Bio

1 ean and standard deviation

There is almost always variation in bio logical data. The amount of variatio n can be show n using a graph called a frequency di stribu tion . M ost var iatio n gives a bell -shaped frequency d istributio n called the normal distribution . The mean value is in the midd le of the di stribution . The mean of a set of values is calc ulated by di vid ing the sum of the values by the numb er of values. For example, the sum of the valu es 7, 9, 11 and 17 is 44 and as here are four values, the mean is 44 divided by 4, w hich is 11. The standard deviation is used to assess how far the values are spread above and below the mean. It is ca lculated by entering data into a graphic display or scientif ic calc ulator and pressing the standard devi ation funct io n key. A high standard deviation shows that the data are w ide ly spread, w hereas a low standard devi ation shows that the data are cl ustered closely arou nd the mean. The standard devi ation ca n be used to help decid e wh ether the difference betw een tw o means is likely to be signi fica nt. Tw o examples are describ ed below .

LEFT AND RIGHT HAND LENGTHS Thirty teenage boys measured the length of their left and right hands, to fi nd out w hether they are different. Indivi d ual boys' left and right hand length varied by as much as 10mm. The results are shown in the frequ ency di stribu tion below .

Hand

Mean length

Standard deviation

left

188.6 mm

11.0 mm

right

188.4 mm

10.9 mm

The normal distribution mean

~

- 2,.0

-1 .0

+1.0

+2.0

,-------1------- ~ -------j----~-o~ 68% of the area is betwe e n - 1.0 a nd + 1.0 sta nda rd deviations.

than 95 % of the

area is betwee n - 2.0 a nd +2.0 standa rd deviation s.

A usefu l rule is that 68% of the values li e w ith in one standard deviat ion of the mean in a norm al di stributi on and approx imate ly 95% of the values lie withi n two standard devi ati ons of the mean (above).

ERROR BARS Bars on graphs extend ing above and below the mean value are used to show the variability of the data. They may show the range of the data, or the standard devi ation .

HAND AND FOOT LENGTHS 12

left

~

10

G c

.--­

8

The same thirty teenage boys w ho measured their hand lengths also measured the length of thei r right foot , to f ind out w hether it was di fferent from their hand lengths. Th e result s are shown in th e f requ ency dis tribu ti on below .


5
6 4

2

o

Mean length

Standard deviation

right hand

188.4 mm

10.9 mm

right foot

262.5 mm

14 .3 mm

~

I

12

~

right 10

G c

8

5-

6

G 12

c ~ 10

g-

8 Lt: 6

I-­


::'

Hand/foot f---

Lt:

right hand

right foot

4

u...

f--­

4

2

o

~

2 0'

I

I I I I I I I I I I I I I I 160 180 200 220 240 260 280 300 Length / mm

160 170 180 190 200 210 Hand Length / mm

Because the standard deviati ons are much less than the di fference in mean length, it is very likely that the di fference in mean length between right hands and right feet is signifi cant.

Because the standard devi ation s are muc h greater than the di fference in mean length, it is very un likely that the di fference in mean length between left and right hands is significa nt.

Statistical analysis 1

Relationships

significance and cause

THE t-TEST

Examples of the use of the t-test

On the previous page, sizes of standard deviations were used to assess whether differences between means were likely to be significant. Biologists often need to decide more objectively whether differences between means are significant. One of the most frequently used methods is called the t-test.

These examples are based on the data for hand and foot lengths described on the previous page. 1. Testing the difference between mean lengths of left and right hands

Mean length of left hands = 188.6mm

Mean length of right hands = 188.4mm

t = 0.082

Critical val ue for t = 2.002 (P = 0.05)

The calculated value of t is much smaller than the critical value, so the difference between the mean lengths of left and right hands is not sign ificant.

The t-test can be used to find out whether there is a significant difference between the means of two populations. A difference is considered statistically significant if the probability of it being due to random variation is 5% or less. t is a statistic that is calculated from the two sets of measurements. The larger the difference between the two means, the larger t is. The larger the standard deviations, the smaller t is. It is not necessary to learn how to calculate t, because a graphic display calculator or computer is nearly always now used.

Stages in using the t-test 1. Enter the values in a graphic display calculator or a spreadsheet program, with values for the two populations entered separately. 2. Use the calculator function keys or computer software to calculate t. 3. Find the number of degrees of freedom. This will be the total number of values in both populations, minus two. 4. Find the critical value for teither using computer software or a table of values of t. The level of significance (P) chosen shou Id be 0.05 (5%) and the appropriate row should be selected according to the number of degrees of freedom. 5. Compare the calculated value of t with the critical value. If the critical val ue is exceeded, there is evidence of a significant difference between the means, at the 5% level.

2. Testing the difference between the mean lengths of right hands and right feet.

Mean length of right hands = 188.4mm

Mean length of right feet = 262.5mm

t = 23.3

Critical value for t = 2.005 (P = 0.05)

The calcu lated val ue of t is much larger than the critical value, showing that the difference between the mean lengths of hands and feet is significant. In these two examples, the t-test confirms conclusions that are reasonably obvious. In biological research, it is often much less clear whether differences between means are significant and the t-test is therefore very usefu I.

CORRELATION AND CAUSE The scattergraph below shows that there is a positive correlation between the lengths of the right hand and right feet of th irty teenage boys - boys with larger hands tend to have larger feet as well.

E 300

E 290

Table of critical values of t

..........

~280 c

Level of significance (P)

E 0

u

(J.)

~ '0

-

~

I

tJ)

(J.) (J.)

M (J.) 0

~

270

o ~ 260

0.2

0.1

0.05

0.02

0.01

0.002

1 2 3 4 5

3.078 1.886 1.638 1.533 1.476

6.314 2.920 2.353 2.132 2.015

12.706 4.303 3.182 2.776 2.571

31.821 6.985 4.541 3.747 3.365

83.657 9.925 5.841 4.604 4.032

318.310 27.327 10.215 7.173 5.893

250

6 7

1.440 1.415

1.943 1.895

2.447 2.385

3.143 2.998

3.707 3.499

5.208 4.785

220

8 9 10

1.397 i.383 1.372

1.860 i.833 1.812

2.308 2.262 2.228

2.896 2.82i 2.764

3.355 3.250 3.169

4.501 4.297 4.144

210

11 12 13 14

1.363 1.356 1.350 1.345

1.796 1.782 1.771 1.761

2.201 2.179 2.180 2.145

2.718 2.681 2.650 2.624

3.106 3.055 3.012 2.977

4.025 3.930 3.852 3.787

15 16 17 18 19 20 30 40

1.341 1.337 1.333 1.330 1.328 1.325 1.310 1.303

1.753 1.746 1.740 1.734 1.729 1.725 1.697 1.684

2.131 2.120 2.110 2.101 2.093 2.086 2.042 2.021

2.602 2.583 2.567 2.552 2.539 2.528 2.457 2.423

2.947 2.921 2.898 2.878 2.861 2.845 2.750 2.704

3.733 3.686 3.646 3.610 3.579 3.552 3.385 3.307

2 Statistical analysis

.. ... ..

240

..

..

. ...

.

..

..

•t

.

.. ..

t

230

200 1 160

170

180

190

200

210

220

Hand length / mm Although there is a positive correlation between hand and foot length, we know that increases in the length of the hand do not cause increases in length of the foot. Instead, both are due to the factors that control growth in teenage boys. This mistake is often made in analysis of data - a correlation between two variables is assumed to show that there is a causal Iink. It is important to remember that correlation is not proof of cause.

2

._ _' _~:.a.-...;....--L

Cell theory INTRODUCING CELLS Cells co nsist of cyto plasm, enclosed in a plasma membrane, usually controlled by a single nucl eus. Two cell types that can be easily looked at under a light microscope are human cheek cells, scraped from inside the mouth (left) and moss leaf cells (right). M oss leaf cell

H uman cheek cell cytoplasm

plasma membrane <::>

' /

'.

chloroplasts cell wall

o

~'-./~

. '~

. .""-J

nucleus

o plasma membrane

<::>

nucleus mitochondria

cytop lasm

sap in vacuole

vacuole membrane

UNICELLULAR ORGANISMS

THE CELL THEORY

Some organisms such as Amoeba (below), Chlorella and Euglen a have on ly one cell. This single cell has to carry out all the functio ns of life: metabo lism - chemica l reactions insi de the cell

response - reacting to stim uli

hom eostasis - co ntrolling co nditions inside the cell

grow th - increasing in size

reproduction - produ cin g offspri ng

nutrition - obtaining foo d.

The cell theo ry includ es these statements: • living organisms are com posed of cells • cells are the smallest units of life • cells com e from pre-exi stin g cells. M any o rganisms have been examined and have been found to co nsist of cells, but there are some casesw here the idea of li vin g o rganisms co nsisting of tin y box-l ike str uctures does not seem to fi t. Fo r example, skeletal muscle is made up of muscle fibres. These are much larger than most ce lls (300 or more mm long) and co ntain hun dreds of nuclei. Most fungi co nsist of t hread-like structures called hyphae, w hich in some species co ntain many nucl ei w ithout d ivid ing wa lls betw een. Man y tissues, suc h as bo ne, co ntain a greater vo lume of ext racell ular mater ial (material outside the cell membr ane) than of cells. Despite these aw kw ard cases, most living ti ssues are co mposed of cells. A lso, w hereas cells taken from an organism often survive fo r a time, smaller parts of an organism do not. Cell s do therefore seem to be the smallest un its of life that are capable of surv iva l. There is also evide nce for the th ird part of the cell theo ry. Some of the classic expe riments in bio logy showed that spontaneous generat io n of life is impossible (below). The first cell s must have been fo rmed in the origin of life from non ­ cell ular material , but today there is no ev idence that cells can be for med exce pt by cell divi sion.

Amoeba '

100

.. ..

-: .. ·:······:···0·:·::".: . :. ': =::. :'. <:>: ~; :..d-:. . :(i) :; . .0 . " :''c2 .. ' . . . ' . :.'. :': · :··~·; o ·: :.:: : .:·::

urn

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. .:"",':':'.: :..~ :>~ :: '~::'." .~'. : '.: : '

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" I ." 0.:_. ' o .... , o.•... , • -. 0--J.·:•• "0""0

..:o.-. (jJ. . '.0,

.'

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. ' c:; .() . 0 .' :

MULTICELLULAR ORGANISMS Mul ticel lular organisms co nsist of many cells. These cells do not have to carry out many different functions. Instead, they can become specialize d for one partic ular function and carry it out very efficiently . Cells in a multice ll ular organism therefore develop in different w ays. This is called different iation . The way in w hich this occurs is described on page 4. Mu lticellu lar organisms are said to show emergent pr opert ies. This means that the who le organism is more than the sum of its parts, because of the co mplex interactions betw een cells.

Steriliz ed soup in an open container decays because bacteria float in

Sterilized soup in a sealed container does not decay as no bacteria are present

Cells 3

Stem cells and differentiation

DIFFERENTIATION

THERAPEUTIC USE OF STEM CELLS

Cells in a multicell ular organism develop in di fferent ways and can therefore carry out different functions. This is called differentiation. The cells need different genes to develop in different w ays. Each cell has all of these genes, so could develop in any way, but it only uses the ones that it needs to follow its pathway of development. O nce a pathway of development has begun in a cell, it is usually fixed and the cell cannot change to follow a different pathway. The cell is said to be committed. The draw ings (below) show three of the hundreds of d ifferent types of d ifferentiated cells in humans.

In the future, many therapies may invo lve the use of stem cell s. Some therapeutic uses have already been int roduced. O ne example is given here. 1. The placenta and umbilical co rd of a baby is used as a source of stem cells. At the end of childbirth, the placenta is taken and pl aced on a stand, w ith the umb ilical cord hanging dow n from it. Blood drains out of the umbi li cal co rd and is co llected - about 1OOcm 3 . The co rd blood co ntai ns many hematopoi etic stem cells. These cells can di vid e and di fferenti ate into any type of blood cell.

H eart muscle tissue

20 i(

urn •

All heart muscle cells contain structures made from protein fibres that are used to contract the cell and help to pump blood in the heart. Sensory neuron

2. Red blood cells are removed from the cord blood and the remain ing fluid is t hen tested to f ind its tissue type, checked for di sease-causing organisms and stored in liquid nitr ogen, in a specia l bank of cord bloo d.

Beta cell in t he pancreat ic islets

. . -. "

. - -.

~

. ...~ ••••.••. •.. •.

STEM CELLS Stem cell s are defined as cells that have the capacity to self­ renew by cell di vi sion and to d ifferentiate. Hum an embryos consist entirely of stem cells in their early stages, but gradually the cell s in the embryo co mmit themselves to a pattern of di fferenti ation . O nce comm itted, a cell may still d ivid e several more t imes, but all of the cells formed w ill di fferenti ate in the same w ay and so they are no lon ger stem cells. Small numb ers of embryonic cells remain as stem cells how ever and they are still present in the adult bod y. They are found in most human ti ssues, incl uding bone marrow , skin and liver. They give some human tissues considerable powers of regeneration and repair. The stem cell s in other tissues only all ow limited repair - brain, kidney and heart, for example. There has been great interest in stem cells because of their potential for tissue repair and for treating a variety of degenerative conditions. Fo r example, Parkinson's di sease, mu ltip le scle rosis and strokes all invo lve the loss of neurons or other cell s in the nervou s system. A lthough st ill only at the research stage, there is the potential to use stem cell s to replace them .

4 Cells

3. Cord bloo d can be used to t reat patients, especia lly child ren, wh o have develop ed certain forms of leukemi a. Thi s is a cancer in w hich the cells in bo ne marrow div ide uncont rol lably, produci ng far too many whi te blood cells. The patient's ti ssue type is matched w ith co rd blood in the bank. If suitable cord blood is available, the patient is given chemotherapy d rugs that ki ll bone marrow cells, including the cells causing the leukemia.

transfusion of cord blood

4. The selected co rd blood is taken from the bank, thawed and intr oduced into the patient's blood system, usually vi a a vei n in the chest or arm. The hematopoi etic stem cells establish themselves in the pati ent' s bone marrow , w here they divide repeated ly to build up a population of bone marrow cells to replace those kill ed by the chemotherapy drugs.

Size in cell biology

LIMITATIONS TO CELL SIZE Cells do not carry o n grow ing indef initel y. They reach a maxim um size and then may divid e.

If a cell became too large, it w ou ld develop problems because its surface area to vo lume ratio

wo uld becom e too small .

A s the size of any obj ect is in creased, the ratio between the surface area and the vo lume

decreases. Con sider the surface area to vo lu me ratio of cubes of va ry ing size as an example.

The rate at w hich materials enter or leave a cell depends on the surface area of the cell.

H ow ev er, the rate at w hic h materials are used or produce d depends on the vo lume. A cell

that become s too large may not be able to take in essentia l materials o r exc rete waste

substances qui ckly eno ugh.

The same prin ciple wo rks for heat. Cells that generate heat may not be able to lose it qui ck ly

eno ugh if they grow very large.

Surface area to vo lume ratios are importa nt in bio logy . They help to exp lain many phenomena

apart from maxim um ce ll sizes.

UNITS FOR SIZE MEASUREMENTS M ost S.1. un its d iffer from each other by a facto r of 1000 . O ne mi ll imetre is a thousand times smaller tha n 1 metre. O ne m icrom etre is a tho usand tim es smaller than 1 mi llim etre. On e nanometre is a thou sand tim es smaller than 1 microm etre. The mo st useful units for measurin g the sizes of cells and struct ures w ithi n them are nanometres (nm) and m ic ro metres (IJ m). The typi cal sizes of some important structures in bio logy are shown opposite.

l Ornrn

=

~

I-­ I-­ I-­ f­

1mm f-

f:::

l=ffff-

100 urn

f:::

~

ff-

cells of eukaryotes

f-

I-

10!Am ~

~

lI-

CALCULATING MAGNIFICATION

l-

Photographs or d raw ings of structures seen und er the mi croscope show them larger than they really are - they magnify them. It is useful to know how m uc h larger the image is than the actua l spec ime n. Thi s facto r is calle d the magnif icat ion. It is alwa ys helpfu l to show the magnifi cati on on a draw ing of a bio logical structure. Foll ow these in structi ons to calculate magnification . 1. Choo se an ob vi o us length, for examp le the maximum di ameter of a cell. M easure it on the draw ing. 2. M easure the same length on the act ual spec imen. 3. If the uni ts used for the tw o measurements are different, co nvert one of them into the same un its as the other one. 4 . Di vi de the length on the dr awin g by the length on the actual speci men. The result is the magnif icatio n.

I-­

1urn l=

~

organelles

•

lI­

I-­ f­

100 nm

f::: •

l=f-

size of image

size of speci men

vi ruses (sizes va ry)

f-

I-­ f-

I­

Mag nificatio n =

bacteria (sizes vary )

10 nm

=•

Thickness of cell membranes

-==

Thi s equat io n can also be used to calc ulate the act ual size of a speci me n if the magnificati on and size of the im age are kno wn .

-

SCALE BARS A scale bar is a line added to a mi cro graph o r a dr aw ing to hel p to show the actual size of

the structures.

Fo r example, a 10 IJm bar shows how large a 10 IJ m object w ould appear.

The figure below shows is a scanning electron mi crograph of a leaf w ith the magnification and a

scale bar both shown.

Scanning electron micrograph of leaf ( x 480 )

1 nm

=• -= -

f-

molecules (e.g. DNA molecule is 2nm in diameter)

I-

0.1 nm

~ '­

1000 mm == 1 m 1000 IJm == 1 mm 1000 nm == 1 IJm

Cells 5

Prokaryotic cells

ULTRASTRUCTURE OF CELLS

FUNCTIONS OF PARTS OF A PROKARYOTIC CELL

From the 1950s onwa rds, ce ll structure co uld be studi ed in much greater detai l than before, using elect ron m icroscop es. W hat was revealed is ca lled the ultrastructure of the cell. Cells were d ivided into two types acco rding to thei r structure, prokaryotic and eukar yoti c. The first cells to evo lve we re prokaryot ic and many organisms still have prokaryotic cells, includi ng all bacteri a. These cells have no nucl eus and the name prokaryotic means befo re the

Stru cture

Function

Cell wa ll

Form s a protective outer layer that prevents damage from outside and also bursting if internal pressure is high .

Plasma membrane

Controls entry and exit of substances, pum pi ng some of them in by active transport.

Cytoplasm

Co ntains enzymes that catalyse the chemica l reaction s of metabo li sm and co ntains DN A in a region called the nucl eo id .

Pili

Hair-li ke struct ures proj ectin g from the ce ll w all, that can be ratcheted in and out; w hen co nnected to anot her bacterial ce ll th ey can be used to pull cells togeth er.

Flagell a

Solid protein structu res, w ith a corkscrew shape, project ing from the ce ll wa ll, w hich rotate and cause locom ot ion.

Rib osomes

Small granular structures th at synthesise prot ein s by translating messenger RNA . Som e prot ein s stay in the cell and others are secreted.

Nucleoid

Regio n of the cyto plasm that contains naked DN A, wh ich is the genetic in fo rmati on of the cell.

nucleus. The fun ctions of struct ures w ithin pro karyotic ce lls are shown (right). Prokaryoti c cells di vid e in tw o by a process called binary f issio n.

'------_ -----'II

L--.-

_

Electron micrograph of Escherichia coli (1-2 pm in length )

Drawing to help interpr et th e electron micrograph

ribosomes

cell wall

plasma membrane

Electron micrograph of Escherichia coli show ing surf ace features

.' "

6 Cells

.

"

nucleoid (region containing naked DNA)

EUkaryotic cells

STRUCTURE OF A EUKARYOTIC CELL Electron mic rograph of a li ver cell ( X 6000)

D rawing to interpret parts of t he elect ro n microgra ph

°QCP DoC)

,(O\JY~~

a

. .. • -.

.'

'

plasma membrane free ribosomes

nucleus mitochondrion

COMPARING PROKARYOTIC AND EUKARYOTIC CELLS Feature

Prokaryotic cells

Eukar yot ic cells

Type of genetic mate ria l

A naked loop of D NA

Chromosom es co nsisting of strands of D NA associated w ith protein. Four o r mo re chromosomes are present.

Locat io n of genetic materi al

In the cyto plasm in a regio n called th e nucl eo id

In the nucl eus inside a do uble nucl ear membrane ca lled the nucl ear envelope

Mit ochondria

Not present

A lways present

Ribosomes

Small sized - 70S

Larger sized - 80S (S = Svedberg units - related to the size of organelles)

In tern al memb ranes

Few or no ne are present

M any internal membranes that compartmentalize the cytoplasm incl udi ng ER, Go lgi apparatuses, Iysosomes

COMPARING PLANT AND ANIMAL CELLS Feature

Ani mal

Plant

Cell wa ll

No cell w all, o nly a plasma membr ane

Cell wa ll and plasma membr ane present

Chl or opl ast s

Not present

Present in cells th at photosynthesize

Pol ysaccharides

Glycogen is used as a storage com po und

Starch is used as a sto rage compound

Vacuol e

Not usually present

Large flu id-fill ed vacuo le often present

Shape

Able to change shape. Usuall y rounded

Fixed shape. Usually rather regular

Cells 7

Membrane structure and membrane proteins

Fluid mosa ic mod el of a biological membran e hydrophil ic phosphate head

hydrophobic hydrocarbon tail

glycoprotein

cholesterol

~ ~ ~ ~~~~~ ~~~ ~~~~ ~ ~ ~ ~ ~ ~~~~~ ~~~ ~~ ~~ ~ ~ ~ ~~

phospholip id bilayer

integral proteins embedded in the phospholipid bi layer

peripheral protein on the surface of the membrane

~

PHOSPHOLIPIDS

FLUIDITY OF MEMBRANES

H ydrophi li c molecu les are attra cted to wate r. H ydr oph obi c mo lecu les are not att racted to wa ter, but are attracted to each other. Phospho li pi d mol ecul es are unu sual because they are partl y hydr oph il ic and partly hydrophobi c. The phosphate head is hydr oph ili c and the tw o hydrocarbon tail s are hydr ophobi c. In w ater, pho spho lipids form doubl e layers w ith the hydr oph ilic heads in co ntact w ith w ater on both sides and the hyd roph obi c tai ls aw ay from w ater in the centre. Thi s arrangement is foun d in bi ol ogical membr anes. The attract io n betwee n the hydr oph o bi c tails in the centre and betw een the hyd rophi li c heads and the surround ing w ater makes membr anes very stab le.

Phosph ol ipi ds in mem branes are in a fluid state. Thi s allows me mbranes to change shape in a w ay that wou ld be im po ssible if they we re sol id. The fluidity also allows vesicl es to be pin ch ed off from memb ranes or fuse w ith them .

MEMBRANE PROTEINS Some electro n mi crographs show the positions of pro teins w ithin membranes. The pro teins are seen to be dotted ove r the memb rane. This gives the mem brane the appearance of a mosaic. Because the protein mo lecules fl oat in the f luid ph ospholipid bilayer, bio log ica l membranes are called fluid mosaics. The fig ure (above) is a di agram showing the f luid mosaic model of a bio log ica l membrane. Some of the functio ns of membrane protein s are shown below.

Funct ions of membran e pro tein s HO RMO NE BIND ING SITES

ENZYMES

e

EL ECTRON CARRIERS

CHANN ELS FOR PASS IVE TRANSPORT

PUMPS FOR ACTIVE TRANSPORT

~ O UTSIDE

OUTSIDE

INSIDE

INSIDE

ATP

ADP+ P A site exposed on the outside of the membrane allows one specific hormone to bind. A signal is then transmitted to the inside of the cell

8 Cells

Enzymes located in membranes either catalyse reactions inside or outside the cell, dependi ng on w hether the active site is on the inner or outer surface

Electron carriers are arranged in chains in the membrane so that electrons can pass from one carrier to another

Channels are passages through the centre of membrane proteins. Each channel allows one specific substance to pass through

Pumps release energy from ATP and use it to move specific substances acrossthe membrane

Passive transport across membranes

DIFFUSION

SIMPLE AND FACILITATED DIFFUSION

Soli ds, liquids and gases co nsist of particles - atoms, ion s and molecu les. In liqui ds and gases, these particles are in co nt inual motio n. The d irect ion t hat they move in is rando m. If particles are evenly spread then their movement in all directions is even and there is no net movement - they remain evenly spread despit e co ntinuall y mov ing. Someti mes particl es are unevenly spread - there is a higher conce ntratio n in one region than another. This causes di ffusio n.

M embra nes all ow some substances to diffuse thro ugh but not others - they are parti ally permeable. Som e of t hese substances move betwee n the phospho lipid mo lecules in the membrane - this is simple diffusion. Other substances are unable to pass betw een the phospho lip ids. To allow these substances to d iffuse thro ugh membranes, channel protei ns are needed . Thi s is call ed facilitated diffusion . Chann el proteins are speci fic - they o nly all ow one typ e of substance to pass thro ugh. For example, chlo ride channels only allow chlo ride ions to pass thro ugh. Cells can con trol w hether substances pass thr ou gh their plasma membranes by facil itated diffusio n, by the typ es of channel pro tein that are produ ced and in serted in to the membrane. Cells cannot cont ro l the d irectio n of movement. Faci litated d iff usion alw ays causes parti cles to move from a region of higher con centration to a region of lower co nce ntratio n. Both simple and facilit ated diffu sion are passive processes - no energy has to be used by the cell to make them occ ur. There are sodium and potassium channel protein s in the membranes of neuron es that open and close, dependin g o n the vo ltage across the membrane. They are called vo ltage­ gated channels and are used duri ng the transm issio n of nerve impulses.

Diffusion is the passive movement of particles from a region of higher conce ntration to a region o f lower co nce ntration, as a result of the random motio n of particles. Diffusion occurs because mo re parti cles mov e fro m the region of higher co ncentration to the region of low er conce ntratio n than move in the opposite directi on. D iffu sion can occur across mem branes if there is a conce ntratio n grad ient and if the mem brane is permeable to the particl e. For example, membr anes are f reely permeable to oxyg en, so if there is a low er conce ntration of oxyge n inside a cell than outside, it wi ll di ffuse into the cell. M embranes are not perm eable to cellulose, so it does not d iffuse across, even if there is a hi gher conce ntrat ion o n on e side of a membrane than the other.

.•••• .••

membrane consisting of phospholip id bilayer

-.­

• •• • •••• • ••• ••••• •• •••• • • •

higher concentration

.....

membrane containing channel proteins

lower concentratio n

• • • •• • ••· I~· .... •••• ... ··1 • ••• • • •

. ··1

........

. ..

·.. . ... ... ·· .. .. .

I • •

Solute unablJo diffuse through membrane

Facilitated diffusion through membrane containing channel proteins

Solute able to diffuse through membrane

OSMOSIS Plasma memb ranes are usuall y free ly perm eab le to wa ter. Th e passive moveme nt of wa te r across memb ranes is different f rom d if fusio n ac ross membran es, because wa ter is th e solvent. A solvent is a liquid in whi ch part ic les d issolve. D isso lved particles are called solutes. The direct io n in w hic h w ate r moves is due to t he co nce ntr at ion of solutes, rather than t he co ncentrat io n of wate r mo lecules, so it is ca ll ed osmosis, rather than diffusion .

Osmos is is the passive m o vem ent of water mo lecules from a region of lower solute concentration to a region of higher solute conce ntration, across a partially permeable membrane. Attr actio ns betw een solute particles and wate r molecules are the reaso n for w ater mov ing to regio ns wi th a higher solute co nce ntration.

-~.

Solute molecules cannot diffuse out as the membrane is impermeable to them

.

e• • • •

..

..'e. .. ~ <: • •• • • • • ••• • • ~ • • • • • •• • • • • •

.

••

.\. •

•

• •••

••

...••••.•..

•••

• ••

••••••

·:Mtf·· •• •

•

•

region of low er solute concentration (in this case pure water) partially permeable membrane region of higher solute concentration

~

W ater molecu les move in and out through the membrane but more move in than out. There is a net movement from the region of lower solute concentratio n to the region of higher solute concentration

Cells 9

Active transport across membranes

PUMP PROTEINS AND ACTIVE TRANSPORT Active transport is th e mo vement of substances across membranes using energy fro m ATP. Ac tive tr ansport can move substances against the con centr ati on gradient - from a region of low er to a region of hi gher co nce ntratio n. Protein pumps in the membrane are used fo r active transpo rt. Each pump onl y transports parti cular substances, so cells can co ntro l w hat is absorbed and w hat is expelled . Pump s w ork in a specific directi on - the substanc e can on ly enter the pump on one side and can only exit on the other side.

Particle enters the pump from the side w ith a lower concentration

Particle binds to a specif ic site. Other types of particle cannot bind

Energy from ATP is used to change the shape of the pump

Particle is released on the side w ith a higher concentration and the pump then returns to its original shape

TRANSPORT OF MATERIALS BY VESICLES IN THE CYTOPLASM Proteins are synthesized by ribosomes and then enter the rough endoplasmic reticulum

Vesicles bud off from the rER and carry the proteins to the Golgi apparatus

The Golgi apparatus modifies the proteins

Vesicl es bud off from the Golgi apparatus and carry the modified proteins to the plasma membrane

ENDOCYTOSIS

EXOCYTOSIS

Part of the plasma membrane is pulled inw ards

Vesicles fuse w ith the plasma membrane

A droplet of fluid

becomes enclosed

w hen a vesicle is pi nched off

The contents of the vesicle are expelled The membrane then flattens out again

Vesicles can then move through the cytoplasm carrying their contents

EXTRACELLULAR COMPONENTS The pl asma membr ane is the barri er that separates a cell from its surround ings. Cells somet imes produce com po nents and then place them outsid e the pl asma membr ane, using exocy tosis. These are called extracellular co mponents. Tw o examples of the rol es of extracellular components are outli ned here: Cytoplasm containing intrace llular components

plasma membrane

Structures outside the membrane are extracellular

10 Cells

1 . Th e plant ce ll wa ll Plants co nstruct thei r cell w alls by sy nthesising cellu lose fibres in vesicle s and add ing them to the inn er surface of the cell wa ll. O ther substances are secreted to intercon nect the cellulose fib res. The strength of the cellulose allow s plant cell w alls to have these rol es: • maintaining the cel l's shape • allow ing hi gh pressure to bui ld up in the cell w it hout it bur sting • high pressure in pl ant cells prevents excessive wat er uptake by osmosis • hi gh pressure in plant cells (turgor pressure) makes the ce ll almost ri gid , help ing to support the plant.

2. Gl ycop rot ein s M any animal cells secr ete glyc oproteins, consisti ng of a protein to wh ich carbohydrate is attac hed. Thi s form s an extracellular matri x. Ti ssues t hat co nsist of a single layer of cells pro duce a thi n layer of ext racellular matri x called the basem ent membr ane, for example around blood capilla ries and around alveo li in the lungs. The matr ix is a gel and has these roles: • suppo rting single layers of th in cells, w hich mi ght oth erwi se tear or perfo rate • cell to cell ad hesio n, fo r example, a basement membra ne helps capillary wa ll cells to adh ere to alveolus wa l l cells.

Cell division

THE CELL CYCLE IN EUKARYOTES New cells are produ ced by di vi sion of existing ce lls. If many new cells are needed, cells go through a cycl e of events again and agai n. Th is is called the cell cyc le. The longest phase in th is cycle is interph ase. Thi s is a very act ive period, during w hich the cell carries out many biochemi cal reacti on s and grow s larger. The D NA mo lecu les in the chromoso mes are uncoil ed and the genes on them can be transcrib ed, allow ing the protein synthesis that is needed fo r grow th. There is an increase in the num ber of mi tochondria and in plant cells in the numb er of chlo rop lasts. There are three stages in int erph ase: G 1 - a period of grow th, D NA transcription and protein synthesis 5 phase - the period during w hic h all D NA in the nucl eus is repli cated G 2 - a period in w hich the cel l prepares fo r divisio n. At the end of int erphase, the cell begins mitosis - the pro cess by w hich the nucl eus divides to for m tw o genetically identical nuclei . Tow ards the end of mitosis, the cytoplasm of the cell starts to di vid e and eventua lly tw o cells are formed, each co ntaining o ne nucl eus. The process of di vidin g the cyto plasm to fo rm tw o cells is cytokinesis. The tw o cells begin int erphase w hen mit osis and cytok inesis have been completed.

Interphase

r

Sph,;,

'~ G,

~

cell The cycle

~~..r()

-,Ei

-o

';0?>"e

<, iL-tetaphase

'1 \

/

"Q,

8!

t-.0:o.\!\\~~

"iL-t,.Itosis and cyto --fIIIIII'" . eS\S \<.\n

THE PHASES OF MITOSIS


Q) Late prophase Each chro mosome consists of two identical chromatids formed by DNA replication in interphase and held together by a centromere

Spindl e m icrotubu les are grow ing

Q) M etaphase Spindle microtubules extend from each po le to the equator

Spin dle microtubules from both po les are attached to each centromere, on opposite sides

The nucl ear membrane has broken down and chromosom es have moved to the equator

Chromosomes are becoming shorter and falle r by superco iling

@ Anaphase

The centromeres have di vided and the chromatids have become chromo somes

~ Early telophase Al l chromo somes

have reached

the poles and

nuclear memb ranes

for m arou nd them

Spindle microtubu les pu ll the genetically identical chromosomes to opp osite

poles

(\.\ \ .11;

@ Late telophase Spindl e mic rotub ules break dow n Chromosom es uncoi l and are no longer indiv idual ly visib le

,,~)

The cel l di vi des (cytokinosis) to form tw o cells w ith geneticall y identical nucle i

USES OF MITOSIS

TUMOUR FORMATION

M itosis is used in eukaryotes w henever genetically identi cal cells are needed : • du ring grow th • du ring embryonic developm ent, w hen the large cell produ ced by ferti lization (zygote) di vid es repeatedly to produ ce many small er cells • w hen ti ssues have been damaged and need to be repai red • to repro du ce asexually.

Som etimes the norm al co ntro l of mitosis in a cell fai ls, due to a change in the genes of the cell. Thi s cell di vides into two , w hic h inh erit the change in the genes. The tw o daughter cells d ivide to for m fo ur cells. Repeated uncont roll ed di vi sions soon produ ce a mass of cells called a tu mour . Thi s can happen in any ti ssue and in any organ. Tumours can grow to a large size and can spread to other parts of the bod y. The d iseases caused by the grow th of tum our s are called cancer.

Cells 11

EXAM QUESTIONS ON TOPICS 1 AND 2 The photomi crog raph below shows a transverse sectio n of part of a liver cell.

a) Identi fy the organelles labelled X and Y.

[2 ]

b) On the photomicrograph, identify the nucl ear memb rane and show its position w ith a clea r label.

[lJ

c) The liver cell show n in the photo micrograph w as making large amo unts of tw o substances. Dedu ce w hat the tw o substances were, giving reason s for your answe r based o n the o rganelle s visible in the photom icro graph.

[2]

2 The d iagram below represents the f lui d model of a cell memb rane.

III

a) (i) State the name of the mo lecule labelled I. (ii) Label the diagram to show w hich part of mo lecu le I is hydrophobi c and w hi ch part is hyd rophilic. b) (i) Identi fy w hether mo lecule 1/ is an int egral or a perip heral protei n. (ii ) Descr ibe the part played by mol ecul e III in active transport.

rn [1] [1] [2]

3 Ten teenage boys, aged 17 or 18, estimated their body fat percentage by measurements of skin fold th ick ness. The estimates (%) we re: 25.6, 12.9,8.1, 10.2, 10.0,8.9, 8.1, 15.3, 11.2, 13.7 . a) (i) Calculate the mean est imated body fat percentage. (ii) Calculate the standard deviatio n.

[2] [2]

The boys also measured their blood pressure. The boys w hose estimated body fat percentages we re higher tended to have higher blood pressure. b) (i) Wh at is this type of relationship betw een two variables called? (ii) D iscuss w hether th is relation shi p proves that beco ming obese causes high blood pressure.

12 18 Questions ­ Cells

[2] [2]

3 Water POLARITY OF WATER

HYDROGEN BONDING IN WATER

W ater mol ecules consist of two hydrogen atom s bonded to an oxy gen atom. The hydr ogen atoms have a slight positive charge and the oxyge n atom has a slight negativ e charge. So, water mol ecul es have two poles - a positive hydr ogen po le and a negative oxyge n po le (below) . This feature of a mol ecul e is called polarity.

A bond can for m between the positive po le of one wa ter mo lecu le and the negative po le of another. Thi s is called a hydrogen bond . In liquid water many of these bonds form, giv ing w ater pro perties that make it a very useful substance fo r livin g organisms. The d iagram (below) shows a hydrogen bond betw een two water mol ecu les.

W ater molecule hydrogen bond

:JI

Hydrogen pole is

s lig ~~ Iy

positive

l

.L

}

Oxygen pole is slightly negative

r ""'

THE PROPERTIES OF WATER Name of the property

Outline of the properties of water

Relat ion ship between the properties of water and it s uses in living or ganisms

Cohesion

W ater mo lecu les stick to each other

because of the hydrogen bond s that for m

betw een them .

Stro ng pu llin g fo rces can be exerted to suc k co lumns of water up to the to ps of the tallest trees in their transpo rt systems. These co lumns of wa ter rarely break. W ater is used as a tran sport medium in the xy lem of plants.

Solvent pr operties

M any d ifferent substances di sso lve in wa ter

because of its pol arity (below) .

Ino rganic particles w ith positive o r negative

charges di ssolve, for examp le sod ium ion s.

Or gani c substances with po lar mo lecu les

dissol ve, for example glucose.

Enzymes also di sso lve in wate r.

Most chemica l reacti on s in liv ing o rganisms take place wi th all of the substances invol ved in the reactio ns disso lved in wate r. W ater is the medium for metaboli c reactions. The so lve nt properti es of w ater allow many substances to be carried di ssolved in w ater in the blood of animals and the sap of plants. W ater can be used as a transport medium .

Thermal properties: heat capacit y

W ater has a large heat capaci ty - large

amo unts of energy are needed to raise its

temperatur e. The energy is needed to break

some of the hyd rogen bond s.

Blood, w hic h is mai nly co mposed of wa ter, can carry heat from war mer parts of the bod y to coo ler parts. Blood is used as a transport medium for heat.

Thermal properties: boiling point

The bo il ing point of wa ter (1OOQC) is high,

because to change it from a li quid to a gas

all of the hydro gen bond s betw een the

wate r mo lecules have to be broken.

W ater is below bo ilin g po int almost everyw here on Earth, and in most areas it is above freez ing po int. As a liquid, rather th an a solid or a gas, it can act as the medium for metabolic reaction s.

Thermal properties: the coolin g effect of evaporation

W ater can evapo rate at tem peratu res below

bo iling poi nt. Hydro gen bond s have to be

broken to do thi s. The heat energy needed

to break the bo nds is taken from the liq uid

wa ter, coo ling it dow n.

Evaporatio n of wate r from plant leaves (transpiration) and from the hum an ski n (sweat) has useful coo ling effects. Wa ter can be used as a coolant.

cg v

~

Ions wit h positive or negative charges dissolve as they are attracted to the negative or positive poles of water molecules.

cQ;:, ~rU - -cg ,

CQi1:', cO

~

M any molecules are polar so are

attracted to water molecules and dissolve.

The chemistry of life 13

Elements and compounds in living organisms

ELEMENTS IN LIVING ORGANISMS

CHEMICAL ELEMENTS AND THEIR ROLES

Living organisms contain many chemical elements, some in large quantities and some in very small amounts. The four commonest chemical elements of Iife are carbon, hyd rogen, oxygen and nitrogen. They are part of all the main organic compounds in living organisms. Examples of other elements that are needed are shown in the table opposite.

Element and symbol

Role in plants, animals and prokaryotes

Sulphur

Needed to make two of the twenty amino acids that proteins contain

S

ORGANIC AND INORGANIC COMPOUNDS Living organisms contain many chemical compounds. Some of them are organic and some are inorganic. Organic compounds are defined as compounds containing carbon that are found in living organisms. There are a few carbon compounds that are inorganic even though they can be found in living organisms. These are all simple carbon compounds that are also widely found in the environment. Carbon dioxide, carbonates and hydrogen carbonates are three examples of inorganic carbon compounds. All compounds that contain no carbon are inorganic. Three types of organic compound are found in large amounts in living organisms ­ carbohydrates, lipids and proteins.

SUBUNITS OF ORGANIC MACROMOLECULES

Calcium Ca

Acts as a messenger, binding to cal mod u lin and other protei ns that regulate processes inside cells, including transcription

Phosphorus P

Part of the phosphate groups in ATP and DNA molecules

Iron Fe

Needed to make cytochromes -proteins used for electron transport during aerobic cell respi ration

Sodium Na

Pumped into the cytoplasm to raise the sol ute concentration and cause water to enter by osmosis

These elements have other specific roles in some organisms. For example, iron is needed to make hemoglobin in many animals and calcium is needed to make the minerals that strengthen bones and teeth.

The molecules of many organic compounds are large and so

are called macromolecules.

They are built up using small and relatively simple subunits.

Some important subunits are shown below.

Subunits of proteins, carbohydrates and lipids

CH20H CH20H 0

H

I

I/~I C C 1\ H H /1 H\\ l/oH

H

I

I OH

I

I

I

H

OH

I

;f

\OH

H-C-H I H-C-H

glucose (a monosaccharide)

0

N--C--C

HI

I

H

I

amino acids (each of the twenty amino acids in proteins has a different R group)

14 The chemistry of life

H-C-H I H-C-H I H-C-H I H-C-H H-C-H I H-C-H I H-C-H I H-C-H I H-C-H I H-C-H I H-C-H I H-C-H I H-C-H

R

\

H

H

\1C I\?H III OH C - - C OH

ribose (a monosaccharide)

H

I/~

C

C--C

OH

c--o

O,\- /OH C I

I H

fatty acids (general structure)

fatty acid (number of carbon atoms and bonding between carbon atoms varies)

Building macromolecules

CONDENSATION REACTIONS In a condensation reaction two molecules are joined together to form a larger molecule. Water is also formed in the reaction. For example, two amino acids can be joined together to form a dipeptide by a condensation reaction. The new bond formed is

a peptide linkage. Condensation of two amino acids to form a dipeptide and water H

R

-.

I

0

H

/

R

-,

N-C-C

H/

I

I

0

/

N-C-C----.

-.

H

OH

/

I

H

H

-,

H~

H/

R

0

R

I

II

I

0

/

N-C-C - N - C - C

OH

I

I

I

H

H

H

+H0

-,

2

OH

Further condensation reactions can link amino acids to either end of the dipeptide, eventually forming a chain of rnany arnino acids. This is called a polypeptide. In a similar way, condensation reactions can be used to build up carbohydrates and lipids. The basic subunits of carbohydrates are monosaccharides. Two rnonosaccharides can be linked to form a disaccharide and more monosaccharides can be linked to a disaccharide to form a large molecule called a polysaccharide. Fatty acids can be linked to glycerol by condensation reactions to produce lipids called glycerides. A maximum of three fatty acids can be linked to each glycerol, producing

a triglyceride.

HYDROLYSIS REACTIONS Large molecules such as polypeptides, polysaccharides and triglycerides can be broken down into smaller molecules by hydrolysis reactions. Water molecules are used up in hydrolysis reactions. Hydrolysis reactions are the reverse of condensation reactions. ~ dipeptides or amino acids polypeptides + water polysaccharides + water

~

disaccharides or monosaccharides

glycerides + water

~

fatty acids + glycerol

EXAMPLES OF CARBOHYDRATES Examples

Example of use in animals

Example of use in plants

Monosaccharides

glucose galactose fructose

Glucose is carried by the blood to transport energy to cells throughout the body

Fructose is used to make fruits sweet-tasting, attracting animals to disperse seeds in the fruit

Disaccharides

maltose lactose sucrose

Lactose isthe sugar in milk, that provides energy to young rnarnmals until they are weaned

Sucrose is carried by phloem to transport energy to cells throughout the plant

Polysaccharides

starch glycogen cellulose

Glycogen is used as a short-term energy store in Iiver and in muscles

Cell ulose is used to make strong fibres that are used to construct the plant cell wall

FUNCTIONS OF LIPIDS

CARBOHYDRATES AND LIPIDS IN ENERGY STORAGE

• Energy storage - in the

Both Iipids and carbohydrates have advantages as energy storage compounds in living organisrns. Carbohydrates are usually used for energy storage over short periods and lipids for long-term storage.

form of fat in humans and oil in plants • Heat insulation - a layer of fat under the skin reduces heat loss • Buoyancy - lipids are less dense than water so help anirnals to float

Advantages of lipids

Advantages of carbohydrates

1. Lipids contain more energy per gram than carbohyd rates so stores of lipid are lighter than stores of carbohydrate that contain the same amou nt of energy

1. Carbohydrates are more easi Iy

2. Lipids are insoluble in water, so they do not cause problems with osmosis in cells

2. Carbohydrates are soluble in water

digested than lipids so the energy stored by them can be released more rapidly

so are easier to transport to and from the store

The chemistry of life 15

Introducing DNA

THE NUCLEOTIDE SUBUNITS OF DNA Although DNA is the genetic material of living organisms and is therefore of immense importance, it is made of relatively simple subunits. These are called nucleotides. Each nucleotide consists of three parts - a sugar (called deoxyribose), a phosphate group and a base. In diagrams of DNA structure these are usually shown as pentagons, circles and rectangles, respectively. The figure (below) shows how the sugar, the phosphate and the base are linked up in a nucleotide.

~ /""....

Pho~~Vi-_I~

I

base

sugar

DNA nucleotides do not all have the same base. Four different bases are found ­ adenine, cytosine, guanine and thymine. These are usually simply referred to as A, C, G and T.

BUILDING DNA MOLECULES Two DNA nucleotides can be linked together by a covalent bond between the sugar of one nucleotide and the phosphate group of the other. More nucleotides can be added in a similar way to form a strand of nucleotides. DNA molecules consist of two strands of nucleotides wound together into a double helix. Hydrogen bonds lin k the two strands together. These form between the bases of the two strands. However, adenine only forms hydrogen bonds with thymine and cytosine only forms hydrogen bonds with guanine. This is called complementary base pairing.

DNA REPLICATION DNA replication is a way of copying DNA to produce new molecules with the same base sequence. It is semi-conservative ­ each molecu Ie formed by repl ication consists of one new strand and one old strand conserved from the parent DNA molecu Ie.

Stage 1 The DNA double helix is unwound and separated into strands by breaking the hydrogen bonds. Helicase is the main enzyme involved. \

~

Stage 2 The single strands act as templates for new strands. Free nucleotides are present in large numbers around the replication fork. The bases of these nucleotides form hydrogen bonds with the bases on the parent strand. The nucleotides are linked up to form the new strand. DNA polymerase is the main enzyme involved. Stage 3 The daughter DNA molecules each rewind into a double helix.

16 The chemistry of life

The two daughter DNA molecu les are identical in base sequence to each other and to the parent molecule, because of complementary base pairing (A pairs with T - - ­ and C with G). Each of the new strands is complementary to the template on which it was made and identical to the other template.

Transcription and translation

GENES AND POLYPEPTIDES

DIFFERENCES BETWEEN DNA AND RNA

Pol yp eptid es are lon g c hains of am ino acids. Ther e are tw enty di fferent am ino aci ds th at can fo rm part of a pol ypepti d e. To make o ne parti cul ar po lyp eptid e, am ino aci ds m ust be linked up in a p rec ise seque nce . Genes sto re th e in form ati on needed fo r makin g pol yp eptid es. The info rmatio n is sto red in a co ded fo rm . The seq uence of bases in a gene codes for the sequenc e of am ino aci ds in a po lypepti de. The inform ati o n in the gene is decod ed duri ng th e maki ng of the po lypeptid e. T here are two stages in this process: transcr ipt io n and t ranslati on .

DNA and RNA bo th co nsist of cha ins of nucl eoti des, each co m posed of a suga r, a base and a p hosphate. T here are three differences betwe en them . Feature

DNA

RNA

umber of strands in the mol ecul e

Two str ands form in g a do ub le heli x

O ne strand o nly

Typ e of sugar in eac h nucleotid e

Deoxyribose

Ribose

Typ es o f bases co ntained

A, C, G and T

A, C, G and U U racil rep laces thym in e

TRANSCRIPTION 1. The DNA double

helix uncoil s and the

Instead of th e D NA of genes bein g used d irect ly to d irect th e synt hesis of po lype pt ides, a copy is made. The cop y is RNA. It carries th e informatio n needed to make a polypepti de out into the cytoplasm, so is ca lled mRNA (messenger RNA). The copy ing of the base sequence of a gene by mak in g an RNA mo lecul e is ca lle d t ranscri pt ion . In transcri pti on , the same ru les of co mp lementary base pairi ng are fol low ed as in rep lic atio n, except that uracil pair s w ith ade nine, as RNA does not co ntain th ym in e. The RNA mo lecu le p roduced therefo re has a base sequence that is com plementary to the transcribed st rand and id entical to th e other D N A stra nd exce pt that U rep laces T.

,,"0

"" "~" . ,. ,.: ;:;: ;: ;: : ;: :; : ;: ;: ;: ,. ,~

Transcription moves along in this direction.

Y

2. Free RNA

>T -c

nucleotides are assembled using one of the two DNA strands as the temp late (the transcribed strand).

T

T

~ 4 . Th e m R NA separates from the DNA.

T

Y

3. The RNA nucleotides are linked up to form a strand of RNA.

Stages 1, 2 and 3 are all carried o ut by th e enz y me RNA pol ym erase.

TRANSLATION Translation is ca rried out by ribosomes, using mRNA and tRNA . It is th e genet ic code that is being translated . The genetic co de is a trip let co de - three bases co de for one amino aci d. A group of th ree bases is called a co do n. 1. Messenger RNA binds to the small

subunit of the ribosome. The mRNA

contains a series of codons, each of

w hich codes for one amino acid.

anticodon

~~ 2. Transfer RNA molecules are present around the

ribosome in large numbers. Each tRNA has a special

triplet of bases called an

antico don and carries the

amino acid corresponding

to this antico don.

-----=

4 . The two amino acids carried by the tRNA molecules are bonded together by a peptide linkage. A dipeptide is formed, attached to the tRNA on the right. The tRNA on the left detaches. The ribosome

moves along the mRNA to the

next codon. Another tRNA

carrying an amino acid binds. A

chain of three amino acids is

formed. These stages are repeated

until a polypeptide is formed.

amino acid

\

I

/

J

~~

~

small subunit of ribosome mRNA

•

direction of movement of ribosome

/ :' . . 3. tRNA molecules bind to the ribosome. Two can bind at once. tRNA can only bind if it has the anticodon that is complementary to the codon on the mRNA. The bases on the codon and anticodon link together by forming hydrogen bonds, following the same rules of complementary base pairing as in replication and transcription.

The chemistry of life 17

Genes, polypeptides and enzymes

ONE GENE-ONE POLYPEPTIDE HYPOTHESIS Genes determ ine th e ami no ac id sequence of pro teins. How ever, some prot ein s co nta in mo re than o ne typ e of po lyp ept ide. Hemoglob in is an exa mple of thi s - it co nta ins two different typ es of po lyp ept ide. It was fo und t hat a d ifferent gene is needed to make eac h po lyp ept ide. Further research has shown that there is almost always a single gene to co de fo r a po lypept ide, w hic h does not code fo r any other po lypepti de. This di sco very led to an im portant hyp othesis in mo lecu lar bio logy - the one gene-o ne po lyp eptid e hypoth esis. There are some excep tio ns to this general rul e: • Some genes code fo r transfer RNA o r messenger RNA, not for polypept ides. • Some DNA sequences act as regulato rs of gene expression and are not translated into pol ypeptides. • In lymphocytes, pieces of D NA fro m di fferent parts of the genome are spliced together and t ranscrib ed and translated to produce antibod ies. Di fferent lymphocytes produ ce di fferent antibodies by splic ing together DN A inh erited from parents, in different way s.

Stages in enzyme cata lysis

substrate

Substrate molecules are in continual random motion. If one coll ideswith the active site it can bind to it. enzyme-substrate complex

INTRODUCING ENZYMES Catalysts speed up chemica l reacti on s w ithout bei ng c hanged themselves. Livi ng organisms make bio logical catalysts called enzymes. Enz ymes are globular proteins which act as catalysts of

chemical reactions. Wi thout enzy mes to catalyse them, many chemica l processes happen at a very slow rate in living organisms. By making some enzy mes and not others, cells can co ntro l w hat chemica l reactio ns happen in their cytop lasm. The structure of enzy mes is quite delicate and can be damaged by vario us substances and co ndit ions. Thi s is called denaturati on .

The substrate fits the active site. If other molecules collide with the active site they do not fit and fail to bind.

Denaturation is changing the structure of an enzyme (or othe r protein) so that it can no longer carry out its function. Denaturat io n is usually permanent.

In chemica l react ion s, one or more reactants are conve rted

into one or more products. In reactions catalysed by enzy mes,

the reactants are called substrates.

ENZYME-SUBSTRATE SPECIFICITY M ost enzy mes are speci fi c - they catalyse very few d ifferent reacti ons. They therefore only have a very small number of possible substrates. Thi s is called enzy me-s ubstrate spec ifi ci ty. The substrates bind to a spec ial regio n on the surface of the enzy me called the active site. An active site

is a region on the surface o f an enz ym e to which substrates bind and which catalyses a chemical reaction involving the substrates. The active site of an enzy me has a very intricate and precise shape. It also has d istin cti ve c hemical pro perti es. Active sites match the shape and c hemica l properties of their substrates. M o lecules of substrate fit the act ive site and are chemically att racted to it (right). Other mo lecu les either do not fit or are not chemica lly attracted. They do not therefore bind to the act ive site. This is how enzy mes are substrate-specific. The way in wh ic h the enzy me and substrate fit together is similar to the way in w hic h a key fit s a lock. The enzyme is Iike the lock and the substrate is Iike the key that fits it.

18 The chemistry of life

The active site catalysesa chemical reaction. The substrates are turned into products. enzyme

I products

~ The products detach from the active site, leaving it free for more substrate to bind.

Enzymes in action FACTORS AFFECTING ENZYME ACTIVITY

EFFECT OF SUBSTRATE CONCENTRATION

W herever enzymes are used, it is important that they have the co nd itio ns that they need to w o rk effect ively. Temp eratur e, pH and substrate concentrat io n all affec t the rate at w hic h enzymes catalyse chem ica l react ions. The fi gures (below and ri ght) show the relatio nship s betwee n enzy me act ivity and substrate co nce ntratio n, temperature and pH .

At low substrate concentrations, enzyme activity increases steeply as substrate concentration increases. This is because random coll isions between substrate and active site happen more frequently with higher substrate concentrations.

EFFECT OF TEMPERATURE Enzyme activity increases as temperature

increases, often doubling w ith every 10 °C rise.

This is because col lisions betw een substrate and

active site happen more frequently at higher

temperatures due to faster molecular motion .

.c :~ uco (l)

E >­ N

C

LLJ

~ At high substrate concentrations most of the active sites are occupied, so raising the substrate concentration has littl e effect on enzyme activity.

1

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Substrate concentration - . .

(l)

E >­ N

C

LACTASE AND LACTOSE-FREE MILK

LLJ

Temperature

•

At high temperatures enzymes are denatured and stop wo rking. This is because heat causes vibrations inside enzymes w hich break bonds needed to maintain the structure of the enzyme.

EFFECT OF pH Optimum pH at whi ch enzyme

activity is fastest (pH 7 is

optimu m for most enzymes).

Lactose is the sugar that is natur ally present in mi lk. It can be co nve rted into glucose and galactose by the enzyme lactase. lactase Lactase is obta ined fro m Klu verom yces lactis, a type of yeast that grow s naturally in m il k. Biotec hnology companies culture the yeast, extract the lactase from the yeast and purify it, for sale to food manufa cturin g co mpanies. There are several reasons fo r usin g lactase in food pro cessing: • Some peopl e are lactose int ol erant and cannot d rink more th an about 250 m l of m ilk per day un less it is lactose­ reduced. • Galactose and glucose are sweeter than lacto se, so less sugar needs to be added to sweet foods cont aining m ilk, suc h as mi lk shakes or fru it yog hurt. • Lactose tend s to crystalli ze du rin g produ ction of ice cream, givi ng a gritty textur e. Because glucose and galac tose are mor e soluble than lactose they remain di ssolved, giving a smoo ther textu re.

1

.c :2: u '"

• Bacteri a ferme nt glucose and galac tose mor e qui ck ly than lactose, so the production of yog hurt and cott age cheese is faster.

E >­ N

Lactase is used in two w ays during food processing:

(l)

C

LLJ

pH ----~.

As pH increases or decreases from the optimum, enzyme activity is reduced. Both acids and alkalis can denature enzymes.

1. It can be added to milk. The final produ ct co ntains the enzym e. 2. It can be immobi lized on a surface or in beads of a porous materi al. Th e milk is then allowe d to flow past the immobi lised lactase. This avoids contam inatio n of the produ ct with lactase.

The chemistry of life 19

Cell respiration and energy

ENERGY AND CELLS All living cells need a continual supply of energy. This energy is used for a wide range of processes including active transport and protein synthesis. Most of these processes require energy in the form of ATP (adenosine triphosphate). ATP is a chemical substance that can diffuse to any part of the cell and release energy. Every cell produces its own ATP, by a process called cell respiration. In cell respiration, organic compounds such as glucose or fat are carefully broken down. Energy from them is used to make ATP. Cell respiration is defined as controlled release of energy, in the form of ATP1 from organic compounds in cells. Cell respiration can be aerobic or anaerobic. Aerobic cell respiration involves the use of oxygen and anaerobic cell respiration does not.

THE USE OF GLUCOSE IN RESPIRATION Glucose is often the organic compound that is used in cell respiration. Chemical reactions in the cytoplasm break down glucose into a simpler organic compound called pyruvate. In these reactions a smarr amount of ATP is made using energy

released from gl ucose.

Glucose

Small amount of ATP

ANAEROBIC CELL RESPIRATION If no oxygen is available, the pyruvate remains in the cytoplasm and is converted into a waste product that can be removed from the cell. No ATP is produced in these reactions. In humans the waste product is lactate (lactic acid). In yeast the products are ethanol and carbon dioxide.

Humans

Pyruvate

--------------------------l.~

Lactate

Ethanol

Pyruvate

Yeast Carbon dioxide

AEROBIC CELL RESPIRATION If oxygen is available, the pyruvate is absorbed by the mitochondrion. Inside the mitochondrion the pyruvate is broken down into carbon dioxide and water. A large amount of ATP is produced as a result of these reactions. Aerobic cell respiration therefore has a much higher yield of ATP per gram of glucose than anaerobic cell respiration.

Carbon dioxide Pyruvate Water

Large amount of AlP

20 The chemistry of life

Photosynthesis

INTRODUCING PHOTOSYNTHESIS Photosynthesis is the process used by plants and some other organisms to produce all their own organic substances (food), using only light energy and simple inorganic substances. It involves many stages and some complex chemical reactions, but it can be outlined in a series of statements. • Photosynthesis involves an energy conversion. Light energy, usually sunlight, is converted into chemical energy. • Sunlight is called white light, but it is actually made up of a wide range of wavelengths, including red, green and blue. • Some substances called pigments can absorb light. The main pigment used to absorb light in photosynthesis is chlorophyll. • The structure of chlorophyll allows it to absorb some colours or wavelengths of light better than others. Red and blue light are absorbed more than green. • The green light that chlorophyll cannot absorb is reflected. This makes chlorophyll and therefore chloroplasts and plant leaves look green. • Some of the energy absorbed by ch lorophyll is used to prod uce ATP. • Some of the energy absorbed by chlorophyll is used to split water molecules. This is called photolysis of water. • Photolysis of water results in the formation of oxygen and hydrogen. The oxygen is released as a waste product. • Carbon dioxide is absorbed for use in photosynthesis. The carbon from it is used to make a wide range of organic substances. The conversion of carbon in a gas to carbon in solid compounds is called carbon fixation. • Carbon fixation involves the use of hydrogen from photolysis and energy from ATP.

MEASURING RATES OF PHOTOSYNTHESIS

Effect of light intensity on photosynthesis

Photosynthesis involves the production of oxygen, the uptake of carbon dioxide and an increase in biomass. Any of these can be used as a measure of the rate of photosynthesis.

At high Iight intensities the rate reaches a plateau. I

Production of oxygen Aquatic plants (e.g. Myriophyllum) release bubbles of oxygen when they carry out photosynthesis. If these bu bbles are collected, their volume can be measured.

Uptake of carbon dioxide

CJ'l

Leaves take in CO 2 from the air or water around them, but this is difficult to measure directly. If CO 2 is absorbed frorn water, the pH of the water rises. This can be monitored with pH indicators or with pH meters.

'Vi Q.)

At low to medium light intensities the rate is directly proportional to Iight intensity.

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Increases in biomass

Q.)

If batches of plants are harvested at a series of times and the biomass of the batches is determined, the rate of increase in biomass gives an indirect measure of the rate of photosynthesis in the plants.

~

~

Light intensity -

~

Effect of temperature on photosynthesis

Effect of CO 2 concentration on photosynthesis

At very high CO 2 concentrations the rate reaches a plateau.

As temperature increases the rate increases more and more steeply.

Optimum temperature

Above the optimum temperature the rate falls steeply.

I

No photosynthesis at very low CO 2 concentrations. CJ'l

CJ'l

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Q.)

At Jow to fairly high CO 2 concentrations the rate is positively correlated with CO 2 concentration.

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Temperature ­

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The chemistry of life 21

EXAM QUESTIONS ON TOPIC 3 1 The table below shows the base composition of genetic material from ten sources. Source of genetic material Cattle thymus gland Cattle spleen Cattle sperm Pig thymus gland Salmon Wheat Yeast

E. coli (bacteri a) human sperm influenza virus

Base composition (%) Adenine

Guanine

Thymine

Cytosine

Uracil

28.2 27.9 28.7 30.0 29.7 27.3 31.3 26.0 31.0 23.0

21.5 22.7 22.2 20.4 20.8 22.7 18.7 24.9 19.1 20.0

27.8 27.3 27.2 28.9 29.1 27.1 32.9 23.9 31.5 0.0

22.5 22.1 22.0 20.7 20.4 22.8 17.1 25.2 18.4 24.5

0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 32.5

a) Deduce the type of genetic material used by (i) cattle

[1 ]

(ii) E. coli

[1]

(iii) influenza viruses.

[1]

b) Suggest a reason for the difference between cattle thymus gland, spleen and sperm in the measurements of their base composition.

[1]

c) (i) Explain the reasons for the total amount of adenine plus guanine being close to 50% of many of the species in the table.

[3]

in the genetic material

(ii) Identify two other trends in the base composition of the species that have 50% adenine and guanine.

[2]

d) (i) Identify a species shown in the table that does not follow the trends in base composition described in (c).

[1]

(ii) Explain the reasons for the base composition of this species being different.

2 The graph (right) shows the results of a data logging experiment. Chlorell«, a type of alga that is often used in photosynthesis

[2]

I 0...

experiments, was cultured in water in a large glass vessel. Light intensity, temperature and the pH of the water were monitored over a three-day period. The changes in pH were due to changes in carbon dioxide concentration. An increase in CO 2 concentration causes a decrease in pH.

7.5 7.0 6.5

a) State the relationship shown in the graph between (i) Iight intensity and CO 2 concentration

6.0

[1]

(ii) temperature and CO 2 concentration.

[1]

20

b) Deduce, from the data in the graph, whether the effect of light intensity or temperature on carbon dioxide concentration is greater. [2] x

~

(i) rises in CO 2 concentration

[2]

(ii) falls in CO 2 concentration.

[2]

.~

100 2

3

days COOH

I R-C- H

I

NH 2

22 18 Questions - The chemistry of life

300 200

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400

c) The graph shows both rises and falls in CO 2 concentration. Explain the causes of

3 The diagram shows the basic structure of amino acids

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__

Genes and chromosomes GENES Genetics is the study of variation and inh eritance. The basic un it of in her itance is the gene. A gene is a heritable factor that contro ls a specific characteristic. A typ ical animal or plant cell nucleus contains thou sands of genes. The total numb er of genes in humans is not yet known but is probab ly between 30 000 and 40 000. A ll of the genes of an organism are known co llectively as the genome. A genome is the whole of the genetic information of an organism.

CHROMOSOMES Gen es are made of D N A . They are part of mu ch larger D NA mo lecu les called chro mo somes. In eukaryotes, prot eins are alw ays associated with the D NA in chromosomes. A typi cal anima l o r plant chromosome co ntains abo ut a 1000 genes, w hic h are arranged in a linear seque nce. In any particu lar type of chromosome the same genes are found arranged in the same sequence. The positi on of a gene o n a chromosome is call ed the gene locus.

Sickle cell anem ia - the consequences of a base substitution mutation Hb is a gene that codes for a polypeptide of 14 6 amino acids forming part of hemoglobin Base substitution

Pa rt of

H b~~y

y

REPLICATION OF CHROMOSOMES

~:\%rtof

Hbs

Transcription

ALLELES A lthou gh one parti cul ar chromoso me type always has the same genes in the same sequence, the genes themselves can vary. D ifferent form s of many genes can be found. These are called all eles of the gene. An allele is a form of a gene, differing from oth er alleles of the gene by a few bases at most and occup ying the same locus as the other alleles of that gene.

.:

•

from A toT

in the triplet

coding for the

sixth amino

acid. The

mutation

changes HbA

into a new

allele, Hbs

/

If a nucleu s is go ing to d iv ide by m itosis or meiosis, all D NA in the nucl eus is replicated . W hen m ito sis or meiosis begins, each chromo some is v isible as a doub le structure (see below). The tw o parts are called chromat ids and are co nnected by a centrom ere. Som e types of chromoso me have a centrome re in the centre and others have a centromere nearer to on e end .

Transcription

j

/

One codon in

the mRNA is

different and

therefore one

amino acid

in the poly­

peptide is

altered

Translation

Translation

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~ Q~y

~

V '?­ 0

,

I

Effect on the phenotype

Effect on the

PhTY'"

j

":,';

©-, 0© 'I U . . . , -.

GENE MUTATION Genes are almost always passed from parent to offsp ring w itho ut bein g changed. Occasio nally genes do change and this is called gene mutati on . Gene mutation is a change to the base sequence of a gene. The small est possible change is w hen one base in a gene is replaced by another base. Thi s type of gene mutation is ca lled a base subst it utio n. A ltho ugh only on e base is changed , the co nsequences can be very significant. Ma ny gene mut ations cause a genetic d isease. More than four thousand genetic di seases have been discovered in hum ans. O ne example is sick le cell anem ia (rig ht).

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,

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Normal red blood cells that carry oxygen efficiently but are affected by malaria

cred~nn~ft~~ s ~~ blood

2J

cells containing

the altered

hemoglobin

become

sickle shaped

Sickle cells may carry oxygen less efficiently but can give resistance to malaria

The allele Hb>that causes sickle-cell anemia has become quite common in some partsof the world affected by malaria. In these regions the malaria resistance that it causes is an advantage

Genetics 23

Meiosis

Chromosomes of a human female

HAPLOID AND DIPLOID In most ce lls the nucl eus co ntai ns tw o of each type of c hromo some (right). The cell therefore has tw o fu ll sets of chromosomes. Th is is called dipl oid . Some cells only con tai n o ne of each typ e of chromosome and therefore have ju st one set. This is ca lled hapl oid . In di ploid ce lls each pair of chromosomes have the same genes, arranged in the same sequence. Ho wever, they do not usually have the same alleles of all of these genes. They are therefore not identi cal but instead are hom ol ogous.

Homologous chromos omes have the same genes as each other, in the same sequence, bu t not necessarily the same alleles of those genes. The numb er of chromoso mes in a cell can be redu ced fro m dip loid to haploid by the process of meiosis. M eiosis is describ ed as a redu cti on di vi sion . Livi ng organisms that reprodu ce sexu ally have to halve their c hromosome number at some stage in the life cycle because the fusion of gametes durin g ferti lization doub les it.

STAGES OF MEIOSIS

Chromosom es pair up .The chro moso mes in eac h pair a re hom ologou s

Prophase I

Nuclea r membr ane will soo n break down

M etaph ase I

A naphase II

Prophase II

24 Genetics

Each chromosome stiIIco nsists of two c hromat ids

l

The cell mem brane a round the equator will soo n be pu lied inward s to divide the cell

Telo phase II

The ce ntro meres have divided making the chromatids into separate chro mosomes which move to o ppo site poles

The ce ll has divided to form two hap lo id ce lls. These imm­ ed iately divide aga in - meios is invo lves two di vision s

An aph ase I

Homologous q_--'~ chromoso mes are pu lled to opposite po les. This ha lves the c h romo so me num ber

Spind le microtubul e s from the two poles attac h to d ifferent ch romo somes in ea c h pair, ens uring that o ne is pulled to o ne po le a nd the other to the othe r pole

Spind le microtu bu les grow from each po le to the equator as in mitos is

The pa irs of chromoso mes line up o n the eq uator

Each nucl eu s now has ha lf as many chro moso mes as the nucleu s of the paren t ce ll

Nuclear membranes reformed

New spind le microtubules grow from the po les to the eq uator

The ce ll membran e is pu lled inwards agai n to divide the ce lls

Both cells have divided again to form four haploid ce lls

Karyotypes

KARYOTYPES AND KARYOTYPING

ANALYSIS OF KARYOTYPES

The numb er and appearance of the chromosomes in an organism is called the karyotype. Living organisms that are members of the same species usuall y have the same karyotype. The karyotyp e of a human female is shown o n page 24 . From a karyotype , the gender of a person can be deduced and chromosome abno rmalit ies can be detected. The most useful time to do this is befo re birth. Cel ls have to be obtained from the fetus. There are two way s of doi ng this: 1. Amniocen tesis A sample of amniotic fluid is removed from the amniotic sac around the fetus. To do this, a hypod ermi c needl e is inserted th rough the wa ll of the mot her's abdo men and wa ll of the uterus. Am niot ic flu id is draw n out into a syringe. It co ntains cells from the fetus. 2. Chorionic villus sampling Cells are removed from fetal tissues in the placenta cal led chorio nic villi. As wi th amnioce ntesis a hypod erm ic need le, inserted through the mother' s abdomen and uterus wal l, is used to obtain the cells.

The gender of the fetus can be determin ed from the sex chromosomes. Gender determ ination is descr ibed o n page 28 . Karyot ypes can also be analysed to f ind out w hether a fetus has chro mosome abnormalitie s. Sometimes chromoso mes that should separate and move to opposite po les during mei osis do not separate and instead mov e to the same po le. This can happen in either the first (below left) or the second div isio n of meiosis (below right). No n-separati on of chro mosomes is called non-disjunction. The result is that gametes are prod uced w ith either on e chro mosom e too many or too few .

Anaphase I

Anaphase II

~ ,\ (K? ~ Z-J ~< ~

Gametes w ith one chromosome too few usuall y qui ck ly d ie. Gametes w it h one chromoso me too many sometimes survi ve. W hen they are fertili sed, a zygo te is prod uced w ith three chromosomes of o ne type instead of two . For example, in the karyotype (below ) there are 4 7 chromoso mes in total with three c hromoso mes of type 21, rather than two . This causes Dow n syndrom e. It can be due either to non-d isj unct io n d uring the form ati on of the sperm or egg. The chance of Dow n synd rome increases w ith the age of the parents.

O nce fetal cells have been obtai ned, they are inc ubated w it h chemicals that sti mulate them to di vid e by mitosis . Another chemical is used w hic h stops mitosis in metaphase of mitosis. Chromosomes are most easily visible in metaphase. A f luid is used to burst the cells and spread out the chromosom es. The Durst ce lls are examined using a microscope and a photograph is taken of the chro mosomes from one cell below). The chromosomes in the photog raph are cut out and arranged into pairs acco rding to thei r size and struct ure. Th is is called kar yot yping.

..

.-

Genetics 25

Monohybrid crosses

MENDEL'S MONOHYBRID CROSSES

DEFINITIONS OF TERMS USED IN GENETICS

G regor M endel is often regard ed as the father of genetics. He investigated inheritance by crossing var ieties of pea plants that had different charac teristic s. For examp le, he crossed a variety th at had round seeds w ith a va riety that had w ri nk led seeds. He fo und th at all the offspring (call ed the F1 generatio n) had the same characte ristic as o ne of the parents. He all owed the F1 generatio n to self-fertilize - each plant prod uced offspr ing by ferti lizi ng its female gametes w ith its ow n male gametes. The offspri ng (call ed the F2 generat io n) contained bot h of the original parental typ es. The characteristic that di sap peared in the F, generation reappea red in a qu arter of the F2 generatio n. M endel dedu ced that inh eritance is based o n factors that can be passed on from generat io n to generatio n. W e now ca ll these facto rs genes. Di fferent fo rms of a gene are called alle les. The figur e below shows an examp le of M end el's mon oh yb rid cro sses.

There are tw o pairs of terms that are often used by geneticists : • Hom ozygou s - having two iden tical alleles of a gene. A ll the gametes of a homozygote have the same allele. • Hetero zygou s - having two differen t alleles of a ge ne. Half of the gametes of a heterozygote have one of the alleles and half have the other allele. • Do mi nant alle le - an allele that has the same effect on the phenotype in a heteroz ygous ind ividual (w here it is com bined w ith a recessive alle le) as in a homoz ygou s individual (where there are tw o co pies of the dominant alle le). • Recessive allele - an allele that only has an effect on the p he no type in hom oz ygou s individ uals (w here the re are two cop ies of the rece ssive alle le). In hetero zygous ind ivi d ua ls the recessive allele is hidden by the domi nant al le le.

Monohybrid cross between smooth and wrinkled seed pea plants P = parental generatio n.

= the alleles possessed by an organism.

Genotype

ss

P genotype - - ­

phenotype - - ­

characteristics gametes ___

F1 = the first fil ial generatio n- the offspri ng of the P generation. F, plants are heterozygous but all have smoot h seeds because S is the domin ant allele and s is recessive.

o

!.I

smooth seed

Phenotype = the of an organism.

ss

F, genotype ___ phenotype ___

w rinkled seed

1

1

®

s

Vo

Gametes are produced by meiosis so are haploid and only have one copy of each gene.

ss

smooth seed

gametes - - ­

Seed shape is determined by a single gene. O ne alle le of this gene (S) gives smooth seeds and the other (s) gives w rinkled seeds. The pea plants are dip loid so they have two copies of each gene. The parental varieties are both homozygous.

/\

W hen the F1 hybrid plants produce gametes, the two alle les separate. This is called segregation.

Segregation occ urs during meiosis. The two alle les of a gene are located on

hom ologous chromosomes F2 genotypes ~_ The grid show n and phenotypes ~ here is called a Punnett grid. It is used to show all - ---jf-- - - - - - - - - <. the possib le outcomes in a cross. In this case both the male and female gametes can be or O , giv ing four possible F2 genotypes. There is a 3:1 rati o of smooth and w rinkled seed F2 plants.

Crosses between two heterozygous individuals give a 3:1

ratio if one of the all eles is dom inant and the other is recessive.

®

26 Genetics

w hich move to opposite poles, causing the segregation (see below).

0@

Inheritance of blood groups

The principles of inheritance discovered by Mendel in pea plants also operate in other plants and in animals. There are, however, sometirnes differences and two of these are demonstrated by the inheritance of ABO blood groups in humans ­ codominance and multiple alleles.

CROSS INVOLVING CODOMINANT ALLELES

P phenotype

)

genotype

)

gametes

Group A

)

X

Group B

IAI A

181 B

1 0

1 0

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F1 genotype

)

phenotype

)

IAIB

IA is the allele for blood group A and I B is the allele for blood group B. Neither allele is recessive, so both are given upper case letters as their symbol.

If IA and 18 are present together, they both affect the phenotype because they are codom inant. Codominant alleles are pairs of alleles that both affect the phenotype when present together in a heterozygote.

--­

Group AS

CROSS INVOLVING MULTIPLE ALLELES P phenotype

)

Group A

Group S

genotype

)

IAi

IBi

gametes

(encircled)

~

(~0 8

IA 18

0/) IAi

...

...

_ Group S

alleles.

8

Group AS

8 1 i

F1 genotypes and phenotypes shown on Punnett grid

The gene that controls ABO blood groups has a third allele: i If there are more than two alleles of a gene, they are called multiple

Group A

A 8 j is recessive to both I and 1 so IA i gives blood group A and 18 i gives blood group O.

~

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ii

Group 0

DEDUCING GENOTYPES FROM PEDIGREE CHARTS :\ pedigree chart shows the members of a family and how they are related to each other. Males are shown as squares and females as circles. If the phenotypes of the rnembers of the family are known, the genotypes can often be deduced. The figure (right) is a pedigree chart that shows the blood group of each individual. All of the genotypes can be deduced. It is also possible to deduce the probabi Iity of the first child of the parents in the third generation being blood group A, B, AB and O.

"

Individuals who are homozygous for i are in blood group O.

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Genetics 27

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--~-

~~~~====::=::===

Genes and gender SEX CHROMOSOMES AND GENDER

Inheritance of gender in humans

¥ xx

• Two chromosomes determine the gender of a child (whether it is male or female). These are called the sex chromosomes. • The X chromosome is relatively large and carries many genes. • The Y chromosome is much smaller and carries only a few genes. • If two X chromosomes are present in a human embryo and no Y chromosome, it develops into a girl. • If one X chromosome and one Y chromosome are present, a human embryo develops into a boy. • When women reproduce, they pass on one X ch romosome in the egg. • When men reproduce, they pass on either one X or one Y chromosome in the sperm, so the gender of a child depends on whether the sperm that fertilizes the egg is carrying an X or a Y chromosome (right).

..

x

xx

Xy

¥

xx

¥

cf

Xy cf

¥ = Female cf = Male

SEX LINKAGE

CHOOSING SYMBOLS FOR ALLELES

If a gene is carried on the X chromosome, the pattern of inheritance is different for males and females - there is sex Iinkage. Sex linkage is the association of a characteristic with

These rules are usually followed when choosing symbols for alleles:

1. One dominant and one recessive allele of a gene

gender, because the gene controlling the characteristic is located on a sex chromosome. Sex-linked genes are almost always located on the X chromosome. Females have two X chromosomes and therefore have two copies of sex linked genes. Males on Iy have one X ch romosome and therefore only have one copy of sex linked genes. In humans, hemophilia (below) and red-green colour blindness are examples of sex-I inked characteristics.

A letter is chosen. The dominant allele is shown with the upper case, and the recessive allele with the lower case letter (e.g. A and a)

2. Co-dominant alleles A letter is chosen. This letter and a superscript letter represent each allele. (e.g. CW and C')

3. Sex-linked dominant and recessive alleles The letter X is used to show the X chromosome. Each allele is shown superscript. (e.g. X H and Xh)

Example of a cross involving sex linkage

The mother is heterozygous but is not a hemophiliac because H is dominant and h is recessive. She is a carrier of the allele for hemophilia.

The diagram below shows how two parents, neither of whom have hemophilia, could have a hemophiliac son.

H

x" X chromosome carrying

A carrierhas a recessive allele of a gene

but it does not affect the phenotype because a dominant allele is also present.

the allele for hemoph ilia.

1---+-----

normal

carrier None of the female offspring are hemoph iliac because they all inherited the father's X chromosome wh ich carries the allele for normal blood clotting (H), but there is a 50% chance of a daughter being a carrier.

28 Genetics

KEY

X X chromosome carryi ng the allele for normal blood clotting

'>----+----

hemophiliac

ef

The Y chromosome does not carry either allele of the gene.

There is a 50% chance of a son being hemophiliac as half of the eggs produced by the mother carry Xh. The chance of a daughter being hemophiliac is 0 % , so the overall chance of offspring being hemophiliac is 25%.

Deducing genotypes

USING PEDIGREE CHARTS

USING TEST CROSSES

Pedigree charts can be used to deduce w hether a character is caused by a dom inant or recessive allele and w hether it is sex-linked or not. They can also be used to deduce the genoty pes of ind ividuals. The f igures (below) are pedi gree charts that each show a di fferent pattern of in herit ance. Squares represent males and ci rcles represent females. Shaded symbols represent ind iv idua ls affected by the co nd itio n and unshaded symbo ls represent unaffected indiv iduals. The probab ili ty of the different phenoty pes in the offspring of some of the co up les in the pedigrees (marked w ith an asterisk *) can be determin ed.

It is not always possible to di scover w hether an ind ividu al has a gene, or does not have it, by looking at the indi vidu al's phenotyp e. If one alle le of a gene is domin ant and another alle le is recessive, an individu al w ith two co pies of the dominant alle le has the same phe noty pe as an indi vidu al w ith one domin ant and one recessive all ele. These two genotypes can be di stinguished by carryi ng out a test cross.

MUSCULAR DYSTROPHY

In a test cross an individual that might be heteroz ygous is crossed with an individual that is hom oz ygous recessive. Example of a test cross A farmer is unsure wh ether his bull is a pur ebred Hereford or w hether it is a Hereford x Abe rdeen A ngus hybr id . Hereford catt le have a w hite head caused by a domi nant alle le (H). A berdeen Angus catt le have blac k heads caused by a recessive alle le of the same gene (h). The farmer crosses his bu ll with 100 Aberdeen An gus cows . The fi gures below show the possib le outco mes.

x

n

6 2J

ALBINISM

Whit e-headed bull

Black-headed cows

WW

ww

j

j

e

@

Ww All offspring have w hite heads

x

HUNTINGTON'S DISEASE W hite-headed bull

Black-headed cows

Ww

ww

/\e @ Ww

j

e

ww

1:1 ratio of wh ite and black heads

Genetics 29

DNA profiling

PCR - POLYMERASE CHAIN REACTION

GEL ELECTROPHORESIS

In the po lym erase chain reacti on, D NA is co pied again and again to produ ce many co pies of the o rigi nal mo lecu les. Mi lli on s of cop ies of the D NA can be produ ced in a few hour s. Thi s is very usefu l w hen very small qu antities of D NA are fo und in a samp le and larger amounts are needed for analysis. DN A fro m very small samples of semen, blood or other tissue or even from long-dead speci mens can be amplifie d using PCR. PCR is carried out at high temperatures using a D NA po lym erase enzy me from Thermu s aquaticus, a bacterium that lives in hot springs.

Gel electro phoresis is a method of separating mi xtur es of protein s, DN A or other mo lecu les that are c harged. The mixtur e is pl aced o n a thin sheet of gel, w hic h acts like a mo lecu lar sieve. An electric fi eld is applied to the gel by attaching electrodes to both ends. Dependin g on w hether the particl es are posit ively or negati vely charged, t hey mov e tow ards o ne of the electro des or the other. The rate of movement depends o n the size and charge of the mo lecul es ­ small and highl y charged mo lecules move faster than larger or less charged ones.

DNA PROFILING Hum ans and ot her o rganisms have short seq uences of bases that are repeated many tim es ca l led satelli te D N A . This satel lit e DNA vari es great ly between different indi vidu als in th e number of repeats. If it is co pied using PCR and then c ut up into short fragments using restr ict io n enzy mes, th e lengths of th e fragments vary greatly betw een individu als. Ge l elect ropho resis ca n be used to separate fragmented pieces of D NA acco rd ing to th eir c harge and size . The patte rn of band s o n the gel is very unli kely to be t he same for any two individ uals. This techniqu e, ca lled DN A prof i ling o r D NA fi ngerprinting has many app licatio ns, in cludin g forensi c inv estigations (o bta ining ev ide nce to use i n court cases) and investigating paternity (w ho the father of a c hi ld is).

For en sic use of DNA profiling a

b

s

Testing paternit y using DN A p rofiling

c

d

e s

F

G kb

"I

-

20

-

10

The f irst use of DN A profi ling was in the Enderby doub le murder case. The D NA profil es show cl early w hether the prim e suspect was guilty . a = hair roots from the first victim b = mi xed semen and vaginal flui ds fro m the f irst victim

c = blood of second victim

d = vaginal swab from second victim

e = semen stain o n second victim

s = blood of prim e suspect.

The tw o bands indi cated by arrows are from DNA in the culprit's semen.

30 Genetics

The D NA profi les of a fami ly of dun nock s (Prunella modu laris) are show n above. Dunnocks are small bird s fo und in Europe, North Afri ca and Asia. The tracks from left to right are: the female, tw o resident males that mi ght have been the father of the offspring and four offspring. The resuIts show that the f3 maIe fathered three of the fo ur offspri ng (D , E and F), despite bein g less domin ant than the a male.

Genetic modification

GENETIC MODIFICATION AND ITS USES The genetic code is universal, so genes can be tr ansferred from one organism to anoth er, even if they are members of different speci es. A gene codes for a po lypeptide with the same am ino aci d sequ enc e, w hether it is in a hum an cell, a bacterium or any oth er cell. Org ani sms that have had genes transferred to them are called genetically modifi ed or gani sms (GM O) o r tr ansgenic organi sms. The process of tr ansferrin g genes is calle d genetic mo dif icatio n. O ne exam ple is the transfer of a gene for factor IX (a blood cl ottin g factor) from hu mans to sheep, w here it is produc ed in th e sheep's milk . An other example is the transfer of the gene fo r resistance to the herbicid e glyphosate from a bacterium to cro p plants, so that the crop can be sprayed w ith the herbicid e.

Techniques used for gene transfer into bacteria Human insulin

Plasmids are small loops of DNA found in bacteria.

Messenger RNA coding for insulin is extracted from human pancreas

cells that make insuli n.

DNA copies of the messenger RNA are made using the enzyme reverse transcriptase.

Sticky ends are made by adding extra G nucleotides to the ends of the gene.

1

oj

Plasmids are

cut open using restricti on enzymes.

j

1

Restriction enzymes cut DNA at specific base sequences.

U

-j

Sticky ends are made by adding extra C nucleotides to the ends of the cut plasmid.

~

The insulin gene and the plasmid are mixed. They link by complementary base pairing (C - G), between the sticky ends.

~~

~~

The recombinant plasmids are mixed w ith the host cells. The host cells absorb them.

CJ DNA ligase seals up the nicks in the DNA by making sugar-

I

The plasmid w ith the human insulin gene inserted is called a recomb inant mid

d h",''h" b:"c=r

The E. coli bacteria start to make human insul in, which is extracted, purified and used by diabetics.

The genetically modi fied E. coli are cultured in a fermenter.

A suitable host cell is chosen to receive the gene, in this case a strain of E. coli bacteria.

~~

~&

BENEFITS AND RISKS OF GENETIC MODIFICATION The production of hum an in sulin using bacteri a has enormous benef its and no obv iou s harmfu l effects. Th ere are oth er examp les of genetic mod ifi cation that are mo re controversial. M aize crop s are often seriously damaged by corn borer insects. A gene from a bacterium (Baci ll us thuringiensis) has been transferred to maize. Th e gene codes for a bacte rial prot ein called Bt to xin that kills corn borers feedin g on the maize. Pot enti al benefits of Bt maiz e

Possibl e harmful effec ts of Bt maize

1. Less pest dam age and therefor e hi gher cro p yields to help to reduce food shortages

1. Huma ns o r farm anima ls th at eat the genetica lly modi fi ed maize m ight be harmed by the bacterial DNA in it, or by the Bt to xin

2. Less land needed fo r crop prod uct ion , so some co uld becom e areas for w ild li fe con servation

2. Insects that are not pests co uld be ki ll ed. M aize pollen containing the tox in is blown ont o wild pl ants grow ing near the maize. Insects feedin g on the wi ld plants, in clud ing M on arch butt erf ly caterpill ars, are therefor e affected even if they do not feed on the maize

3. Less use of insecti c ide sprays, w hic h are expensive and can be harmfu l to farm w o rkers and to w iJdJife

3. Populatio ns of w ild plants m ight be changed. Cross-po lli natio n wiJl sp read the Bt gene into some wi ld plants but not others. These plants wo uld then produ ce the Bt toxin and have an advantage over other wi ld plants in the struggle for survival

Genetics 31

Cloning

CLONES AND CLONING

PLANT AND ANIMAL CLONING

Clo ni ng is produ cin g identi cal co pies of genes, cells or organisms. The produ cts of cloning are called a clone. A clo ne is a gro up of genetica lly identical organisms or a gro up of genetica lly identical cells derived from a single parent cell . Cloning is very useful if an organism has a desirabl e combinatio n of c haracteristics and mo re organisms with the same characterist ics are wa nted - th is is reprodu ctive cl on in g. Sometimes cl oning is used to produ ce skin or other tissues needed to treat a pat ient - this is therapeutic cl on ing.

Most pl ants can be clon ed qui te easily from pieces of root, stem or leaf. A nimals cannot be cl oned in the same way from parts of thei r bodi es. If animal embryos are di vided up at an early stage into several pieces, each piece can develop into a separate anima l. (This happens natu rall y w hen identica l tw ins are fo rmed .) However, it is hard to predict w hic h em bryos w ill develop into animals w ith desirabl e c haracteristics and should therefore be clo ned. The first successful reprodu cti ve clon ing of an adult w ith kno wn characteristics produ ced Doll y the sheep (below).

Techniques for cloning using differentiated cells The egg cells w ithout nuclei were fused wi th the donor cells using a pulse of electricity. The fused cells developed like

zygotes and

became embryos.

Udder cells were taken from a

donor sheep. The cells were cultured in a low nutrient medium to make them switch off their genes and become dormant.

The nucleus was removed from each egg

t

:'U ······ · C>V

~

.

.

i

_

,

.~ '/ ."0

cell using a •. micropipette.

I"

.

_.

oJ

·' .

~

_•.

One lamb was born

successfulIy and was

named Doll y. Doll y is

genetically identical to

the sheep w hose udder

cells were used.

Unfertili zed egg cells were taken from another sheep.

The embryos were imp lanted into another sheep who became the surrogate mother.

THERAPEUTIC CLONING IN HUMANS Techniqu es are bein g developed to create hum an embryos, from w hic h emb ryonic stem cells can be obt ain ed for medical use. These stem ce lls have the capac ity to di vid e and differenti ate into any ty pes of hum an ce ll. They co uld be used to repl ace t issues o r even o rgans that have beco me damaged o r lost in a pati ent. There are many ethica l issues inv olv ed and research into therapeutic cl onin g has been banned in some co untries. Arguments for therapeutic cloning

Arguments against therapeutic cloning

1. Embr yoni c stem cells can be used for therapies th at save lives and reduce suffering.

1. Every hum an embryo is a potenti al hum an being, w hic h should be give n a chance of developi ng.

2. Cells can be removed from embryos that have stopped develop ing, so would have di ed anyway.

2. M ore embryos may be produ ced than are needed, so some may have to be ki lled .

3. Cells are removed at a stage w hen embryos have no nerve cells and cannot feel pain.

3. There is a danger of embryo nic stem cells developin g into tumour cells.

THE HUMAN GENOME PROJECT The hum an genome has been estimated to co nsist of between 25 000 and 30 000 genes. The Human Genom e Proj ect aims to fi nd the location of all of these genes on the hum an chro mosomes and the base sequence of all of the DN A that makes them up. The project is an internation al coo perative one, w it h labor atori es in many co untries invol ved .

32 Genetics

The sequencing of the enti re human geno me w ill make it easier to study how genes influence hum an developm ent. It wi ll allow easier identif ication of genetic di seases. It wi ll allow the produ cti on of new dru gs based on DN A base sequences of genes o r the structur e of prot eins coded fo r by these genes. It w il l give us new insights into the o rigins, evo lution and migrations of hum ans.

EXAM QUESTIONS ON TOPIC 4

In hum ans the blood groups A, B, AB and 0 are determ ined by three alleles of an autosomal gene: lA, IB and i. A lleles lA and IB are codo minant and allele i is recessive. The phenotypes of some ind ivid uals in the pedigree below are show n.

B

2

3

~

0/

D

o

= male

= female

a) Exp lain the co ncl usio ns th at can be drawn abo ut the genotypes of the indi vid uals in the ped igree in generatio ns 2 and 3.

[3]

b) Exp lain to w hich blood groups the parents of t he bl ood group 0 female in the pedi gree co uld have belonged.

[3J

c) Suggest o ne reason for testing the blood groups in humans.

[1 ]

2 W hen red and w hite flowered Mirabilis jalapa plants are crossed together, all the offspring have pink f lowers . The symbo ls for the two alle les invo lved are C' (red) and CW(w hite). a) State the genotypes of the red- and w hite-flowered parents and the pi nk-flowere d offspring.

[1J

b) W hen Me ndel c rossed red- and w hite-flowe red pea plants together, all of the offspring had red f lowe rs. Suggest a reaso n for the difference in results betwee n pea plants and Mirabilis jalapa plants.

[1]

c) Predi ct the outco me of a cross betwee n tw o pi nk-flowered Mirabilis jalapa pl ants, using a Punnett grid.

[3]

3 a) Defi ne clo ne.

[1]

b) O utli ne one tec hnique fo r clo ning animals, using differentiated cells.

[2]

1 2 U C D 3 4 5 6 7 8 9 10111 2

The D NA profiles of sheep are show n (right). U = d ifferenti ated cells taken fro m the udder of a sheep that was used in cl onin g experiments

<; .t;..

C = cells in a culture derived fro m the udder cells D = blood cells taken from Do lly the sheep 1-12

= resuIts from

kb

• -

12

-

10

12 other sheep.

c) (i) Explain w hether DNA fragments in the prof iles had moved upw ards or down w ards.

- 8

[2J

(ii) Expl ain the co ncl usions that can be draw n from the DNA profil es of the sheep. [3J

-6

18 Questions - Genetics 33

5 Identifying living organisms

USING KEYS TO IDENTIFY ORGANISMS

Constructing a key

The first stage in many eco logica l investigations is to find out w hat spec ies of orga nism there are in the area bein g studie d. Thi s is called species identifi cati on . Th is can be don e using keys. Keys fo r species identification are usual ly co nstructed in thi s way: • the key consists of a series of num bered stages • each stage co nsists of a pair of alternative characteristics • some alternatives give the next stage of the key to go to • some alternat ives give the ident ifi cation .

The five animals shown below are fo und in beehives. It wo uld be usefu l to co nstruct a key to allow a beekeeper to identify them, as some of them are ve ry harmful and others are harmless to hon ey bees.

Identifying aquarium plants using a key

Galleria mellonella

M any aquatic plants in aquariums in biology labo rator ies belong to one of these fo ur genera:

• • • •

Cabo m ba Ceratophyllum Elodea M yriophyllum

A ll of these plants have cy lindr ica l stems with w horls of le aves. The shape of fo ur leaves is shown in the figure (left). A key can be used to ident ify w hic h of the fo ur genera a plant belon gs to, if it is known to be in one of them. 1. Simp le undi vid ed leaves

.Elodea

Le aves forke d o r divid ed into segments

2

Acarus siro

Braula caeca

Acarapis woodi

Varma jacobsonii

2. Leaves forke d once or twi ce to fo rm tw o or fo ur segments

Ceratophyllum

Le aves di vid ed into mo re than four segments

3

3. Leaves d ivid ed int o many fl attened segments .. . . Cabo mba Leaves d ivi ded into many f ilamento us segments

Myr iophyllum

Some species of Elodea have recently been mo ve d by

taxo nomists to other genera:

Elodea den sa is now Egeria den sa.

Elodea crispa is now Lagarosiph on m ajor.

Leaves of aquarium plants BINOMIAL NOMENCLATURE In the cl assificat ion of living organisms, the basic group is the species.

A species is a group of organisms w ith simi lar characte ristics, which can interbreed and produ ce fertile offs pring. Every specie s is cl assified into a genus. A genus is a gro up of simi lar species. Each specie s needs an international name, so that bio log ists throu ghout the wo rld can refer to it. The naming of species is called nom enclature. The nom enclature th at bio logists use is called the bin omial system because two names are used to refer to each species. The key features of the bin omial system of nomencl ature are: • the first name is the genus name • the genus name is given an upper case first letter • the second name is the species name • the specie s name is given a lower case fir st letter • itali cs are used w hen the name is prin ted • the name is underli ned if it is hand-written.

34 Ecology and evolution

Classification of plants and animals

CLASSIFICATION FROM SPECIES TO KINGDOM A group of organisms, suc h as a species or a gen us is ca lled a taxon . Species are classified into a se ries of taxa, eac h of w hich incl udes a wider range of species than the previou s one . This is ca lled the hierarchy of taxa. Animal exa mple Balaen optera musculu s - th e blue wh ale (left)

Balaenoptera musculus

Plant example Sequoia sem pe rvirens - the coast redwood (right)

Species that are similar a re gro uped into a ge nus

Ge nus Balae nop tera

Ge nus Seq uo ia

Genera that are simila r a re gro uped into a famil y

Fa mily Balae no pte ridae

Fam ily Taxod iaceae

Families th at are simila r are gro uped into an ord er

Or de r Cetacea

O rde r Pina les

Orders that a re similar are grouped into a cla ss

Class Mamm a lia

Class Pinop sida

Cla sses th at ar e simila r ar e gro uped into a ph ylum

Phylu m Cho rda ta

Phylum Co nifero phyta

Phyla that are similar ar e grouped int o a kingdom

Kingdo m Anima lia

Kingdom Plan tae

Plant classification There are four main phyla of plan ts, w hich ca n be easi ly distingu ished by studyi ng their external structure. Root s, lea ves and stems

Ma ximum height

Repr oductive structu res

Bryophyte s - mo sses

Bryo phytes have no roots, on ly struc tu res sim ilar to root hairs ca lled rhizoids Mosses have sim ple leaves a nd stems Liver worts consist of a flatt en ed tha llus

0 .5 met res

Spores are produ ced in a ca psu le. The ca psu le deve lops at the e nd of a sta lk

Filicinophyte s - fern s

Fern s have roots, leaves a nd short non -wood y ste ms. The leaves are usual ly c urled up in bu d a nd a re ofte n pinn ate ­ div ided into pai rs of leaf lets

15 met res

Spores are pro d uced in spora ngia, usua lly o n the un derside of the leaves

Coniferophytes - conifers

Co nife rs are shrubs o r trees w ith roots, leaves a nd woody stems . The leaves are often na rrow w ith a thick waxy c uticle

100 met res

Seeds are produced. The seeds deve lop from ov ules o n the surface of the sca les of fema le cones. Ma le co nes pro d uce po llen

Ang ios pe rmo ­ ph ytes ­ flow ering plants

Flowe ring p lants are very va riab le but usu a lly have roots, leaves a nd ste ms . The ste ms of flowe ring plan ts tha t deve lop into shrubs a nd trees a re woody

100 metres

Seeds a re prod uc ed . The see ds deve lop from ov ules inside ova ries. The ova ries a re pa rt of flowers. Fruit s deve lop from the ovaries, to dispe rse the seed

ANIMAL CLASSIFICATION There are ove r th irty ph yla of a nima ls. The exte rna l recogni tion fea tures of six of these ph yla a re shown here . Cnid aria • radia lly symmetric • te ntacl es • sting ing ce lls • moutn but no an us Examp les: jellyfish, corals, sea anemo nes

Pori fera • no clea r symmetry • attac hed to a surface • pores th ro ugh bo dy • no mouth o r a nus Exam p les : spo nges Plat yhelminths • bilate ra lly symmetric • flat bod ies • un segment ed • mouth but no a nus Exam ples: Planaria, tapeworms, liverflukes Mollu sca • muscu lar foot a nd man tle • she ll usu ally present • segmentation not visible • mo uth and anus Exam p les: slugs, snails, clams, squids

~-;;

/ / r- ----:/",;:::;:'// I

.. ...r~/

»>

~ -",.

//1

\. /'

:--.'----r-r>-

.-

.

/" '. ':~\

/1

Annelida • b ilatera lly symmetric • bristles ofte n prese nt • seg me nte d • mou th a nd anus

Examp les: earthwo rms,

leeches, ragworms

Art h ro poda • bilate rally symmetric • exoskeleto n • segme nted • jo inted appendages Examples: insects, spiders, crabs, m illipedes

Ecology and evolution 35

Population dynamics

CHANGES TO THE SIZE OF A POPULATION A popu latio n is a gro up of organisms of the same species, who li ve in the same area at the same time .

There are four ways in which the size of a population can change: • Offspring are produced and are added to the populatio n - natality. • Individuals die and are lost from the population - mortality. • Individuals move into the area from elsew here and are added to the population - immigration. • Individuals move out of the area to live elsew here - emigration . Populations are often affected by all four of these things and the overall change can be calcu lated using an equation : Population change = (natality + immigration) - (mortality + emigration)

POPULATION GROWTH CURVES

If the size of a popul ation is measured regular ly, a curve can be plotted. W hen a species spreads into a new area, the pop ulation growth curve is often sigmoid (S­ shaped). The three phases of this curve are exp lained by changes in natal ity and

morta lity.

2. Transitional phase The natal ity rate starts to fall and/or the morta lity rate starts to rise. Nata lity is still hig her than mortality so the popu latio n still rises, but less and less rapidly.

\

1. Exponential phase The population increases

expo nential ly because the

natal ity rate is higher than the mortality rate. The resources needed by the pop ulatio n such as foo d are

abu ndant, and di seases and predators are rare.

Natali ty and mortali ty are equal so the .

.. popu lation size is constant. Something

has lim ited the pop ulation such as:

o

o o

shortage of resources, e.g. food.

mo re predators.

more disease or parasites.

Q)

N

All of these factors lim it population

C

increase because they becom e more intense as the po pulation rises and becomes more crow ded. They eit her reduce the natality rate or increase the mortality rate.

' Vi

o

.~

::l Q.

o c,

If the pop ulation is lim ited by a shortage of resources, it has reached the carrying capacity of the environme nt. The carryi ng capacity is the maximum population size that can be supporte d by the environment.

Time - - -- - +

36 Ecology and evolution

Evidence for evolution

EVOLUTION OF POPULATIONS

HOMOLOGOUS ANATOMICAL STRUCTURES

The wo rd evo lutio n has several meani ngs, all of w hic h involve the gradual developm ent of things. In bio logy, the wo rd has come to mean the changes that occur in livin g o rganisms, ove r many generations. Evolu ti o n happens in popu lation s of livi ng o rganisms. It only happens w ith characterist ics th at can be in herited .

There are also remarkable similariti es betw een some groups of organisms in their structure. For example, bon es in the limbs of vertebrates are strik ingly similar, despite being used in many di fferent ways (below) . The structure is ca lled the pentadactyl li mb.

hi

k,,\. Hum an

Evolution is the cu mulative change in the heritable characteristics of a population.

•

~--<;

Po rp oi se

~

f' ~~ (~

A lthough it is not possib le to prov e, using the scientific method, that the organisms on Earth today are the result of evolutio n, there is much ev ide nce that makes it very li kely. Three types of evidence are illu strated on th is page.

~

M O I ' ~~ I ( ~ .

fH

t:~~.V ~

~, ~~~ ~ Bat

The most likely explanation for these structural similarities is that the organisms have ev olved from a commo n ancesto r. Structures that have developed from the same part of a common ancesto r are called homol ogous structures.

THE FOSSIL RECORD - PALAEONTOLOGY Fossil of Acanthostega

Eight fingers

\

"<, Seven

toes

The existe nce of fossils is ve ry diffi cult to explain w itho ut evo lution . A n example of this is Acanthostega. The figure (left) is a d raw ing of a 36 5 mill ion year o ld fossil of Acanthos tega. It has similarities to other vertebrates, with a backbone and fou r limbs, but it has eig ht fingers and seve n toes, so it is not identical to any existi ng organism. Th is suggests that verte brates and other organisms change over tim e. A canthostega is an example of a " missing li nk" . A lthough it has fou r legs, li ke most amp hibians, rept iles and mammals, it also had a fish-like tai l and gi lls and lived in wa ter. This shows that land vertebrates co uld have ev o lve d from fi sh via an aquatic animal w ith legs.

SELECTIVE BREEDING OF DOMESTICATED ANIMALS The breeds of ani mal that are reared for human use are clearly related to w ild species and in many cases can sti ll interbreed w ith them . These dom esticated breeds have been developed fro m w ild speci es, by selecting indi vid uals w ith desirable traits, and breedin g from them . The strik ing d ifferences in the heritable character ist ics of dom esticated breeds give us evidence that spec ies can evo lve rapid ly .

/

I /.~

Spanish, Hamburgh and Polish Fowl, illustrated in Breeds of Animals and Plants under Domestication by Charles Darwin

Ecology and evolution 37

Natural selection

DARWIN , WALLACE AND EVOLUTION BY NATURAL SELECTION Charles Darwi n developed the theory that evo lution occ urs as a result of natur al selectio n. He exp lained his theory in The Origi n of Species, pub lished in 1859. He had do ne many years of research and had collected much evidence fo r the theo ry befo re then. Darwi n delayed pub lication of his ideas fo r many years, fearing a hostil e reactio n. He mi ght never have pub li shed them if another bi ologist, A lf red W allace, had not w ritten a letter to him in 1858 suggesting very sim ilar ideas. The theory of evo lut ion by natural select ion can be explained in a series of observations and deduct io ns. The photograph on the right shows a statue of Charles Darwin at Shrewsbury Schoo l, w here he was a pupi l from 1818 to 1825.

Ob servati ons

Deduct ions

* Populatio ns of livin g organisms tend

* Mo re offspring are produced

than the enviro nment can suppo rt

* There is a struggle for existence

in w hich some ind ivid uals

survive and some di e

to increase expo nentially

* Yet, on the w hole, the numbe r of

ind ividuals in popul ations remains

nearly constant

* Living organisms vary. The members

of a species are di fferent from each

other in many ways

* Some indi vidu als have characterist ics

that make them we ll adapted to their

enviro nment and other ind ivid uals have

characteristics that make them less

we ll adapted to their environment

* The better adapted

ind ividuals tend

to surv ive and reproduce more than

the less we ll-adapted ind ividu als

This is natural selection

* Mu ch variatio n is heritable -

* The better-adapted indi viduals pass on

it can be

passed o n to offspring

their characteristic s to mo re offspring

than the less we ll adapted ind ivid uals.

The results of natural selectio n

therefore accumulate

* As one generatio n fo llow s another,

the characteristics of the species

gradually change - the species evo lves

In 1828 Darwin, as a yo ung man was struggling to learn enough mathematics to pass a unive rsity exam. The extract below is from a letter that he w rote to Charles W hitley, a fr iend and emi nent mathematic ian. , I am as idle as id le can be: one of the causesyou have hit on, viz irresol ution the other being made full y aware that my noddl e is not capacio us enough to retain o r co mprehend M athematics. - Beetle hunting & such thi ngs I grieve to say is my prop er sphere... r (1 !

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38 Ecology and evolution

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Evolution in action EN~RONMENTALCHANGEANDEVOLunON Since D arwin developed hi s theo ry of evo lut io n by natur al selectio n, c hanges have been ob served in some species . In eac h case, th e evo lut io n has been in respon se to env iro nme nta l change . Two exa mp les are descri bed here - th e devel opment of ant ibio tic resistance in bacteri a and melani sm in ladybu gs. Other exa mp les include the devel opm ent of metal tol erance in pl ant s grow ing on was te m ateri al fro m minin g metal ore s, and cha nges to th e beaks of finc hes on th e Ga lapagos Island s in respon se to EI N ino eve nts. All these recent cases of obse rved evo lutio n in vol ve rel ati vely sma ll cha nges, but th ey do non eth eless add to the ev ide nce for evolution .

SEXUAL REPRODUCTION AND EVOLUTION Vari ation is essentia l for natur al selec tio n and therefor e fo r evo lutio n. Althou gh mu tation is th e o riginal so urce of new genes or alleles, sexual repr odu cti on prom otes va riatio n by allowing the fo rmatio n of new co mbinatio ns of alleles. Tw o stages in sexu al repr odu cti on pr om ote var iatio n. 1. M eio sis allows a hu ge va riety of genetica lly differen t gametes to be produ ced by eac h individu al. 2. Fertilizati on allows alle les from tw o different indi vidu als to be bro ught togeth er in o ne new indi vidu al. Prokaryotes do not reprodu ce sexua lly but have other ways to prom ot e variatio n by exc hang ing genes. Some species of or gani sms o nly repr odu ce asexually.

Mutationsstill produce some variation in these species, but w itho ut sexua l repr odu cti on th e variatio n and th e capaci ty for evo lutio n is less.

Multiple antibiotic resistance in bacteria

Evolution of melanism in ladybugs

Antibiot ics are used to co ntrol di seases caused by bacteria in humans. There have been increasing probl ems wi th di sease­ causing bacteria being resistant to antibiot ics. The figure belo w shows the percentage of casesof gonorrhea (a sexually transm itted di sease) in the United States that we re caused by antibiotic ­ resistant strains of Neisseria gonorrhoeae between 1980 and 1990. The trend w ith many other di seases has been sim ilar.

Adalia bipunctata, th e tw o- spot lad ybu g (o r ladybird ), is a

9 ~

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sma ll beetl e, which usuall y has red w ing cases w it h tw o bl ack spots. Th e red co lo ur wa rns pred ator s th at it tastes unpleasant. Me lanic form s also ex ist, w ith bl ack w ing cases. The mel ani c fo rm abso rbs heat more eff ic ie nt ly th an th e red form . It therefor e has a selec tive adva ntage w hen sunlig ht level s are low and it is difficul t for ladybu gs to wa rm up . Th e mel ani c fo rm of Adalia bip un ctata becam e co mmo n in industri al areas of Brit ain , but declin ed again after 1960 . Th e decline co rrelates w ith decreases in smo ke in th e air (be low) . In air dark ened by smo ke, th e melani c fo rms wi ll be able to wa rm up more quickl y, but if th e smo ke is no lon ger present thi s adva ntage is lost and wa rn ing co lo uratio n is mor e im po rta nt.

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Gen es th at give resista nce to an antib iotic ca n be fo und in

th e m icro-or gani sms that natur all y m ake that antib iotic.

Th e evo lutio n of multiple antib io tic resistan ce in vol ves th e

follo w in g steps.

o A gene that gives resistance to an ant ibiotic is transferred to a bacterium by mean s of a pl asmid or in so me ot her way. There is th en va riatio n in thi s typ e of bact erium - so me of the bacteri a are resistant to th e ant ibiotic and some are not. o Doctors o r vets use the ant ibio tic to co ntro l bacteri a. Na tural selec tio n favours the bacteri a that are resistant to it and kill s th e non-resistant o nes. o Th e antib iot ic -resistant bacteri a repr odu ce and spread,

repl acin g th e non-resistant on es. Eventu all y, mo st of th e

bacteri a are resistant.

o Docto rs o r vets change to a different antibiotic to co ntro l bacter ia. Resistance to this soo n develop s, so anothe r antibiotic is used, and so on until mu ltipl y resistant bac teria have evo lve d . Th e mor e an anti bio t ic is used, th e mor e bacteri a resistant to

it th ere w ill be and the fewe r non-resistant.

,

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50 E

annual average o , »>: summer levels e-- 0 of smo ke

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Adalia 2-punctata (f. typical

Adalia 2-punctata (f. quadrimaculata)

2-spo t ladybird (typi cal)

2-sp ot ladybird (melani c)

Ecology and evolution 39

Trophic levels

Popu lation s do not li ve in isolatio n - they li ve together w ith other popu lation s in communities. A community is a group of populations li ving together and interacting w ith each other in an area. There are many types of interac tio n betw een popu lations in a community. Trophi c relation ships are very im port ant - w here one pop ulation of organisms feeds o n another pop ulatio n. Sequences of troph ic relationships, w here each membe r in the sequence feeds on the previou s o ne, are called food chains. An example from rainfor est at Iguazu in north-east Argenti na.

Passion flow er (Passiflora schummania na)

Helico nius butterfly (He lico nius erato)

.....

tegu lizard (Tup inambis tegu ixin )

jag uar (Panthera onca)

An example f rom chalk grassland and th e air above it in Euro pe.

carrot plant ..... carro t fly..... flycatcher (D aucus (Psila (M usci capa carota) rosea) striata)

.....

sparrowhawk (A ccip iter nisus)

goshaw k (A ccip iter gentilis)

The first organism in a food chain does not feed on ot her organisms so must be a pro ducer - an organism that makes its ow n foo d . The ot her organisms are al l co nsumer s and are called primary, secondary , tertiary and so on, depend ing on thei r positi on in the chain. Produ cer, primary co nsumer, seconda ry co nsumer and terti ary co nsumer are examples of trophic levels. The trophic level of an organism is its posi tio n in the foo d chain. Exampl e: Produ cer Sea lettuce (Ulve lactuca)

Prim ar y consumer ------. Second ar y consumer M arine iguana Galapagos snake (Ambly rhyncus cristatus) (Dromiscus biserialis)

------. Tertiary consumer Galapagos haw k (Buteo galapagensis)

A food chain show s only some of the trophi c relatio nships in a community. Organi sms rarely feed on only one ot her o rganism and are usually fed o n by more than o ne organism. The complex network of trop hic relationship s in a co mmunity is show n in full in a co mp lex d iagram called a food web . An examp le of a food web is shown on page 42 .

40 Ecology and evolution

Energy flow

AUTOTROPHS The organisms in a co m munity all need a supply of energy . Organisms are div ide d in to tw o groups acco rding to their source ­ autotrophs and heterotrophs.

Energy flow through producers heat

A utotrophs are organisms that synthes ize their own organic molecu les (food) from simple inorganic substances .

Release of energy by cell respiration for use in the producer then loss as heat.

A utotrophs make their ow n food , so are also called producers. O ak trees, ma ize plants, algae, blue-green bacteria are examples. Al l food chains start w ith a produce r. In alm ost all comm uni ties, the produ cers make organic matter by phot osynt hesis.

. 1energy in organic matter in producers

J

Death of the producer so the energy passes to detritivores and

Light is therefor e the initial energy source for the w ho le com munity. Producers co nve rt light energy int o the chem ical energy of sugars and ot her o rganic compo unds. Thi s energy trap ped by the produ cers eventua lly leaves them in one of thr ee ways, show n in the f low c hart (rig ht).

energy in organic matter in prim ary consumers

\

E

n.ergy passes to a

pn m a ~y consumer

when It eats the

saprotrop hs w hen they digest the

producer.

producer energy in organic matter in detri tivores and saprotrophs

HETEROTROPHS Heterotrophs are organisms that obtain organic molecu les (food) from othe r

organisms .

Energy flow through consum ers

heat

There are three types of heterot roph: con sumer s, detritivores and sapro t rophs.

Consumers are organisms that ingest organic m atter that is living or recently killed. Prim ary co nsume rs eat prod ucers and so obtain energy from them . The y do not absorb all of the energy in the food that they eat. The energy that they do not take into thei r tissues leaves them in one of th ree ways, show n in the flow chart (right). There are sim ilar energy losses from seco ndary and tertiary co nsumers in the food chain. Locu sts, sheep and lion s are examp les of co nsumers.

Oetritivores ingest dead organic matter.

Release of energy by cell respiration for use in the primary consumer then loss as heat. energy in organic I matter eaten by primary consumers Some organic matter is not digested, so energy is lost in feces and passes to detrit ivores and saprotrophs.

Dun g beetles and earthworms are examples of detritivores.

The energy that passes to detritivo res and saprotrophs is eventua lly released by cell respiratio n and lost as heat. In most comm unit ies all the light energy that was trapped by prod ucers is ultimatel y lost as heat after fl ow ing through the food chain. A sum mary of energy flow for a three-stage food chain is show n (right).

,

energy in organic matter eaten by

\

consumers

secondary consumers

En ergy passes to a secondary consumer w hen it eats the primary consumer.

\1

energy.in organic "---­ matter In detritivores and

Saprotrophs live on or in dead organic matter, secreting enzymes into it and absorbing the produ cts of digestion. Bread mou ld and mushrooms are examp les of saprotro phs.

energy in organic

.1 matter in the tissues ofprimary

sap rotrop hs Energy flow through a food chain

~

photosynthesis

t

c~z l

cell respiration

death, loss of ti ssues and feces

__________ r-~---'--4c I

---L--- ,

detritivores and saprotrophs

Ecology and evolution 41

Food webs and energy pyramids

FOOD WEBS A food we b is a d iagram that shows all the feedin g relation ships in a co mmunity . The arrows indicate the direction of energy f low. Co mplete foo d we b di agrams are very co mp lex. The figu re (below) shows a simp lified food web for a com mun ity that lives in an area of Ar cti c tundra in Ogo to ruk Valley.

Food web for Arctic tundra Secondary consumers

EJ

r

,

Wolverines

EJ B

[ W. ., I,

~

Grizz ly bear

Owls and haw ks

"\ \

Primary consumers

Caribou

Voles and lemmings

\

Ground squirrels

\ \ I

I I I

I I I I I I I

Producers

Plants (mainly cotton sedges)

ENERGY PYRAMIDS Energy pyramid s are di agrams that show how much energy fl ow s throu gh each trophi c level in a co mm un ity . The amo unts of energy are shown per square metre of area occupi ed by the com munity and per year (k] m -l year" ). The figure (right) is a pyr amid of energy for Silver Springs, a stream in Flo rida. The f igure (below right) is a pyramid of energy for a salt marsh in Geo rgia. Pyram ids of energy are always pyramid shaped ­ each level is smaller than the one below it. Thi s is because less energy flows through each successive troph ic level. Energy is lost at each trophic level, so less remains for the next level. Note that mass is lost as we ll as energy, so the energy co ntent per gram of the t issues of each successive troph ic level is not low er. Energy is lost in vario us ways. In each of the f irst three ways the energy is not co mplete ly lost from the co mmunity as it passes to detritivores and saprotrop hs. • Some organisms die before an organism in the next trophi c level eats them . • Some parts of organ isms such as bones or hair are not eaten. • Some parts of organisms are indi gestible and pass out as feces. • M uch of the energy absorbed by an organism is released in cell respiratio n. The energy, in the for m of ATP, is used in processes suc h as muscle co ntractio n or active transport that require energy. These processes invo lve energy transfo rmations, w hic h are never 100% effic ient. Some of the energy is co nverted to heat. 10- 20% is a typi cal efficiency level. Most of the energy released by ce ll respiration is lost from the organism as heat. Energy absorbed by li ving o rganisms is only availab le to the next troph ic level if it remains as chemica l energy in the growt h of the organism. Thi s is only a small prop o rtion of the energy absorbed .

42 Ecology and evolution

Energy py ramid fo r a stream

tertiary consumers

67 1602

secondary consumers primary consumers producers

r l 14 000

I

I 87 000

L...­

----J

Energy pyr amid for a salt marsh

secondary consumers primary consumers producers

I

117 1278 1 152 000

'----- - - -- - -- -----'

Nutrient recycling

ECOSYSTEMS, ECOLOGISTS AND ECOLOGY

NUTRIENT RECYCLING IN ECOSYSTEMS

Cornrnunities of living organisms interact in many ways with the soil, water and air that surround them. The non-living surroundings of a community are its abiotic environment. A community and its abiotic environment function together as a system called an ecosystem. An ecosystem is a

The recycling of nutrients is one example of the interactions between living organisms and the abiotic environment in an ecosystem. Energy is not recycled. It is suppl ied to ecosystems in the form of light, flows through food chains and is lost as heat. Nutrients are not usually resupplied to ecosystems - they must be used again and again by recycling. Carbon, nitrogen, phosphorus and all the other essential elements must be recycled. They are absorbed from the environment, used by living organisms and then returned to the environment. The processes involved in the carbon cycle are shown below.

community and its abiotic environment. Ecologists study the complex relationships within ecosystems. This area of study is called ecology. Ecology is the study of

relationships in ecosystems - both relationships between organisms and between organisms and their environment.

The carbon cycle

combustion

,

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--------------

-----~

CO 2 in air and water

C

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in fossiI fuels, e.g. coal, oi I and gas

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incomplete \ decomposition \ and fossiIization \

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C

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in organic compounds in saprotrophic bacteria and fungi

death

C in organic compounds in producers

C

feeding

in organic compounds in consumers

feeding

THE ROLE OF SAPROTROPHS IN RECYCLING OF NUTRIENTS Saprotrophic bacteria and fungi have an essential role in nutrient cycles. They feed by secreting digestive enzymes into dead organic matter, including dead plants and animals and feces. The enzymes gradually break down the organic matter and the nutrients that were locked up in complex organic compounds are released. The saprotrophs absorb the substances that they need from the digested organic matter.

Without saprotrophs, nutrients would remain locked up permanently in dead organic matter and organisms that need the

nutrients would soon become deficient.

Ecology and evolution 43

Global warming and the greenhouse effect

RISING CARBON DIOXIDE LEVELS

Gr aph of at mospheric CO 2 co ncent rat io ns

The carbo n dioxid e concentration of bubb les of air trapped in Antarct ic ice at d ifferent dates have been measured. These show that for two thousand years befo re 1880 the carbon d ioxide co ncentratio n of the atmosphere remained fairl y co nstant at about 270 parts per millio n (ppm). Fro m 1880 o nwards the co ncentratio n rose. Since 1958, the co ncentratio n has been monitored continuo usly at M auna Loa, Haw aii (right). There is an annual fluctuatio n, but the overall trend has been upw ards and the co ncentrat ion is now mor e than 100ppm higher than in 1880.

Mauna Loa observatory, Hawaii monthly average carbon dioxide concentration E 390 0­ 0­

c

380

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370

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ON U

If/JlV\ VV ' .yNVWyVV

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340 330

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GREENHOUSE GASES Carbon di oxid e is one of a group of gases that cause heat to be retai ned in the Earth' s atmosphere: • carbo n di oxi de

• methane

• oxides of nitrogen (NO X)

• sulfur dio xide

Heat retent ion by gases is called the greenhouse

effe ct. The processes invo lved are show n in t he f igure

(right).

The greenhouse effect is not a new phenom enon .

Natural processes prod uce greenhouse gases, so they

are a natural part of the Earth' s atmosphere. The

c hange in recent years is that human activities have

increased the productio n of greenhouse gases and so

thei r atmospheric conce ntratio ns and their

co ntribut ion s to the greenhouse effect have been

rising (below right). Th is is cor related w ith rising

temp eratures on Earth - global w arming.

year Cause of th e greenho use effec t Light from the su n has short wave lengths an d ca n mo stly pass through the atm osphere

Gree nho use gases in the atmo sphe re inclu ding CO 2 , met hane, wate r vapo ur a nd sulfur d ioxide trap some of the long-wave " . -. " . -. . "'w " rad iation , ca using the Earth . '. . to be wa rmer than if the "' ~ radiat io n esca ped.

I'. +'. -. -. .

" I\~;"\'/ ~' J'~'< Sunlight wa rms up the surface of the Earth w hic h em its lo ng-wave rad iation

Incre ases in effect s of greenhouse gases 2.0

RISING GLOBAL TEMPERATURES Temperatu re record s have been analysed to find the mean for th e w ho le w or ld in each year from 1850 o nwa rds. The figure (right) show s the di fference betw een t he mean temp erature for each year and an ov erall mean temp eratu re for the years 1961-1 990 . The trends are th at • From 1856 unt il about 1910 temp eratures we re relatively stable. • From 1910 unt il 1940 temperatur es rose and we re t hen stable. • From 1970 th ere has been a rapid ri se. • A ll ten of the hottest years since records began in 1850 have been since 1990. • 1998 was the hottest year in that period and 200 5 wa s the seco nd hott est year. • Over the past centu ry, global temp eratures have risen by O.7°C on average, w hic h takes us out of the range of average temp eratur es experienced on Earth ove r the last 1000 years. These c hanges in temp erature are statistically significant. There co uld be variou s causes, but the most likely cause is an increased greenhouse effect, du e to human acti vities.

Increase in 1.5

t he warmin g

effect of th e

1.0 gas betw een

1750 and

2000/ Wm -2 0.5

0-'-- ' - --'--<----1---1-_ --'---'- - ­ halo N,o

CO, carbo ns

A nnual glo bal t emperatures 1850- 200 5 0.6

Long-term trend

0.2 0.0 - 0.2 - 0.4 -0.6 - 0.8 1850

44 Ecology and evolution

Annual average

0.4

1872

1894

1916

1938

1960

1982

2005

Responses to global warming

HABITATS The Earth provides places for millions of livi ng organisms to ex ist. These places are called habitats.

A habitat is the environment in which a species normally lives or the location o f a living organism .

CONSEQUENCES OF GLOBAL WARMING The effects of glo bal wa rming are already being felt, but they are likely to becom e much more extreme du ri ng the 21't century. Habitats thro ugho ut the w orld w ill be affected, but the effects on Arcti c ecosystems co uld be parti cu larly catastrop hic. • Glaciers w ill melt and po lar ice sheets w ill break up into icebergs, w hic h w ill also eventually melt. The Arc tic ice cap may d isappear complete ly . • Permafrost w ill melt dur ing the summer, increasing the rates of decomp osit ion of trapped organic matter, includ ing peat and detrit us. This w ill cause release of carbon d ioxid e, fu rther inc reasing atmospheric concentrations. • Species adapted to temperate co nd itio ns w ill spread no rth, altering food chai ns and affecting anim als in the higher tro phic levels. • M arin e species of animal in Arct ic waters may becom e ext inct, as they can be very sensitive to temperatu re changes in seawater. • Po lar bears and ot her animals w ill lose their ice habi tat, w here they feed and breed. • Pests and d iseases may becom e more prevalent, w ith wa rmer temperatures. • Sea levels wi ll rise and low- lyin g areas of land w ill be f lood ed. • Extreme weather events, such as storms, wi ll becom e more frequent, w ith harmfu l effects on species that are not adapted .

THE PRECAUTIONARY PRINCIPLE In a co urt of law , prosecuto rs try to prove that the defendant is gui lty . If they cannot do this, the defendant is assumed to be innocent. Wh en the precautio nary princ iple is fo ll ow ed, the opposit e po licy is adopted - people plann ing to do something must prove that it w ill not do harm, before actually do ing it. The precauti onary principle should be fo ll owed w hen the possib le co nsequences (risks) of hum an actio ns are very large or co uld even be catastrop hic.

Ice sheet br eakin g up, with Gr eenland in the background

Mu sk ox (O vibos moschatus) a speci es of mamm al w hic h nearly became extinct through over-hunting in the early 20 th century. Protection by the Canad ian government has allowed them to increase, w ith the populatio n now over 60 000 . They have a very thic k coat and are adapted to the co ld co nditions of Arcti c regions. The co nsequence of global w arming fo r musk ox can be deduced fro m the distrib ution map (below) .

A lthough there is strong evidence that greenho use gas emissio ns are causing glo bal w arming, there is no pro of. Some po liticia ns and business leaders have argued against measures to combat global wa rmi ng, because it is not ce rtain that greenho use gasesare causing it. Oi l compa nies and airlines in parti cu lar have vo iced opposition. M any scie ntists have argued that if w e wa ited for proof of the effects of greenhouse gas emissions befo re reactin g, the co nsequences w ould probably have reached a catastrop hic level. The risks are so great that the precautio nary pr incip le should be fo ll owe d : anyone advoc ating co ntinuing to emit greenhouse gases at current levels, or even to increase emissio ns, should be requir ed to prove that thi s wi ll not cause a damaging increase in the greenhouse effect.

Di stribution map of mu sk ox in the Arctic

Ecology and evolution 45

EXAM QUESTIONS ON TOPIC 5 The graph below shows the growth of a population of ring-necked pheasants (Phasianus colchicus) on Protection Island off the north west coast of the United States. The original population released by the scientists consisted of two male and eight female birds. Two of the females died immediately after release.

-E

2250

[Source of data: Elinarson A. S., Murrelet, (1945) 26: pages 39-44]

:..0

'0

2000

Q:j

..D.

E :J

/

1750 I

C

'Vi-

C 1500 ~

ro Q)

..c

/

1250

0.

uQ) ..::L.

U

1000

/

Q)

C

0.0

/

500

1/

c

250

:J

0.

et

0

I /

1/

C

o

~

V

I

750

.~

'0

/

~

o

--

V

1/

/ 3

2

4

5

6

7

8

9

10

Time/years a) State the term used to describe the shape of a growth curve of this type.

[1 J

b) (i) The scientists predicted that the population would reach its carrying capacity of 2000 by year 8. Draw a line on the graph to show the population growth between years 6 and 10.

[2J

c) (i) Predict how the population growth would change if all the female birds in the original sample had survived.

[1 ]

(ii) Predict the effect on the carrying capacity if all the female birds in the original sample had survived.

[1 J

2 The diagram below shows in simplified form the transfers of energy in a generalized ecosystem. Each box represents a category of organisms, grouped together by their troph ic position in the ecosystem.

Sun

~""""'I--------.-------~ III

~""""'1---- --------.. II

u c

ro QJ tJl

..c

:....

0

0.>

e :-2

e~

0.0

~"""",j------~

ro

Cf)

a) Deduce the trophic levels of the organisms in boxes I, II and III.

[3J

b) State the form in which energy enters organisms in box 1.

[1]

c)

[1 ]

Identify which arrow represents the greatest transfer of energy per unit of time. (Add a large X to the arrow).

d) Explain what is represented by the dotted arrows leaving each box.

3

[3]

Methane acts as a greenhouse gas in the atmosphere. The main sources of methane are the digestive systems of cattle and sheep, bacterial action in rice paddies, burning of biomass (e.g. forest fires), bacterial action in swamps and marshes, burning of coal and release of natural gas. a) Discuss whether methane emissions from these sources will cause a change in the Earth's temperature.

[3J

b) Discuss whether release of methane is a natural process or an example of a human impact on the environment.

[3J

c) Suggest measures that could be taken to reduce the emission of methane.

[3J

46 18 Questions - Ecology and evolution

6 Digestion

TAKING IN FOOD

THE NEED FOR DIGESTION

Hum ans take foo d into their di gestive system throu gh the mou th and the esophagus. How ever, this foo d is not truly inside the body unti l it has passed th ro ugh a layer of cells into the body' s ti ssues. This happ ens in the small intestines and is called absorpt io n. Small finger-like proj ecti o ns from the w all of the small intestine called vil li are speci ally adapted to absorb foo d mol ecul es. The structure of a vill us is show n below . After food has been abso rbed it is assimilated - it become s part of the ti ssues of the body.

The food that humans eat co ntains substances made by oth er organisms, many of w hich are not suitab le for hum an tissues. They must therefore be broken dow n and reassembled in a form that is suitable. A second reason for di gestion is th at many of the mo lecu les in food s are too large to be absorbed by the villi in the small intest ine. These large mol ecu les have to be broken dow n into small molecu les th at can then be absorbed by di ffu sion , faci litated diffusion or acti ve tra nsport. The thr ee main types of foo d mo lecu le that need to be di gested are starch, protein and triglycerides (fats and oils). Di gesti on of these large mol ecul es happens naturall y at body temperature, but only at a very slow rate. Enzym es are essential to speed up the process. Enzym es of digest ion

Structure of a vill us

lacteal (a branch of the lymphatic system)

Example of this enzyme Source

Amylase Salivary amylase Salivary glands

Substrate

Sta rch

Products

Maltose

Optimum pH

pH 7

Protease Pepsin Wall of stomach Proteins Small polypeptides pH 1.5

Lipase Pancreatic lipase Pancreas Triglycerides (fats or oils) Fatty Acidsand Glycerol pH 7

The hum an digestive system goblet cells (secrete mucus)

esophagus

stomach

RElATIONSHIP BETWEEN STRUCTURE OF A VILLUS AND ITS FUNCTION • Vil li increase the surface area over w hich foo d is absorbed. • An epithelium, co nsisting of o nly o ne thin layer of cells, is all that food s have to pass through to be absorbed . • Prot rusions of the exposed part of the plasma memb ranes of the epithelium cells increase the surface area fo r absorption. These projectio ns are called microv illi. • Protein channels in the mi crovill i mem branes allow rapid absorptio n of foods by faci litated di ffusion and pump s allow rapid absorptio n by active transport. • M itocho ndria in epithelium cell s provid e the ATP needed fo r active transport. • Blood capillaries inside the villus are very close to the epithelium so the di stance for diffusion of foods is very small. • A lacteal (a branch of the lym phatic system) in the centre of the vil lus carries awa y fats after abso rptio n.

FUNCTIONS OF THE STOMACH AND INTESTINES Di gestion of proteins begins in the stomach, catalysed by pepsin. Bacteria, w hic h could cause food poison ing, are mostly ki lled by the acid co nditions of the sto mach. The aci dity also prov ides opti mum co nditions for pepsin to w ork. Enzymes secreted by the wa ll of the small intestine complete the process of di gestion . The end prod ucts of digestion are absorbed by the villi protruding from the wa ll of the small intestine. The indi gestible parts of the food, together w ith a large volume of w ater, pass on into the large intestine. W ater is absorbed here leaving solid feces, w hic h are eventually egested through the anus.

Human health and physiology 47

The cardiovascular system

Structure of the heart

HEART STRUCTURE The heart is a do ub le pump , w ith the right side pumpi ng blood to the lungs and the left side pumpi ng bloo d to all other o rgans. The wa lls of the heart are composed of card iac muscle. Contr act io n of cardiac muscle is myogenic - it can co ntract on its ow n, w itho ut being st imulated by a nerve. There are many capi llaries in the muscu lar wa ll of the heart. The blood running th rough these capillaries is supp lied by the coronary arteries, w hic h branc h off the ao rta, c lose to the semilunar valve. The blood brou ght by the coronary arteries brings nutrients. It also brings oxygen fo r aerob ic cell respiration, w hic h provides the energy needed fo r cardiac muscle contractio n.

aorta vena cava

(superior)

left atrium right atrium

.--:-::::",---_ _ ~ pulmonary veins

semil unar valves-- - \-T-- - '

atrio-ventricular valve

vena cava

(inferior)

atrio-ventricular valve

left ventricle right ventricle

BLOOD VESSELS

THE ACTION OF THE HEART

Arteries ./ Thick layers of . / circular elastic and muscle fibres to help pump the blood on after each heart beat

Thick outer layer of longitudinal collagen and elastic fibres to avoid bulges and leaks

Narrow lumen to help maintain the high pressures

Thick wall to w ithstand the high pressures

Veins Thin layers w ith a few ci rcular elastic and muscle fibres because blood does not flow in puIses so the veins wall cannot help pump it.

Thin wa ll allows the vein to be pressed flat by adjacent muscles, helping to move the blood Thin outer layer of longitudi nal collagen and elastic fibres because there is little danger of bursting

Wide lumen is needed ~~~~v to accomodate the slowflowing blood N.B. veins have valves to prevent back-flow

The atria are the co llecti ng chambers - they co llec t blood from the veins. The ventr icles are the pumpin g chambers - they pump blood out into the arteries at high pressure. The valves ensure that the blood alwa ys f lows in the co rrect d irecti on. Every heartbeat consists of a sequence of action s. 1. The wal ls of the atria contract, pushing blood from the atria into the ventricles thro ugh the atriove ntricular valves, w hic h are op en. The semilunar valves are cl osed, so the ventricl es fi ll with blood . 2. The wa lls of the ventricl es co ntract pow erfull y and the blood pressure rapid ly rises inside them. This rise in pressure first causes the atriove ntr icular valves to close, preventing back-fl ow of blood to the atria and then causes the semilunar valves to open, allowing blood to be pumped out into the arteries. At the same t ime the atria start to refill as they co llect blood from t he veins. 3. The ventricle s sto p co ntracti ng and as pressure falls inside them the semilu nar valves close, prevent ing back-flow of blood from the arteries to the ventricl es. W hen the ventric ular pressure drops below the atrial pressure, the atri oventri cu lar valves open. Bloo d entering the atrium from the veins then flows on to start filling the ventr ic les. The next heartbeat begi ns w hen the wa lls of the atr ia cont ract again.

THE CONTROLOFTHE HEARTBEAT Capillaries Wall consists of a single layer of t hi n~ cells so the distance for diffusion in or out • is small. ~ Pores between cells in I I the wall allow some of the plasma to leak out and form tissue fluid. / ' Phagocytes can also squeeze out.

~) ~/~

Very narrow lumen ­ only about 1Ourn ac r~ss s.o that. caplillarles fit Into sma Many small capil laries have a larger surface area than fewer Wider ones

48 Human health and physiology

s pa~e s.

Heart muscle ti ssue has a spec ial property - it can co ntract on its own w ithout being stim ulated by a nerve. O ne regio n is respo nsib le for initiating each co ntractio n. Th is regio n is ca lled the pacemak er and is located in the wa ll of the right atrium . Each tim e the pacemaker sends out a signal the heart carries o ut a co ntractio n or beat. Nerves and hormones can transmit messages to the pacemaker. • O ne nerve carries messages from the brai n to the pacemaker that tell the pacemaker to speed up the beating of the heart. • A nother nerve carries messages from the brain to the pacemaker that tell the pacemaker to slow dow n the beating. • Ad renali n, car ried to the pacemaker by the bloodstream, tells the pace maker to speed up the beating of the heart.

Blood, transport and infections

THE COMPOSITION OF BLOOD

PHAGOCYTES

Blood is compose d of plasma, erythrocy tes (red blood cells),

leukocytes and platelets. The figure below shows the

appearance of blood as seen using a li ght mi croscop e. Tw o

types of leukocyte are show n.

Som e of the leu kocytes in bloo d are phagocytes. These cells can identify pathogens and ingest them by endocytosis. A pathogen is an organism or virus that causes d isease. The pathogens are then ki ll ed and digested inside the cell by enzymes fro m Iysosomes. Phagocytes can ingest pathogens in the blood . They can also squeeze out th rou gh the wa lls of blood cap illa ries and move through tissues to sites of infectio n. They then ingest the pathogens causing the infecti on. Large numbers of phagocytes at a site of infect ion form pus. Some pathogens are able to avoi d being ki lled by phagocytes, so another defence is needed .

lymPhOCyte }

phagocyte

f1

l," kO,~"J

(white blood cells) platelets plasma transporting nutrients, carbon dioxide, hormones, antibod ies and urea

erythrocytes (red blood cells) transporting oxygen

\

~ ~

pathogens phagocytic leukocyte

ingested pathogens

FUNCTIONS OF BLOOD

ANTIBODIES

Blood has tw o main functio ns: transport and defence against infectious disease. Red bloo d cells transport oxyge n fro m the lun gs to respir ing cells. Blood plasma transports • nutrients

• carbon dioxid e

• hormones

• antibodies

• urea.

The blood also transports heat from parts of the body that

prod uce it, to the skin, w here it is lost to the envi ronment.

Leukocytes (white blood cells) defend the bod y against

infecti ous diseases. The roles of phagocytes and leukocytes are

described on th is page and the next page.

Antibod ies are protei ns that recognize and bind to speci fic antigens. A ntige ns are fo reign substances that stimu late the prod ucti on of ant ibodies. A ntibod ies usually only bi nd to one specif ic antigen. A ntigens can be any of a w ide range of substances inclu di ng cell w alls of pathogenic bacteria or fungi and prot ein coats of antigen ~ pathogenic viruses. b i n di ng ~ An tibodi es defend the bod y against site pathogens by bindi ng to antigens on Antibody mol ecul e surface of a pathogen and stimu lating made up of four its destructi on. The figure (on page 50) polyp eptid es shows how antibod ies are produ ced.

BARRIERS TO INFECTION

ANTIBIOTICS

The skin and muco us memb ranes fo rm a barrier that prevents most pathogens from enteri ng the body . The outer layers of the skin are tou gh and form a physica l barri er. Sebaceo us glands in the skin secrete lactic acid and fatty acids, w hic h make the surface of the skin aci dic. This prevents the growth of most pathogenic bacteria. M uco us memb ranes are soft areas of skin that are kept moi st w ith mucus. M ucous membr anes are fou nd in the nose, trac hea, vagi na and urethra. A lthough they do not for m a strong physica l barrier, many bacteria are kil led by lysozyme, an enzy me in the mucus. In the trachea pathogens tend to get caught in the sticky mucus and cil ia then push the mucus and bacteri a up and out of the trachea. Despite these barriers to infecti o n, pathogens do somet imes enter the body so another defence is needed.

Ant ibiot ics are chemica ls produced by microorganisms, to ki ll or co ntro l the grow th of other microorganisms. For example, Pen icillium fungus produces penici llin to ki ll bacteria. M ost bacterial diseases in hum ans can be treated successfully w ith antibio tics . For example, tu bercul osis has been treated w ith strepto myci n. There are many differences betw een hum an cells and bacterial cells and so there are many anti biotics that block a process in bacterial cells w ithout causing any harm to human cells. Viruses carry out very few processes themselves. They rely instead o n a host cell such as a human cell to carry out the processes for them . It is not possible to block these processes w ith an antibiot ic w itho ut also harmin g the human cel ls. For this reason virus d iseases cannot be treated w ith ant ibiotics.

Human health and physiology 49

Antibodies and AIDS

PRODUCTION OF ANTIBODIES

CD Antibodies are made by lymphocytes, one of the two main types of leukocyte.

~

Variety of antibodies on~ lymphocyte surfaces.

sss.

phagocyte

@ W hen antigens bind to the antibodies on the surface of a lymphocyte, this lymphocyte becomes active and divides by mitosis to produce a clon e of many identical cells.

Q) W hen a pathogen enters

Q) A lymphocyte can only make one type of antibody so a huge number of different lymphocyte types is needed. Each lymphocyte puts some of the antibody that it can make into its plasma membrane w ith the antigen-combining site projecting outwards. ~ ~ ..::cLr:. ...t--X-X.. ~

~ ..x-=.:r:.. ~

~

.::LY-.::L.

~ i n ac t i ve l y mp h OCy te

(0) -

m;lo; ;;

- \ active lymphocyte

the body, its antigens bind to the antibodies in the plasma membrane of one type of lymphocyte.

~

@ ~

~

.....:

' ®©@~~~

@ @) ~~': :. ' @ ©@.{~5~ ...

AIDS - A SYNDROME CAUSED BY A VIRUS A IDS shows how vital the bod y's defences against di sease are. Destruction of the imm une system leads inevitably to death. A IDS is an example of a syndrome. A syndrome is a group of symptoms that are found together. Indi viduals w ith acquired immunodeficiency syndrome (AIDS) have low numbers of one type of lymphocyte together w ith we ight loss and a variety of diseases caused by viruses, bacteria, fungi and protozo a. These di seases weaken the body and eventually cause death.

@ The clo ne of cells starts to produce large quantities of the same antibody - the antibody needed to defend the body against the pathogen.

Structu re of HIV single stranded RNA

reverse transcriptase

Cause HIV (human imm unodefi ci ency virus) causes A IDS. The virus infects a ty pe of

lymphocyte that plays a vital rol e in antibody prod uctio n. O ver a period of years these

lymphocytes are destroyed and antibodies cannot then be produ ced. W ithout a

fu nctioni ng immu ne system, the bod y is vulne rable to pathogens that w ould norm ally

be contro lled easily .

Transmiss ion

HIV does not survive for long outside the body and cannot easily pass through the ski n.

Transmission invol ves the transfer of body fluids from an infected person to an uninfected

one.

• Through small cuts or tears in the vagina, penis, mo uth o r intesti ne during vaginal, T-Iymph ocyte infect ed with HIV( X 3500) anal or oral sex. • In traces of blood on a hypodermi c needle that is shared by int ravenou s d rug abusers. • Acro ss the placenta from a mother to a baby, o r thro ugh cuts du ring chi ld birth or in mil k during breast-feeding. • In transfused blood or w ith blood prod ucts suc h as Facto r VIII used to treat hemophili acs.

Social imp lications • Families and fr iends suffe r grief. • Fami lies beco me poo rer if the indi vidua l w it h A ID S was the wage earner and is refused life insurance. • Indivi duals infected w ith HIV may becom e stig mati zed and not fin d partners, housing or employ ment. • Sexual activ ity in a populatio n may be reduced because of the fear of A IDS.

50 Human health and physiology

Gas exchange

THE NEED FOR GAS EXCHANGE

THE VENTILATION SYSTEM

AND VENTILATION IN HUMANS Cell respiration happens in the cytoplasm and mit ochond ria of cells and releases energy in the fo rm of ATP for use inside the cell. In humans oxygen is used in ce ll respiration and carbo n di oxid e is produ ced. Hum ans therefore must take in oxyge n fro m thei r surround ings and release carbo n dioxid e. Thi s process of swappi ng o ne gas for another is ca lled gas exchange. Gas exchange happens in the alveo li of human lun gs. Oxyge n diffuses from the air in the alveo li to the blood in capillaries. Carbon di oxid e diffu ses in the opposite dir ection . The fi gure (below) shows the adaptat io ns of the alveolus for gas exc hange. Di ffusion of oxygen and carbon dioxid e happens because there are co nce ntrat ion gradients of oxyge n and carbo n dioxide betw een the ai r and the blood . To maintain these co ncentratio n grad ients, the air in the alveoli must be refreshed frequently. The process of bringing fresh air to the alveo li and removin g stale air is called vent ilatio n.

trachea intercostaI muscles

ADAPTATIONS OF THE ALVEOLUS TO GAS EXCHANGE Although each alveolus is very small, the lungs contain hundreds of mill ions of alveoli in total, giving a huge overall surface area for gas exchange.

The alveolus is covered by a dense network of blood capillaries wit h low oxygen and high carbon dioxide concentrations. Oxygen therefore diffuses into the blood and carbon dioxide diffuses out.

The wall of the alveolus consists of a single layer of very thin cells. The capi llary wall also is a single layer of very thin cells, so the gases only have to diffuse a very short distance.

Cells in the alveolus wall secrete a fluid which keeps the inner surface of the alveolus moist, allowi ng the gases to dissolve. The fluid also contains a natural detergent, which prevents the sides of the alveoli from sticking together.

left lung

l--~ ri b s

bronchio les (ending in microscopic alveoli)

~

diaphragm

VENTILATION OF THE LUNGS Air is in haled into the lun gs throu gh the trachea, bron chi and bron ch iol es. It is exhaled via the same rout e. M uscles are used to lower and raise the pressure inside the lun gs to cause t he mo vements of air. Inh aling

Exhal ing

• The external intercostal muscles contract, moving the ribcage up and out

• The internal intercostal muscl es co ntract, movi ng the ribcage down and in

• The diaphragm co ntracts, becomin g fl atter and mo vin g down

• The abdominal muscl es co ntract, pushin g the di aph ragm up into a dom e shape

• These muscle mov ements increase the vo lume of the thorax

• These muscle mov ements decrease the vo lume of the thorax

• The pressure inside the t horax therefore drop s below atmospheric pressure

• The pressure inside the thorax therefo re rises above atmospheric pressure

• Ai r flows into the lungs fro m outside the body until the pressure inside the lungs rises to atmosp heric pressure

• Air flows out from the lungs to outside the body unti l the pressure inside the lungs fall s to atmospheric pressure

Human health and physiology 51

--

-

- - --

-

- - - -

Neurons and synapses

ORGANIZATION OF THE NERVOUS SYSTEM

SENSORY AND MOTOR NEURONS

The nervo us system is co mposed of cel ls called neurons. These ce lls are often very elongated and can carry messages at high speed in the fo rm of elect rica l impul ses. There are two parts of the nervous system • th e central nervous system (CNS), co nsisting of the brain and spinal co rd • periph eral nerves that co nnect all parts of the body to the central nervou s system.

Neu rons carry elect rica l impu lses long d istances in the body, using elo ngated struct ures ca lled nerve fib res (axo ns). • Sensor y neuron s carry nerve impulses from receptor s (sensory ce lls) to the CNS. • M otor neuron s (below ) carry impu lses from the CNS to effectors (muscl e and gland cells). • Relay neurons carry impulses w ithi n the CNS, fro m one neuron to another.

Structure of a motor neuron motor end plates

cell body

nucleus

direction of transmission of impulse along the axon

axon (nerve fibre)

I

length of neuron omitted

skeletal muscle fib res

dendrites

Stages in synaptic transmission

SYNAPSES A synapse is a ju ncti on betw een two neuron s. The plasma membr anes of the neurons are separated by a narrow fluid-filled gap ca lled the synaptic cl eft . M essages are passed across the synapse in the fo rm of c hemica ls ca lled neurotr ansmitters. The neurotransmitt ers always pass in the same directi on from the pre-synapti c neuron to the post-synapti c neuron . M any synapses fun ction in the following w ay. (D A nerve impul se reaches the end of the pre-synaptic neuron . Depo lariz ation of the pre-synaptic membra ne causes vo ltage-gated calci um channels to op en. Calc ium io ns di ffu se into the pre-synaptic neuro n. Q) lnflux of calci um causes vesicl es of neurotransmitter to move to the pre-synaptic membrane and fuse w ith it, releasing the neurotran smitter into the synaptic cl eft by exocytos is. 8) The neurotr ansmitter diffuses across the synaptic cl eft and binds to receptors in the post-syn apti c membr ane. @ The receptors are transmitter-gated ion channels, w hich open w hen neurotransmitter binds. Sodium and other positively charged ions diffuse into the post­ synaptic neuron . This causes depol arizati on of the post-synaptic membra ne. @ The depo lariz ation passes o n down the post­ synaptic neuron as an actio n pote ntia l. Neurotransmitter in the synapti c cl eft is rapid ly broken down , to prevent co ntinuous synaptic transmission . For example, acetylcho lin e is broken down by cho linesterase in synapses that use it as a neurotr ansmitter . Calci um ions are pumped out of the pre-synapti c neuron into the synaptic cl eft. The f igure (right) shows the events th at occ ur dur ing

synaptic transmissio n.

o

o

52 Human health and physiology

Q) Vesicles of neurotransmitter move to the membrane and release their contents

CD Nerve impulse reaches the end of the pre-synaptic neuron

CZJ Calci um is pumped out. Neurotransmitter is broken dow n in the cleft and reabsorbed into the vesicles

synaptic knob

vesicles of neuro­ transmitter

i® @

Q) Calcium diffuses in through calci um channels

@

".

@ L,~ r

~~~

?'-:-

->:::.c,,= . -, ------:;AHI~.

Ca2+ Ca2+

@)Neuro­ transmitter diffuses across the synaptic cleft and binds to receptors

0) Sodium ions

@ Nerve imp ulse setting off along the post-synaptic neuron

enter the post­ synaptic neuron and cause depolarization

Nerve impulses

RESTING POTENTIALS The resting potential is the elec trical pot ential across the plasm a mem brane of a cell that is not conducting an imp ulse.

action potential

+50

Neuron s pu mp ions across their plasma membranes by acti ve transport. Sodium is pumped out of the neuron and potassium is pump ed in . Con centr ation grad ients of both sodium and potassium are established across the membrane. The inside of the neuro n develop s a net negative charge, co mpared w ith the outside, because of the presence of chlori de and other negatively charged ion s. There is therefore an electrica l potenti al or vo ltage across the membr ane. Thi s is called the resting potenti al.

+30

+10 zero

>

E -10

<,

.~

.ACTION POTENTIALS

c Q)

An action potential is the reversal and restoration of the electrical po tential across the plasm a me mb rane of a ce ll, as an electrical imp ulse passes along it (depolariz ation and repolariz ation).

"0 -30

CL

threshold level

- 50

W hen an impu lse passes alo ng the neuron , sodi um and potassium ions are allo wed to d iffuse across the membr ane, thr ough vo ltage-gated ion channels. The electrica l potentia l across the membrane is ini ti ally reversed but is then resto red . This is called an action potential. The figure (right) shows th e changes in memb rane po larization that occur du ring an action potenti al. The way in w hic h action potenti als pass down nerve fib res is explained below .

-70 I

L

resting potential

\m m

:.----:.

--­

_

-90 ~~ -~' '-v-'

(l)

CD

~ ~~~

Q)

@

STAGES IN THE PASSAGE OF A NERVE IMPULSE

CD An actio n potenti al in one part of a neuron causes an actio n potential to develop in the next sectio n of the neuron . This is due to diffusion of sod ium io ns betw een the region w ith an actio n potenti al and the region at the resting potenti al. These io n movements, loca l currents, redu ce the resting potent ial. If the potenti al rises above the threshold level, vo ltage­ gated channels open .

CD Sodi um channels open very quickly and sodium ions diffuse into the neuron down the concentration gradient. This reduces the membrane potential and causes more sodium channels to open. The entry of positively charged sodi um ions causes the inside of the neuron to develop a net positive charge compared to the outside - the potential across the membrane is reversed. This is called depolarization.

Potassium channels open after a sho rt delay. Potassium ions d iffu se out of the neuron down the co ncentratio n grad ient th rough th e opened channels. The exit of positi vely charged potassium ions cause the inside of the neuron to develop a net negative c harge again compared w ith the outside - the potenti al across th e membr ane is restored. This is called repolarization.

:\

©

©

8) Concentration gradients of sodium and potassium across the membrane are restored by the active transport of sodium ion s out of the neuron and potassium ions into the neuron . This restores the resting potential and the neuron is then ready to conduct another nerve impulse. As before, sodium ions diffuse along inside the neuron from an adjace nt region that has already depo larized and in itiate depolarizatio n.

SG~a >8 "" 8

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Ion movements during an action potential

Human health and physiology 53

Maintaining the internal environment

HOMEOSTASIS Blood, and tissue flui d derived from blood , flow around or cl ose to all cells in the body. Blood and tissue fluid for m the internal environment of the body. Thi s internal envi ron ment is controlled and varies very little despite large variation s in the external environment. The co ntro l process is called hom eostasis.

The endocrine and nervous systems Endocrin e system

Ne rvo us system

pituitary gland

th yroid gland

Hom eostasis is maintaining the internal environment of the bod y between limits. The parameters contro ll ed include • bod y temp eratu re • bl ood p H • carbo n di oxide concentration • blood glucose concentration • w ater balance The nervou s system and the endoc rine system are bot h invol ved in controlling the internal env ironment. The endo crine system co nsists of glands, w hic h release hormon es that are transported in th e b lood .

iqrl

.:

II

islets in th e pancreas

testes (ovaries in females)

CONTROLLING LEVELS BY NEGATIVE FEEDBACK 1. Feedback In feedback systems, the level of a product feeds back to control the rate of its ow n production .

I

Level of product feeds back to affect the rate of production .

2. Negat ive feedback Negative feedback has a stabilizing effect because a change in levels always causes the opposite change. A rise in levels feeds back to decrease production and reduce the level. A decrease in levels feeds back to increase productio n and raise the level. These are both negative feedback.

Processes that cause the

production of something.

3. Mo nito ring levels Wh en the level falls signif icantly

below the set point, it is

increased by negative feedback.

Levels above set po int

Set point

- - - - - - --- - - - - -- -- --- - - - - - - - - - --- - -- - - - ---- - -- -- - -- ~- - - - --- - - - -- - - - - _. - _r_----''__-- -- - -- ----*~

f--"~----;;,.,c.----""~-_7'''------------==.__

- - - ----- - -- -~- -- --- --- -- - --- - - - - - - -- -1- -- - - - - --- - - - -- - - - - ----- ---- ----- -- -Levels below set point

Small fluctuations above and below the set point do not cause a response.

W hen the level rises

signifi cantly above the set

point, it is reduced by negative feedback.

54 Human health and physiology

Body temperature and blood glucose

CONTROL OF BODY TEMPERATURE The hypoth alamus of the brain monito rs the temperatur e of the blood and compares it w ith a set point, usually close to 37QC. If the bl ood temperature is low er or higher than the set point the hypoth alamus sends messages to parts of the bod y to make them respond and bring the temperature back to the set point - negati ve feedback . These messages are carried by neuron s. The responses affect the rate at w hic h heat is produ ced, the rate at w hich it is transferred betw een parts of the bod y in the blood , or the rate at w hic h it is lost from the bod y. Responses to overh eat in g

Respon ses to chilling

Skin arterio les becom e wi der, so mo re blood flow s throu gh the ski n. Thi s bloo d tr ansfers heat from the co re of the bod y to t he skin. The temperatu re of the skin rises, so more heat is lost fro m it to the environment.

Ski n arterio les become narrow er and they bring less blood to the skin. The blood capillaries in t he skin do not mo ve, but less blood f lows throu gh them. The tem perature of the ski n falls, so less heat is lost fro m it to t he env ironme nt.

Skeletal muscl es rem ain relaxed and resting so that they do not generate heat.

Skeletal muscl es do many sma ll rapid co ntractio ns to generate heat. Thi s is called shive ring.

Sw eat glands secrete large amo unts of sweat making the surface of the skin damp . W ater eva pora tes from the damp skin and this has a coo ling effec t.

Sweat glands do not secrete sweat and the skin remains dry .

nnn

sweat on skin

---

secretion ~ from sweat gland \

skin / arterio le dilated

(w idened)

warm skin so much heat lost

i~

iv---..

,i

JijF 'l0J :;~~~/J

dry skin rapid blood flow in capi llaries keeps the skin warm

-

sweat duct closed up

III

cold skin so little heat lost little blood flows through capilIaries so skin cools dow n

no sweat secretion

,~

shunt vessel closed I

sub-cutaneous adipose tissue for insulation

skin arteriole

constricte d

artery

vein

,-

r,

\ ~

shunt vessel open so blood can bypass capillaries

~

CONTROL OF BLOOD GLUCOSE

I

Blood glucose concentration cannot be kept as steady as bod y temp eratu re. Instead it is usuall y kept betwee n 4 and 8 m i/Jimo les pe r drn" of bloo d . Cells in the pancreas mon itor the concentratio n and send hormon e messages to target organs w hen the leve l is low or high. Respon ses by the target organs affect the rate at w hic h glucose is loaded into the blood or unloaded from it. The mechanisms rnvotved are anothe r example or negative reedoaoc,

\

Responses to hi gh blood glucose levels

13 cells in the pancr eati c islets prod uce in sulin .

I Responses to low blood glucose levels a cells in the pancreatic islets prod uce glucago n.

Insul in stim ulates the liver and mu scle cells to absorb glucose G lucago n stim ulates li ver cells to break glycogen dow n into from the blood and co nve rt it to glycogen. Gr anu les of glucose and release the glucose into the blood . glycogen are sto red in the cyto plasm of these cells. O ther Thi s raises th e blood glucose level. cells are stim ulated to absorb glucose and use it in ce ll respiration in stead of fat. These processes low er the blood glucose level.

DIABETES In some peop le the co ntrol of blood glucose does not wo rk effective ly and the co ncentration can rise o r fall beyo nd the normal limits. The fu ll name for this co nd ition is diabet es mellitus. There are tw o forms of this co ndi tion, w hic h are compa red in the tab le below: Typ e I di abet es

Type II diab etes

The onset is usuall y du ring childhoo d.

The o nset is usually after c hildhoo d.

a cells produce insuffi ci ent i nsuli n.

Target ce lls become insensitive to i nsu lin .

Insulin inj ecti ons are used to co ntro l glucose levels.

Insuli n inj ect ions are not usually needed .

Di et cannot by itself co nt rol the co nditio n.

Low ca rbohy drate d iets usuall y co nt rol the co nditio n.

Human health and physiology 55

Reproductive systems

THE FEMALE REPRODUCTIVE SYSTEM

FEMALE SEX HORMONES

ovary

oviduct ce rvix

uterus

vagina

bladder

large intestine

urethra vulva

TESTOSTERONE Ce lls in the testes of males produ ce testoste rone - the male sex ho rmo ne . Testoste rone has seve ral ro les. • The deve lopin g testes of a male fetu s secrete testoste rone , whic h ca uses ma le ge nitalia, includin g a pe nis, to develop in the fetus • Leve ls of testosteron e rise dur ing pube rty a nd cause ma le seco nda ry sexual c haracte ristics to deve lop - pubic hair, a n e nla rged peni s a nd growth of skeleta l muscles for exam ple • During ad ulthood, testosterone maintain s the sex drive, the instinct whi ch e nco urages men to have sexua l intercour se a nd the refo re pass o n thei r ge nes to offsprin g. Testoste rone is a lso o ne of the hormon es needed to stimulate spe rm produ ction by the testes.

The pituitary gla nd prod uces FSH a nd LH . These two horm on es affect processes in the ovary. FSH stimu lates the deve lo pment of follicles - fluid filled sacs that co ntain an egg ce ll. LH stimu lates fo llicles to beco me mature, release their egg (ovulatio n) and then deve lop into a structure ca lled the co rpus lute um. The ova ry produ ces estroge n a nd progeste rone. These two horm on es stimul ate the develop ment of fem a le seco nda ry sexua l c ha racte ristics durin g pu berty. They also stimulate the development of the ute rus lining that is needed d uring pregnan cy. Unless a wo ma n is pregnant the levels of the fem ale sex horm on es rise a nd fa ll accord ing to a cycle , which is descr ibed o n page 57 .

THE MALE REPRODUCTIVE SYSTEM

seminal vesicle

bladder

sperm duct

- --

i----fl

+ - - - -- - - -- - -----,I-- -

erectile tissue

prostate gland

penis - ­ - -I ~-l-----------f------ e pi di d ym i s

urethra -

­

-

-t1l----H

scrotum

foreskin

56 Human health and physiology

testis

The menstrual cycle

Between puberty and t he menopause, wome n who are no t pregna nt fo l low a cycle called t he me nstr ual cycl e. Th is cycl e is co ntr o l led by ho rmon es FSH and LH prod uced by t he pitu itary gland and est roge n and progesterone prod uced by t he ovary. Th e fi gure below shows t he leve ls of t hese ho rmo nes d uring t he menstru al cycl e. It also shows t he c han ges in t he ova ry and i n the uteru s.

CD

@

LH rises to a peak and causes the egg to be released fro m the fo llic le - ovul ation .

FSH level rises and stimu lates fo lli cl e develop ment and estrogen secretion by cells of the fo ll icle.

j

,...

FSH and LH levels

'\

"".

.' • • ,

H igh progesteron e and estrogen levels in hibit FSH and LH secretion. Thi s is negative feedback because FSH and LH stimulated estrogen and prog esterone secretion.

I

' .~

®

FSH levels rise again, starting t he next menstru al cycle . I

v

i

• ".

®

@ LH causes the fo lli c le cel ls to secrete less estrogen (negative feedback) and mor e progesteron e. Aft er oval ution LH causes the foll icl e to develop into the co rpus luteum.

I

~ .................... •.

I \..

.:

" , .._. . , .. ...

' ..----.:., .FSH LH

, .'

:

CjJ GJ CjJ GiJ GJ CjJ QO

ova ry develop ment

follicle starting to develop

follicl e nearly mature

corpus

luteum

I

•• , " " 1

I I

I

!

,,'

I

••'

estrogen and pro gesterone levels

• •

.......... .....

I

•• r "

•

:

• ••••• , •• ~ . . . . .. I

@

This positive feedback makes estrogen levels rise and stimu late the repair of the uterus lining.

@)

Estrogen levels rise to a peak and stimu late LH secretion by the pitu itary gland.

MEN STRUATIO N

0

1

2

3

4

1 5

l101I1l: R~'"~~

~

~

,,\

~~

; , " . _;

~'."! ~.~ '';' - :''''''''~

, '..·. ," ·1 -::}'-; ". ~, .

.~; \ ' ~

._ -\ ~, . ,':

," ,

7

8

}~ :-;~

',

: . -\ ' I, " ' .

~:"":.~. ; : . ,.; : " _ . .~ ., .,. ~ . <: :'

'('::'. " ~ " " L:~ .,,,-J.;:.~ .' .;

O V ULATIO N

6

.

~ ~-----,

: : I I,

uterus w al l development (en do metri um)

e'"

~so~ .•

:;"

progesterone

I

7 - \ ,\

Estrogen makes the fo l licl e cells produce more FS H receptors and so respond more strongly to FSH.

~

I

I

a>

I I

".

:

l

MENSTRUATION

r

9 10111213 141516 171 819202 1222324252627282930 3 1 323 334 DAYS AFTER THE START OF MENSTRUATION

Human health and physiology 57

In vitro fertilization

INFERTILITY Som e couples do not achieve fertil ization and pregnancy w hen they wi sh to, despite sexual interco urse during the period in the midd le of the menstrual cycle w hen ovulatio n usually occurs. This is calle d infertil ity. It may be temporary, because the causes can be reso lved, or permanent. Approximately one in six co uples have some experience of temporary or permanent infertil ity. M any of these couples can be helped to have a chil d by in vitro ferti Iization - IV F. For example, blocked oviducts in a wo man prevent concept ion, but IV F can overco me thi s prob lem . Ot her prob lems cannot be resolved by IV F, fo r example low or zero sperm co unts in men . The process of IVF is outlined (right).

Timetable for IVF _- -- G) Adrug is injected once a day for three weeks, to stop the wo man's normal menstrual cycle.

, _ @ Large doses of FSH are injected once

a day or 10-1 2 days to stimulate the

ovaries to develop many foll icles.

" -Q) HCG (another hormone) is injected

" :

21.00

" :' :'

36 hours before egg collection, to loosen

the egg in the foll icles and to make

them mature.

@ The man provides semen by

ejaculating into a jar. The sperm are

processed to concentrate the healthiest ones.

, : -: ~ The eggs are extracted from the 9.00 :: foll icles using a device inserted through 10 .00 ' the wall of the vagina. 14 .00

" - ® Each egg is mixed with sperm in a week 6 -

8 .00

,

shallow dish. The dishes are kept overnight in an incubator.

" -0 The dishes are checked to see if

week 7

14 .00

fertil ization has worked.

", ® Two or three embryos are selected and

placed, via a long plastic tube, into the

uterus.

week 8

--,-------- ® A pregnancy test is done to see if any embryos have implanted. week 9

, __ , _-- -,- - - - ----

----.@ A scan is done to seeif the pregnancy is continuing normally. The heart should be visible beating.

ETHICAL ISSUES ASSOCIATED WITH IVF Som e issues are controversial and around the wor ld the v iew s held by peop le may vary co nsiderably . Ethical issues invo lve questio ning w hether something is w rong or right. Deci sion s cannot be made using scienti fic method s, but scie nti sts have an obliga tio n to consider ethica l issues.

Ethical arguments against IVF

Ethical arguments for IVF

• Inherit ed form s of inferti lit y mi ght be passed on to ch ild ren, w hic h means that the suffering of the parents is repeated in their offspring. • More embryos are often produ ced than are needed and the spare embryos are sometimes killed, denyin g them the chance of life. • Embryologists select embryos to transfer to the uterus, so hum ans are decid ing w hether new indi vidu als survive or die . • IV F is an un natural process, carried out in laboratories, in contrast to natural conceptio n occurr ing as a result of an act of love. • Inferti lity should be accepted as the wi ll of God and it is w rong to try to circumvent it by using IVF to have a chil d .

• M any form s of inferti lit y are due to environmental facto rs, so offspring w ill not inh erit them . • Any embryos that are ki lled dur ing IVF are unable to feel pain or suffer, because their nervous system has not developed . • Suffering due to genetic disease could be red uced if embryos we re screened before bei ng transferred to the uterus. • Parents w ill ing to go thro ugh the pro cess of IVF must have a strong desire for ch ildren and so are likely to be loving parents. • Infertility brin gs great un happ iness to parents w ho wa nt to have child ren, w hic h in some cases can be ove rcome by IVF.

58 Human health and physiology

EXAM QUESTIONS ON TOPIC 6 Respiration in humans and other mammals generates heat which can be used to keep the body temperature above that of the surrou ndi ngs. Many mammals found in the southern hemisphere, including marsupials, vary their body temperature according to a daily cycle. The mouse lernur (Microcebus myoxinus) is an example of such a mammal. To investigate this daily cycle, M. myoxinus was studied in its native habitat in Madagascar. Data-loggers which recorded body temperature (Tb) over 24-hour periods were implanted in the bodies of several of these mammals. Air temperature (Ta) was recorded at the same time. A typical set of results is shown in the graph below. Darkness -------,

40

Tb

!g-- -----­

35 ~ Cl)

Ta

30

--:r-a----i----------------------------------------i---\----------------t ~- ~,:- ~~,- ----------.

25

-------\A;~ --------------------------------------t ---_t------------k:_ -----------------­

~

~

Q)

Q.

E

\

~

20

. '"

.. J

- - ------ - ~ --- - -- ~..- ~ :..!-,-r~ ~-,- - - -- - ---( --- - - -- - -- ---\ .. 4,\ " " " \

15

-

- -- --- - - - -- - - - -- - -- - -- - - -- - - -- - -

r------------,-,- -------------------------­

~l\

,"

_: - -'-~~\.~ _\",: -~;.~ ~-;/: - - -- - - - -- - - - --- - - -- - - - -- - -- -­

10 16:00

20:00

24:00

04:00

08:00

12:00

16:00

Time of day [Source: Cossins and Barnes, Nature (1996), 384, page 582]

a) Using only the data in the graph, state two differences between Ta and T b during the hours of darkness.

[2]

b) T b rises from 08:00 to 12:00. Explain briefly how this temperature rise occurs.

[2]

c) Predict, with a reason, whether M. myoxinus is active in the hours of dayl ight or the hours of darkness.

[1 ]

2 a) (i) State the function of phagocytic leukocytes.

[1 ]

(ii) Outline where in the body phagocytic leukocytes carry out their function.

[2]

b) Explain briefly the need for small numbers of many types of B-Iymphocyte in the body.

[2]

3 The diagram right shows part of the human gas exchange system. a) State the name of the parts labelled I and II.

[2]

b) I and II allow the lungs to be ventilated. Explain briefly the need for ventilation.

[2]

c) Draw and label a diagram of alveoli.

[3]

II

'

(­

18 Questions - Human health and physiology 59

7 DNA structure and replication

DNA STRUCTURE At one end of each

$

Hydrogen bonds (show n as - ) lin k the

bases. Tw o bonds form between adeni ne and thym ine and three bonds betw een guanine and cytosine. On ly these pairs can form hydrogen bon ds.

strand is a

phosphate li nked to ?H carbo n atom 5 of -0 - P = 0 deoxyrib ose. This is I the 5' termin al. 0 Cs

0

/~

C4

\ c3-

ci

C1

o

2

Adjacent nucl eotid es --~F;:::---~ are linked by a bond betw een the phosphate group of one nucl eotide and carbon atom 3 of the other nucl eotide.

r 0= p - o-

I

o guanine

N

\

cytosine

/

N - H-O

~

/=\ N-C

At one end of each strand is a hydroxyl group attached to carbon atom 3 of deoxyr ibose.

Thi s is therefore the 3'

OH

/

~

/ C""' N/ H

/ ~

C-C

O-

L

'-~

l - N\

N -H -N

C -H I;

C -C / \ H -N \ H

~

~ _-----~)

termin al.

H

Two of the bases in D NA are purines: adenine and guanine. They have tw o ri ngs in their mol ecu les. Two of the bases in DNA are pyrimidines. Cytosine and thymi ne are pyrimid ines. They have one ring in their mol ecul e. O nly a purine plu s a pyrimi dine w ill fit in the space between

the sugar-phosphate backb ones.

-----'Y~----~./

\.~-----~

The two strands have their 3' and 5' terminals at opposite

ends - they are anti-parallel. D NA replication can only occur in a

5 ' ~ 3' direction so a different method is needed for the tw o strands.

DNA REPLICATION

CD The cell produces many free nucl eotides fo r DNA replicati on. Each has three phosphate groups - they are deoxyrib onucl eoside tripho sphates. Tw o phosphates are removed durin g repli cation to release energy.

Q) Helicase uncoils the DNA doubl e helix and splits it into two temp late strands.

Q) DNA polym erase III adds nucl eotides in a 5'­ 3' directi on . On o ne strand it moves in the same dir ecti on as the repl ication fo rk, c lose to hel icase. O n the other templ ate strand it moves in the opposite di rection.

@ Short lengths of D NA are

@ DNA ligase seals up

formed betw een RNA prim ers on this strand, - ----, called Ok azaki fragments.

the nick by makin g another

"'' 'Pho\Ph'', bond,

CV D NA polymerase I removes the RNA primer and replaces it wi th DN A. A nick is left w here two nuc leotid es are still unconnected.

60 Nucleic acids and proteins

~ D NA pol ym erase III

starts repli cation next to the RNA prim er and adds nucl eotid es in a 5'-3 ' direction. It therefore moves away from the repli catio n fo rk on th is strand.

® RNA prim ase adds a sho rt length of RNA attached by base pairing to the template strand of DN A. This acts as a primer, all ow ing DNA pol ymerase to bi nd and begi n replica tion.

Organization of DNA in eukaryotes

DNA IN PROKARYOTES AND EUKARYOTES A ll eukaryotes and prokaryotes use D NA as thei r genet ic materi al and use the same genetic code , but there are differences in the way that the DNA is organized and used. Prokaryotes have naked D NA, w hic h co nsists mostly of single co py genes that are tr anscri bed and translated w itho ut mod if ication . The situatio n in eukaryotes is mor e co mplex :

Nucleosome structure

nucleosome core consisting of eight histone protein molecul es

DNA linker

Replication init iat ion sites Repli cati on of D NA begin s at specia l in iti ation points. Eukaryotes have many of these initi ation points alo ng each chromoso me. M ost pro karyot es have o nly on e po int on their D NA mol ecul e w here repli cation is initiated.

Nucleosomes In eukaryotes, the D NA is associated w ith protei ns to form nucl eoso mes - glob ular structures that co ntain eight histone protei ns, wi t h DN A w rapped around. A not her hi ston e prot ein bond s the structure together (a bove right). In an interphase nucl eus in eukaryotes the DN A resembles a str ing of beads (right). N uc leoso mes have tw o functio ns: • they help to package up the DNA durin g mitosis and meio sis by the process of supercoi li ng • they can be used to mark parti cul ar genes, either to promote gene expressio n by tr anscripti on and translation , or to cause silenc ing of a gene by prevent in g transcr ipt ion.

another histone protein holdi ng the nucleosome together DNA w rapped tw ice around the nucl eosome core DN A linker conti nuing towards the next nucleosome

Repetitive sequences Mu ch of the D NA in eukaryotes consists of repetiti ve base sequences, whi ch are not translated. Hi ghl y repetiti ve sequences, sometimes calle d satelli te D N A, are sequences of betw een 5 and 300 bases, that may be repeated as many as 10 000 times. These co nstitute 5- 45% of typi cal eukaryote DNA. Its fun cti on is not yet cl ear. A surprisingly smal l pro portio n of eukaryo tic D NA is sing le copy, or un iqu e genes.

DNA strand

nucleosomes

Introns and exons M any genes in eukaryotes co ntain intron s - seque nces of bases t hat are transcr ib ed, but not translated. Exons are sequences of bases that are tr anscribed and translated. A typical eukaryote gene co nsists of a series o f exons and intron s. Af ter transcr iption of the w ho le gene, the intro ns are remov ed to form mature mRNA, in a process called po st­ transcription al modification (below right). Prokaryotes do not usual ly have introns in their genes. percentage of genes

nucleosomes can

~ be tagged wi th

proteins to promote or repress transcripti on

100 80

Saccharom yces cerevis iae (a yeast)

60 40 20 0 11

1=

40

DNA

30

__ _ j

Drosophila melanogaster (fruit fly)

20

10

ojl II II II II 1

==

DO

=

=

20

transcription

~ -,- - " ~====j introns

~

'post-transcriPtional modification

mRNA exon mature

15

=

10 5

ojl,lI ,II,II ,II,II ,II ,IOI, II, II,II,b Q'7 , '7'7, ,1, 10 '7'7 4

9

11 10

13 12

15 14

17 16

19 18

<30 <60 20 <40 >60

1"'0<'' ' 00 ~

mRNA

protein

nu m b er of exons

Nucleic acids and proteins 61

Transcription of DNA

RNA POLYMERASE AND TRANSCRIPTION DNA is split into two strands by RNA polymerase. On e of these strands forms the templ ate for transcri ption. The base sequence of the mRNA is complementary to it. The other strand has the same base sequence as the mRNA (except for T instead of U) and is therefore called the sensestrand. The strand that forms the template and is transcrib ed is called the antisense strand.

DNA is rew ound into a double heli x by the rear of RNA polymerase

DNA is unw ound by the front of RNA polymerase

3'

GTACCGT TAG

Part of { 5 ' the DNA of a gene 3 '

3' G U A C C GU U A G 1

I I I I I I I I

C A TGGCAAT

5'

CI

RNA polymerase

antisense strand

mRNA molecule produced by RNA polymerase

5' Free nucleoside triphosphates are used by RNA polymerase to extend the grow ing mRNA molecule. Two phosphates are removed as they are li nked on, converting them into RNA nucleotid es. The 5' end of the nucleotid e is added to the 3' end of the grow ing chain - transcri ption thus moves in a 5 ~ 3' direction.

TRANSLATING THE GENETIC CODE M essenger RNA ca rries th e in form ati on needed for making po lyp eptid es out from th e nucleu s to th e cytopl asm of eukaryotic ce lls. The informati on is in a coded form , whi ch is decod ed during tr anslati on. The base sequence of mRNA is tr anslated int o the amino aci d sequence of a pol yp eptid e. Key featur es of the co de are describ ed (below left). The meaning of each co do n is shown in the tab le (below right). The genetic co de is a triplet code - thr ee bases co de for one am ino aci d. A group of thr ee bases is called a codon. There are 64 different co do ns (4 3) . Thi s gives more than eno ugh cod on s to code fo r th e tw enty am ino acids in pr otei ns. If codons cons isted of two bases there wou ld be sixteen (4 2 ) - not enou gh . No ne of the 64 codons are unu sed . Instead, the genet ic cod e is degenerate. Thi s means that it is possibl e for tw o o r mor e codons to code for the same am ino aci d. The genet ic cod e is universal. With ju st a few minor exceptions, li v ing organisms use p recise ly th e same code. Viru ses also use this co de.

First base of codon (5' end) U

C

A

G

62 Nucleic acids and proteins

Second base of codon on messenger RNA

I

I

I

U Phenyl alanine Phenylalanine Leucine Leucine

C Serine Serine Serine Serine

A

G

Tyrosine Tyrosine STOP STO P

Cysteine Cysteine STO P Tryptophan

Leucin e Leuci ne Leucine Leucin e

Proline Prol ine Prol ine Proline

Hi stidine Hi stid ine G lutamine G lutamin e

Arginine A rginine Arginin e Arginine

Isoleucine Isoleucin e Isoleucin e Methionine I START

Threonine Threon ine Threonin e Threonine

Asparagine Asparagine Lysine Lysine

Seri ne Serin e Arginine Argin ine

Valin e Valin e Valine Valin e

A lani ne Al anine Alanine A lanine

Aspartic acid Aspartic acid Glutamic acid G lutamic acid

G lycine Glycine Glycine Gl ycin e

Third base of codon (3' end) U C A

G U

C

A

G

U C

A

G

U

C

A

G

Ribosomes and transfer RNA

tRNA AND tRNA ACTIVATING ENZYMES

tRN A st ructure

There are many different types of tRNA in a cell, w hic h have an imp ort ant ro le in translation . All tRN A mo lecul es have: • sect io ns that becom e doubl e stranded by base pairin g, creating loop s (above right) • a tripl et of bases called the antico don , in a loop of seven bases • two other loops • the base seque nce CCA at the 3' termi nal, w hic h forms a site for attac hing an ami no aci d. These features allow all tRNA mo lecu les to bind to three sites on the ribosome. The base seque nce of tRNA mo lecu les varies and th is causes some variable features in its structure : • an extra small loop is sometimes present • the base paired sect ions are sometimes heli cal. The variable features give each type of tRNA a distinct ive three-di mensional shape and d istincti ve c hemica l prop erti es (below right). Th is allows the cor rect amino acid to be attached to the 3' terminal by an enzy me called a tRNA activati ng enzyme . There are twe nty different tRNA act ivatin g enzy mes - o ne for each of the tw enty different amino acids. Each of these enzy mes attac hes o ne particu lar amino acid to all of the tRNA mo lecu les that have an anticodon co rrespo ndi ng to th at amino acid . The tRNA activat ing enzy mes recogni ze these tRNA mo lec ules by thei r shape and chemica l properti es.

A

5'

3' site for attaching an amino acid

C C

loop of seven nucleotides

double stranded sections linked by base pairin

extra loop loop of eight nucleotides

anticodon loop antic odon

I Thr ee-dim ensional view of tRN A

helical section

loop of seven nucleotides

\'

loop of eight

nucleotides

site for attaching an amino acid

Energy from AT P is needed fo r the attac hment of amino acids. A hi gh-energy bond is created betwee n the amino acid and the t RNA. Energy from this bond is later used to link t he ami no acid to the grow ing po lypeptide chain d uring translatio n.

antico don loop

STRUCTURE AND FUNCTION OF RIBOSOMES Ribosomes have a co mplex structure, w ith these features. • Proteins and ribosoma l RNA mo lecules (rRNA) bot h form part of the struct ure. • There are two subunits, one large and one small. • There are three bind ing sites fo r tRNA on the surface of the ribosome. Two tRNA mo lecules can bin d at the same ti me to the riboso me. • There is a binding site for mRNA on the surface of the ribosome. The structure of a ribosome is show n in o ut line in the fi gure (right), w ith the three tRNA bind ing sites. Ribosomes in th e cyto plasm are called free ribosom es. They synthesize protei ns for use w ithin the cell. Ribosomes can also be attached to membr anes of the endo plasmic retic ulum. They are called bound ribosomes and synthesize proteins for secretion from the ce ll or for Iysosomes.

position of growi ng polypeptide

\\

}

}

binding sites for tRNA

large subunit

small subunit

position of mRNA

PEPTIDE BONDS Ribosomes are the site of po lypeptide synthesis. Thi s invo lves li nking am ino aci ds together by a co ndensatio n reacti on (shown on page 15). The lin kage betw een the amino acids is a peptid e bond . Perhaps unexpected ly, it is rRN A and not protein s in the ribosom e th at catalyse the reacti on in w hic h the peptid e bond is formed. The diagram (right) shows a peptid e bond betw een tw o am ino acids.

H"

R

0

R

0

H

OH

I II I ~ N -C -C- N-C -C N/ I I I <, H

H

~

peptide bond

Nucleic acids and proteins 63

=

=

=

=

=

-

-

---------~===----------,

-

-

,

Polysomes and polypeptide elongation The figure (right) is an electron m icrograph showing groups of ribosomes ca lled pol ysomes (or pol yribosomes). A po lysome is a group of ribosomes mo vin g alo ng the same mRNA, as th ey simu ltaneously translate it. Each ribo some foll ow s a series of steps that is repeated many times to translate th e mRNA. O ne am ino ac id is added to the elongating polypeptide each tim e the cycle of steps is repeated (see below). As ribosom es move alo ng the mRNA towards the 3' end, the po lyp eptid e is gradually elo ngated. (x 180000)

POLYPEPTIDE ELONGATION

CD O ne of the binding sites for tRNA is vacant. The

/

•• •••

••• •••••

5'

small subunit of the ribosome ensures that only a tRNA with the antico don that is complementary to the next codon binds to it.

•• ••• ••

••• • •••• •

•

-+-'

....I ~....I....I....I- 3 '

5'

"l"""'

-jooI

- 3'

@ The tRNA shown on the left has been displaced to the

Q) The large subunit of the ribosome advances over the

third bind ing site, and detaches from the ribosome. It can be used again in translation after a tRNA activati ng enzyme has added another amino acid to it.

small subunit and detaches the polypeptid e fro m the tRNA show n on the left. The pol ypeptid e is attached by a peptide lin kage to the single amino acid held by the tRNA show n on the right.

•• •••

••• ••••• ••

•• •••

••• ••••• ••

Q) The small subunit slides across the large subunit. At the same tim e it moves three nucl eotides on along the mRNA in a 5' to 3' dir ection. Translation always occurs in a 5' to 3' di rection along mRNA.

64 Nucleic acids and proteins

Starting and stopping translation

Special steps are needed to sta rt the process of trans lat ion and to sto p it. These ste ps are ca lled initiation a nd termin ation. The three stages of translation are th us initiation , e longation and termination .

INITIATION OF TRANSLATION

cQJ

(a)

1

(b)

tRNA with the anticodon com plementary to the sta rt codo n binds to the sma ll subunit of the ribosome

The small subunit, carrying the tRNA binds to the 5' end of the messenger RNA

5'

end

AUG

_

3' end

_

3' end

_

3' end

_

3' end

The sma ll subunit slides along the mRNA until it reaches the start codo n, which shows where translation should be started

(c)

5'

end

The large subunit of the ribosome binds to the small subunit

(d )

5'

end

Another tRNA, with the ant icodon co mplementary to the next codon on the mRNA, binds to the ribosome.

Elo ngation of a polypept ide can now start

(e)

5'

end

TERMINATION OF TRANSLATJON

.....

The ribosome moves a long the mRNA in a 5'- 3' d irection, translating ea ch codo n into an amino acid on the e longating polypeptide

,

(w)

I _

I

.....

from 5' end

3'end

UGA

.........................

The ribosome reaches a stop codon. No tRNA mo lecule has the com plementary anticodo n

(x)

_

... ..... : . . .-----\.......-... -.......... The released polypeptide has ---usually already sta rted folding ...... up to form the protein's final shape

I

-

The large subunit advances over the sma ll subun it. The po lypeptid e is released from thetRNA

-

(y)

( _

3' end

J

from 5' end

'-/

)

3' end

from 5' end

aCsma hesa n d th~oro The ll subunit '. largems~~A all separate and

tRNAu ~~:

~ '"

(z)

_

from 5' end

UGA

Proteins synthesized by free ribosomes mostly remain and are •••••••• used in the cytoplasm. Prote ins synthes ized by ribosomes bound - - - - l.. to the ER are mostly secreted from the ce ll or are used in Iysosomes ••••••••

X"•••••

Nucleic acids and proteins 65

Intramolecular bonding in proteins

Po lypeptides have a mai n chain co nsisting of a repeating sequence of covalently bonded carbon and nitrogen atoms: N- C - C- N- C - C, and so on. Each nitrogen ato m has a hydrogen atom bonded to it ( N - H ). Every seco nd carbon atom has an oxygen ato m bo nded to it ( C = 0 ).

H-N

o=c

0

I

II

II

H

0

\

\

/

/ \

C-H

/

c =o

H- N

\

H- C

\

/

/ \

\

H- N

\ /

O'
Hydrogen bond s can fo rm between N - H and

C = 0 groups, if they are bro ught cl ose together.

\

C-H

/

\

\

/

N- H lIlllIIIIIIIIO=C

/

\

\

/

/ \

\

/

C=O IllIIlIIIlIUH-N

/

N-H '''''''' '''O=C

\

C- H

I

N- H

/

C- H

H-C

\

c=o

/

\

For example, if sectio ns of po lypeptid e run parallel, hydr ogen bo nds can fo rm betw een them . The structure that develops is calle d a B­ pl eated sheet. If the pol ypept ide is wo und into a right-handed hel ix, hydr ogen bo nds can fo rm betw een adj acent turn s of the hel ix. The structure that develops is called an a -helix . Because the groups fo rm ing hyd rogen bo nds are regularly spaced, secondary struct ures always have the same dim ensions. In add itio n to the hyd rogen bondin g in B-pleated sheets and a -helices, there are many other typ es of bond ing. Most of these invo lve the R groups of the am ino acids. The figure (below) shows some of these bonds.

c- o

C = O IlIIlIIl IlIl IH- N

H- C

/

N- H

/

C - HlIllI lIlllllIH -C

C = O IIlIIIlIIIlIlH - N

/

C- H

N - HUlIIIIllIllIO = C

N- HIIIII IlII IIII O = C

/ \

N-C- C -N -C - C

I

/

H-C

H

a::-HELIX

J3-PLEATED SHEET

H

H

Bond angles give the sheet a pleated shape

Types of intramolecular bond in proteins Ionic bonds can form between positively and negatively charged R groups

Acidic amino acids have R groups that can lose an H+ ion and so become negatively charged

, ,,." ',,

~HO\

H

'b-<-~y.'0'b /'\ _ --~~~:~~----r-~:o~O 1ff of----,: 'b y. 0 -, \\

'y/

'b~I)"

/

Basic amino acids

"

1)-

"

have R groups that can accept an H+ ion and so become positively charged

,'-,

_ :

is iD I ?i : I

oI :.'('. .

"'!', ~

I -Z

'\ \

~. \

/

/ ';"7"'\

" !?' "' 0

=f

N

I

""I

\..--- -z; ,, ?/~ "\ \ / .-y<. 0",(> '0

/ C'--'<,

C<-,,~

~~

~

./ 1--

./~ " -S-

1

'h 'S-

H

I

i: Gf:/b- - - - - -, _"'_llJ.:Jsl.:J

//

° I

C/-i. /

/

3

S

H

HO SHO/

v

I

:

I

Asparagine

Cr\ 3

;-­

I

!UJ t!Jnl:j~ -::- o'-:.- _J H H S

HO L1

N f I

.

0-

C/-i.

- - - - -,

, "',..,.---N'

H HI II

Pt;-e"':J-----f.!. :

\

< S . e C"::>-... 3 1_--------------- \H 0 rS ' ·C/-i. --r - ~~I.'.'- - - l - - Cr\ " I H II : "'" I/ -Y / < I 0 I \ I N I C I : 1-\ II \ " C/ {-lit(I ~ -Y

/

(1 /

/ '

/

I

9'--cJ\ H

II \ 0 I

I

:

: Lt ..y}!\ '7

Disulfide bridges wh ich are strong' covalent bonds can form between pairs of cysteines

\

/'

I \ \ H _- ----J-- CH~ _ ( o / ~, Q. (>thi~~;n'- Q - L - l1 - - CI-\ 2- J - -~~\i(\e ~ ~ 0>,cl/~ / " \%,

tl-t, <,

/

e

I

\ 01-\

Hydrophobic interactions, which are weak bonds, can form between R groups that are non-polar including all those projecting inwards here

0 ::;'-- ' NH2~'\ .sf.: '"

~<"

i

0

j:.

Hydrogen bonds can form between some R groups

\ '0' .

'"

\~

'0. . .---°",

o~ /'~ J,-

'"

66 Nucleic acids and proteins

f0

.JI°/I

I

P!::J!? ::J!J.it!ds - ~ - - GH : /I If - - - - I.. 0

',,_/' , I-f;IV-litF\! \ / C""\"" N/I C-r-- N-C

,, ---°/

H

" N..J--O , i . I " O_N" o I 0 ""'- t >.

f ,0,

\

0 »< ; ' ;

! /I

Ho

I

"o=~/ _.;\~. \

i .--6

\('._l,:-' \ eU'J .- -1, I n O·---- .H :

'//cI I-O -O~O-o \

H

N

,.0'J",-- ,: /

I~

G

"'U!::Jn"'7

G

0

--- -

-:;:::.0\ <"

_ S- - - -~ I

Protein structure

Protein s have a co mplex structure, whi ch can be explained by defin ing four levels of structure, primary, secondary , tertiary and quaternary structure.

PRIMARY STRUCTURE Primary structure is the number and seq uence o f am ino acids in a polypeptide. M ost polypept ides consist of betw een 50 and 1000 amino aci ds. The prim ary structure is determin ed by the base sequence of the gene that codes for the po lypeptide. The fi gure (below) shows the primary structure of B-endorphin, a protein co nsist ing of a single pol yp eptid e of 31 amino acids that acts as a neurotransmitter in the brain.

-+ Isoleucine -+ Isoleucine -+

Asparagine -+ Alanine -+ Histidine Lysine Glycine

Leucine

Lysine Lysine

-+ Glycine -+ Glutamine -+ Tyrosine -+ Glycine -+ Phenylalanine ... Methionine

Threonine -+ Serine

-+

Tertiary structure is the three-dim ension al conforma tion o f a pol ypep tide. It is fo rmed w hen the po lypeptide fo lds up after bein g pro duced by translatio n. The con fo rmation is stabilized by intramole cu lar bonds that for m betwe en amino acids in the po lyp eptid e, especi ally betw een their R groups. These include ionic bonds, hydr ogen bond s, hyd rophobic interactions and di sulfid e bridges. The intr amol ecul ar bond s are oft en fo rmed betw een amino acids that are wid ely separated in the pr imary struct ure of the po lypep tide, but w hich are brou ght together during the foldin g proc ess. The figur e below show s the terti ary structur e of lysozyme using the sausage mod el. Sausage model of lysozym e

Prim ary st ruct ure of B-endo rphin Alanine

TERTIARY STRUCTURE

Serine -+ Glutamic acid-+

Lysine

-+ Glutamine -+ Threonine -+ Proline -+

Valine

Phen ylalanine -+ Lysine

-+ Threonine -+ Leucine -+ Asparagine

SECONDARY STRUCTURE

QUATERNARY STRUCTURE

Secondary structures are regular repeating structures, including f5-pleated shee ts and a -he lices stabilize d by hydrogen bonds be twee n groups in the main chain of the polypeptide. In many protein s, parts of the po lyp eptid e form

Quaternary structure is the linking together o f two or more pol ypeptides to form a single protein . For example, insul in

secondary stru ct ures and oth er parts do not. In some prot eins seco ndary structu res do not for m at all. In a few proteins almost all of the polypept ide forms secondary struct ures. Fo r example almost all of myosin mol ecu les is a -helix and almost all of fibr oin (silk protein) is B-p leated sheet. The fi gure (below) show s the position of second ary structures in lysozyme, using the ribbo n model. Sections of a -helix are represented by helical ribbons and sections of B-p leated sheet are represented by arrows .

co nsists of tw o pol yp eptid es linked together, co llagen co nsists of three po lypeptides and hemo globi n consists of four . In some cases prote ins also co ntain a non-po lypeptide structure called a pro stheti c gro up. Each of the four po lyp ept ides in hemo globin is linked to a heme gro up, w hic h is not made of am ino aci ds. Proteins w ith a prosthetic group are called conj ugat ed proteins. The figure (below) shows the quaternary structure of hemoglobi n.

Sausage model of hemo globin

Ribbon model of lysozym e

Nucleic acids and proteins 67

Protein functions

FUNCTIONS OF FIBROUS AND GLOBULAR PROTEINS Protein s can be divided into tw o types acco rding to their shape - fibrous or globular. Fibro us protein s have a lon g and narrow shape. They are mostly insolub le in wa ter. G lobu lar prot ein s have a roun ded shape. They are mostly solub le in wa ter. Tw o exam ples of both fibrous and glo bular proteins are given in the table (below) . Protein s have a huge range of fun cti on s in livi ng organism s. Some prot eins are located in membr anes - their fun ction s are listed on page 8. Four of the fu nction s of non -membr ane proteins are li sted in the table (below) . Proteins can also be used as foo d stores, fo r examp le casein in milk, as pigments, for example opsin in the reti na, as toxin s as in some snake venom, as horm on es, fo r example insulin, and as enzy mes.

Function

Example

Structural

Co ll agen

Transport

Hem oglo bin

M ovem ent

M yosin

Defence

Im mu noglo bu li n

Details

Shape

The funct ion of co llage n is to strengt hen bon e, te ndo n and skin. These ti ssues all produce tou gh co llage n fibres in the spaces betw een their ce lls The fun cti on of hemoglo bin is to bind oxygen in the lun gs and to t ranspo rt it to respi ring ti ssues

Fib rous

G lobu lar

Th e function of myo sin (w ith anot her prot ein ca lle d act in) is to cause co ntract io n in mu scle fi bres and as a result ca use mov ement in an ima ls The fun ction of immu noglob uli n is to act as anti bod ies. Part of the im m unoglobu lin mol ecu le ca n be varied, so th at an almost end less variety of di fferent ant ibo d ies ca n be produ ced

Fibrous

G lo bu lar

POLAR AND NON-POLAR AMINO ACIDS IN PROTEINS A min o aci ds can be d ivided into two ty pes accordi ng to the c hemica l characterist ics of the ir R group. Po lar am ino aci ds have

hydrophi li c R groups and non- pol ar amino acids have hydr ophobi c R gro ups. The distributi on of po lar and no n-po lar amino

aci ds in a prot ein mo lecu le inf luence w here the prot ein is located in a cell and w hat functio n it can carry out.

The figures (below) show examples of th is.

Supero xid e di smutase - an enzyme found in all aerobic or gani sms Positions of proteins in and out of membranes

Non-polar amino acids in the centre of water­ soluble proteins stabilize their structure.

:th

Polar amino acids on the surface of proteins make them water soluble.

.. ' -. ..

A ring of amino acids w ith negatively charged R-groups repel the negatively charged superoxide ions and help to direct them to the active site.

Non-polar amino acids cause proteins to remain embedded in membranes.

The active site is a cleft containing amino acids wi th positively charged R-groups w hich attract the negatively charged superoxide ions that are the substrate of the enzyme. Lipase - an enzyme that works in th e small intestine

_ - -­ Polar amino acids ----",::::::::::;L----"<;--;:\'{. create channels thro ugh w hich hydrophilic substances can diffuse. Positively Polar amino acids cause charged R groups parts of membrane proteins allow negatively charged to protrude from the ions through and vice versa. membrane. Transmembrane proteins have two such regions.

68 Nucleic acids and proteins

polar region

The active site is a cleft containing amino acids w ith non-polar R-groups w hich bind non-polar triglycerides.

-

Part of the enzyme molecule acts as a hinged lid w hich can cove r the active site w hen not in use, hiding the non-polar R-groups.

non-polar region A protein cofactor binds to the enzyme, and helps lipase to bind to the surface of lipid drop lets because it has non-polar R-groups on its surface.

Enzymes and activation energy

ENERGY CHANGES DURING CHEMICAL REACTIONS Duri ng chemi cal reactio ns, reactants are co nverted into prod ucts. Before a mol ecul e of the reactant can take part in the reacti on, it has to gain some energy. Thi s is called the act ivati on energy of the reacti on . The energy is needed to break bond s w ith in the reactant . Later during the pro gress of the reactio n, energy is give n out as new bonds are made. M ost bio logical reactions are exothermic - the energy released is greater than the activa tion energy . Enzymes reduce the activation energy of the reactions that they catalyse and therefore make it easier fo r these reactio ns to occ ur. The graph (below ) shows energy changes d urin g uncatalysed and catalysed exothermic reactio ns. The chemical environment provided by the act ive site fo r the substrate causes changes w ithin the substrate mol ecu le, w hich weake ns its bo nds. The substrate is changed into a t ransiti on state, w hic h is different from the transition state du ring the reactio n w hen an enzy me is not invo lved. The transition state achieved during bi ndi ng to the active site has less energy and thi s is how enzy mes are able to red uce the acti vatio n energy of reactio ns.

,"b'~

active site of enzyme

As the substrate binds, the conformation of the protein is altered and the shape of the active site becomes complementary to that of the substrate

Energy changes during a chemical reaction

Activation

energy

w ith no

enzyme Activation energy w ith enzyme

c-,

on

iii c:

UJ

-.- - - - - - -- - - ' } Net energy product Progress of reaction _

released by the reaction is not changed by the enzyme

THE INDUCED FIT MODEL Biochemi sts have inv estigated many enzy mes and fo und that the lock and key model does not fu ll y explain the bindi ng of the substrate to th e active site. Unti l the substrate bi nds, the active site does not fit the substrate preci sely. As the substrate approac hes the act ive site and binds to it, the shape of the active site changes and only th en does it fit the substrate. The substrate ind uces the acti ve site to change, weake ni ng bonds in the substrate du ring the process and thu s reduci ng the activat ion energy. The fi gure (right) shows the indu ced f it model of enzy me activ ity. Som e enzyme s can have quite broad specifici ty, for examp le some protea ses. The induced fit model explai ns th is better than the lock and key model - if the shape of an active site alters wh en substrates bind , several di fferent but similar substrates co uld easily bind successful ly to it.

pm~

Weakening of bonds in the substrate helps the reaction to occur, converting it into the products. These dissociate from the active site and the enzyme returns to its original conformation

Nucleic acids and proteins 69

Enzyme inhibition

Some chemica l substances reduc e the activ ity of enzy mes or even prevent it co mpletely . These substances are called enzy me inhibitors. Some enzy me inhibi to rs are competiti ve and some are non-competiti ve. Figures below are a comparison of these types of in hib itor , w ith an example of each.

Competitive inhibition

Non-competitive inhibition

The substrate and in hibi tor are c hem ica lly very similar

The substrate and active site are not similar

The inhi bitor bind s to the active site of the enzyme

The inhib itor binds to the enzy me at a different site from the active site

Wh ile the inh ibitor occ upies the active site, it prevents the substrate from bindin g and so the activ ity of the enzy me is prevented until the inhibitor dissoci ates

The inhib ito r changes the co nfor mat io n of the enzy me. The substrate may still be able to bi nd, but the act ive site does not catalyse the reaction, or cata lyses it at a slower rate

6 o/

Substrate

Inhibitor

Inhibitor

Substraty()

)~t~~~ sti~e

OJ"

0;;:, ..

cannot

Enzyme

With no inhibitor the subst rate is co nverted to product at the act ive site

CJ

Inhibitor bou nd the e nzyme awa y / from the

Substrate binds but is not con verted

"'~ ~ ~;~,d

V

altered.

w ith no inhibitor

w ith no inhibitor

with a non­ competitive inhibitor

w ith a competitive inhibit or

Su bstrate concentration ­

Substrate concentration ­

W it h a fixed low co ncentrat ion of inh ibito r, increases in the substrate co ncentration gradually redu ce the effect of the inhibitor . The inhib ito r and substrate compete fo r the active site. W hen the substrate bind s to the active site, the in hibitor cannot bi nd, so the proportion of enzy me mo lecul es that are inh ibited becom es less and less. W hen there are many more substrate molecu les than in hibitor molecules, the substrate always wi ns the competit ion and bind s to the

With a fi xed low concentration of in hib itor, increases in substrate co ncentration increase enzy me activ ity. How ever, the substrate and in hib itor are not co mpet ing for the same site. The substrate cannot prevent the bindin g of the inhibitor , even at very high substrate co ncentratio ns. Som e of the enzy me molecules therefore remain inhi bited and the maxi mum enzyme activi ty rate reached is lower than w hen there is no inh ib itor

active site. The same maximum enzyme activity rate is then reached as w hen there is no in hi bitor .

EXAMPLE

EXAMPLE Succi nate

Fumarate

coo-

coo­

I

CH 2 I

9H2

COO-

Nitric oxide synthasecatalyses this reaction: )0 citrulli ne + nitric oxide arginine

I

- - - - _. CH

II Succinate dehydrogenase CH I

COOSuccinate dehydrogenase is inhibited by malonate

70 Nucleic acids and proteins

Malonate

coo­ I CH2 I

COO­

Op ioids are chemicals that resem ble morphine. They are inhib itors of nitric oxide synthase. They do not resemble arginine and bind to a different site on the enzyme, so they are non-competitive inhibitors. Nitric ox ide has many signallin g roles in human physiology.

Controlling metabolic pathways

METABOLIC PATHWAYS

Chains and cy cles of reactions

initia l substrate

Metaboli c pathw ays have these features: • They co nsist of many chemi cal reactions that are carried out in a part ic ular sequence. • A n enzyme catalyses each react io n. • A ll the react ions occ ur inside cells. • Som e pathways bu ild up organic compou nds (anabo lic pathw ays) and some break them down (catabolic pathw ays). • Some metabolic pathways consist of chains of reactio ns. G lyco lysis is an example of a chain of reactions - a chai n of ten enzy me-contro lled reacti ons converts glu cose into pyruvate. • Som e metabo li c pathways consist of cyc les of reaction s, w here a substrate of the cycl e is cont inually regenerated by the cycl e. The Krebs cycle is an examp le. The figure (opposite) shows the general patte rn of reactions in a chain and a cycl e.

substrate

1

;7 m ed;.r:'>: ", cod pmd",\

intermediate

1

"b",,"

intermediate intermediate

1

1

intermediate

\

intermediate

J

intermediate

intermediate

~

intermediate

1

product

end product

ALLOSTERY AND THE CONTROL OF METABOLIC PATHWAYS In many metabo lic pathways, the produ ct of the last reaction in the pathw ay inhi bits the enzy me that catalyses the first reacti on . This is called end-pro duct inhibition . The enzyme that is inhi bited by the end prod ucts is an example of an allosteric enzyme . A llosteric enzymes have two non-overlapping binding sites. One of these is the act ive site. The other is the allosteric site. In this case the alloster ic site is a bind ing site for the end product. W hen it binds, the struct ure of the enzyme is altered so that the substrate is less likely to bind to the act ive site. Th is is how the end-p roduct acts as an inhib itor. Bindi ng of the in hibitor is reversible and if it detac hes, the enzyme returns to its o rigina l co nfo rmatio n, so the active site can bind the substrate easily again (right).

The advantage of this method of controll ing metabolic pathways is that if there is an excess of the end-pro duct the w hole pathw ay is switched off and intermediates do not buil d

up. Conversely, as the level of the end-product falls, mo re and more of the enzymes that catalyse the first reaction w ill start to wo rk and the w hole pathway wi ll becom e activated. End product inhib ition is an examp le of negative feedback (see example below).

End-product inhibit ion Substrate binds to the active site and is converted to the product.

Substrate could bind to the active site as the allosteric site is empty.

Substrate is not likely to bind to the active site as the inhibitor has bound to the allo steric site.

COw wo •

·-· 0

- - ---.~

0

-----. Q

-- - ---~

,,

,,

0

The substrate of the first enzyme in the metabolic pathway is converted by the pathway into an inhibitor of the enzyme.

An exampl e of end pr odu ct inh ibition

CH3

H

I I H-CH-OH I

NH2-C-COOH

CH3

I

0

c=o

I I

OH-C -COOH -

• C-COOH threonine dehydratase CH2

I

CH3

I I

CH2

I

CH3

H

o

I I

C- COOH -

C- OH

CH

OH-C- COOH - -

~~

CH3

I

3

I

NH2 - C- COOH

I

I

CH

~~

f H2

CH

threoni ne

H

CH3

CH2

~~

CH3

CH2

I

I

CH3

i,() lp lir in p- i, th of the pathway and inhibits threonine -- p- p_.nrJ . -- product ,­ . hydratase w hich catalyses the first step del

CH3 isoleucine

~

,-- - -- - - -- -- - -- - - -- - - - - - - - -- - - -- - - - -- - - - -- - ---- - - -- - - - - - - - - - - - - - - - - - - - - - - - - - ~

,,

,

Nucleic acids and proteins 71

EXAM QUESTIONS ON TOPIC 7 An enzyme experiment was conducted at three different temperatures. The graph shows the amount of substrate remaining each minute after the enzyme was added to the substrate. W shows the results obtained at a temperature of 40°C.

0.45 M

I

E

0.4

u

0

0.35

c

0.3

S 0

•.j:i

~

C Q) u c

0

u

0.25 0.2 0.15

Q)

~

0.1

:::::l

0.05

...0 (j')

0 0 Time (min)

a) (i) Explain whether the temperature used for X was higher or lower than 40°C. (ii) Estimate the temperature that was used for Y.

[3] [2]

b) Draw a curve on the graph to show the expected results of repeating the experiment at 40°C with (i) a fixed low concentration of non-competitive inhibitor.

[1 ]

(ii) a fixed low concentration of competitive inhibitor.

[2]

2 Reverse transcriptase is an enzyme found only in cells infected by certain viruses.

3

a) ) Distinguish between the 3' terminal and 5' terminal in a chain of nucleotides.

[2]

b) Nucleic acids contain purines and pvrirnidines. Compare purines and pyrimidines.

[3]

c) Distinguish between translation and transcription.

[5]

The diagram below represents the structure of lysozyme, a protein consisting of a single polypeptide, found in egg white. a) State the name given to the shape of this type of protein.

[1]

b) State what is meant by the primary structure of a protein.

[1]

c) In the regions labelled X and Y two different types of secondary structure are found. (i) Identify each type of secondary structure:

[2]

(ij) State the type of bonding that is used to stabilize

these structures.

[1]

d) Explain the importance of the tertiary structure of this

protein to its function.

72 18 Questions - Nucleic acids and proteins

[2]

8 Glycolysis

INTRODUCING GLYCOLYSIS Cell respir ation in vol ves the produ cti on of ATP using energy released by the ox idatio n of glucose, fat or other substrates. If glucose is the substrate, the first stage of cell respiration is a metaboli c pathway called glycolysis. The pathway is catalysed by enzy mes in the cyto plasm. G lucose is partiall y ox id ized in th e pathw ay and a small amo unt of ATP is produced . This partial oxi dat ion is achieved w itho ut the use of oxyge n, so glycolysis can fo rm part of both aerob ic and anaerob ic respiration .

Comparison of ox idation and reduction Oxid ati on react ions

Redu cti on reacti ons

Additi on of oxyge n atom s to a substance.

Removal of oxyge n atoms from a substance.

Removal of hyd rogen ato ms from a substance.

Add itio n of hydr ogen atoms to a substance.

Loss of electro ns from a substance.

Add itio n of elect rons to a substance.

OXIDATION AND REDUCTION IN CEll RESPIRATION Cell respiration invol ves many ox idatio n and reduct ion reactions. The figure (top right) co mpares the ways in w hich chemica l substances can be oxi di zed and redu ced. Hyd rogen carriers accept hydrogen ato ms remove d from substrates in cell respiration . The most co mmo nly used hydrogen carrier is NA D+ (nicotinamide adeni ne d in ucl eot ide). Hydrogen atoms co nsist of one proton and one electron. W hen tw o hydr ogen ato ms are removed from a respiratory substrate, NAD+ accepts the electrons from both ato ms and the proto n from one of them. NA D+ + 2H

........

NA D H + H+

Examples of ox idat io ns and reduct ion s in cell respir ation Fe3 + + electron ........ Fe2+

Fe2+ ........ Fe3 + + elect ron

succinate + FAD ........ fu marate + FADH 2 malate + NAD+ ........ oxa loacetate + NAD H + H+

pyruvate + NA D H + H+ ........ lactate + NA D+

The fi gure (right) shows equations for some of the chemica l changes that are part of cell respiratio n. It is possib le to use the inf orm ation in the figure (to p ri ght) to deduce w hether each of them is an ox idatio n, a redu cti on or both .

Stages of glycolysis hexose (glucose)

CONVERTING GLUCOSE TO PYRUVATE IN GLYCOLYSIS There are fou r main stages in glyco lysis. 1. Tw o phosp hate groups are added to a mo lec ule of glucose to form hexose biphosphate. Addin g a phosphate group is called phospho ry lation . Tw o mol ecu les of ATP provide the phosphate groups. The energy level of the hexose is raised by phosphorylatio n and thi s makes the subsequent reacti ons possibl e. 2 . The hexose biphosphate is split to form two mol ecul es of triose phosphate. Splitti ng mol ecul es is called lysis. 3. Tw o atoms of hydr ogen are removed from each triose phosphate mo lecul e. This is an oxidat ion. The energy released by thi s ox idatio n is used to li nk o n another phosphate group, pro duci ng a 3-carbon co mpound car rying tw o phospha te groups. NA D+ is the hydr ogen carr ier that accepts the hydrogen ato ms.

Phosphory

''''0"

2 ADP

hexose biphosphate

Lysis

2 triose phosphate molecules

2 NAD+

Ox idation 2 NADH + W

4. Pyru vate is fo rmed by removin g the tw o phosphate gro ups and by passing them to A DP. Th is results in Al P fo rmat io n. The fig ure (right) shows the main stages of glycolysis.

~2 ATP 1"-

4ADP ATP formation 4ATP

SUMMARY OF GLYCOLYSIS • One glucose is co nverted into two py ruvates. • Tw o ATP mol ecu les are used per glucose but four are produced so there is a net yield of tw o ATP mo lecu les. • Tw o NAD +are co nverted into tw o NA D H + H+

2 pyruvate molecules

Cell respiration and photosynthesis 73

Krebs cycle

ANAEROBIC AND AEROBIC RESPIRATION Glycolysis can occur without oxygen, so it forms the basis of anaerobic cell respiration. Pyruvate produced in glycolysis can only be oxidized further, with the release of more energy from it, if oxygen is available (right). This occurs in the mitochondrion. The first stage is called the link reaction. Enzymes in the matrix of the mitochondrion then catalyse a cycle of reactions called the Krebs cycle.

no oxygen

THE LINK REACTION

Summa.ry of the link reaction

Pyruvate from glycolysis is absorbed by the mitochondrion. Enzymes in the matrix of the mitochondrion remove hydrogen and carbon dioxide from the pyruvate. The hydrogen is accepted by NAD+. Removal of hydrogen is oxidation. Removal of carbon dioxide is decarboxylation. The whole conversion is therefore oxidative decarboxylation. The product of oxidative decarboxylation of pyruvate is an acetyl group, which is accepted by CoA (right).

\

CoA

cq

THE KREBS CYCLE In the first reaction of the cycle an acetyl group is transferred from acetyl CoA to a fou r-carbon compound (oxaloacetate) to form a six-carbon compound (citrate). Citrate is converted back into oxaloacetate in the other reactions of the cycle. Three types of reaction are involved. • Carbon dioxide is removed in two of the reactions. These reactions are decarboxylations. The carbon dioxide is a waste product and is excreted together with the carbon dioxide from the link reaction. • Hydrogen is removed in four of the reactions. These reactions are oxidations. In three of the oxidations the hydrogen is accepted by NAD+. In the other oxidation FAD accepts it. These oxidation reactions release energy, much of which is stored by the carriers when they accept hydrogen. Th is energy is later

released by the electron transport

chai n and used to make ATP. • ATP is produced directly in one of the reactions. Th is reaction is substrate-level phosphorylation. The figure (right) is a summary of the Krebs cycle.

Summary of the Krebs cycle

acetyl CoA

CoA

oxoaloacetate (C4 )

NADH + H+

74 Cell respiration and photosynthesis

~NADH

FAD ATP

NADH + H+ ADP

+ H+

Oxidative phosphorylation

THEELECTRONTRANSPORTCH~N

THE ROLE OF OXYGEN

The elect ron transport chain is a series of electro n carriers, located in the in ner membrane of the mitocho ndrion. NAD H suppl ies tw o electro ns to the f irst carr ier in the chain. The elec tro ns come from ox id ation reactio ns in earl ier stages of ce ll respir ation . The tw o elect rons pass alo ng the chain of carriers beca use th ey give up energy each tim e they pass from one car rier to the next. At thr ee points alo ng the chain eno ugh energy is give n up for ATP to be made by ATP synthase. As this ATP produ cti on relies on energy released by oxidatio n it is called oxidative phosphor ylation. ATP synthase is also located in the inn er m itochond rial memb rane. FADH 2 also feeds elect ro ns into the electron transpo rt chai n, but at a slight ly later stage than NADH and at only two stages is sufficie nt energy released for ATP productio n by electrons from FADH 2 .

At the end of the electron transport chain the electrons are given to oxyge n. At the same time oxyge n acce pts hydrogen ion s, to for m wa ter. Thi s happens in the matri x, on the surface of th e inner memb rane. Th is is the only stage at w hich oxyge n is used in cell respiration. If oxy gen is not availab le, electro n flow alon g the electron transport chain sto ps and NADH + H+ cannot be recon verted to NA D+. Suppl ies of NAD+ in the mit ochondri on run o ut and the link reactio n and Krebs cyc le canno t co ntinue . G lycolysis can continue beca use conversion of pyruvate into lactate or ethano l and carbon di oxide produces as mu ch NA D+ as is used in glycolysis. How ever, w hereas aerobic cell respiration gives a yield of abo ut 30 ATP mo lecules per glucose, glycolysis produces o nl y tw o . Oxygen thus greatly in creases the ATP yie ld. The f igure (below) shows the electro n transpo rt chai n and the role of oxygen as the termin al electro n accep to r.

The electron transport chain of mito chondria

matrix of mitochrondri on

lr {

~

inner

mitochondrial

membane

H2 0 H+

,,

1----

\"

­

2.- ---------­

,

:

space between ! inner and outer membranes

t 0 2 + 2H+

NADH

t

H+

THE COUPLING OF ELECTRON TRANSPORT TO ATP SYNTHESIS Energy released as electrons pass alo ng the electron transport chain is used to pum p proto ns (H+) across the inn er mi toc ho ndria l membrane into the space betw een the inn er and outer membranes. A co nce ntrat ion grad ient is fo rmed, w hic h is a sto re of potential energy. AT P synt hase, located in the inn er mi tochon dr ial memb rane, transports the proto ns bac k across the membrane down the co nce ntrat io n gradient. As the proto ns pass across the membrane they release energy and thi s is used by ATP synthase to produce ATP. The co upling of ATP synthesis to electro n tr ansport via a co ncentration grad ient of proton s is call ed chemi osmosis. The figure (right) shows some features of ATP synth ase.

,

,,

,, ,, ,,

~

y

y

H+

H+

Structure of ATP synthase

ADP is phosphorylated to ATP at three identical active sites.

~T P ADP+ U

H+ movement across the membrane causes this part of ATP synthase to rotate. This rotation drives ATP production.

These parts of ATP synthaseare in a fix ed position.

'-

~~~~ ] inner

.. .

lill l \1 mitochondrial

JIL __

LA ~ ~~

membrane

Cell respiration and photosynthesis 75

Mitochondria

The mitocho ndr io n is an exce llent exam p le of the relation ship betwee n structure and funct ion . The fi gure (below) is an electron m icro grap h of a w ho le mitoch ond rio n. T he fi gure (bottom) is a draw ing of the same mitocho ndri on, labell ed to show how it is adapted to carr y out its fu nction.

Outer mitochondrial membrane

Matrix

Separates the contents of the mitochondrion from the rest of the cell, creating a comp artment wit h ideal conditions for aerobic respi ration.

Fluid inside the mitochondr ian containing enzymes for the Krebs cycl e and the link reaction . 70S ribosomes and a naked loop of D NA are present in the matrix.

1- 2 urn

Space between inner and outer membranes

Protons are pumped into this space by the electron transport chain. Because the space is very small, a high proton concentration can easily be formed in chemiosmosis.

Cristae

Inner mitochondrial membr ane

Contains electron transport chains

and ATP synthase, w hich carry out

oxidative phosphorylatio n.

76 Cell respiration and photosynthesis

Tubular or shelf-like proj ections of the inner membrane w hich increase the surface area available for oxidat ive phosphorylation .

Light and photosynthesis

::' ~otosynthesis is the process that plants, algae

100

-=-ld some bacteria use to produce all of the

Action spectrum of photosynthesis

CJ)

=~5anic compounds that they need.

CJ)

C!)

-5

~10tosynthesis involves many chemical reactions.

c >­

~Jme of them need a continual supply of light

(5

~ld so are called

]

light-dependent reactions.

80

60

Q..

Jther reactions need light ind irectly, but can .arrv on for some time in darkness. These are :::alled light-independent reactions. C[ucose, arnino acids and other organic compounds are produced in the light independent ~eactions. The Iight-dependent reactions produce intermediate compounds that are used in the light-independent reactions. In darkness these intermediate compounds are gradually used up.

C

~ 40 '0 C!)

:g

20

::::::: o

o+1---...,--...,.----,---------,-------,.---,.--...,.----­ 6r~~ 6r~~ ~~~ ~~~ ~~
Wavelength of Iightlnm

THE ACTION SPECTRUM OF PHOTOSYNTHESIS A spectrum is a range of wavelengths of electromagnetic radiation. The spectrum of Iight is the range of wavelengths from 400 nm to 700 nm. Each wavelength is a pure colour of light: 400-525 violet-bl ue 525-625 green-yellow 625-700 orange-red The efficiency of photosynthesis is not the same in all wavelengths of Iight. The efficiency is the percentage of Iight of a wavelength that is used in photosynthesis. The figure (top right) is a graph showi ng the percentage use of the wavelengths of light in photosynthesis. This graph is called the action spectrum of photosynthesis. The graph shows that violet and bl ue Iight are used most efficiently and red Iight is also used efficiently. Green light is used much less efficiently.

100

Absorption spectrum of chlorophylls a and b I I

I I

80

KEY

, ,, ,, , , ,, ,, ,,

1:

.~

'0 60 c .Q

Q..

o

.DCiJ 40

chlorophyll a chlorophyll b

I I I

::::::: o

I

I

I I

I

20

I

,,

I

I

o

I

---

400

450

500

550

600

650

700

750

Wavelength of Iightlnm

THE ABSORPTION SPECTRA OF PHOTOSYNTHETIC PIGMENTS The action spectrurn of photosynthesis is explained by considering the light-absorbing properties of the photosynthetic pigments. Most pigments absorb some wavelengths better than others. The figure (centre right) shows the percentage of the wavelengths of visible light that are absorbed by two common forms of ch lorophyll. Th is graph is cal led the absorption spectrum of these pigments. The graph shows strong simil arities with the action spectru m for photosynthesi s. • The greatest absorption is in the violet-blue range. • There is a also a high level of absorption in the red range of the spectrum. • There is least absorption in the yellow-green range of the spectru m. Most of th is Iight is reflected. There are some differences between the action spectrum and the absorption spectra. Whereas little light is absorbed by chlorophylls in the green to yellow range there is sorne photosynthesis. This is due to accessory pigments, including xanthophylls and carotene, which absorb wavelengths that chlorophyll cannot.

Action and absorption spectra of an alga Some algae contain large amounts of accessory pigments. For example, kelp (Laminaria saccharina) contains carotene and fucoxanthin in addition to chlorophylls and so can absorb and use all wavelengths of light with about the sarne efficiency in photosynthesis. The graph below shows the action and absorption spectra for kelp. The colour of kelp can be deduced from the data.

100

1: 80

-_

.

-.:.:

.~

'0

_

~

.....

,

, ,, ,, ,, ,, ,, ,, ,, ,, ,,

C!)

:g 60

v c

(1j

c

o

'R. 40

KEY

o

action spectrum

.D (1j

~

absorption spectrum

20

....

,, , ,_ .... ' /\',

,

O--'-'----,--------r----,-----.....,.--------,---------,.----.,.---------,

400

450

500

550

600

650

700

750

Wavelength of lightJnm

Cell respiration and photosynthesis 77

Light-dependent reactions

LIGHT ABSORPTION

PRODUCTION OF ATP

Chlo rophyll absorbs li ght and the energy from the light raises an electron in the chlo rophyll mo lecu le to a higher energy level. The electron at a higher energy level is an excited electron and the chlo rophyll is phot oacti vated. In single ch loroph yll mo lecu les the exci ted electron soon drop s back down to its original level, re-emitt ing the energy. Chlorophyll is located in thylakoid membranes and is arranged in groups of hundreds of molecules, called phot osystems. There are two types of photosystem - photosystems I and II. Excit ed electrons from absorptio n of photons of light anyw here in the photosystem are passed from mol ecul e to mol ecul e until they reach a specia l chlo rophyll mo lecul e at the reaction centre of the photosystem. Thi s chlo rophyll passes the exc ited electro n to a chain of electron carriers.

An exci ted electron fro m the reacti on centre of photosystem II is passed along a chain of carriers in the thyl akoi d membrane (below) . It gives up some of its energy each tim e that it passes fro m one carrier to the next. At one stage, enough energy is released to make a mol ecul e of ATP. The co up ling of electron transport to ATP synthesis is by c hemiosmosis, as in the mit ochondri on . Electron flow causes a proton to be pump ed across the thylakoid membr ane into the fluid space inside the thyl akoid . A proton gradient is created. ATP synth ase, located in the thylakoid membr anes, lets the proton s across the membrane down the co ncentratio n gradie nt and uses the energy released to synth esize ATP. The produ ction of ATP using the energy from an exci ted electro n from Photosystem /I is cal led non- cycli c phot ophosphorylati on. An alternative method of pho tophospho rylation is show n on page 81.

ADP ATP

Light-dependent reacti ons in t he th ylakoid

W NADP+ NADPH

stroma

photosystem I A

thylakoid space

1 .---- -­

-

-

-t-- - thylakoid membrane

-----[lTrrrl

2W part of adjacent thylakoid

photosystem II

PRODUCTION OF NADP

PRODUCTION OF OXYGEN

After releasing the energy needed to make ATP, the electro n th at was given away by photosystem /I is accepted by photosystem I. The electron replaces one previously given away by photosystem I. W ith its electron repl aced, photosystem I can be photoact ivated by absorbing light and then give away anot her exc ited electron. Th is high-energy electro n passes alo ng a short c hain of carriers to NAD P+ in the stro ma. NADP+ accepts two high-energy electrons fro m the electron transport chain and one H+ ion from the stroma, to fo rm NADP H.

Photosystem /I needs to replace the exci ted electro ns th at it gives away. The special chloro phyll mo lecu le at the react io n centre is positively charged after giv ing away an electron. W ith the help of an enzy me at the reaction centre, water mo lecul es in the thylakoid space are split and electrons from them are given to c hloro phyll. Oxyge n and H+ io ns are form ed as by-produ cts. The splitting of water mol ecu les only happens in the li ght, so is called phot ol ysis. The oxygen produ ced in photosynthesis is all the result of photol ysis of water. Oxyge n is a waste produ ct and is excreted.

78 Cell respiration and photosynthes is

Light-independent reactions

THE CALVIN CYCLE

CARBON FIXATION

The light-independent reacti ons take place w ithin the stroma of the chloro plast. The f irst react ion invol ves a fi ve-carbo n sugar, ribulose bisphosphate (RuBP). RuBP is also a pro duct of the light ind ependent reacti on s, w hich therefore for m a cyc le, called the Calvin cycle . There are many alternative names for the intermed iate co mpo unds in the Calvin cycle . Gl ycerate 3-phosphate is somet imes also called 3-phosphoglyce rate. G lycerate 3-phosphate is sometimes abbreviated as GP, w hic h co uld be confused with glyce raldehyde 3-phosphate, w hic h is a fo rm of tri ose phosphate or w ith glucose phosphate. The abb reviatio n GP should the refore be avoi ded!

Carbon d ioxid e is an essential substrate in the light-independent reactio ns. It enters the chloroplast by diffusion. In the stroma of the chlorop last carbon dioxide combines w ith ribulose bisphosphate (RuBP), a five-carbon sugar, in a carboxy lation reaction. The reaction is catalysed by the enzyme ribulose bisphosphate carboxylase, usually called rubi sco. Large amou nts of rubisco are present in the stroma, because it wo rks rather slowly and the reaction that it catalyses is a very important one. The product of the reaction is a six-carbon compound, w hich im mediately splits to form two molecules of glycerate 3-phosphate. This is therefore the first produ ct of carbon fixation.

Summar y of t he Calvin cycle ribulose bisphosphate

CXf:XX)

ADP+P

CO 2

o

ATP

glycerate 3-phosphate

CD:) CD:)

%

of triose phosphate used to regenerate RuBP

2ATP

triose phosphate

CfX) CD:)

2NADPH 2NADP+

J.e of triose phosphate used to produce glucose phosphate

6

Glucose

phosphate

Cf:DCfX)

REGENERATION OF RUBP

SYNTHESIS OF CARBOHYDRATE

For carbo n fixatio n to co ntinue, one RuBP mo lecul e must be pro duced to replace each one that is used . Triose phosphate is used to regenerate RuBP. Five mo lecu les of tri ose phosphate are co nverted by a series of reacti ons into three molecul es of RuBP. Thi s process requires the use of energy in the form of ATP. The reacti on s can be summarized using eq uatio ns w here o nly the numb er of carbo n atoms in each sugar mo lecul e is show n.

Glyce rate 3-phosphate, formed in the carbon fixation reaction , is an organic acid. It is co nverted into a carbohyd rate by a reduction reaction . Hydrogen is needed to carry out th is reaction and is supp lied by NAD PH . Energy is also needed and is supplie d by ATP. NA D PH and ATP are produ ced in the li ght-d ependent reactio ns of photosynth esis. G lycerate 3-p hosphate is reduced to a three-carbo n sugar, tri ose phosphate (TP). Linki ng together tw o tr iose phosphate molecul es together pro duces glucose phosphate. Starch, the storage for m of carbo hydrate in plants, is for med in the stroma by co ndensation of many mo lecules of glucose phosphate.

C3 C6 C4 C7

+ + + +

C3 C3 C3 C3

~ C6

~

c,

C4 + C7

~ Cs + Cs

~

For every six mo lecu les of tr iose phosphate for med in the light- independent reactions, f ive must be co nverted to RuBP.

Cell respiration and photosynthesis 79

Chloroplasts

The chlo roplast is another example of cl ose relationship betw een struct ure and function . The figure (below) is an electron mi crograph of a chloroplast. The figure (bottom) is a drawing of the same chloroplast, labelled to show how it is adapted to carry out its functi on.

Structure of a chloroplast

granum

stroma co ntaini ng 70S ribsomes and naked DNA

inner membrane

outer membrane chloroplast envelope

starch grain

80 Cell respiration and photosynthesis

lipi d dropl et

Limiting factors in photosynthesis

THE CONCEPT OF LIMITING FACTORS

Light intensity, carbon dioxide concentration and temperature are three factors that can determine the rate of photosynthesis.

If the level of one of these factors is changed, the rate of photosynthesis changes. Usually, only changes to one of the factors

will affect the rate of photosynthesis in a plant at a particular time. This is the factor that is nearest to its minimum and is called

the limiting factor. Changing the limiting factor increases or decreases the rate, but changes to the other factors have no effect.

This is because photosynthesis is a complex process involving many steps. The overall rate of photosynthesis in a plant is

determined by the rate of whichever step is proceeding most slowly at a particular time, This is called the rate-limiting step.

The three limiting factors affect different rate-limiting steps.

The figures on page 21 show the relationship between each of the limiting factors and the rate of photosynthesis.

THE EFFECT OF LIGHT INTENSITY

THE EFFECT OF TEMPERATURE

THE EFFECT OF CO2 CONCENTRATION

At low light intensities, there is a shortage of the products of the Iight­ dependent reactions - NADPH and ATP. The rate-limiting step in the Calvin cycle is the point where glycerate 3-phosphate is reduced. At high Iight intensities some other factor is limiting. Unless a plant is heavily shaded, or the sun is risi ng or seUing, light intensity is not usually the lim iti ng factor.

At low temperatures, all of the enzymes that catalyse the reactions of the Calvin cycle work slowly. NADPH accumulates. At intermediate temperatures, some other factor is limiting. At high temperatures, RuBP carboxylase does not work effectively, so the rate-limiting step in the Calvin cycle is the point where CO 2 is fixed. NADPH accumulates.

At low and medium CO 2 concentrations, the rate-limiting step in the Calvin cycle is the poi nt where CO 2 is fixed to produce glycerate 3-phosphate. RuBP and NADPH accumulate. At high CO 2 concentrations some other factor is limiting. Because the level of carbon dioxide in the atmosphere is never very high, carbon dioxide concentration is often the limiting factor.

Results of an investigation into limiting factors 500

The figure (right) shows the effects of

light intensity on the rate of photo­ synthesis at two different temperatures and two carbon dioxide concentrations. It is possible to deduce which is the limiting factor at the point marked with an arrow (CD - 8)) on each curve.

CJ)

+-'

'c

::J

>-- 400

g

.:.0 ~

'V5

'Vi

CJ.) ..c

300

,; ,; ,; ,; ,; . "1- ..---------------.----­

C

>-­

0

'0 ..c

KEY

x

x

x

x

x

o

0

0

0

0

,

0...

30 DC and 0.15% CO 2 20 DC and 0.15% CO 2 30 DC and 0.035% CO

'0 CJ.)

~

2

~

/"'"

200

~::,..o"o"oxoxoxoxoxoxoxo~xoxoxoxoxoxoxoxoxoxoxoxoxoxoxoxoxoxoxoxo

'~o+

~

100

4

~

20 DC and 0.035% CO 2

0'

o

i i i

i I i

I i i

1

4

8

2

3

5

6

7

9

I

10 11

i

12

Light intensity/arbitrary units

CYCLIC PHOTOPHOSPHORYLATION

Summary of cyclic photophosphorylation

excited electrons Photosystem

j

II

./

r ' \ATP

ADP

~

Photosystem I

When light is not the limiting factor, NADPH tends to accumulate in the stroma and there is a shortage of NADP+. The normal flow of electrons in the thylakoid membranes is inhibited because NADP+ is needed as a final acceptor of electrons. An alternative route can be used that allows ATP production when NADP+ is not available. This pathway is called cyclic photophosphorylation. • Photosystem I absorbs Iight and is photoactivated. • Excited electrons are passed from photosystem I to a carrier in the chai n between photosystem II and photosystem I. • The electrons pass along the chain of carriers back to photosystem I. • As the electrons flow along the chain of carriers they cause pumping of protons across the thylakoid membrane. • A proton gradient is formed and this allows production of ATP by ATP synthase. The figure (left) shows the pathway used in cyclic photophosphoryl ation.

Cell respiration and photosynthesis 81

EXAM QUESTIONS ON TOPIC 8 The electro n mi crograph below shows part of a pl ant root cell , includ ing mitochondri a.

x

[Source: Dr S, E. Jun iper, Dept. of Plant Sciences, University of Oxford]

a) Exp lain brief ly two featu res that allow the mitochondria in the micrograph to be identified.

[2 ]

b) Redr aw the structure of th e mitocho ndr ion marked X.

[2 ]

c) Ann ot ate th e m icrograph (not your draw ing) to show one exam ple of (i)

a region w here th e Krebs cycle takes p lace

(ii) a lo cation of ATP synthetase

[3J

(iii) a region w here glyco lysis takes p lace. 2 a) Dr aw a cur ve of the act io n spectrum for photo synthes is on th e ax is below.

400 vio let

500 blue

green

600 yellow

orange

[2]

700 red

Wavelength/ nm b) Expl ain th e rel ation shi p b etw een the action spectrum and th e absorptio n spectra of photosyn th eti c pigme nts. 3 a) State tw o processes that invol ve chem iosmosis.

[2j

b) Explain the need for a mem brane in chem iosmos is.

[3]

c) Suggest a locatio n w here c hemiosmosis cou ld occ ur in prokaryotes.

[1]

82 18 Questions ­ Cell respiration and photosynthesis

9 L

­

...

_._~---

Leaf structure and function LEAVES AND PHOTOSYNTHESIS

LEAVES AND TRANSPIRATION

The funct ion of leaves is to produce food for the plant by photo synthesis. The leaf is adapted by its structure to carry out photosynthesis eff icie ntly . O n page 5 is a scanni ng electron micro graph of a leaf. The figure (below) is a plan d iagram of tissues in part of a leaf of a dicoty ledonous plant to show the adaptations for photosynthesis.

Photosynt hesis depend s on gas exc hange ove r a moi st surface. Spo ngy mesophyll cell wa lls provid e this surface. Water often evaporates fro m the surface and is lost, in a pro cess called transpirat io n. Transpiration is the 10 55 of water vapour from the leaves and stems of p lants. The fi gure (below) shows adaptat ions to minimize the amo unt of transpiratio n.

Tissues of the leaf and th eir fun cti ons Upper epidermis- a continuous layer of cells covered by a thick waxy cuticle. Prevents water loss from the upper surface even w hen heated by sunlight. Lower epidermis in a coo ler position has a thinner waxy cuticle

Palisade mesophyll - consists of densely packed cylindrical cells wi th many chloroplasts. This is the main photosynthetic tissue and is positioned near the upper surface w here the light intensity is highest

The main part of the leaf is the leaf blade or lamina. It has a large surface area to absorb sunlight but is very -< thin- only about 0 .3 mm. It is composed of four thin tissue layers w ith veins at intervals.

' ..~ '~'" :,\--,::.'

i,'."

! ;-: ~'-'; ::-:-

.. ::;./-.

.;-

· .."

= =

= J­ ".

<:\:~::~ -~~

Xylem- brings water ~ to replace losses due to transpiration

. ~"

~

~

Phloem- transports products of photosynthesis out of the leaf.

......

ctu

Vein is centrally positio ned to be close to all cells.

r>,

­

Spongy mesophyll - consists of loosely packed rounded cells wit h few chloroplasts. This tissue provides the main gas exchange surface so must be near the stomata in the lower epidermis.

~ Stoma- a pore that allows CO 2 for photosynthesis to diffuse in and O 2 to diffuse out.

'>­

Guard cells-this pair of cells can open or close the stoma and so control the amount of transpiration.

FACTORS AFFECTING TRANSPIRATION

TRANSPIRATION IN XEROPHYTES

Plants lose wa ter vapour from their stems and leaves by transpiration . The rate of wat er loss varies depend ing on internal and external conditions. The main internal co nd ition is w hether the stomata are ope n or closed. The plant hormone absci sic acid causes guard cells to cl ose the sto mata. Plants produ ce abscisic acid w hen they are sufferin g water stress. External variab les are called abiotic fact or s - four of these have an effect on the rate of transpiration. • Light - guard cells close the sto mata in darkn ess, so transpirati on is much greater in the lig ht. • Temperature - heat is needed for evaporatio n of wa ter from the surface of spongy mesophyll ce lls, so as temp erature rises the rate of transpiratio n rises. H igher temperatures also increase the rate of diffusion throu gh the air spaces in the spongy mesop hyl l, and reduce the relative humidity of the air outside the leaf. • Hum idi ty - wa ter diffu ses out of the leaf w hen there is a co ncentrat io n gradie nt betwe en the air spaces inside the leaf and the ai r outside. The air spaces are alwa ys nearly saturated . The lower the hum idity o utside the leaf, the steeper the gradient and therefore the faster the rate of transpiration . • Wind - pockets of air saturated w ith water vapo ur tend to form near sto mata in still air, w hic h reduce the rate of transpiration. W ind blows the satu rated air away and so increases the rate of transpiration .

Plants that are adapted to grow in very dry habit ats are calle d xerophytes. Cereus giganteus, the saguaro or giant cactus, is an example of a xerophyte. lt grows in deserts in M exico and Arizon a and shows many xero phyt ic adaptatio ns, w hic h help to reduce transpiration . Vertical stems to absorb sunlight early and late in the day but not at midday when light is most intense.

CAM physiology, w hich involves opening stomata during the cool nights instead of in the intense heat of the day.

11\\11',

Very thick waxy , cuticle covering the stem.

Spines instead of leaves to reduce the surface area for transpiration.

Plant science 83

Transport and support MINERAL UPTAKE BY ROOTS

Structure of xylem vessels

Roots absorb wate r and min eral io ns from the soil. Plants increase the surface area fo r absorpt ion by branching of roots and the grow th of root hai rs. Plants absorb potassium, phosphate, nitrate and other mineral io ns from the soil. The co ncentratio n of these ions in the soil is usuall y muc h low er than inside root cells, so they are absorbed by active transport. Root hai r cells have mitocho ndri a and protei n pumps in their plasma membranes. M ost roots o nly absorb mineral ions if they have a supply of oxyg en, because they produce ATP for act ive transport , by aerobic ce ll respiratio n. The rate of absorptio n of mineral ions is someti mes limi ted by the rate at w hic h the ions move th rou gh the soil to the root. There are three w ays in w hich ions can move: • d iffusio n of mi neral ions • mass f low of w ater carrying io ns, w hen water drain s

through the soiI

• into fungal hyphae, that grow around plant roots in a

mutuali stic relatio nship, and then from the hyphae to

the roots.

No plasma membranes are present in - - --R-7 mature xylem vesse ls, so water can move in and out freely

Lumen of the xylem vessel is filled wi th sap, as the cytoplasm and the nuclei of the original cells break down . End walls also break dow n to form a continuous tube

Helical or ring-shaped thickenings of the cell ulose cell wall are impregnated wi th lignin. This makes them hard, so that they can resist inward pressures

Pores in the outer cell ulose cell wall conduct water out of the xylem vessel and into cell walls of adjacent leaf cells

STRUCTURE AND FUNCTION OF STEMS Stems co nnect the leaves, roots and f low ers of pl ants and transport materials betw een them using xy lem and phloem tissue. Stems support the aerial parts of terrestrial plants. Support is provided in several w ays. • Cell s absorb w ater and high pressure develops inside the

cell. This is cell turgor and it makes the cell almost rigid .

• Some cells develo p thickened cell ulose wa lls, w hic h

strengthen the plant.

• Cell wa lls in xy lem ti ssue are both thic kened and lign if ied

making them very strong (above right). Xylem provides

support especia lly in wo ody stems.

The f igure (below) is a plan d iagram to show the positi on of the tissues in the stem of a young d icoty ledonous plant. Tran sverse section of a stem -

xylem } vascular cambium bundle phloem

epidermis

cortex

,

, ,,

CD

"tl"" c:Y ,

,,

CJP,

.. 9/ -: LX··.,Q...

84 Plant science

WATER TRANSPORT THROUGH PLANTS Xylem vessels co ntain long unb roken co lumns of w ater. W hen transpiratio n is occ urri ng, w ater moves upw ards from t he roots to the leaves. Thi s f low is ca lled the transpiration stream . The fi gure (above) shows the struct ure of a xy lem vessel. M ature xy lem vessels are dead and the f low of wa ter thro ugh them is passive. Heat from the env iro nment provides energy for evaporation of wa ter fro m the cell wa lls of spongy mesoph yll ce lls in the leaf. The water that evapo rates is rep laced w ith wate r from xy lem vessels in the leaf. The w ater is pulled out of xylem vessels and through po res in spongy mesophyll cell wa lls by capill ary action. Low pressure o r sucti on is created inside xy lem vessels w hen wa ter is pull ed out. This is called the transpiration pull. The suctio n extends down th rou gh the co lumns of water in xyl em vessels to the roots. These co lumns of wa ter do not usuall y break because of the cohesion of wa ter molecules. W ater mo lecules are co hesive d ue the hydrogen bonds betwee n them. A nother process that can help w ater to move up in xy lem vessels is the adhesion of wa ter to the wa ll of the vessel. This is particularl y im port ant w hen sap starts to rise, in xy lem vessels of plants that w ere leafl ess throug h the w inter. In these plants, xy lem vessels are empty in w inter and refi ll in spring. Ad hesio n also helps prevent the co lumn of wa ter in wa ter­ f illed xy lem vessels from breaki ng.

TRANSPORT IN PHLOEM Sugars and amino acids are transport ed inside plants by phl oem ti ssue. This process is ca lled active translocation because phloem cells have to use energy to make it happen. Sugars and amino aci ds are load ed into the phloe m in parts of the plant call ed sources and are transloc ated to sinks, w here they are un loaded . Exampl es of sources are parts of the plant w here photo synthesis is occ urri ng (stems and leaves) and sto rage organs w here the stores are bei ng mobilized . Examples of sinks are roots, growing fruits and the developi ng seeds inside them .

Reproduction of flowering plants

STRUCTURE AND FUNCTION OF FLOWERS

FACTORS NEEDED FOR SEED GERMINATION

Flow ers are the struct ures used by flowerin g plants fo r sexual reprod ucti on. Female gametes are co ntai ned in ovules in th e ova ries of the f low er. Pollen grains, produced by the anthers, co ntain the male gametes. A zygo te is formed by the fusion of a male gamete w ith a female gamete inside the ov ule. This process is calle d fertilization . Before fertil izatio n, another process called pollination must occ ur . Pollin ation is the transfer of po llen from an anther to a stigma. Po llen grains co ntaining male gametes cannot mov e w ithout help from an external agent. M ost pl ants use eit her w ind or an animal fo r po llin ation . The structur e of a flower is adapted to its method of pollin ation . The figure (below) shows the st ructure of a flowe r of Lamium alb um, wh ich is adapted to bee po lli natio n. Pollen grains germinate on the stigma of the flower and a pollen tub e contai ning the male gametes grows down the sty le to the ova ry. The pollen tub e delivers the male gametes to an ov ule, w hic h they ferti lize. Fertilized ov ules develop into seeds. The figure (bottom) shows the structure of a seed of Phaseolu s multifl orus. Ova ries co ntaining fertil ized ov ules develop into fruits. The fun ct ion of the fruit is seed di spersal.

Seeds w ill not germinate unless external conditions are suitable. • W ater must be available to rehydr ate the dry tissues of

the seed.

• Oxyg en must be availa ble for aerobic cell respiratio n. Som e seeds respire anaero bica lly if oxyge n is not available but ethano l produ ced in anaerobic respiration usually reaches toxi c levels. • Suitabl e temp eratures are needed . Germinatio n invo lves enzy me act iv ity and at very low and very high temperatures enzy me activity is too slow. Som e seeds remain dormant if temperatures are above or below partic ular levels, so that they o nly germinate du ring favour able tim es of the year. The figure (below ) show s the struct ure of a seedling of Phaseo/us m u/tif/or us, abo ut 2 weeks after the start of germination.

Structure of a seedling of Phaseo/us multiflorus first fol iage leaves are about to open ~

cotyledons provide energy and nutrients

for germination

Structure of Lamium a/bum flower anther

/

bend in the stem protects the leaves as the shoot pushes up through soiI

stem between the - ! - cotyledons and the first foliage leaves has grow n

filament seed coat split w hen the seed absorbed water and swelled

style main root growing down wards into soil

ovaries

Structure of a seed of Phaseo/us multif/orus External structure seed coat (testa) scar where seed was attached to the ovary Internal structure ({~a.

embryo root

(radic le)

seed coat

~" Jl\

embryo shoot (plumule) cotyledon ­ one of two in the seed

branches of the main root increase the surface area for absorption

METABOLIC EVENTS DURING GERMINATION • The first stage in germination is the absorptio n of wa ter and the rehydr ation of living cells in th e seed . Th is allows the cells to becom e metabo licall y active. • Soon after absorbing w ater, a plant grow th hormone called gibberell in is produ ced in the coty ledons of the seed. • G ibberellin stimulates the pro duct io n of amy lase, w hi ch catalyses th e di gestio n of starch into maltose in the foo d stores of the seed . • M altose is transported f rom the food stores to the growt h regio ns of the seed ling, including the emb ryo root and the I embr yo shoot. • M alto se is co nverted into glucose, w hic h is either used in aerobic cell respiratio n as a source of energy, or is used to synthesize cell ulose or other substances needed for grow t h. As soon as the leaves of the seed ling have reached li ght and have opened, photosynthesis can supply the seedli ng w ith food s and the food sto res of the seed are no longer needed.

Plant science 85

Diversity in plant structure

MONOCOTYLEDONS AND DICOTYLEDONS

MODIFIED ROOTS , STEMS AND LEAVES

Flowering plants are d iv ided into two groups, acco rd ing to the num ber of leaves that the emb ryo pl ant has, in side the seed. M onocoty ledon s have o ne coty ledo n (seed leaf) w hereas di cotyl edons have tw o. There are other di fferences:

The normal fun cti ons of the roots, stems and leaves of plants have been descri bed on the previo us pages. In some plants, these organs have becom e modi fi ed fo r other functi on s.

Monocotyledons

Dicotyledons

Leaf veins run parallel to each Leaf vei ns fo rm a net-li ke othe r pattern Vascu lar bund les are spread thr ough the stem random ly Stamens and ot her organs in the flo w er are in multip les of 3

Vascul ar bund les are in a rin g near the outside of the stem Stamens and other fl oral o rgans are in mu ltiples of 4 or 5

1. Bulbs In some monocotyledon plants, leaf bases grow to fo rm an und erground o rgan ca lled a bulb (below) . Plants use bu lbs for food storage. They can be ident if ied from the series of leaf bases fi tt ing inside each ot her, w ith a central shoot apica l meristem. small new bulb, developed from an axillary bud that wil l eventually separate and form a new plant.

fleshy leaves '\~~----:';;7 used for food

storage

Unbranched roots grow from Roots branch off from other stems roots rttI7.rIHh'l+-

Exampl es of plants in each group are shown in the figures (below) .

-

terminal bud from which leaves grow

stem ofbu lb -----,~~~_- roots

2. Stem tubers In so me di coty ledon plants, stems grow down w ards into the soil and sectio ns of them grow into stem tubers (below) . They are used for food storage. They can be identified as stems because despite being swo llen their vascular bund les are arranged in a ring.

Leaves produce food by

photosynthesis.

Phloem in stems transports

food to storage organs.

parallel leaf veins

Tuber grows and stores food.

Tradescantia pallida 3. Storage roots Some roots beco me swo llen w ith sto res of foo d (below) . They can easily be identified from their shape and from vascular tissue being in the centre.

~iW~!j~~/'l,g;r-- branching leaf veins

Carrot

Sweet Pea

4. Tendrils

Caltharanthus roseus

86 Plant science

Tendrils are narrow outgrow ths fro m leaves that rotate through the air until they to uch a solid support, to w hic h they attac h, allowing the plant to climb upw ards (above).

Growth and development in plants

APICAL AND LATERAL MERISTEMS

AUXIN AND PHOTOTROPISM

Plants have regio ns w here ce lls co nt inue to divid e and grow, ofte n thro ughout the life of th e plant. These regio ns are ca lled meri stems. Flow erin g plants all have meristems at the ti p of the root and the tip of the stem (below) . These are ca lled apical m eristem s as they are at the apex of the roo t and stem . Growth in apica l meristem s allows roo ts and stems to elo ngate. The shoot apical meristem also produces new leaves and flow ers. M any di cot y ledo no us p lants also develop lateral meri st ems. In yo ung stems, t his co nsists of camb ium in the vascula r b und les, but as th e stem grows older , a co mplete ring of cam bi um forms. A sim ilar lateral meristem forms in o lder roots. Growth in lateral meristems makes roo ts and stems thick er, wi th extra xy lem and ph loem ti ssue. The growth in th ickness of tr ee trunks is due to th e lateral meri stem, inside the bark.

Plants use ho rmones to co ntro l their growth and their deve lopment. A n exam p le of a p lant hormon e is aux in, w hich acts as a growth pro mo ter. It doe s this by ca using secretion of hyd rogen io ns int o ce ll wa ll s, w hic h loosens co nnections betw een ce ll ulo se fi bres, all ow ing cell expansio n. O ne of th e processes that aux in con tro ls is phot otrop ism ­ directi on al growth in respo nse to the source of li ght. Shoot tips can detect the source of the brightest li ght. They also prod uce auxi n. Acco rding to a lon g-stand ing th eory, aux in is redistributed in the shoo t tip fro m the lighter side to the shad ier side. It then prom otes mo re growth on the shadier side, causing the shoot to bend towa rds the li ght. M olecular mech anisms fo r the actio n of aux in are being discovered . There are pum ps in the plasma membrane calle d aux in eff lux carrie rs. These are di stributed unevenl y and so ca n redi stri but e aux in in a tissue. Plant ce lls co ntain an aux in recepto r. W hen auxi n binds to it, transcri pt io n of speci fic genes is promoted, w hic h affec t the growth of the ce ll in th e w ays descr ibed above .

dome of cells at centre of apical meristem

youngest developing

leaf

PHYTOCHROME AND PHOTOPERIODISM

developing

bud

region of stem growth

PHOTOPERIODIC CONTROL OF FLOWERING Some p lants only flow er at the ti me of year w hen days are short and other pla nts on ly f lower w hen th e days are long . They are ca lled sho rt-day p lants and long-day p lants. Exp eri ments have shown th at it is not th e lengt h of day b ut the length of ni ght that is significa nt. For exam p le, chrysant hemums are sho rt-day p lants and o nly f lower w hen they receive a lo ng cont inuous peri od of d arkness (below) . They t herefor e natu rall y flowe r in the aut umn (fall) . Growe rs can pr odu ce pots of flo w er in g chrysanthem ums at all tim es of the year by keep ing them in gree nho uses w it h b linds. W hen the ni ghts are not lo ng enough to in duce flow eri ng, th e b li nds are cl osed to extend the ni ghts artif ic ia lly . In a sim ilar way, petun ias, w hic h are lo ng-day pla nts, can be indu ced to flower at tim es of the yea r w hen the days are short by bei ng give n extra light in green houses to red uce th e lengt h of the ni ghts.

Plants ca n measure the length of perio ds of dark to an acc uracy of a few m inutes. They do this using a pigment in their leaves ca ll ed ph yt och rom e, w hic h ex ists in tw o int erco nvertib le fo rms. On e form is call ed P, because it absorbs red light w ith a wave length of 660 nm . P, is the inactive fo rm of phyt ochrom e. W hen it absorbs red light it is rap idly converted into the active form, ca lled Pr, . Thi s for m ca n absorb far red light w ith a wave length of 73 0 nm and is then rap id ly co nverte d back to P, . In norm al day light there is much more red light than far red li ght so p hyto chrom e ex ists in th e active Pr, for m . In darkness Pr, reverts very slowly to P, (above). This gradual reversion process is p rob ab ly how th e length of the dark peri od is tim ed . Eno ugh Pr, rem ains in lon g­ day p lants at th e end of shor t nights to st im ulate flowering. In Arabidop sis, whi ch is a long-day p lant, a protein has been found to w hic h Pr, b inds. Th is protein p robably act s as a transcripti on fac tor, causi ng genes involved in flow ering to be sw itc hed on. In sho rt day p lants Pr, presumab ly acts as an in h ibitor of flow eri ng. At the end of long nights, enough Pr, has been co nve rted to P, to allow flow ering to oc cur . Interc on version s of ph yto chrom e

red light (sunlight) rapid conversion

Response of chrysant hem ums t o different li ght/dark regim es

24­ Ught

::::'" I I....... . ../

~

j.. ,.,._-:-

- -.-": : ::~~'_".'•:. j

jl ..,.';

.:

"

o

O

JI~,~.~:.,.~~::.~ .

-

length Criti cal night Flash of light

P,

Pr,

..

, ,, far red light (rapid conversion)

r r

Darkness

.......

J

< \~.~,:.

o D

'.-'. ~. 'I-~...:- ,..,~

slow conversio n duri ng darkness

Plant science 87

EXAM QUESTIONS ON TOPIC 9 Control of flowering in long-day and short-day plants involves inter-conversion of phytochrome between its two forms, Prand Pfr. a) State whether phytochrome is in the P, or Pfr form at the end of the day (sunset) in (i) long-day plants

[1 ]

(ii) short-day plants

[1 ]

b) Explain how long-day and short-day plants time the length of the night.

[2]

c) Distinguish between the effect of Pfr in long-day and short-day plants.

[2]

2 Flowering plants (angiospermophytes) are classified into two groups: monocotyledons and dicotyledons. a) Outline three differences between monocotyledons and dicotyledons.

[3]

b) Distinguish between growth due to apical and lateral meristems in the stems of dicotyledons.

[2]

c) Monocotyledons do not have lateral meristems. Predict the consequences for monocotyledons of not having lateral meristems.

[2]

3 C3 and CAM plants both need CO 2 for photosynthesis. They take in CO 2 through microscopic pores called stomata. The stomata can very from being fully closed (0% open) to fully open (1000/0 open). The circular graph below shows the width of opening of stomata during a 24 hour period in a C3 plant and a CAM plant. 12 pm (midnight)

o

------- C3

- - CAM

6pm (sunset)

6am

(sunrise)

12 am (midday)

a) Identify the hours during which stomata were fully closed in (i) the C3 plant

[1 ]

(ii) the CAM plant

[1 ]

b) One of the two plants is a xerophyte. Use the data in the graph to predict whether the C3 plant or the CAM plant is the xerophyte.

[2]

c) (i) Outline the changes in the stomata of the C 3 plant shown in the graph between 11.00 am. and 2.00 pm.

[2]

(ii) Suggest a reason for the changes.

88 IB Questions - Plant science

[1 ]

10

..\

",:'.! :;:'1.:,.

-.....

",A 'Awn

,.

Mendel's law of independent assortment G regor Me ndel disco vered the Law of Segregation by doin g mo noh ybrid c rosses w ith pea plan ts. He discovered a not her law of inherita nce by doi ng crosses in w hic h the pa rents differed in two c haracteristics, that a re contro lled by two diffe ren t ge nes . These a re ca lled dihybrid crosses. Mendel d id his dih ybrid c rosses w ith pea plants. An examp le of o ne of his c rosses is shown be low . The parents in this c ross d iffer in see d shape, co ntro lled by o ne gene, a nd in see d co lou r, co ntro lled by a differe nt ge ne.

SSyy

P genotype _ I

'0

wrinkled green seed Gametes only co ntain one co py of eac h gene .

1

1

@

gametes ­

The a lleles for smooth seed and yellow seed are do minant so all of the F1 have smooth yellow seeds.

Ssyy

F1 genotype_ phenotype ­

smo~~~e~ l low

\ /I @) ~ 0 sv

~

y

Q V

+-

eac~

O ne copy of ge ne is again passed on In the

gametes, but as the F1

plants are heterozygous for both genes four possible co mbinations of a lleles.

t her~ ar~

@A® SSyy

F2 genotypes and phenotypes

o smooth yellow

o

a llele fo r smooth see d. a llele for w rinkled see d. a llele for yellow see d. a llele fo r gree n see d.

I,i4

smooth yellow seed

gametes­

S= s= Y= y=

Pea plants co ntain two copies of eac h gene.

ssyy

o

phenotype -

KEY TO SYMBOLS

o smoot h yellow

Ssyy

A Punnett grid is the best way to show the genotypes and phenotypes in a dihybrid cross.

The phenotypic ratio in the F2 generatio n is 9 smooth yellow: 3 smooth green: 3 wrinkled yellow: 1 wrinkled gree n

o

smooth yellow

ssyy

o

smooth yellow

o

The 9:3:3:1 ratio shows that the four types of gametes are all equa lly co mmon. The inheritance of the two genes is separate. The presence o f an allele of one of the genes in a gamete has no influence ove r which allele of the other gene is present in the gamete. This is Mende l's Law of Independ ent Assortment.

Genetics 89

Dihybrid crosses

PREDICTING RATIOS IN DIHYBRID RATIOS The 9:3:3 :1 ratio is oft en fo und w hen parents that are heterozygou s fo r tw o genes are crossed together. The ratio is the pro duct of tw o 3: 1 ratio s - each of the two genes wo uld give a 3:1 ratio in a mo no hybr id cross between two heterozygou s parents. In a di hybr id cro ss they fo llow M ende l's Law of Independent Assortm ent because they are unlin ked. Di hyb rid crosses can give other ratios if : • either of the genes has co do m inant alleles, • either of the parents is hom ozygous for one/both of the genes, • either of the genes is sex linked . Sex-linked genes are located on sex chromosomes instead of on autosomes (non-sex chromosom es). The figure (right) shows ratios that these typesof genes could give. A not her cause of unu sual ratios is interactio n betwee n genes. The fi gure (below ) shows an example of a d ihybrid cross w here there is interaction betwee n genes.

Possible ratios in dihybrid crosses

3

phenotypes

3

3

3

3

3

6

1

2

3

I

1

1

2

2

1

1

1

3

2

CcAa

CcAa

3

9

1

P genotypes

2

3

1

Two genes in mice affect coat colour. O ne gene controls w hether the coat is co loured or not. The other gene control s the colour.

KEY C = allele for coloured coat C = allele for albino coat

CCAA

A a

= allele for agouti coat =allele for black coat

Agouti is the normal colour of w ild mice. Each hair has black and w hite bands so the overall colour is grey.

9 agouti ----.~ 3 black 4 albino

All mice that are cc are albino because they are unable to produce pi gment in the hairs in their coat.

90 Genetics

Polygenic inheritance

THE DISCOVERY OF POLYGENIC INHERITANCE

Results of a cro ss between red and white fl ow ered beans

Some characteristics are influ enced by mo re than o ne gene. This is called polygenic in heritance. Gregor Me nde l di scovered an example of pol ygeni c inh eritance, when he

APS P

crossed a purple-flow ered species of bean w ith a w hite­ flowered speci es. The F] offsprin g w ere all purp le, so he

wh ite flo wers and a w ide variety of shades of purple f low er.

APSw

Me ndel suggested that two or three genes might be involved . If these we re codom inant genes, each with two alleles, one fo r pur ple flowers (AP and BP) and one fo r w hite (Aw and BW ), there co uld be f ive shades of flower colour (right).

POLYGENIC INHERITANCE AND CONTINUOUS VARIATION Most examp les of po lygenic in herit ance invo lve more than tw o genes w ith codom inant alleles. As the number of genes invol ved increases, the number of possib le phenotypes increases. Eventually, it becomes impossibl e to divide indi vid uals into di screte gro ups - the variation is co ntinuo us.

AWSP

AWSw

EXAMPLES OF POLYGENIC INHERITANCE

AWS P

AWSw

APA PSPS P

APAPSwS P

AWAPSPSP

AWAPSwS P

;A jl) jl) ~ APAPSwSw

AWAPSPSw

AWAPSwSw

jl) ~ ~ ~

jl) jl) ~ ~

IJ ~ j1 ~

APAwSPS P

APAwSwS P

AWAwSPS P

AWAwSwS P

APAwSPSw

APAwSwSw

AWAwSPS w

AWAwSwS w

Distribution of grain colo ur in whe at

Gr ain co lour in wh eat Wheat grai ns vary in co lour fro m w hite to dark red, depe ndi ng on the amount of a red pi gment they co ntai n. Th ree genes co ntro l the co lour. Each gene has two alleles, o ne that causes pigment pro duction and o ne that does not. Wh eat grain s can therefore have between 0 and 6 alleles for pigment produ ction . The figu re (right) show s the expected distributi on of grain co lo ur fro m a cross betw een two plants that are heteroz ygous for each of the thre e genes.

APS w

APAPSPSw

expected a 3:1 ratio of purple to w hite flow ers in the F2 offspring. Instead, he found a much smaller proportion of

APS P

20

15

15

c-,

u

c


OJ

u

.!

Skin colour in hum ans The co lo ur of human skin depends on the amo unt of t he black pi gment melanin in it. There is a con ti nuo us d istribution of ski n co lour f rom very pale (little melani n) to black (much melani n). At least fo ur and possibly mor e genes are invo lved, each w ith alle les that promote melanin production and alleles that do not. There is therefor e a w ide range of possib le genoty pes with anythi ng from no alleles promotin g melani n produ ctio n to many. The fi gure (below ) shows humans w it h a range of skin co lou r.

6

w hite •

6

• red

Skin colour variation in hum ans

Genetics 91

Genes - linked and unlinked

UNLINKED GENES

GENE LINKAGE

Mendel's law of independent assortment can be explained in terms of chromosome movements during meiosis. If pairs of genes are located on different types of chromosome, when homologous chromosomes pair up in meiosis the genes are on different pairs. The pairs of homologous chromosomes are called bivalents. The bivalents are orientated randomly on the equator, so the pole to which alleles on other bivalents are moving does not affect the pole to which alleles on a bivalent move. Random orientation of bivalents allows combinations of alleles to be broken up, so that new combinations can be formed when gametes fuse during fertilization. If two parents with the genotypes AAB Band aabb are crossed together, the gametes that they produce (AB and ab) wi II fuse together to give an F1 hybrid with the genotype AaBb. The figure below shows the possible gametes that could be produced by meiosis in this F1 hybrid. The parents could not have produced two of the gametes (Ab and aB).

Some pairs of genes do not follow the law of independent assortment. The expected 9:3:3:1 ratio is not found when parents that are heterozygous for the two genes are crossed. The figure (below) shows the first example of this to be discovered. The results show that there were more offspring than expected with the parental character combinations ­ purple long and red round. There were fewer than expected with the new combinations - purple round and red long. Combinations of genes tend to be inherited together. This is called gene linkage. Gene linkage is caused by pairs of genes being located on the same type of chromosome. New combinations of alleles can only be produced if DNA is swapped between chromatids. Th is is called recombination and involves a special process called crossing over, which happens during the early stages of meiosis. Individuals that have a different combination of characters from parents, as a result of crossing over, are called recombinants.

Independent assortment of unlinked genes

Gene linkage in Lathyrus odoratus

P genotypes

~

ppll

PPLL

phenotypes ~ purple flowers long pollen

red flowers round pollen

prophase I

j 50% / probability

50% probability

F1 genotype ~ phenotype ~

j @ C§ ~

~

j

PpLi

purple flowers

long pollen

Self-polIination of F1 plants to produce F2 generation.

metaphase I

Expected F2 ratio

9 purple long

3 purple round

3 red long

1 red round

~

Expected results (6952 plants in total)

3910.5

1303.5

1303.5

434.5

~

Observed resuIts

390

393

1338

C§)

C§

telophase I

92 Genetics

pi

PL

4831

Crossing-over

EYENTSINPROPHASEI OF MEIOSIS

Th e pr oc ess of crossi ng ove r

Homol ogous chromosomes pair up in prop hase I of meiosis. Each homologous chromosome co nsists of two sister chromatids. Chromatids of different chromosomes are called non-sister chromatids. Wh ile the chromosomes are paired, sections of ch romatid are exchanged in a process called crossing-over. The figure (right) shows how crossing-ov er occurs.

At one stage in prop hase I all of the chromatids of two homo logous chromosomes become tightly paired up together. This is called synapsis.

!

[ : : fou

r chromatids in total,

long and thin at this stage

The DNA molecul e of one of the chromatids is cut. A second cut is made at exactly the same point in the DNA of a non-sister chromatid.

+±3

E

T

BENEFITS OF CROSSING-OYER Crossing-over has two important co nsequences. 1. It creates chiasmata w hic h hold hom ol ogou s chro moso mes to gether in pairs called biva lents, dur ing t he later stages of p rophase I and metaphase I un til mi crotubul es have attached. 2. It allows recom bin ation of linked genes. A ll of the genes that have their loci on the same chromoso me type for m a lin kage gro up. Recom bin ati on of genes in a lin kage gro up ca nnot occ ur w it hou t cr ossing-over. The poi nt w here crossing-ove r occurs along chromoso mes is random - it ca n occ ur at a vast number of di fferent points. M eiosis ca n therefo re pr odu ce an almost in fin ite amo unt of genetic variety . The figure (below) shows how crossing-over ca n cause recomb inat ion of linked genes. Th e figure (right) shows an examp le of a cross in volv in g gene lin kage, using bars to represent the chromoso mes on w hich the genes are linked . A test cross was do ne on the F, p lants. Recom bin ati on of linked genes

DNA is cut at the same point in tw o non-sister chromatids The DN A of each chromatid is jo ined up to the DN A of the non­

sister chromatid. This has the effect of swapping sections of DNA

between the chromatids.

:z: In the later stages of prophase I the tight pairin g of the homol ogous chromosomes ends, but the sister chromatids remain tightly connected. W hen each cross-over has occu rred there is an X­ shaped structu re call ed a chiasma.

~ ~ i

:

AN EXAMPLE OF GENE LINKAGE AND TEST-CROSSING IN ZEA MAYS

. w.

c

P genotypes

C

Parental gene combinatio ns are AB and ab

1

a

a

,

Locus of gene A

~ ~ Locus of gene B

I

phenotypes

j

t.rossmg occu rs between

the loci of the

two genes

x:

chiasma

W

gametes

~

KEY

c

w

C

.~

V 1

W = allele for starchy kernels

w

.

\

!

[

!

[

,

\

Test crossusing a plant that is homozygous recessive for both genes

w

•

c w w hite waxy

C~~ ~~c '

= alle le for waxy kernels

c

1

w

c

= alle le for purple kernels

c = allele for wh ite kernels

w

purple starchy

phenotype

gametes

.

c

W

'------'-

F, genotype

w

wh ite waxy

purple starchy C

c

•

r---r

A A

::E

\

-. . c

[

•

,

w

~

C F1 genotype

•

c phenotype numbers

w

purple starchy

14 7 Parental combination

c

w

purple

c

w

w hite

waxy

starchy

65

58

Recombi nants formed as a result of crossing over.

c

w

w hite

waxy 133

'-.­

Parental combination

Genetics 93

Phases of meiosis

M eiosis involves tw o divisions. Each division is divided into four phases. The main events of each phase are listed below .

PROPHASE I o

o o o o o

PROPHASE II o

o

Chromosom es start to co il up and so become shorter and thicker. Homologous chromosomes pair up. Crossing over occ urs. Centrioles move to the po les in animal cells. Nu cleoli break down . At the end of prophase I the nuclear membrane breaks down .

METAPHASE I Chromosomes cont inue to shorten and th icken. Spindle microtu bules attach to the centromeres. o Bivalents line up on the equator. o Chiasmata slide tow ards the ends of the chromo somes, causing the shapes of the bivalents to change. o At the end of metaphase I the chromosomes start to move.

o

Chromosomes become shorter and thi cken again by coiling. Centrio les move to the poles in animal cells. At the end of prophase II the nuclear membranes break dow n.

METAPHASE II o o o

Spindle microtub ules attach to the centromeres. Chromosomes line up on the equator At the end of metaphase II the centromeres divi de.

ANAPHASE II o

The two chromatids of each chromosome move to opposite poles. At the end of anaphase II the chromatids reach the poles.

o

o

o

TELOPHASE II

ANAPHASE I o

o

The tw o chromosomes of each bivalent move to opposite poles. Thi s halves the chromosome number. Each chromosome consists of tw o chromatids. Because of crossing over the two chromatids are not identical. At the end of anaphase I the chromosomes reach the poles.

TELOPHASE I Nuclear membranes form around the groups of chromosomes at each pole. o The cell divides to fo rm two haploid cells. o The chromosomes uncoi l partially. o At the end of teloph ase I the tw o cells either enter a brief period of interphase or immediately proceed to the second division of meiosis. The DNA is not repl icated. o

Nuclear membranes form around the groups of chromatids at each pole. Each chromatid is now co nsidered to be a chromosome. o The two cells each di vide to form to fo ur cells in total. o The chromosomes uncoi l. o Nuc leoli appear. o In most organi sms the cells fo rmed at the end of telop hase II develop into gametes. o

SUMMARY OF MEIOSIS 1. Meiosis involves two divi sions. O ne cell or nucl eus divid es to fo rm four cells or nuclei . 2. The chromosome numb er is halved, from dip lo id to haploid. 3. An almost infi nite amount of genetic variety is produ ced, as a result of crossing-over in prop hase I and the random orientatio n of bivalents in metaphase I. The figure (below) shows micrographs of four stages in meiosis in cells from the testis of a locust.

Earl y prophase I

l ate prophase I

to urn

Anaphase II

Anaphase I

x

94 Genetics

~~ .... ~.

-.... l'

•

EXAM QUESTIONS ON TOPIC 10 In some pl ants tw o genes co ntro l flower co lo ur . [No te : - repr esents any allele] Plants wi th th e geno type A_B_ have b lue flo w ers. Plants w ith the genoty pe A_bb have red flowers. I.

Plants with the genoty pe aa __ have w hite f low ers. a) State th e name given to the ty pe of inh eritance w here mor e th an on e gene co ntro ls a single phenoty p ic characteristic.

[1]

A hom ozy gous b lue-f lowered plant (AA BB) is cr ossed w ith a homozygou s w hite-flowered pl ant (aabb). b) State th e genoty pe and phenotype of th e F1 offspring.

[2]

c) The F1 plants are allow ed to pol lin ate eac h othe r. D educe, using the Punnett grid below, th e genotypes of th e gametes prod uced by th e F7 p lants and the geno types and p henotypes of all th e possib le F2 offsprin g.

[5]

gametes ---+­

t

d) State th e expected rati o of flower co lo urs in th e F2 offs pri ng.

[1]

e) The tw o genes code for enzy mes used to co nvert a whi te substance into a red pi gment and th e red pi gment into a blu e pigment. Dedu ce th e effec t of the enzymes prod uced from gene A and gene B.

[1]

2 a) Def ine reco mb inatio n.

[1]

When grey bodi ed lo ng w inged D rosoph ila f lies we re test crossed w ith black bodi ed vestigial w ing f li es the F1 generatio n was found to co ntain:

40 7 grey bodied lon g w inged f li es

39 6 blac k bodi ed vest ig ial w inged fli es

75 black bodi ed lon g w inged fli es 69 grey bod ied vest igia l w inged fli es b) Ident ify w hic h of th e f lies we re reco mb inants.

[2J

c) The F1 generation does not fo llow Me nde l's Second Law (Law of Independ ent Assortment). Explain how th e observed ratio co uld have arisen.

[3]

d) Suggest how genetici sts co uld mak e use of ex perimenta l results of the typ e shown above .

[2]

3 The mi cr ograph below show s a pair of hom ol ogou s chromosomes in a ce ll carr yi ng out meiosis in the grasshopper

(Charthippus parallelus). tu um

a) Identi fy th e stage of meiosi s of th e cell that co ntai ned th e pair of chromosomes.

[2J

b) In th e pair of chromoso mes in th e mi crograph dedu ce th e num ber of (i) chro mati ds

[1]

(i i) ch iasmat a

[1]

c) Outlin e how chiasmata are produ ced.

[3]

IB Questions - Genetics 95

11 Antibody production STAGES IN ANTIBODY PRODUCTION

3. Activation of B-cells

The production of antibo d ies by the im mun e system is o ne of the most remarkabl e bio log ica l processes. W hen a pathogen invades the body, the immune system gears up to produce large amo unts of the specific antibodies needed to combat the pathogen . This process only takes a few days. The production of antibodies by B-ceffs is show n in a simp fified form on page 50 . A ntibody production usually depends on other types of lymphocyte, including macrophages and helper T-cel ls. The ro les of these cells are explained here.

Inac t ive B-ce lls have ant ibodies in their plasma membrane . If these antibodies match an antigen, the ant igen binds to the antibody. An activated helper T-ce ll with receptor s for the same antigen ca n then bind to the B-cell . The activated hel per T-cell sends a signal to the B-cell , caus ing

it to change from an inactive to an active state. This is activation of B-cells . inactive B-cell

1. Antigen presentation Macrop hages take in antigens by endo cytosis, process them and th en attac h them to membr ane proteins called MH C prot eins. The MHC protein s carry ing the antigens are then moved to the plasma membrane by exocytosis and the antigens are displayed on the surface of the macrophage. This is antigen presentation . antigen is absorbed .--and then displayed by the macrophage

inactive helper T-cell MHe protein

4. Production of plasma cells 2. Activation of helper T-cells Helper T-cells have receptors in their plasma membr ane that can bind to antigens presented by macroph ages. Each hel per T-cell has receptors w ith the same ant igen-bindi ng dom ain as an antibody . These receptors allow a helper T-cell to recognize an antigen presented by a macrop hage and bind to the macro phage. The macroph age passes a signal to the helper T-cell cha nging it fro m an inact ive to an active state. Thi s is activatio n of helper T-ce lls.

Activated B-cell s start to divide by mito sis to fo rm a cl on e of cells. These cells becom e act ive, w ith a mu ch greater vo lume of cyto plasm. They are then know n as plasma cells. They have a very extensive netw ork of rough endo plasmic reticulum . Th is is used for synthesis of large amo unts of antibody, w hic h is then secreted byexocytosis.

Help er T-cell bind s to

macro phage pr esentin g

th e antigen

plasma

cell

activated helper T-cell

96 Human health and physiology

5. Production of memory cells M emory ce lls are B-ce lls and T-ce lls that are formed at the same tim e as activa ted helper T-cell s and B-cell s, w hen a di sease challenges the im mune system. Afte r the activa ted cells and the antibod ies produ ced to fight the di sease have di sappeared, the memor y cells persist and allow a rapid response if the di sease is enco untered again . M emor y cells give long-term immunity to a d isease.

Immunity and vaccination

ACTIVE AND PASSIVE IMMUNITY

PRINCIPLES OF ANTIBODY PRODUCTION

Resistance to infectio n is called immunity. A ntibod ies give immuni ty to disease - thi s is someti mes called specific imm uni ty, because one type of antibody gives protecti on against o nly one disease. Immunity can either be act ive or passive.

The imm une system has the potenti al to produce a vast range of different types of antibody - perhaps 10 15 d ifferent types. It wo uld be imp ossible to make large q uantit ies of all of these antibod ies. Instead, a few B-cells that can make a type of ant ibody are produ ced and if these cells enco unter an ant igen to w hich their antibody binds, they mu lti ply to form a clone of many cells. This is called clon al select ion. Sometimes several d ifferent types of antibody can bi nd to the same antigen, so more than o ne c lo ne of cells is formed. Thi s is called po lyclo nal selectio n. A cl one of B-cells can produ ce large amounts of antibody quick ly and so give immun ity to the di sease w ith w hich t he antigen is associated. Immunity to a d isease is only develop ed if the di sease challenges the im mune system. This is call ed the principle of chall enge and response. These two prin cip les do not fully explai n antibody di versity. Research is ongoing into tw o addi tio nal processes: • how lym phocytes splice together DNA taken from various parts of the genome, to produce a huge variety of genes coding for anti bod ies • how rapid mutation occ urs in antibody genes in lymphocytes that have been activa ted by antigen binding ­ this gives the chance of produci ng antibodies that fit the antigen better.

Active immunity is due to produ ction of antibod ies by the organism itself after the body's de fence mechanisms have been stimulated b y antigens. An example is w hen infecti on w ith rubell a viru s causes immun ity to rubell a to develop and re-in fecti on is very rare.

Passive imm unity is due to the acquisition of antibodies received from another organism, in which active imm unity has been stimulated. Examp les of passive imm unity : • During pregnancy, antibodies are passed across the placenta from mother to the fetus. • The fi rst mil k prod uced after birth, called co lostrum, co ntai ns antibodies that line the gut of new born babies, help ing to prevent infection. • Antib odi es are somet imes injected as an emergency treatment for virul ent di seases, such as rabies.

VACCINATION A vacci ne is a modified form of a d isease-causing microorganism that stim ulates the body to develop imm uni ty to the di sease, w ithout fu lly develop ing the d isease. Vacci nes co ntai n weakened form s of the m icroorganisms, killed form s or chemica ls produ ced by the microorganism that act as antigens. The vaccine is either injected into the bod y or sometimes swa llo wed. The prin cipl e of vacci nation is that antige ns in the vacci ne cause the produ ct ion of the ant ibod ies needed to co ntrol the d isease. Som etim es two or more vacci natio ns are needed to stimulate the produ ctio n of enough antibod ies. The figure (right) shows a typical response to a fi rst and second vacci natio n against a disease. The first vaccination causes a little anti body prod uct ion and the prod uction of some memory cells. The seco nd vacci natio n, sometimes called a booster shot, causes a respo nse from the memory cells and therefo re faster and greater prod uction of antibodies. M emory cells should persist to give lo ng-term immunity.

Response to first and second vacci nat ions

.£ I o

(b) Secondary response

.0

c: '0'" c

.2 "@ C

::l c

I

(a) Primary response

o

U

o

t First encounter w ith antigen

10

20

30 40 Time/d ays

t

50

60

Second encounter with antigen

VACCINATION - BENEFITS AND DANGERS There are huge benefits from vacci natio n: 1. Epidemics and pandemi cs can be prevented and some di seases can be comp letely erad icated - smallpox was the fir st and polio may be the seco nd. 2. Deaths d ue to di sease can be prevented. For examp le, measles is a major cause of death of unvaccin ated c hildren in some parts of the wo rld. 3. D isabi lity due to di sease can be prevented, decreasing health care co sts, for example deafness and blind ness in babies w hose mothers w ere not vacci nated and so contracted rubella during pregnancy .

Immunization is the most effective of all pub lic health interventio ns. A ll vacci nes are very carefully tested before being introduced and the risks of the di seases that they prevent are much greater than any adverse effects associated w ith vacc ines themselves. Unfortunately, the diseases that vacc ines prevent become rare so that parents worry mor e about the vaccin e than the disease. As a result unfounded stories of the dangers of vacci nes easily tip public op inio n against vacci natio n, w ith very serious co nsequences for chil d health . Serio us adve rse reactio ns wh ic h are caused by vacci nes, such as severe al lergic reactio ns (anaphylaxis), are very rare. M ost ot her vacci ne reactions are min or and recover w ithout treatment: fever, o r pain, swelling and redness at the site of vacci nation .

Human health and physiology 97

Monoclonal antibodies and blood clotting

PRODUCTION OF MONOCLONAL ANTIBODIES Large quant ities of a single type of antibo dy can be made using an ingenious techniqu e. • Anti gens that co rrespond to a desired antibody are inj ected int o an animal. • B-cell s produ cin g the desired antibody are extracted from the animal. • Tumour cells are obtained. These cells grow and di vide end lessly . • The B-cells are fused w ith the tumo ur cells, produc ing hybrido ma cells that di vide endlessly and prod uce the desired ant ibody. • The hybrid oma cells are cultured and the ant ibo d ies that they produ ce are extracted and purified . The f igure (right) shows a factory used fo r the industrial produ cti on of mon ocl onal ant ibod ies. There are many ways in w hic h mono clon al antibo dies can be used. Two examples are described here.

Treatment of anthrax Anthrax is a disease caused by a bacterium that produces tox ins. It is often lethal, even w hen antibiotic treatments are given. A nthrax spores have sometimes been used deliberately to infect peopl e and cause death. M onocl on al antibo d ies are being developed w hich neutralize one of the toxin s and therefore sustain the patient' s life unti l their immune system produ ces antibodies naturall y.

Diagnosis of malaria Tests using mo nocl o nal antibodies have been develop ed for many d iseases, inclu ding malaria. Mo noclonal antibodies are produ ced that bind to antige ns in malarial parasites. A test plate is coated w ith the ant ibod ies. A sample is left in the plate long eno ugh for malaria antigens in the sample to bind to the antibodies. The sample is then rinsed off the plate. A ny bound ant igens are detected using more mo noclo nal ant ibo d ies w ith enzy mes attac hed that cause a co lo ur change. This is called an ELISA test. It can be used to measure the level of infecti on and to d isti nguish between di fferent strains of malar ia, eithe r in humans or in mosquitoes.

BLOOD CLOTTING Wh en human tissue is inj ured and blood escapes from blood vessels, a semi-solid is formed from liqu id blood to seal up the wou nd and prevent entry of pathogens. The semi-solid is called a blood clot and the process is called clotting. Platelets have an import ant role in clotting. Platelets are small cell fragments that ci rculate w ith erythrocytes and leukocytes in the bloo d plasma. The cl ottin g process begins with the release of c lotting facto rs either f rom damaged tissue cells or fro m platelets. These clotting facto rs set off a series of reacti ons in w hich the produ ct of each reactio n is the catalyst of the next reacti on . This system helps to ensure that clo tting on ly happens w hen it is needed and it also makes it a very rapid process. In the last reactio n fi brinogen, a soluble plasma protein is altered by the removal of sect io ns of pepti de that have many negati ve c harges. This allows the remainin g po lypepti de to bind to others, formin g lo ng protein fibres calle d fibr in. Fibr in fo rms a mesh of fibres across wo unds. Blood cells are caught in the mesh and soon form a semi-so lid cl ot. If exposed to air the clot dri es to form a protective scab, w hich remains until the wo und has healed.

Fibrin and bl ood cells in a bl ood cl ot

Final reactions in blood cl otting Reactions initiated by ciotti ng factors released by platelets or damaged tissue cells prothrombin

activator

A1IIIIIP

~

prothrombin (inactive)

thrombin

(active)

~

fibrinogen (soluble)

98 Human health and physiology

fibrin

(insoluble)

Muscles and joints

MOVEMENT IN HUMANS

JOINTS

The mu scu lar-skeletal system and nervou s system are responsibl e for movement in humans. • Muscles provi de the force needed fo r mu scle co ntractio n. They do th is w hen they co ntract. • Tend on s attac h muscl es to bone. • Bon es provid e a fir m anc ho rage for muscles. They also act as levers, changing the size or di rect io n of for ces generated by mu scl es. • Ligaments co nnect bone to bone, restrict ing movement at joints and hel pin g to preven t di slocation . • Ne rve s stimulate muscles to co ntrac t at a precise time and extent, so that move ment is co-o rd inated.

Junct ions betw een bon es are ca lled jo ints. • Cartil age redu ces fr ictio n betwee n bo nes w here they meet. • Synovial f lui d lubri cates the joi nt to redu ce frict io n. • Join t capsule seals the joint and ho lds in the synov ial fluid . The knee is a hinge jo int. It allows co nsiderable movement in o ne plane: bendi ng (f lexio n) o r straightening (extensio n), but little movement in the other two planes. In co ntrast, the hip jo int allows move ment in thr ee p lanes (protract ion / retraction, abd uct io n/add uct io n and rotat io n). The figure (below) shows the structu re of the elbow joint.

THE ELBOW JOINT biceps - the flexor

muscle, used to bend

the arm at the elbow

tendon of triceps humerus p 'd bone ­

~~}E~~Yg~ ~~ ~th e~ . ---,\

ligaments - tough cords of tissue linking bone to bone, to prevent dislocation

~r~ g ~ ~;:,:~ ",o~'~

radius - bone that _ _ transmits forces from the biceps through the forearm

en the arm

ulna - bone that _ _ transmits forces from the triceps through the forearm

capsule ­ seals the joint

cartilage - a layer of smooth and tough tissue that covers the ends of the bones where they meet to reduce friction

synovi al fluid ­ lubricates the joi nt to reduce friction

STRUCTURE OF STRIATED MUSCLE FIBRES Wh en viewed w ith a light mic rosco pe skeletal m uscle is seen to co nsist of large mu lt inucl eate cells called muscle f ibres. W ithin each mu scl e fibre are cy li ndrica l struct ures called myofibr il s. The myofib rils consist of repeatin g uni ts called sarc omeres, w hic h have light and dark bands. The light and dark bands extend across al l the myofib rils in a muscl e fibr e, giv ing it a striated (striped) appeara nce . Arou nd each myo f ibri l is a special type of endo plasm ic reticulum, called sarcop lasm ic retic ulum, v isible in the electro n m icrograph (right). There are also mitoc ho ndria between the myofibri ls.

• -, " ';" 0,"''''

sarcolemma (membrane

Y\A.~\

,

" ,

~f muscle

" '" f bre)

myofib rils

nucleus

dark bands

light bands

Human health and physiology 99

Muscle contraction

STRUCTURE OF A SARCOMERE A sarcom ere is a subunit of a myofibril. At either end is a Z line to w hi ch narrow actin filaments are attac hed. The actin fi lam ents stretc h inw ard s towards the centre of the sarco mere. Betw een them, the re are thicke r myosin f ilaments, w hich have heads that can bind to the actin. The pa rt of the sarco mere co ntaining myo sin is the dark band and the part co ntaining on ly actin fi lame nt is the light band . The figure (right) shows the structur e of a sarcomere.

/

Z line

'"

~~~~ in~=: ~ ~~ ~ il :~~o

t!

.. r: ...

filaments

~p

~ r,:~

~f~~e:===~~~ a light band ,

~

........

k~ ~jm

.~ :,, ~

dark band

one sarcomere

i@

- V­

myosin heads

CONTRACTION OF SKELETAL MUSCLE W hen a motor neurone stimulates a striated muscle fibre, calcium ions are released from the sarcop lasmic reti cu lum . The calci um causes bi nding sites on actin to be revealed, allow ing myosin heads to bi nd. A cycl e of events occurs, w hi ch causes actin filaments to slide inw ards towards the centre of the sarcom eres. Thi s makes the light bands narrower and the sarcomeres shorter - the musc le fibre co ntracts. The figure (below) show s the events that cause mu scle contraction. The electron mIG O~\ o.?'W' .,n ow .,\\lo.\eO mu.,c.\e In \e\o.)(.eo \'oo\\om \ eh) o.n o. c.o n\\o.c.\ eo. \'oo\\ om \1'5n\) ,,\o.\ e.,.

CD Myosin filaments have heads w hich form cross-bridges w hen they a ~e a.ttached to bindin g sites on actin fil aments.

MOVEMENT

~

/

~ ~ ADP + P ~

® The ADP and phosphate

are released and the heads push the actin fi lament inwards towar ds the centre of the sarcomere. This is called the pow er stroke.

Q) ATPbinds to the

----=:=

myosin heads and causes them to break the cross­ bridges by detaching from the bindin g sites. -.

~ )

\ ~

~+P

~AD P+ P

~

@ The heads attach to binding sites on acti n that are further from the centre of the sarcomere than the previous sites.

Relaxed muscle

100 Human health and physiology

Contracted muscle

(] ATP is hydrolysed to ADP and phosphate, causing the myosin heads to change their angle. The headsare said to be 'cocked' in their new position as they are storing potential energy from ATP.

Kidney structure and ultrafiltration

FUNCTIONS OF THE KIDNEY

ULTRAFILTRATION IN THE GLOMERULUS

The kidney has tw o functions - excre t io n and

osmoregulation.

Ex cretio n is the remo val from the bod y of the waste products

of metabo lic pathways.

Osmoregulation is the co ntro l of the water balance of the

b lood, tissue or cy top lasm of a living organ ism.

The funct io n of the glo merulus is productio n of a filtr ate fro m blo od by a process called ultrafiltration . Part of the blood plasma escapes throu gh the w all s of all capilla ries, but in the glomerulus 20% escapes, w hi ch is mu ch greater than usual. There are two main reason s fo r thi s. • The blood pressure is very high, bec ause the vessel takin g blo od aw ay from the glomerulus is narrow er than the vessel brin gin g bl ood. • The capill aries in the glome rulus are fenestrat ed - they have many pores th rou gh them. These pores are large enough to allow any molecu les through, but on the outside of the capillary wa ll is a basement membrane, composed of a gel of glycoproteins (below ). The basement membrane acts as a fi lter as it only allow s molecu les w ith a molecular mass below 68 000 to passthrough. It lets all substances in blood plasma through except pl asma proteins. The fluid produced by ultrafiltration is collected by the Bow man's capsule and flows on into the proximal convo luted tubule.

THE STRUCTURE OF THE KIDNEY The kid neys produ ce urine. The figure (below ) show s the struct­ ure of the kidney. The cortex and medu lla of the kidney contain many narrow tu bes called nephrons. The figure (below) show s the structure of a neph ron, together wi th the associated glomerulus. Structure of a kidney in vertical section =::", <

cortex

Structure of the nephron renal artery

glomerulus

I

afferent medulla

a rte rio le~

efferent arteriole

I

renal vein pelvis of kidney

/

CORTEX ------------ ---MED ULLA

/1

Descending li mb loop of Henle { AscendiIng I'irnb

J [

ureter - - -+-­ (carries urine to the bladder)

Jr

collecti ng

Structure of part of a glomerulus

basement

membrane ­

the filter

Podocytes - strangely shaped cells wi th fi nger-like projections w hich wrap around capi llaries in the glomerulus and provi de support

du ct~

(

COMPARISON OF FLUIDS IN THE KIDNEY The physio logy of the kid ney can be stud ied by co mparing the content of blood flo wi ng to and from the kid ney w it h the co ntent of glomerular filtrate and urin e. Content (mg per 1 OOml of bl ood ) Blood in re nal artery

fenestrated wall of capillary

plasma

red blood cell

nucleus of capillary wa ll cell

Glomerular Blo od in filtrate renal vein

Glucose

90

o

90

90

Ur ea

30

2000

30

24

740

o

o

740

Protein s

b l ood ~

Urine

G lu cose is often present in the urine of untreated diabetic patients. This is because the gluc ose co ncentration of bl ood rises much higher than 90 mg per 100 m l, so the pu mp s in the proxim al convo luted tubu le cannot reabsorb all the glucose that is filtered out in the glomerulus.

Human health and physiology 101

Urine production and osmoregulation

SELECTIVE RE-ABSORPTION IN THE PROXIMAL CONVOLUTED TUBULE

Structure of the proximal convoluted tubule

-.

microvill i

Large vo lumes of glomerular fi ltrate are produ ced - about 1 litre every 10 minutes by the two kidn eys. As we ll as waste products, the filtrate co ntains substances th at the bod y needs, w hic h must be re-absorbed into the blood . M ost of this selective re-absorp tion happens in the proximal convo luted tub ule. The wa ll of the nephron consists of a single layer of cell s. In the pro xim al convo luted tubule the cells have mi crovi lli proj ectin g into the lum en (right), givi ng a large surface area for absorptio n. Pumps in the membrane re-absorb useful substances by act ive tran sport, using ATP produced by mitochondria in the cells. A ll of the glucose in the filtrate is re-absorbed. A bout 80% of th e min eral ions, includ ing sod ium is re-absorbed. Ac t ive tra nsport of so lutes makes the total solute co ncentratio n higher in the ce lls of the w all than in the f iltrate in the tub ule. W ater therefore moves from the filtrate to the cell s and on into the adj acent blood capillary by osmosis. Abo ut 80% of the wate r in the filtrate is re-absorbed, leavi ng 20% of the o riginal vo lume to fl ow on into the loop of Hen le.

mitochondria

lumen containing filtrate

I

basement membrane

OSMOREGULATION IN THE COLLECTING DUCT

THE ROLE OF THE LOOP OF HENLE G lo merular fil trate flows deep into the medu lla in descendin g limbs of the loop s of Hen le and then back out to the co rtex in ascend ing lim bs. Descendin g lim bs and ascend ing li mbs are opposi te in terms of permeability. Descend ing limbs are permeable to wa ter but not to sod ium ions. Asce nding limbs are permeabl e to sodi um ions but not to w ater (right). Ascendin g limbs pump sod ium ion s from the fiItrate into the medull a by act ive transpo rt, creat ing a high solute co ncentration in the med ulla. As the fi ltrate flows down the descend ing li mb into thi s region of high solute co ncentratio n, some wa ter is d raw n out by osmosis. Thi s di lutes the fluids in the medulla slightly . How ever the filtrate that leaves the loop of Henle is mo re dilute than the f luid entering it, showing that the overa ll effect of the loop of Hen le is to increase the solute co ncentratio n of the medull a. This is the rol e of the loo p of Henl e ­ to create an area of high solute co ncentratio n in the cells and tissue fluid of the medul la. After the loop of Henle, the filt rate passes through the di stal co nvo luted tu bul e, w here the io ns can be exchanged betwe en the filtrate and the blo od to adj ust blood level s. It then passes into the co llecting duct.

50%

100%

Na+ 100%

H2O

Na+ 150% 150% 150%

Na" 150%

H2O

Na+

H2O

200% 200% 200%

H2O

2000/.

Na+ H2O 250 0/0 2500/0 250%

H2O

250%

Na+ 300%

H2O

300%.

Movements of water and sodium ions in the loop of Henle and the collecting duct. Solute concentrations inside and outside the nephron are show n as a percentage of normal blood solute concentration

102 Human health and physiology

Osmoregulation is the control of water and solute leve ls. The col lecting duct has an important role in osmoregulatio n. If the water content of the blood is too low , the pitui tary gland secretes ADH . This hormo ne makes the cells of the collecting duct produce memb rane channels called aquaporins, w hich makes the collecti ng duct permeable to water. As the filtrate passes down the collecting duct through the medull a, the high solute co ncentration of the medul la causes most of the water in the filtrate to be re­ absorbed by osmosis. A small volume of concentrated urine is produced. If the w ater co ntent of the blood is too high, A D H is not sec reted, aquapor ins are brok en down and the co llect ing duct becom es much less permeable to w ater. Litt le wa ter is reabsorb ed as the filtrate passes down the co llect ing duct and a large vo lume of dilute urine is produ ced . In this w ay the wa ter co ntent of the bloo d is kept w ithin narrow li mits.The urin e produ ced by the co llecting du cts drains into the renal pelvi s and down the ureter to the bladder.

Spermatogenesis

Spermato genesis is th e pr oducti on of spermato zo a. Spermato zo a are usuall y sim ply called sperm. Spermatogenesis occurs in the testes, in narrow tubes ca lled sem iniferous tubules . The fi gur es (below and right) show th e struct ure of testis tissue, in cl udin g the sem inifero us tubules. The f igure (bottom) shows th e processes invo lved in spermatogenesis.

Structure of testis tissue wall of seminiferous tubule

blood vessel

interstitial cells (Leydig cells) secrete testosterone

-,

Micrograph of testis tissue (x 90)

o STAGES OF SPERMATOGENESIS spermatogonium

CD A n outer layer called germin al epithelium cells (2n ) divide endlessly by mit osis to produce more dip loid cells.

Q) Dipl oid cells grow larger and are then called p rim ary spe rmatocytes (2 n)

primary spermatocyte

It

",

secondary spermatocyte

J Q)

Each primary . spermatocyte carries out the fi rst division of meiosis to produce two secondary spe rma tocy tes (n).

@) Each secondary

®

spermatocyte carries out the second di vision of meiosis to produce tw o sp ermatids (n).

Sperm detach from Sertoli cells and eventually are carried out of the testis by the fluid in the centre of the seminiferous tubul e.

spermatids

(i) Spermatids become associated \I

If

--j

with nurse cell s, called Sertoli cells, w hich help the spermatids to develop into spe rmatozoa (n). This is an example of cell di fferentiati on .

Human health and physiology 103

Oogenesis

Oogenesis is the p rod uctio n of an ov um . Ova are often simp ly ca lled eggs. Oogenesis occurs in the ova ries.

The figures below show the structure of ova ry tissue.

The figure (bottom) shows the processes invo lved in oogenesis.

ovary

Micro graph of the of a rabbit

Structure of the of a rabb it

region w here

blood vesse ls

enter and leave

ovary

medulla (containing blood

_-===========:::::::::""

vess\

~=====:::::======'\=--

outer layer of germina l epitheli um cells

cortex

(containi ng

primary foll icles)

secondary oocyte inside a mature follicl e

STAGES OF OOGENESIS @ Primary oocytes start the first di vision of meiosis but stop during prophase I. The primary oocyte and a single layer of follicle cells around form a primary foll icle .

a> Dip loi d cells grow into larger cells called pri mary oocytes

@ W hen a baby gi rI is born the ovaries contain about 400 000 primary follicles.

® Every menstrual cycle a few primary foll icles start to develop . The primary oocy te completes the fi rst division of meiosis, forming two haploid nuclei. The cytoplasm of the primary oocyte is divided unequall y formi ng a large secondary oocyte (n) and a small po lar cell (n ). developi ng foil icles

I

~ o

(2 n ).

primary oocyte

G) In the ovari es of a female fetus, germinal epit helium cells (2 n ) divide by mitosis to form more dip loid cells (2 n).

~-

secondary oocyte

® The secondary

flap of tissue connecting ovary to abdomen corpus luteum (develops from the follicl e after ovulatio n)

egg released at ovulation

~ three layers secondary

of follicle oocyte in cells prophase II

I

® After fertil ization the secondary oocyte completes the second division of meiosis to form an ovum, (w ith a sperm nucl eus already inside it) and a second polar cell or body. The first and seco nd polar bod ies do not develop and eventually degenerate.

104 Human health and physiology

first polar cell

follicular fluid

mature fo llicl e

CD W hen the mature follicle bursts, at the ti me of ovulation, the egg that is released is actually still a secondary oocyte.

oocyte starts the second divi sion of meiosis but stops in prop hase II. The follicle cells meanw hi le are proliferati ng and fo llicular fluid is forming .

Gametes

STRUCTURE OF HUMAN SPERM acrosome haploid nucleus

co

c ..Q

mid-piece (Zurn long)

E

tail (40[!m long, two-thirds ci it omitted from this drawi ng)

-1

"

C ill (J)

"'j: E

:::!.

8

".s:

helical mitochondria

ill

(J)

microtubules in a protein fibres to 9+2 arrangement strengthen the tai I

plasma membrane

HORMONAL CONTROL OF SPERMATOGENESIS

PRODUCTION OF SEMEN

Three hormon es are involved in the pro ductio n of sperm.

Three structures help to prod uce semen - the epididy mis, semina l vesicles and prostate gland Wh en sperm from the testis arrive in the epid idymis, they are unable to sw im. The sperm undergo a matu rin g process w hile they are stored in the epid idy mis and becom e able to swim. The two seminal vesicles and prostate gland produce and sto re fluids and expel them during ej aculat ion. The fluid mixes w ith the sperm and increases the vo lume of the ejac ulate. The flu id from the semi nal vesicles co ntains nutr ients for the sperm incl uding fru ctose. It also co ntains mucus w hic h protects the sperm in the vagi na. The fluid fro m the prostate gland co ntains m ineral io ns and is alkali ne so protects the sperm from the aci d co ndit io ns in the vagina.

Hormone

Source

Rol e

FSH

Pituita ry gland

Stimulates primary spermatocytes to undergo the first division of meiosis, to form secondary spermatocytes

Testosterone

Interstiti al cells in the testis

Stimu lates the developm ent of secondary spermatocytes into matur e sperm

LH

Pituitary gland

Stim ulates the secretion of testosteron e by the testis

COMPARING SPERMATOGENESIS WITH OOGENESIS

STRUCTURE OF A HUMAN EGG haploid nucleus

first polar cell

cytoplasm

(or yolk)

containing

droplets of fat

There are many sim ilarit ies betwee n the formation of sperm and eggs. • Both start w ith pro liferatio n of ce lls by mi tosis. • Both in vol ve the cell grow th befo re meiosis. • Both invo lve the two di vi sion s of meiosis. The table below shows some of the di fferences. Spermatoge nesis

O ogenesis

M i ll ions produced dai ly

On e produced eve ry 28 days

Released dur ing ejac ulatio n

Released on abo ut day 14 of menstrual cycle by ov ulatio n

Sperm fo rmat io n starts du ring puberty in boys

The early stages of egg produ cti on happen during fetal develop ment in fema les

Sperm pro ductio n co ntinues throu ghout the adult life of men

Egg producti on beco mes irregular and then sto ps at the menopause in wo men

Fou r sperm are produced per meiosis

O nly on e egg is produ ced per meiosis

plasma membrane layer of follicle cells (corona radiata)

layer of gel composed of glycoproteins (zona pellucida)

Di ameter of egg cell

= 11 0 urn

Human health and physiology 105

Fertilization

Summary of spermatogenesis

8

Stages in the fertilization of a human egg

germina l epithelium cells

2n

1\ 8 2n

8 2n

/\

/\

mitosis

8 8 88

sperm try to push through \ the layers of \ fo llicle cells around the egg

7, Arrival of sperm Sperm are attracted by a chem ica l signal and sw im up the ov iduct to reach the egg, Fertili zation is only successful if many sperm reach the egg.

2n 2n 2n 2n

cell growt h

8

prim ary spermatocyte

fo llicle - ---f cell

2. Binding The fir st sperm to break throug h the layers of foll icl e ce lls binds to the zo na pellu cid a. Th is tri ggers the acrosome reacti on .

2n

/\ 88 n

j

n

n

~

n

~ ~

2nd division of meiosis

spermatids

n

~

!!! n

n

-----I

plasma membrane of egg

n

8 8 8 8

n

zona - pelluci da

secondary spermatocyte

/\ /\

1

1st division of meiosis

n

3. Acrosome reaction acrosomaI --+-+----T---1-----r--T-/I.:// cap

cell differentiation

spermatozoa tai l and mitochondri a

Summary of oogenesis

8

2n

i,n i t 1 usually remt outside

germinal epithelium cells

1\

8 2n

8 2n

/\

/ \

mitosis

cell growth

j primary oocyte

2n

1\ 8

j

1st division of meiosis

n

secondary oocyte and first polar body

/\

j

8~ n

o

n

o~ ;/O~'o ~

D

4. Fusion The plasma membranes of the sperm and egg fuse and the sperm nucl eus enters the egg and join s the egg nucl eus. Fusion causes the co rtica l reaction.

cortical granules

8888 2n 2n 2n 2n

8

The co ntents of the acrosome are released, by the separatio n of the acrosomal cap from the sperm. Proteases from the acrosome di gest a rout e for the sperm through the zo na pelluc ida, allowing the sperm to reach the plasma membrane of the egg.

hardened zona pell ucida

~ ~ , :..:".:, D

exocytosis of contents of cortical granules

106 Human health and physiology

".

__

';"

- - - sperm nucleus

two polar -----:rii'fi&l!lil cells

2nd division of meiosis

ovum and second

polar body

5 . Cortical reaction

two haploid nuclei from the sperm and the egg

Sma ll vesicles ca lled co rt ica l granules move to the pl asma membr ane of the egg and fuse w ith it, releasin g thei r co ntents byexocytosis. Enzy mes from the co rtica l granules cause c ross-li nking of glycoproteins in the zo na pellucid a, makin g it hard and prevent in g the entry of any more sperm.

6. Mitosis The nucl ei f rom the sperm and egg do not fuse together. Instead, both nucl ei carry out mitosis, using the same centrio les and spindle of mi crotu bul es. A two-ce ll em bryo is produced .

Pregnancy and childbirth

FERTILIZATION AND EARLY EMBRYO DEVELOPMENT

4-cell embryo

If a couple wan t to have a ch ild, they have sexual intercourse w ithout using any method of contrac eption . The bio logic al term for sexual interco urse is copulat ion. During cop ulation, semen is ejacu lated into the vagina. Sperm sw im th rough the cervix, up the uterus and into the ovidu cts. If there is an egg in the ovid ucts, a sperm can fuse w ith it to produce a zy gote. The fusion of an egg wi th a sperm is called fertilizat ion . The zyg ote prod uced by fertilization in the oviduct is a new hum an indi vid ual. It starts to di vide by mitosis to form a 2-ce ll embr yo, then a 4-cell embryo (right) and so on unt il a holl ow ball of cells called a bl astocyst is form ed . W hile these early stages in the developm ent of the embryo are happ ening, the embr yo is tra nsported dow n the ovid uct to the uterus. Wh en it is about 7 days o ld, the embryo imp lants itself into the wa ll of the uterus, w here it cont inues to grow and develop .

DEVELOPMENT OF THE FETUS

Female repr odu ct ive system duri ng pregnancy

amniotic

sac

amnioti c fluid

placenta uterus wall

---L----\

umbilical cor d

vagina cervix

CHILDBIRTH Throu gh the 9 mont hs of pregnancy, the hor mone progesteron e ensures that the uterus develop s and sustains the grow ing fetus. The level of progesterone in the mot her becom es increasingly high. The end of pregnancy is signalled by a fall in progesterone level. This allows the mot her's bod y to secrete anot her horm one - oxy toci n. Oxytoc in causes th e muscle in the uterus wa ll to co ntract. Uter ine co ntract io ns stimulate the secretion of more oxytoc in. The uterin e co ntract io ns therefore beco me stronger and st ronger. Thi s is an example of posit ive feedbac k. W hile the muscle in the wa ll of the uterus is contracting, the cervix relaxes and becomes w ider. The amniotic sac bursts and the amniotic fluid is released. Finally, often after many hours of co ntractions, the baby is pushed out through the cerv ix and the vagina. The umbili cal co rd is cut and the baby begins its independent life. Contractions co ntinue for a time until the placenta is expelled as the afterbirth.

By the tim e that embryo is about 8 weeks o ld, it starts to develop bone ti ssue and is known from then onwa rds as a fet us. The fetus develop s a placenta and an umb ilical co rd (left). The placenta is a d isc-shaped structure, w ith many proj ectio ns called placental villi embedded in the uterus wa ll . In the placenta the blood of the fetus flow s cl ose to the blood of the mother in the uterus wa ll. M aterials are exchanges betw een maternal and fetal blood. For example, oxygen passes from maternal to fetal blood and carbon dioxid e passes from fetal to maternal blood . The fetus also develops around itself an amnio tic sac co ntaining amniotic fluid . The fetus floats in this amniotic f luid and is supported by it. The delicate tissues of the fetus are prot ected from inju ry by the amniotic fluid , w hic h acts as a shock absorber. This is needed if an everyday event or an acci dent causes an impact to the moth er's abdomen. A samp le of fluid can be taken from the amniotic sac by inserting a hypodermic needl e throu gh the abdomen wa ll. This procedure is know n as amnioce ntesis. The fluid co ntains fetal cells wh ic h can be cultured to make them di vid e. The chromosomes of the di vidi ng cells can be examined to test for chromosomal abnormalities such as Down 's syndrome.

Childbirth almost comp leted

vagina - the birth canal

Human health and physiology 107

Structure and function of the placenta

HORMONAL CONTROL

STRUCTURE AND FUNCTION OF THE PLACENTA

OF PREGNANCY

The figure (below) shows the struct ure and functio ns of the placenta.

The fig ure (bottom) shows how materi als are exc hanged betwee n maternal and fetal bloo d at

the surface of v illi in the placenta.

Estrogen and progesteron e are needed throu ghout pregnancy to stimulate the deve lopme nt of the uterus lin in g. During the first few days after ov ulatio n the co rpus luteum secretes these hor mon es w hether or not there has been ferti lizati on . After impl antin g in the uterus wa ll, the emb ryo starts to secrete a horm on e called HC G (human cho rio nic gonado trophin). HCG prevent s degeneration of the corpu s luteurn, w hich wo uld happen at the end of a menstrual cy cle . HCG stim ulates th e co rpus luteum to grow and to co ntinue secretion of estrogen and progesteron e. Thi s is essential to allow the pregnancy to co ntinue. By the middle of the pregnancy, the co rpus Iuteum starts to degenerate, but by then cells in the placent a are secreting estrogen and progesteron e and these ce lls secrete in creasing amo unts unti l the end of the pregnancy.

Structure of the placenta Placenta - a disc-shaped structure, 185 mm in diameter and 20 mm thic k w hen fully grow n.

Placental villi - small projections that give a large surface area (14m' ) for gas exchange and exchange of other materials. Fetal blood flows through capillaries in the vi lli.

I

Deoxygenated fetal blood flows from the fetus to the placenta along two umbilical arteries.

LfrlllH­

-

Inter-vill ous spaces­ maternal blood flow s thro ugh these spaces, brought by uterine arteries and carried away by uterine veins.

Oxygenated fetal blood flows back to the fetus from the placenta along the umbilical vein.

Myo metrium - muscular wa ll of the uterus, used during childbirth.

En dometrium - the lining of the uterus, into w hich the placenta grows.

EXCHANGE OF MATERIALS ACROSS THE PLACENTA Maternal blood in the i nter­ vi lIous space

nV

P\ ~

[J U (?\, (j ·

(J

°2' glucose, lipids, water, minerals, vitamins, antibod ies, hormones

~ O c? © O ©~

Chorion ­ forms the placental barrier, controlli ng w hat passes in each dir ection Cytoplasm of chorion produces estrogen and progesterone and secretes them into the maternal blood

Basement membrane (freely permeable) Capillary carryi ng fetal blood is close to the vill us surface and has a very thin wa ll of single cells

Connective ti ssue inside the villus

~

108 Human health and physiology

small distance separating maternal and fetal blood

CO 2 , urea, hormones, water

NB Maternal blood does not flow along the umbilical cord or through the fetus.

EXAM QUESTIONS ON TOPIC 11 a) Defin e excretion.

[2]

b) Compare the co mpositio n of blood pl asma and urin e, by giving two di fferences in the table below.

[2]

Blood in the renal artery

Blood in the renal vein

c) Exp lain briefly the function of the loop of Henle in the hum an kidney.

[2]

d) Deduce w hich part of the kid ney has been damaged if prote in is fo und in the urin e.

[1]

2 The electron micrograp h below shows part of a myofibri l, taken fro m a skeletal muscle. The parts marked M contain myosin filaments. Three ot her regions are labelled I, II and III. M

A

(~-~

M ~-~\

( - -

-

-

A

~--~\

'-y---J"-.,---/'-------v-----­

I

II

III

[Source: Dr G. Newman, EM Unit, University of Wales College of Medicin e]

a) (i) State one type of fi lament, apart from myosin, whi ch is present in myofibrils. (ii) Identify in w hich of the regions label led I, II and III these other fi laments can be found.

[11 [1 ]

b) The myofibri l is partly contracted. Deduce w hich of the regions wo uld increase in length if (i) the myofibr il co ntracted more

[1]

(ii) the myofibril relaxed

[1]

3 a) Compare the structure of human sperm and eggs.

[4]

b) Compare the role of FSH in men and wo men.

[3]

c) Compare the roles of LH and HCG in wo men.

[3]

18 Questions - Human health and physiology 109

12

...._ _........

~

...............

_~_u..-..---

~ _

Components of the human diet

NUTRIENTS IN THE HUMAN DIET

VITAMIN D AND THE BALANCING OF RISK

N utr ients are chemical substances fo und in foods that are

used in the hum an bod y.

M any nutrients are needed in the human d iet:

am ino aci ds, fatt y acid s, min erals, vitamins and water .

Carbo hyd rates are almost alway s present in human di ets but

specific carbo hyd rates are not essent ial.

Minerals and vitamins are bot h needed in small quant it ies,

but they are chemica lly very d iffe rent :

• minerals are chemic al elements that are obta ined in an io nic fo rm, for example sodi um as Na" ions and phosphorus as PO l - io ns • vitamins are organic compo unds that cannot be synthesized by the bod y.

If there is insuffi c ient vitamin D in the bod y, ca lci um is not absorbed from foo d in the gut in large enough quantiti es. Symp toms of calc ium defi ciency ca n develop (rickets). Vitami n D is co ntained in oily fish, eggs, mil k, butt er, cheese and liver. Plant products do not co ntain vitamin D, but it is usually added du ring the manufacture of soya mil k, margari ne and breakfast cereals. U nusually fo r a vitam in, it ca n be synthesised in th e skin, but th is o nly happens w it h ultra-vio let li ght (UV). The intensity of UV is too lo w in w inter in high lat itudes for much v itamin D to be synthesized, but the liver can stor e eno ugh duri ng the sum mer to avo id a defi cie ncy in w inter. Even w hen there is br ight sunlight, three thin gs can prevent absorpt io n of enough ultra-v iol et li ght by the skin fo r adeq uate synthesis of vita min D : • avo id ing exposure to sunlight e.g. staying indoo rs • cove ring most of the skin w it h clo thing • apply ing sun creams to block ultra vio let light These things are all ways of reduci ng the risk of mali gnant melanom a - a form of ski n cancer that can be fatal. This is because UV can cause the mutation s that turn skin cells into tum our cells. A delicate balance must therefore be struck, betw een over-exposure to UV and an excessive risk of malignant melanoma, and under-exp osure, w hich brings the risk of vitam in D defic iency.

RECOMMENDED VITAMIN C INTAKES The recommended daily intake of a mineral or vi tamin is the min im um amo unt that should be co nsumed per day to ensure health . Tw o types of experiment have been do ne to determine this amo unt for vitam in C. 1. A small mammal called a guinea pig has been used, w ith groups of guinea pigs fed diets w ith different levels of vitamin C for a trial period . The level of vitamin C in the blood plasma and urine of the experimental anim als was then measured. Also the strength of co llagen in bone and skin was measured, to test for signs of scurvy (vitamin C deficiency). The results can be used to estimate the amount of vitamin C that humans require per kilogram of body tissue. 2. Experim ents we re done in Britain during the Second W orld W ar, using volunteers w ho we re co nscien tio us ob jectors to milit ary service. Fo r six wee ks all the vo lunteers wer e give n a di et lacki ng vitami n C plus a dai ly supplement of 70m g. The vo lunteers were then d ivided into three groups and give n 70 mg, 10 mg or no vitami n C per day, for eight months. They we re given skin cuts, to test for wound healing and were checked fo r other signs of scurvy . The 10 mg and 70 mg groups did not develo p scurvy, but all those in the Omg group did. The results of the human trial suggest that 10 mg of v itamin C per day is suffic ient, but in most co untries much higher reco mme nded daily intakes have been set. There are two main reasons fo r th is. • To give a safety margin so that the risk of scurvy is minim ized • To allow fo r variatio ns betwee n ind ividua ls in their general health and in thei r ability to absorb and use vitamin C Some sci entists have suggested that the recommended level should be increased, because vitam in C may give protecti o n against upper respirato ry tract infecti ons (co lds). For examp le, Linus Pauling, a Nobel prize-wi nnin g Am erican chemi st, advocated levels of 1000 mg or more of vi tam in C per day. There is littl e scientifi c evide nce to bac k up the theor y that thi s gives protectio n against co lds. There is ev idence that if the bod y adj usts to high rates of intake by excreting the excess and intake drop s back to norm al levels, this exc retion co nt inues, causing scurv y to develop - this is called rebo und malnutri tion . Dai ly intake of about 50mg is prob ably suffic ient.

110 Human nutrition and health

IODINE AND DIETARY SUPPLEMENTATION A rti fi cial nutr ient supplementatio n is used w hen a diet co ntains insufficie nt quantit ies of a nutrient. The nut rient can be added to a food, or can be supplied in a pure form. Iod ine is one of the best examples of the benefits of artificia l di etary supplementation . Iod ine is needed for the synthesis of the hormone thy roxin , by the thyroid gland. A n obv ious symptom of iodi ne defic iency di sorder (lD D) is swell ing of the thy roid gland in j' the neck, called go itre (see f igure). ID D also has some less obvio us but very serio us consequences. If wo men are affected du ring pregnancy, their child ren are born w ith perm anent brain damage. If chi ld ren suffe r from ID D after birth, their mental development and intelligence are impaired . In 1998 U N ICEF estimated t hat 43 mi ll ion peopl e wo rldwide had brain damage due to IDD and 11 millio n of these had a severe co nd ition call ed cretinism. 40 % of the wo rld's po pu lation was est imated to show some mental im pairment because of ID D, w ith hi ghest rates in areas w here the soil used to grow crops and the drin king wa ter cont ain litt le iod ine. At the W or ld Children's Summit in 1990 a campaign wa s started to eliminate IDD by add ing it in small quantiti es to salt so ld for human consumption. This is a highly effective way of prevent ing ID D at a cost of only about 5 cents per person per year. By the year 2000 iodi zed salt was reaching mor e than 3.3 bi lli on peop le. If the campaign to prov ide iod ized salt th roughout the w orld is successful, no childre n in the fut ure w i ll suffer from ID D .

Amino acids and fatty acids AMINO ACIDS IN THE HUMAN DIET

PHENYLKETONURIA

Twenty different amino acids are needed to make proteins.

Phenylalanine is an essential amino acid, but tyrosine is non­
'rrurnans can maKeabDUt na\~ D~ tn~~~ \n ~\J~\~\een\ ~'Uctl)\\\\ee'S by conversion from other nutrients in the diet. These are the

non-essential amino acids. A shortage of any of the other amino acids in the diet causes protein deficiency malnutrition. Often this deficiency disease is caused by a general shortage of protein in the diet, which results in a lack of most or all of the essential amino acids. One of the most obvious consequences of protein deficiency malnutrition is the swelling of the abdomen, often seen in photographs of children in areas of famine. The swelling is caused by tissue fluid retention, or oedema. In a well­ nourished person, plasma proteins in the blood cause all tissue fluid to be reabsorbed in blood capillaries. If these proteins cannot be synthesized, because of a lack of one or more of the essential amino acids, then fluid builds up in the tissues, including the abdomen. Protein deficiency mal nutrition has many other effects, as proteins have so many roles in the body. The overall effect is that growth is retarded and if energy is also lacking in the diet there can be wasting - loss of body mass.

phenylalanine

tyrosine hydroxylase

-..;......-_.....:...._-.:...---I.~

. tyrosine

High levels of phenylalanine in the blood are a symptorn of the genetic disease phenylketonuria. In this disease, there is a deficiency or complete lack of the enzyme tyrosine hydroxylase, because of a mutation of the gene coding for the enzyme. In a fetus, the levels of phenylalanine are kept down by the mother's metabolism, but after birth the levels rise and soon have harmful effects. In many countries, phenylalanine levels are tested by a simple blood test soon after birth, allowing very early diagnosis of phenylketonuria. This allows a special diet to be fed, containing low levels of phenylalanine, preventing most if not all of the harmful effects of the disease.

STRUCTURE OF FATTY ACIDS

FATTY ACIDS AND HEALTH

All fatty acids have a carboxyl group (COOH) and a hydrocarbon chain. Fatty acids are variable in the bonding between the carbon atoms and the number of hydrogen atoms bonded to the carbons. Saturated - all of the carbon atoms in the chain are connected by single covalent bonds so the number of hydrogen atoms bonded to the carbons cannot be increased. Unsaturated - one or more double bonds between carbon atoms in the chain, so more hydrogen could be bonded to the carbons if a double bond was replaced by a single bond.

Many claims have been made about the health consequences of the various types of fatty acid but the evidence for many of these claims is scanty.

Saturated fatty acids • There is a positive correlation between diets with high

levels of saturated fatty acids and CHD mortality.

• Correlation is not proof of cause - it could for exarnple be

the low fibre content of most diets high in saturated fat that

causes CHD.

Cis-monounsaturated fatty acids

H

H H

H

H

H

I

I

I

I

I

I

~

I

I

I

-, OH

H-C-C-C-C~C-C-C-C

I

H

H H

I

H

I

H

H

0

Unsaturated fatty acid

(naturally occurring ones have more carbon atoms)

• Rates of CHD are typically low in people who eat a

Mediterranean type diet, rich in olive oil, which contains

cis-monounsaturated fatty acids.

• Other factors vary between people, apart from the arnount

of cis-monounsaturated fatty acids in their diets, including

genetic factors, and these could explain differences in rates

of CHD.

Omega-3 fatty acids Monounsaturated - only one double bond.

Polyunsaturated - two or more double bonds.

The position of the nearest double bond to the CH 3 terminal

is significant. In omega-3 fatty acids, it is the third bond from

CH 3 whereas in omega-6 fatty acids it is the sixth.

Cis unsaturated - hyd rogen atoms are bonded to carbon

atoms on the same side of a double bond.

Trans unsaturated - hyd rogen atoms are bonded to carbon

atoms on opposite sides of a double bond.

H I

H

H

I

I

-C~C

I

-C~C-

cis

H

trans

• Much of the tissue of the eye and brain is made up of long­ chain fatty acids. These are synthesized in the body from essential fatty acids, including omega-3 fatty acids. It seems reasonable that a deficiency of these would impair brain and eye development. • There is no clear evidence that omega-3 dietary

supplements improve brain and eye development.

Trans fatty acids • There is a positive correlation between diets with high levels of trans fatty acids and CHD. Analysis has shown that other factors cannot explain the correlation, leaving trans fatty acids as the only risk factor. • In autopsies after deaths from CH 0, most of the fat in

arterial plaque has been found to be trans fat.

• Consumption of trans fats is associated with raised LDL

levels and reduced HDL levels, which are associated with

increased rates of CHD.

Human nutrition and health 111

Energy in human diets

ENERGY CONTENTS

APPETITE CONTROL

The three types of nutrient that supply most energy in human diets are carbohydrates, fats (I ipids) and proteins. Of these, fats provide the most energy per gram. Carbohydrates and proteins have a similar energy content.

The brain has an appetite control centre. It is located in the hypothalamus. Its role is to make us feel satiated when we have eaten enough food. The appetite control centre does this when it receives hormonal stimuli: • insulin, secreted by the pancreas when blood glucose levels are high • PYY3-36 secreted by the small intesti ne, when there is food in it • leptin secreted by adipose tissue, with more secreted as amou nts of stored fat increase. The role of the appetite control centre is very important. People whose appetite control centre does not function properly find it much harder to avoid obesity.

Nutrient

Energy content per 100 g

Carbohydrate

1760 kJ

Fat

4000kJ

Protein

1720 kJ

DIFFERENCES IN ENERGY SOURCES

BODY MASS INDEX

Diets vary around the world, especially between ethnic groups that eat traditional diets. Usually a few foods are the main energy sources in the diet and these foods are eaten in large quantities. • Rice - in tropical and temperate areas, for example in China and Japan • Wheat - in areas with a temperate climate, for example in the Ukraine • Cassava - in high rainfall areas in the tropics, for example the Yoruba tribe in Nigeria • Fish - where crop growth is impossible, for example the Inuit tribe in the far north of America • Meat - in ethnic groups with a nomadic lifestyle, for example the Maasai of Kenya.

It is not possible to assess whether a person's body mass is at a healthy level simply by weighing them, because of natural variation in size between adults. Instead, body mass index is calculated. The units for BMI are kg/rrr'.

ENERGY SOURCES AND HUMAN HEALTH There are health consequences of diets rich in carbohydrates, fats and protei ns. Carbohydrates Consumption of large amounts of sugar can increase the risk

of obesity, Type II diabetes and tooth decay.

Consumption of large amounts of starch can cause obesity,

but there is Iittle evidence of other health problems,

especially if the starch is in a formulation in which it is slowly

digested, preventing rapid glucose absorption into the blood.

Dietary fibre is mostly complex indigestible carbohydrate.

The health benefits of eating it are described on page 114.

Fats Consumption of fats in large quantities carries a significant risk of obesity. It has also been known for many years that there is positive correlation between fat intake and the risk of death from coronary heart disease (CHD). The type of fat is very significant, with trans fats associated with the greatest risk; saturated fats also probably increase the risk of CHD. Causes of CH D are complex and genetic factors and other dietary factors also have major influences. Proteins Large amounts of protein are sometimes consumed, especially as a part of some slimming diets that are intended to reduce body mass. Although controlled trials have not been done, there may be some associated health risks, especially with animal protein. These include kidney stones (composed of uric acid), gout, reduced kidney function in people who already have impaired kidney function, and loss of calcium in urine, increasing the risk of osteoporosis.

112 Human nutrition and health

mass in kilograms BM 1 = - - - - - - ­ (height in metresl/ The table below can be used to draw conclusions from a person's BM!. Body mass index

Conclusion

below 18.5

underweight

18.5-24.9

normal weight

25.0-29.9

overweight

30.0 or more

obese

CLINICAL OBESITY When a doctor diagnoses that a patient is obese, it is called clinical obesity. The World Health Organization has reported an obesity epidemic, with rates rising rapidly in some countries. Over 300 million adults worldwide are clinically obese. The reasons for this are complex and include these factors: • foods with a high content of fat and/or sugar are cheap and widely available and smaller quantities of low energy and high fibre foods are eaten • economic growth and cheaper foods have allowed larger portion sizes to be served • more people are using automated means of transport, such as cars or buses, and fewer people are walking or using other active means of transport • many people now have physically undemanding jobs, for example in offices, instead of labouring work, for example on farms • many tasks that were done in the home by hand are now done by a mach ine • the most popular pastimes have become less active, for example watching television or playing computer games, instead of active games or sports. In summary, more food is being eaten, but less of the energy in it is being used up in daily activities.

Issues in nutrition (Part 1) HUMAN MILK AND ARTIFICIAL MILK

TYPE II DIABETES

Hum an mi lk is produced by a mother' s breasts after birth and w hile the baby is st ill suckling. Arti fici al milk, o r infant for mula, is prod uced w ith a co ntent as sim ilar as possible to human mil k, but it cannot be identi cal in co mpositio n. The diffe rences are summarized below .

This is the type of di abetes that usuall y develops in adults rather than children and is not treated by inj ection s of insuli n.

Human milk

Artificial milk

Carbo hydrate

lactose

lactose OR glucose pol ym ers

Protei n so urce

65 % human w hey proteins 35% casein

18% bovi ne whe y and 82% bovine casein O R soya proteins

Fatty aci ds

human butterfat

palm , coco nut, soy or safflower o ils

Antibodies

antibodies present in the fi rst mil k - co lostrum

no antibod ies for fight ing human diseases are present

BENEFITS OF BREAST-FEEDING M ost mo thers are advised to breast-feed (nurse) their babi es, rather than bottle-feed with artifici al milk, because of the benefits: • breast-feedi ng avo ids the all ergies to prote ins in cows' mi lk or soya that can develo p w hen babi es receive artif ici al mil k • breast-feeding prom otes bond ing betw een mother and baby • freq uent breast-feeding acts as a natural birth-co ntro l method, reduci ng the chance of co nception w hi le the mo ther is lactatin g and th erefore allowing more tim e betwee n th e birth of one child and the next • breast milk is naturally sterile so is safer in areas w here it is impossible to sterilize w ater used to prepare art if icia l mil k • milk product ion helps mothers to lose weight after pregnancy.

ANOREXIA NERVOSA Anorexia nervosa is a di seaseth at most ly affects gir ls and wo men. It usually starts in the mid-teens w hen the emo tio nal and psych ological changes of ado lescence are occu rring. It has co mplex causes, making the condit ion a chall enge fo r all those invo lved . The consequences fo r friends and famil y include anxiety about the physical harm that the condit io n causes, feelings of guilt about di ffi cult relationships, powerlessness w hen treatment seems to be failing, and hurt at the desire for isolatio n show n by many peop le w ith anorexia. Because peop le w ith ano rexia do not eat enough carbo hyd rate or fat fo r use in cell respiratio n, pro tein is broke n down . Mu scles lose mass and beco me w eaker, w ith feelings of fati gue. Hair becom es mo re brittle and thinner and there can be hair loss. The ski n beco mes dry and bruises easily, w ith a grow th of fine hai r all over the bod y. Blood pressure drops, with a slow heart rate and poo r cir culation. M enstrual cycles often stop, wi th no peri ods or ov ulatio n, mak ing girls w ith anorexia infertil e.

1. Causes

Alt hough beta cells in the pancreas sti ll secrete insulin in

response to high blood gluco se levels, bod y cell s beco me less

responsive to the insuli n. The causes of this are not entirely

understood , but seem to be associated w ith increased bloo d

concentrations of fatty aci ds. The foll owi ng factor s all

increase the risk:

• di ets rich in fat, and low in fibre

• obesity, d ue to ove reating and lack of exerci se

• genetic facto rs, w hic h affect fat metabolism.

These risk factors vary betwee n et hnic groups and there is

therefo re huge variat io n in rates of Type II d iabetes, from less

than 2% in China to 50 % among the Pim a Indi ans.

2. Symptoms

The sympto ms of Type II di abetes are usuall y mi ld and

sometimes develop very gradually ove r a perio d of years, so it

is not alw ays d iagnosed qui ck ly. These are the main

sympto ms that are used to diagnose the condition :

• elevated levels of blood glucose

• glucose in the urine - this can be detected by a simple test • ti redn ess, increased appetite and loss of bod y mass • needi ng to exc rete urine freq uently, due to pro duction of large vo lu mes of urine • dehyd ration and thirst - fro m loss of w ater in uri ne.

3. Dietar y advice Changes to the di et are an obvio us way of trying to co ntro l Type II di abetes. Adv ice usuall y incl udes: • reducin g the intake of saturated fats • reducing the intake of sugar, especia lly in sweets (candy), snack foo ds and dr inks • eat ing more foods that are high in fibr e, incl uding vegetables and fr uit • eating regular small meals throughout the day, each meal including mod erate amounts of carbo hydrate, to prevent high blood sugar levels after a large meal • eati ng carbohyd rates w ith a low glyc emic index (G I), because they are digested and absorbed slow ly. The graph (below) shows the effects on blood glucose levels of eating high G I and low G I foods .

1:

high GI e.g. potatoes, cakes, cornflakes, white bread

':l

o

8­

E E

I

'l'­

~

U

2

00 ':l

7­

o .2

co

10w GI e.g. sweetcorn, beans, peanuts,

6­

5­ ~,

a

I 50

I 100

Z I

150 M inutes after intake

Human nutrition and health 113

Issues in nutrition (Part 2)

ETHICS OF EATING ANIMAL PRODUCTS

CHOLESTEROL AND CHD

M any peop le choose w hat to eat, based on li kes and dislik es,

availability and cost. Som e peop le also have ethica l reasons

fo r not eating certain foods.

Cho lesterol is a steroid and is mainly foun d in ani mal prod ucts. It is an essential comp onent of memb ranes. Som e investigations have shown that as the amo unt of cho lestero l in the blood plasma rises, the risk of death from CHD (coronary heart d isease) increases. A 10% increase in blood cholestero l is associated w ith a 30% increase in the ri sk of death fro m CH D . Other stud ies have suggested that total blood cho lestero l is less significa nt than levels of cholesterol in LDL . Neve rtheless, it seems reasonable that reducin g the amo unt of cho lesterol in the d iet sho uld cut blood plasma co ncentratio ns, lowering the risk of CH D . In practice, dietary cho lesterol only has a small effect on blood cholesterol levels so the effects of reducing dietary cholesterol are li kely to be minimal. Cho lesterol can be synthesized by the li ver and the rate of thi s varies as a result of genetic d ifferences. In some fami lies, high blood cholestero l levels are very co mmo n, even w ith diets very low in cho lesterol . The main co rrelation between di et and blood cholesterol levels is w ith saturated fat int ake. As d ietary saturated fat increases, both LD L and total bloo d cho lesterol levels tend to increase. CHD rates are also cor related positively with saturated fat int ake. It is not cl ear w hat, if any, the causal links are, but most physici ans adv ise reduci ng saturated fat intake, to try to reduce blood cho lesterol and the risk of CHD .

Meat

Anim als have to be kill ed to obt ain meat, usually after reari ng

them on a farm.

• Is it right fo r one animal to take the life of another animal to obt ain food ? • Is the pain caused to animals during transport and slaughter ju stifi able? • Is the suffering of animals reared fo r meat in unnatur al and crow ded co ndi tio ns j usti fiable?

Milk Cow s and oth er mammals produce mi lk after giv ing bir th. Th is mi lk can be used for human co nsump tio n if th e calf or young mamm al is separated from its mother soo n after birth. • Is the huge milk product io n of the cows that have been bred acceptab le, given that it is often associated w ith health problems and a short life expectancy? • Is the suffering of cows w hose ca lves are taken away from them soo n after birth j ustif iable? • Is it acceptable to make cows have calves in ord er to stim ulate m ilk productio n, w hen t hese calves w ill almost certainly have to be kil led eventually?

Eggs Most eggs co me from hens (female birds) that have been specia lly bred for pro lific egg produ cti on. • Is it acceptable to breed and keep hens that produce far greater numbers of eggs than their w ild relati ves? • Is the suffering of egg-layi ng hens kept in unnatu ral co nditio ns ju stifi able - either in small cages o r in artificia lly large groups in most free-range systems? • Is it acceptable to kill male chicks at 1- 3 days o ld because they do not lay eggs? Hon ey Bees are kept in hives and surplus honey is removed w hen available. • Is it ju stifiable to take honey from bees that have sto red it for thei r ow n use w ithin the bee co lo ny? • Is it acceptable to keep bees in an area w here the bees wi ll co mpete w ith wi ld insects that forage on nectar from flowers?

THE IMPORTANCE OF FIBRE Fibre is materi al that ca nnot be d igested in the small intesti ne. Cell ulose from plant ce ll wa lls is the main co mponent of d ietary fibre, but there are others incl uding chitin from fungi and crustaceans. M any invest igatio ns have show n that fibre helps to prevent co nsti patio n, by increasing the bulk of materi al in the large intestine. There are ot her possible advantages, but the ev idence for these is weake r. • Fibre might help to prevent obesity by increasing the bul k in the sto mac h, w hic h redu ces t he desire to eat more food . • Fibre may reduce the risk of d iseases of the large intestine incl udin g appendicitis, cancer and hemo rrho ids. • Fibre might slow the rate of sugar absorptio n and so help the prevent ion and treatment of di abetes.

FOOD MILES AND FOOD TRANSPORT Food mi les are simp ly a measure of how far a food item has been transpo rted from w here it was produced to w here it is eaten. M uch food is now transport ed hund reds of ki lo metres by road o r rai l, or t hou sands of ki lometres by air. Thi s causes air po ll ution , traff ic co ngestio n and the release of greenho use gases. At the other extreme, if urbanizati on was reversed and food was grow n w here we live, no energy would have to be used to transpo rt the food . Some co nsumers now refuse to buy foods w ith high food miles, hoping that supermarkets and shops w i ll start selling locall y pro duced food instead.

114 Human nutrition and health

O ther co nsumers are not co ncerned about food miles and instead wa nt co ntinuity of supply throughout the year and maxim um choice of w orld foo ds. So me env ironmentalists po int out that there are ot her energy costs in food produ cti on , suc h as produ cti on and app licatio n of ferti lizers. As an exa mple, this migh t make th at the ov erall ene rgy costs of lam b p rodu ced using low energy input systems in New Zealand and t ranspo rted aro und t he wo rld by sea, low er than the energy costs of lo ca ll y prod uced lamb. During fami nes, transport of food is j ustifiable on hum anitarian grounds, w hatever th e food mi les.

EXAM QUESTIONS ON OPTION A - HUMAN NUTRITION AND HEALTH A 1 The nom ogram be low shows the rel ation shi p between mass in kilog rams, height in ce ntimetres and bod y mass ind ex for adu lts.

140 00

135

1: OJ)

130

3:

125

~

'w

120 11 5 110 105 100 95 90 85 80 75 70 65 60 55 50 45 40 145

150

155

160

165

170

175

180

185

190

195

200

205

height (cm) a) Use the nom ogram to est im ate the bod y mass ind ex of adults w ith (i) a mass of 70 kg and a height of 170 cm

[1]

(ii) a mass of 90 kg and a height of 200 cm

[1]

b) (i) Calc ulate the bod y mass index fo r the adults in (a) using the standa rd equat ion.

(ii) Co m pare the calculated va lues fo r body mass index w ith the est imated values fro m the nom ogram . c) Expl ain the significa nce of the lines on the nom ogram for bod y mass indices of 18.5, 25 and 30.

[2] [1] [3]

A2 a) D istingu ish between (i) mon ounsatur ated and poly unsaturated fatty aci ds

[1 J

(ii) trans and c is unsatur ated fatty aci ds

[1 J

b) Evaluate the health co nsequences of d iets rich in satu rated fatty acids .

[3]

A3 Female mamma ls prod uce m ilk fo r their offspr ing, co ntain ing almost all the nutri ents needed by a young mamm al. a) Dedu ce the types of nut rien t co ntained in m il k.

[3]

b) Human mo thers can either feed their bab ies on their own m il k or on artif icia l m ilk . D iscu ss the benefits to bab ies of feedin g on mi lk from their mot her.

[31

c) Cow's mi lk fo rms part of the human di et, in some parts of the w orld. D iscuss th e ethics of co nsuming co w's mil k.

[2]

IB Questions - Human nutrition and health 115

13 Muscles and fitness MUSCLES AND MOVEMENT

FITNESS

The inform ati on on mu scles and movement described on pages 99- 100 of Chapt er 11 is part of Option B.

The result of a successful trainin g programme is a cond it io n called f it ness. Fitness is the p hysical co nd ition of the bod y that all ows it to perfo rm exercise of a pa rtic ular type .

FAST AND SLOW MUSCLE FIBRES Skeletal muscles co ntain two main types of mu scle fibre, fast fibres and slow fibres. Fast muscle fib res are sometimes called Type li b fibres, and slow fibres are Type I. The di fferences betwee n the two types of fibre are shown below . Fast fibres

Slow fibres

Blood supply

M oderate, w ith some blood capillaries

Excell ent, w ith many blood capillaries

Myoglo bi n

Little present

Large stores

M itochondria

Few present

Ma ny present

Cell respir ation

Large amo unts of the enzymes of glyco lysis, giving a high anaerobic capacity

Large amounts of ox idative enzy mes in mitochondria, so aerobi c capacity is high

Stamina

Low

Hi gh

Strength

High

Mo derate

PERFORMANCE ENHANCING SUBSTANCES

Fast mu scles fibr es co ntract more rapid ly and exert mo re

force per unit of cross-sectional area than slow muscle fibr es.

Fast f ibres can release large amounts of energy for a short

period of t ime by anaerobic respiration, so are useful in high­

intensity exerci se, for example 100 m sprint races.

Slow fibres release energy more slowly by aerobic cell

respiration, but can co nt inue fo r longer, so are useful in

endurance events, for example marathons.

M uscles vary in the proport io ns of the di fferent types of fibr e,

both w ithin a person's bod y and between people. Exercise

can affect the proporti o ns w ithin a person's muscles.

Mo derate-intensity exercise, such as long-di stance run ni ng or

sw imming, encourages the development of slow fibres. Hi gh­

intensity exercise, for example sprinting or we ight lifting,

enco urages the developm ent of fast muscl e fibres.

As a result of natural variati on and the effects of trainin g

programmes, elite athletes vary greatly in the proportion s of

fast and slow fibr es. The figure (below) shows the mean

percentage of fast and slow fibres in a thigh muscl e in fi ve

groups of athletes.

fast

slow

sprinters, throwers jumpers

I I

800m runners

~

alpine skiers cross-country

skiers

long-distance runners

..

10 20 30 40 50 60 70 80 90 % of fibres

116 Physiology of exercise

Dru gs can be used to enhance perform ances in sport, but there are strong ethical arguments against their use. 1. The lo ng-term health of spo rtsmen and wo men w ho are encourage d to take them may be damaged. For example, anabolic stero ids can cause men' s testes to becom e smalle r and sperm co unts to be low. Because anabo lic steroids resemb le testosterone, they can int erfere w ith wo men's reprod uct ive system and cause abno rmal menstrual cycles. H igh doses can cause liver di sease and there have been reports of athletes wh o take anabo lic stero ids suffering from emotional prob lems, w ith inap propri ately aggressive o utbursts. Increased muscle strength allows athletes to generate forces so strong that muscl es and tendon s can be torn . 2. Dr ug-users gain an unf air advantage in co mpetitio ns. For example, in M en' s 100m fin als in a recent O lympic Games, a high proportion of athletes had prob ably been taking anabo lic stero ids. 3. Crimin als profit from the sale of banned dr ugs. For example, there have been prosecutio ns of peop le w ho have been making substant ial profit s from the illega l sale of anabo lic steroids. If athletes decided not to use these anabo lic steroids, these profits co uld not be made. There are some ethical arguments in favour of legalizing perform ance enhancin g substances, but few genuine arguments, based on ethics, for their use. 1. Thei r use might overcome natural variation in physiol ogy, for example, variation in testosterone levels. If all athletes we re able to use them, competition might be fairer.

1

1

It is important to note th at fitness is specific to a particular

type of exerci se.

Dur ing training programmes, it is useful to measure fitness.

Various types of measure are used. These often invol ve

measurin g speed o r stamin a.

• Speed is the rate at w hic h a movement is perfor med. The tim e taken for a mov ement mu st be measured. Speed depends mostly on fast muscle fi bres. Speed is import ant in sprinti ng and football. • Stamin a is the abil ity to cont inue an exerci se for a lon g tim e. The maxim um dur ation t ime is measured. Stamina depends mostly on slow muscl e fib res. Stam ina is important in row ing and in lon g-di stance runnin g. Both speed and stamina have their uses as measures of fi tness­ whi ch is better depends on the type of fitness that is being assessed.

2. If they do enhance perform ance, spectators might gain more enjoy ment from w atchi ng sports.

Exercise and cell respiration GLYCOGEN AND MYOGLOBIN IN MUSCLE G lycogen is a po lysacc har ide th at is stored in muscle fib res.

It is made by linking together glucose mo lecul es and can be

broken down to provid e a source of glucose for cell

respiration . It avoi ds glucose shortage in mu scles durin g

int ense or long-duration exercise.

Some muscle fibres co ntain a red pigmen t called myoglobin.

Oxygen binds to it w hen the oxyge n level in mu scle is hi gh.

Oxygen is released by myoglobin wh en the ox ygen level in

mu scle is very low . The ro le of myoglobin is to act as an

oxygen store, allowing mu scl e fib res to co nti nue aerob ic

respiration for longer and delayin g the fo rmati on of lactate.

Causes of mu scle fat igue in races KEY

D

Blood lactate concentration

D

Glycogen breakdown %

%

20

M

100 0)

'E

u

0) 0

80

15

] :::J

E c::

:;~~s 10

"' E

60

c:: 3:

.- 0 c::u 0) c::

o n:l 00'= c 0)

0 ';:;

40

u

u

5

c::

o

u

MO)

a

l

o ~

0

>- ~

As the int ensity of exercise in cr eases, the bod y requires more oxyge n for aerobic cell respirat io n in mu scle fibr es.

V0 2 is the volume of oxygen that is absorbed by the body per minute and supplied to the tissues. As the intensity of exercise increases, V0 2 rises, until V02 max is reached .

V0 2 max is the maximum rate at which oxyge n can be absorbed by the body and supplied to the tissues. The i nten sity of exerc ise can rise above the level w he re V0 2 max is reac hed, by usin g anaerobic respirat io n. Thi s does not happen as a sudde n swi tch fro m one ty pe of respir ation to t he ot her: as inten sity of exe rci se in cr eases, the pe rce ntage of aerob ic respir ati on decr eases and the pe rcentage of anae rob ic ce ll resp iratio n in cr eases. Aerob ic ce l l respirati on can use fat o r ca rbo hyd rate as the substra te, but anaerobic cel l respiratio n ca n o nly use car bo hydrate . For this reason, as th e inten sity of exerc ise in creases, t he use of fat in cell respiration falls and the use of carbo hy drate ri ses until it reach es 10 0% .

cn..Q

~

I

r

20 0 ~ c

1 4 15 60 180 >360 a Duration of race or other endurance event I minut es

SOURCES OF ATP IN MUSCLES Mu scl e co ntract io n requires a supp ly of energy, It is obtai ned by co nverting ATP to A D P, The ADP th at is produ ced mu st be co nve rted back into ATP, for mu scle co ntractio n to co ntinue. There are th ree ways of doin g th is: 1. Cr eat in e ph osphate Mu scle fi bres co ntain sto res of creatine phos phate, w hic h can be used to pho sphoryl ate ADP by th is reactio n: creati ne + ADP phosphate

EFFECTS OF INCREASING THE INTENSITY OF EXERCISE

•

creatine + ATP

This reactio n allows AT P to be regenerated fo r abo ut 8-10 seconds of intense exercise - eno ugh for a 100 m sprint fo r example, If the dur ati on of exercise is longer then cell respiration must be used. 2. A naero bic cell respir ation Hi gh-int ensity exercise , such as sprint ing or we ight li ftin g, requir es ATP to be supp lied at suc h a rapi d rate, that oxyge n cannot be supp lied fast eno ugh for aerob ic cell respiration. An aerobi c cell respir ation t herefore has to be used. Lactate (lact ic acid) is produ ced by th is process and at the same tim e, hyd rogen io ns acc um ulate. A naerobic respiration can on ly be used to produce ATP for a maxi m um of tw o minu tes. Beyond thi s duration, hydrogen io n co ncent ratio ns prevent fu rther anaero bic respira tion , so hig h-intensity exercise canno t be co ntinued . 3. Aerobic cell respir ati on Oxygen for this type of respirati on is brought by bl ood pu mp ed to the muscle . If oxyge n levels in the mu scl e becom e low , oxyge n supp lies can be supp leme nted for a tim e by release fro m my oglobin sto res. Ae robic cell respir ation can produ ce ATP continuo usly at a rapid eno ugh rate for low -intensity exercise, suc h as wa lking or joggin g, how ever lon g the dur ati on .

REPAYING THE OXYGEN DEBT Lactate is car ried by bloo d fro m muscl es to the li ver, w here it is co nve rted to pyru vate. Oxygen is needed to do thi s, so if lactate is present in the bod y there is an oxyge n debt. If a large amou nt of lactate builds up during v igorous exercise, a large amo unt of oxyge n is needed to repay the oxygen debt. Th is is the reason for deep venti lation s and a rapi d venti lati on rate fo r a time after the exercise. The py ruvate pr odu ced w hen the ox ygen debt is bein g repaid can either be conve rted to glucose o r can be absorbed by mitochondri a and used in aerob ic respira tio n.

CREATINE PHOSPHATE SUPPLEMENTS Som e athletes use creatine as a d ietary supplement. An evaluatio n of its effect iveness is given below, An sw er

Qu esti on Is creati ne absorbed from the gut?

Yes.

Can dietary sup pleme ntation increase creat ine co nce ntrations in m uscle?

Yes, but only in athletes wi th natur all y low conce ntrat io ns. O nly sma ll doses of creatine are needed to reach maxi mal mu scle co nce ntratio ns.

Is the maximum int ensity of exercise in creased ?

There is some evidence of an increase in maxi mum intensity ove r sho rt du ration s.

Can in tense exercise be co ntinued for a longer time?

Endurance, invo lv ing aerobic cell respir atio n, is not increased .

Some studies have shown that creatin e phosphate supp leme nts cause we ight gain by water retenti on . If thi s happened, perform ance mi ght be im paired .

Physiology of exercise 117

Training and the pulmonary system

MEASURING PULMONARY FUNCTION

EFFECTS OF TRAINING ON VENTILATION

The pulmo nary system co nsists of the lun gs, the associa ted muscles and the airways lead ing to and from the lungs. There are various measures of pulmo nary fu nctio n w hich are used both duri ng the trainin g of athletes and also in the assess ment of patients w ith di seases of the pulmo nary system.

Train ing in vo lves repeating exercises that bring the body int o the desired state of fitness. There can be effects on the specific muscles used during trainin g and also more general effects on the pulm onary and card iovascular systems. Trainin g can reduce the ventilat io n rate at rest from abo ut 14 to 12 inhala tio ns per minute. Thi s is not because less gas excha nge is needed, but because the effic iency of oxy gen absorpt io n and carbo n d ioxide excretio n can be increased . Trainin g can increase the maximum vent ilat io n rate from about 40 to 45 inh alations per minute. Thi s is due to strengt hening of the muscles used fo r venti Iatio n. Trainin g m ight be expected to increase the vital capac ity of the lungs, but if there is any increase, it is o nly small. Lung capac ity appears to be unaffected by traini ng prog rammes.

Total lung capacity is the volum e of air in the lungs after a maximum inhalation . Vital capacity is the maximum volume of air that can be exhaled after a maximum inhalation. Tidal volume is the volume of air that is taken in or out with each inhalation or exhalation. The term venti lat io n wa s def ined in Chapter 6 on page 51 . Ventil ation has a clea rer meanin g than breathin g, so is used in IB Biol ogy.

Ventilation rate is the number o f inhalations or exhalations per minute.

I ventilation rate at rest

I

EFFECT OF EXERCISE ON VENTILATION Dur ing exercise, inc reases in ventilatio n rate and tid al vo lu me usuall y occu r. • Increases in ventilatio n rate and tid al vo lume bring more fresh air to the lun gs per minute du rin g exercise. • This ensures that the co ncentration of oxyge n in air in the alveo li remains high and the co ncentratio n of carbo n di oxid e remain s low . • Blood returnin g to the lungs during exercise has a higher carbo n d ioxide co ncentratio n and a low er oxyge n co ncent ratio n th an at rest. • Concentration gradients of oxygen and carbon dioxide between alveolar blood and air are therefore steep, maintainin g a high rate of gas exchange, w ith more carbon dioxide diffu sing into the alveoli per minute and more oxygen absorbed into the blood, than w hen the body is at rest. • Thi s is needed because during exercise the rate of aerobic respir ation in muscl e fib res increases, w ith more oxyge n used and more carbo n di oxi de pro duced per minute. • W hen the amo unt of oxygen supplied per minute to muscl es is insuffici ent, anaerob ic respiration has to be used, and the maxim um dur ati on of the exercise is not as long as wh en aerobic respiration is supply ing the energy that is needed. The chart (below) shows the ventilation rate and tidal vo lume of an athlete runnin g at diffe rent speeds.

E 3.00

80 o<

"'0

~.

..... ~ 2.7 5

70

:::J

tidal volu m. ~ e-€

0

>

~

2.5 0

X

"'0 ';:;

/

"",

60

/ / /

X

50

/ / / /

2.00 1.75

/x

---~

/

-- - -< / ventilation rate

40 30

1.50 --'-----r-----,----, -- ,------,------r- -..--'- 20 11 15 17 19 7 9 13 speed / km h:'

118 Physiology of exercise

* 3

/ /

2 .25

~

o

:::J

=t

maximum ventilation rate

o

vital capacity

-15

-10

- 5 0 +5 percentage change after training

+10

+15

WARM-UP ROUTINES M ost sportsmen and women use wa rm-up routin es to prepare themselves for exercise, w hether in a training sessi o n o r a com peti tive event. For examp le, tenni s players may do stretching exerc ises and then spend several minut es hitt ing the ball acro ss the net gently and practising serves, wh il e not under match press ure. Variou s reasons are give n to ju stify wa rm-up routin es: 1. Improving performance - bl ood f low to muscles is increased, supp ly ing mo re oxyge n; muscles becom e wa rmer ; the rate of respirat io n can increase, allowing mo re vi go rous and rapid muscle co ntractions w hen the co mpetitive event begins. 2. Psychological preparation - if a specific wa rm-up routine is used every time befor e an event, it may help to get the body mentally ready for physical act iv ity and fo r co mpetitio n, by adrenalin secretio n or other means. 3. Preventing injuries- muscles th at have been war med up and tend ons and ligaments th at have been gently stretched may be less vulnerable to injuries. The ev idence for the effectiveness of warm -up routines is rather thin and is based mostly on small numb ers of ind ividu al cases (anecdotal ev idence) rather than on co ntrolled tri als wi th large numbe rs. Athletes are understandably reluctant to com pete w ithout wa rmi ng up, fo r research purposes. Some anecdotal evidence suggests that war ming up may not be essential - reserves often co mpete successfully in matc hes, after littl e or no wa rmi ng up!

Training and the cardiovascular system

MEASURING HEART FUNCTION

EFFECTS OF TRAINING ON THE HEART

The card iovascular system con sists of the blood, the heart and the bl ood vessels. Heart function can be assessed using these measures: Heart rate is the number of contractions o f the heart per

Training can in crease the thickness of the heart wa ll and the vo lume of the ventricles. The stroke vo lume is therefore larger, both at rest and during exercise . The bod y does not need a larger cardiac output at rest, so the heart rate can be lower. Trainin g can reduc e the heart rate at rest to 50 beats per minute. At any level of intensity of exercise, the heart rate is lower after training, because of the larger stroke vo lume . The max im um heart rate is not greatly affected by traini ng, but because of the greater stroke vo lum e, card iac output is much greater at maximum heart rate after training . Thi s allows the train ed athlete to perform a much greater intensity of exercise.

minute. Stroke volume is the volume of blood pumped out with each contraction of the heart. Cardiac output is the volume of blood pumped out by the heart per minute. Venou s return is the volume o f blood returning to the heart via the veins per minute.

EFFECTS OF EXERCISE ON THE CARDIOVASCULAR SYSTEM

RISKS AND BENEFITS OF EPO

1. Venou s return increases durin g exerci se. Wh en muscl es in the legs and arms co ntract, th e muscles becom e sho rter and w ider and so exert pressure o n adjacent veins. There are valves in these veins, ensuring that blood f low s towa rds th e heart. Pressure therefore causes blood to be squeezed alo ng veins to the heart, increasing venou s return . Thi s allows card iac outpu t to be increased. 2. Cardiac output increases as a result of incr eases in heart rate and stroke vo lum e. Exercise involves a rise in carbon dioxide produ ction by muscles. Abso rption of this extra carbon di oxid e into the blood causes a decrease in blood pH . The brain detects the pH decrease and sends impu lses to the heart's pacemaker, causing the increase in cardiac output. 3. The di stribution of blood changes w hen exerci se starts. Art eriol es supp lyin g the o rgans of the bod y can narrow or w iden, decreasin g or increasing the flow of blood . The li sts below show w hic h organs receiv e more blood during exercise than at rest, wh ich receive less blood and w hic h receives the same volume. M or e dur ing exercise

l ess during exercise

Same volu me

skeletal muscle s

kidneys

brain

heart w all

sto mach

ski n

intestines

Ath letes sometimes increase the amo unt of red blood ce lls, as a proporti on of the volum e of their bl ood . This is called the pac ked cell volum e (PCV). At sea level a norm al PCV is 0.4-0 .5. There are several wa ys of increasing PCV above 0.5, inclu di ng the fo llowing: 1. Injecti o ns of EPO (erythropo ietin), a natu rall y prod uced ho rmon e that stimulates red blo od cell produ cti on. 2. Blood transfusion s, shortly befor e an event. Often the transfused blood was removed from the at hlete's bod y long enou gh before the event for the blood cell s to have been replaced. There are clear benefits in terms of perform ance of inc reasing PCV . As these cell s transport oxygen, the larger the numbers of them, the greater the rate at w hich oxyge n can be carried around the bod y by the blood. With more oxygen, skeletal muscl es can co ntract more vigoro usly . There are also so me risks. Hi gh levels of PCV increase the chance of blood clot fo rmatio n (thrombosis). Blood cl ots cause heart attacks and stro kes. There have been deaths among cyc lists and ot her athletes, w ho had used one or other of the methods above to in crease PCV.

INJURIES TO MUSCLES AND JOINTS Vi gorou s exercise sometimes causes injuries to mu scles and joints.

In summ ary, dur ing exercise, blood return s to the heart and is pumped out at a greater rate. M uch of thi s blood fl ow s to th e muscles, increasing the supply of oxyge n, allow ing an increase in the rate of aerobic respiration and ATP supply for muscle co ntractio n.

• Torn mu scles - excessive stretc hing causes muscl e fibres, or mor e rarely an entir e muscle, to tear, for example the qu adri ceps or hamstrin gs. • Sprains - abnormal movement at a joint causes stretch ing or minor tearin g of ligaments, for examp le jo ints in the fingers or the ankle (see fi gure, left). • Torn li gament s - large abno rmal movements cause ligaments to tear completely, for example the cru ci ate ligaments in the knee.

Ankle sprai ns

• Di slocati on - abnormal movement at a joint causes th e bones to move o ut of alig nment. Usuall y ligament s w ill be torn at the same tim e.

torn ligament

• Intervertebr al di sc damage - abnormal movements or heavy loads cause the soft centre of a di sc to bu lge out , thr ough a tear in the di sc wa ll (see qu estion 3 on page 120). swelling movement causing

ankle sprain

Physiology of exercise 119

EXAM QUESTIONS ON OPTION B - PHYSIOLOGY OF EXERCISE B1 Hu mans and other mamm als can store ox ygen in the lungs, in m uscles and in the blood . The pie charts below show the vo lume of oxyge n (cm 3 ) per kilogram of body mass sto red in these tissues in hum ans and in a marin e mammal, the W eddel l seal. Human

Wedd ell seal

2.9

o o

D

blood muscle lung

14.2

3.6

a) Compare the tot al amo unt of oxyge n stored per kilogram of bod y mass in seals w ith that in hum ans.

[1]

b) Com pare the pro po rtio ns of oxygen sto red in blo od , muscle and lu ng of seals with those in hum ans. (N o calculat io ns are required).

[3]

c) Suggest t hree facto rs w hich affect how m uch ox ygen can be sto red in m uscle in the bo dy of a ma mmal.

[3]

B2 a) Dr aw a di agram to show the structur e of a sarcome re.

[3]

b) O utli ne the ro le of ATP in muscle co ntractio n.

[3]

c) Compare cardiac output at rest and w hen vi goro us muscle contractions are bein g performed .

[1]

B3 The scan (right) show s damage to intervertebr al disc s in the nec k of a person. Gr ey and w hit e matter in the spinal co rd can be di stingui shed . a) State the number of discs that are damag ed .

[1]

b) Describe the damage to these di scs.

[2]

c) State the othe r part of the person's body that is affecte d by the disc damage.

[1]

d) Suggest how damage to intervertebral d iscs may be caused .

[2]

120 18 Quest ions - Physiology of exercise

14

lAW'"

r? •

FE""OIIl

EXAM QUESTIONS ON OPTION C - CELLS AND ENERGY Topics in Optio n C are covered on pages 66-81. C1 The rate of photosynt hesis in plants can be influenced by many factors . Experim ent s wer e carried out to investigate the effect of hi gh and low light in tensiti es o n photosy nthesis at differe nt temp eratur es. All other factors w ere kept constant. A sum mary of the results is presented in the graph below.

.~ 10 c

::>

>­

~ 8

:0

~ 'V;

6 I (high light intensity)


.c

"E

~

<,

4

.8 o

" (low light intensity)

-E. 2

1 e<:

0

0

10

20

30 Ternperature/X.

40

50

a) State the name of one lim iting facto r of photosynthesis, apart from temp erature and light intensity .

[lJ

b) (i) Dedu ce the facto r limiting the rate of photosynt hesis in experim ent I, betwe en 0 and 30° C. Give a reason for your answer.

[2]

(ii) D iscuss w hic h facto r limits the rate of phot osynthesis in experim ent I, betwee n 35 and 40 °C. c) Suggest o ne exp lanatio n for the difference betw een the results of experiments I and II.

[2]

[2]

C2 Enzym es can be inhi bi ted compe titive ly and non- com petiti vely. a) State one example of : (i) a co mpetitive inh ibi tor

[1]

(ii) a non -com peti ti ve inh ibi to r

[1]

b) Compare competitive and no n-competit ive inhibition by stating o ne similarity and one d ifference in the tabl e below. Competiti ve inhibiti on

[2]

No n-co mpetitive inhibi ti on

Simil arit y

Di fference

C3 The reacti on s of part of aerobic ce ll respiration are show n below.

C3

~

~

I { ), Cs

a) Identi fy the com pounds C3 and Cz.

[2]

b) Identi fy I and II.

[2]

c) State one ot her product of the se react io ns.

[1]

d) State the name of the cycle of reacti on s.

[1]

18 Questions - Cells and energy 121

15 Origin of life on earth

SPONTANEOUS ORIGIN OF LIFE

ORIGIN OF ORGANIC COMPOUNDS

Pasteur showed in an experiment in the 19th century that spontaneous generat ion of life fro m inorganic matter do es not now take pl ace - cells ca n only be form ed from oth er cells. Th is is not surprising, as even the simplest prokaryoti c cells are very co mplica ted. Neve rtheless, w hen the Earth was fir st formed th ere we re no living ce lls on it, so at some stage the fir st living cells must have appeared . Claim s that this happened 3.8 bi llion years ago are now disputed and the o ldest undi sputed bacterial fossils are in the Gun fli nt che rts of O ntario, datin g from 1.9 bill io n years ago. Fo ur proc esses wo uld have been needed for the fir st ce lls to form : • chemical reaction s to produce simple organi c mo lecu les, such as am ino acids, from inorgani c molecul es, such as water, carbo n d ioxid e and ammo nia • assembling of these simple organic mo lecu les into po lym ers, for example, pol ypeptid es fro m am ino acids • fo rmatio n of poly mers that can self-replicate - this allows in heritance of characteristics • develop ment of memb ranes, to fo rm spherical drop lets, w ith an internal chemistry different from the surro undings, including the polymers that held the genetic in formation. The prod uct of these fo ur processes w ould have been cell-like struct ures. Natural selection co uld have op erated on them, allowin g evo lutio n to begin .

Vario us possible locatio ns have been suggested for the synthesis of the organi c co mpounds needed fo r the o rigin of life.

MILLER AND UREY'S EXPERIMENTS

THE ROLE OF RNA IN THE ORIGIN OF LIFE

In 1953, Stanl ey M iller and Harol d U rey investi gated the theor y that organic co mpounds co uld have formed spont aneously on Earth . They recreated the co nd ition s that prob ably existed on Earth before livi ng o rganisms we re present. Inside their apparatus (belo w) they mi xed the gases amm o nia, met hane and hydrogen to form a reduci ng atmosph ere. Electri cal di scharges and the bo iling and co ndensing of wa ter simu lated lightning and rainfall. After one wee k, the cl ear wa ter in the apparatus had turn ed to a mur ky brow n. Analysis revealed many o rganic compounds, incl udi ng f ifteen amino acids. M i ller and Urey co ncl uded that organic compounds co uld have fo rmed spo ntaneously on Earth, before there we re any li ving organisms here.

In modern prokaryot es, the various parts of the genetic mechanism cannot functio n w ithout each other. For example, genes cannot be repli cated w ithout enzy mes and enzy mes cannot be made without genes. It seems incon ceiv ab le that t he w ho le mech ani sm co uld have evo lved at once, but grad ual evo lutio n wo uld have requ ired simpler intermed iate stages. O ne possibili ty is the use of RNA instead of both DNA and enzy mes. RNA may have had a very significant rol e in the origin of life. It has two prop erti es that wo uld have allowed it to do thi s - catal ysis and self-replication .

Miller and Urey's apparatus

2. There are hydrothermal vents deep in the oceans, w ith c hemica ls we lling up from the rocks belo w . A round these vents, there are very unusual chemica l co nd itio ns, wh ich might have allowe d the spo ntaneous synthesis of the organic compo unds from w hic h the first o rgani sms evo lved. 3. Some theories invol ve an extraterrestria l o rigi n for organic compounds. Experi ments by scientists w orki ng wi th NASA have shown that organ ic co mpounds and proto -cells could have form ed in co ld interstell ar space. They might then have been deli vered to the Earth by meteorites, co mets or interp lanetary dust. There was a heavy bomba rdment of the Earth by meteorites 4000 mill ion years ago, w hich mi ght have brou ght the organi c co mpounds that became o rganized into the fir st living organisms.

1. RNA catalyses a bro ad range of chemica l reactio ns. It co uld therefore have taken the rol e that is carried o ut by proteins (enzy mes) in the organisms that now exist on Earth. RNA st ill catalyses some reactions, for example pept ide bond fo rmat ion du ring protein synthesis in the ribosome.

2 . RNA is capable of self-replicatio n - one mo lec ule can for m a templ ate fo r the produ ct ion of another mo lecule, foll owi ng the rules of com plementary base pairin g. If the new ly synthesized mole cul e is then used as a temp late, a repli cate of the o riginal mol ecule w ill be produced .

water vapour

---:~__

122 Evolution

1. M ille r and U rey's experiments suggest that organic co mpounds could have been synthesized by chem ica l react io ns in the atmosphere and in wa ter, o n the surface of the Earth.

cold water in

No biol ogical mec hanisms now exist fo r self-replicati on by RNA mo lecul es, but this is not surpris ing as RNA was superseded, bill ions of years ago, by DNA as the genet ic material and by prot eins as the catalysts of life. There are var ious reasons for the DN A- protein w orld rep laci ng the RN A w o rld . O ne possibi lit y is that the maximu m length of RNA mo lecul es is about 150 0 nucl eot ides - thi s places a severe restriction o n the amo unt of genetic infor mat io n that can be held . RNA viruses, for example, have a very small genome .

Origin of prokaryotes and eukaryotes

MEMBRANES AND PROTOBIONTS

THE ENDOSYMBIOTIC THEORY

To form the fir st cells, membranes we re needed to separate cytop lasm and its metabo li sm from the surroundin g fluid . Phospholip ids natur ally group togeth er to form bi layers in wat er. These bi layers form spherica l structures enc losi ng a d rop let of f luid , simi lar to the vesicl es th at are now found in ce lls.

Eukaryot ic cells co ntain mi tocho ndria and chloroplasts, wh ich are not fou nd in prok aryoti c cells. If eukaryotic cells evolved from prokaryotic cells, the origin of these organelles must be explained.

W ater containin g t hese membr ane-bound micro spheres is call ed coacer vat e and is viscou s and cl o udy in appearance. Because of th eir hydrophob ic prope rti es, bi layers of pho sphol ipid wo uld have all owe d an int ernal env iron me nt to develop , different from the surround in g env ironme nt. These primitive cell-li ke structures, that may have preceded living cells, are called protob iont s. To become cells, they wo uld have had to develop genetic mechanisms to allo w reprod uct io n and the transmissio n of characteristi cs to offsp ring. The details of th is transition are not yet und erstood .

PROKARYOTES AND THE ATMOSPHERE The first organisms on Ea rth to use photosynthesis for the synthesis of organi c compo unds were prokaryotes. Wh en these organisms started to use w ater as source of hydro gen in photosy nthesis, oxygen started being released as a wa ste product into the atmosphere. There is evid ence that before this time there w as littl e ox ygen in the atmosphere. Concen tratio ns of oxygen bui lt up over a relatively short period - about a hundr ed mill ion years! This w as prob ably du e to the activ ity of photosynt hetic pro karyotes. Oth er prok aryot ic organisms w ere able to use aerobi c cel l respiratio n, once the atmosphere co ntained oxygen. Rocks in Greenland datin g from 3.7-3 .8 million ago, called the banded iro n form ation, give evidence of oxygen in the atmosphere. This suggests that prokaryot ic cells had evo lved and were producing oxyge n by then. Among existing organisms, photosynthetic bacteri a in hot springs and ot her extreme environ ments are prob ably most sim ilar to these early prokaryotes .

Accord ing to the endosymbioti c theory , both mito cho ndria and chlo roplasts have evo lved from ind ependent pro karyoti c cells, whi ch w ere taken int o a larger heterotro phic cell by endocy tosis. Instead of being digested, the cells w ere kept alive and conti nued to carry out aerobic respiratio n and photo synth esis. The characteristics of mit och ondri a and ch lorop lasts support the endosymbiotic theory. • They grow and di vid e like cells . • They have a naked loop of DNA, like proka ryotes. • They synth esize some of their own protein s using 70S ribosomes, li ke prokaryotes. • They have doubl e membr anes, as expected w hen cells are taken into a vesicle by endocytosis. Some biologists have suggested that flagella and cil ia also have an endosymbiotic origin, but the evidence for this is less clear. The evolution of eukaryotes from prok aryotes d id not just involve the developm ent of mitochon dria, chlo roplasts and possibly c ilia and flagell a. Eukaryotic chrom osom es, meiosis and sexua l reprodu ction also had to evo lve. On ce th is had happened, evo lutio n could take place at a much more rapid pace th an befor e and there wa s w hat has sometimes been described as an exp losion of life on Earth.

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GENE POOLS AND ALLELE FREQUENCIES •

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A new individual, produ ced by sexual reproducti on, inherits genes from its tw o parents. If there is random mating, any tw o individuals in an interbreeding popu lation cou ld be the two parents, so the indi vidu al could inherit any of the genes in the interbreeding popu lation. These genes are called the gene pool.

I

A gene pool is all the genes in an interbreeding population . Many genes have di fferent alle les. In a typ ical interbreedin g population, some alleles will be commoner than others. How common an allele is can be assessed using allele frequenc y. 2

1 0 billi ons of years ago

Alle le frequency is the frequency of an allele, as a proportion of all alle les of the gene in the population. All ele frequenc y can range from 0.0 to 1.0.

Evol ution always invo lves a change in all ele frequency in a

popu lation 's gene poo l, over a number of generations.

Evolution 123

Species and speciation

WHAT IS A SPECIES?

SPECIATION

Bio logists have been argui ng about the exact meanin g of the term species fo r ov er tw o hund red years. Before the di scovery that species can evo lve, a species w as regarded as a type of livin g organism w ith f ixed characte ristics, w hic h di stinguish it from other species. This is known as the mo rphological defi niti on of a speci es. It is sti ll a useful idea. Species can usuall y be di stinguished from each other by their characterist ics - this is how speci mens are identi fi ed.

The for matio n of new species is called speciatio n. New species are formed w hen a pre-exi sting species splits. Th is usuall y invo lves the iso latio n of a popu lation from the remainder of its species and thus the isolation of its gene pool. The isolated population w ill gradually diverge from the rest of the species if natural selectio n acts differently on it. Eventually the isolated population wi ll be unable to interbreed wi th the rest of the species - it has become a new speci es. Speci ation can either be allopatric or sympatric. 1. A llo patric speciati on occurs w hen members of a species migrate to a new area, forming a pop ulatio n that is geographica lly isol ated from the rest of the species. Interbreedin g is imp ossible - geographical isolation acts as a barrier betw een the gene pool s of the populatio ns. The populatio ns can therefore split to form separate species. This can happen repeatedl y, for example with the lava lizards of the Galapagos.

Howeve r the morp ho logical definitio n does not recogni ze the fact that specie s ev o lve . If two popu lation s w ith similar but not identical characterist ics are geographically separated, they may be in the gradual process of splitt ing from one species into tw o separate ones. It is not easy fo r a taxo nomist to decide wh ether to cl assify them as one or tw o species and some criterio n is needed to deci de. The reason fo r members of a speci es having co mmo n features is that they interbreed w ith eac h other. The reason for the characteristics of o ne species being different from those of another is that the tw o species do not interbreed and are evo lving separately . Bio logists now regard interbreed ing as a mo re imp ort ant criterio n than mor phol ogy. The bio logical defi niti o n of a species is a group o f actually or

Di stribution of lava lizards on the Galapa gos Island s •

~n sa lvado r

Ruddy duck

124 Evolution

W hite-headed duck


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San~ Fe

O nly if two separated pop ulati ons can be shown to be capable of interbreed ing should they be classified as one species.

Two animal species that can interbreed

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potentially interbreeding populations, with a com m on gene pool, which are rep roductivel y isolated from other suc h groups.

The bio logical species defini tion is w idely accepted, but it does cause some prob lems. • M any sibling species have been fo und . These are species that cannot interbreed, but show no significa nt d ifferences in appearance. A lthou gh separate species, they are ve ry d iffi cult fo r eco log ists to identify. For example the Pipi strelle bat in Britain w as recently shown to be two sibling speci es. • Som e pairs of species that are cl early di fferent in their c haracteristics w ill interbreed . M any plant species hybrid ize and some ani mals also, e.g. rudd y d ucks and w hite-headed ducks (below ). • Som e species always reprod uce asexually, so the memb ers of a pop ulatio n do not interbreed . The bio logical spec ies defi nitio n is therefore unusab le. • Fossils cannot be cl assified acco rd ing to the bio logi cal spec ies defi nition, as it is imp ossib le to decid e with w hic h organisms they wo uld have been able to interb reed.

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2. Sympatric speciatio n occ urs wh en tw o varieties of a species live in the same geographica l area, but do not interbreed . Two examp les w il l be co nsidered here: (a) The apple maggot fly (Rhago letis pomonella) of North A merica is an example. It used to lay its eggs o nly on haw thorn fruits, w hic h w ere the foo d of its larvae . It now also infests non-n ati ve apple trees as well . O ne strain of th is spec ies now lays its eggs on apple fruits and other strains o n haw thorn frui ts. Because the fruits ri pen at different ti mes, adults of the tw o strains emerge and mate at different times, so there is a behavioural or temporal barrier betw een the gene poo ls. There are d ifferences in alle le f requenci es of the tw o strains show ing that sympatric speci atio n has started to occur. (b) Barriers betw een gene pools can also occur by hybrid infertility, often due to polyploid y. If there are some tetraploid individuals in a population, the gametes that they produce will be dip loid . Hybrids produced w hen diploids mate w ith tetraploids w ill be triploid. These hybrids wi ll always be sterile as meiosis fails in triploid cells. So, diploids can only produce fertile offspring by mating w ith d iploids and tetraploids by mating w ith other tetraploids. Plants in the genus Rum ex are good examples of speciation by polyploidy . The basic diploid chromosome in thi s genus is 20, but Rumex obtusifolius has 40 chromosomes and so is a tetraploid. Rumex crispus is a hexaploid wi th 60 chromosomes and there is eve n a decaploid species - Rumex h ydrolapathum , with 200 chromosomes!

Trends in evol ution

ADAPTIVE RADIATION

RATES OF EVOLUTION

Speciation often happens repeatedly, to form a group of species from one ancestral species. Sometimes each species then evolves in very di fferent ways. This is called divergent evolution . By becoming adapted to different ecologica l roles, the diffe rent species avoid competi tion with each ot her. If species in a group diverge rapidly in th is way, it is calle d adapti ve radiation . Thi s can happen w hen the group has a characteristic that gives it a co mpetitive advantage over existi ng species or w here there are oppo rtunities that no other species are utilizin g. Darw in's finches on the Galapagos archipe lago are an example. Mam mals are another group that demo nstrate adaptive radi ation . The figure (below) shows examp les of the mamma lian pentadacty l li mb, derived from one ancestral mammal.

There has been much discussion among biologists about rates of evolution. O ne idea, called gradualism , is that evolutio n proceeds very slowly, but large changes can gradually take place over long periods of tim e. This does not fit in wi th the fossil record, w hich shows periods of stability, with fossils showi ng littl e evolut ion, fo llowed by periods of sudden major change. The periods of stability may be due to equi librium w here living organisms have become we ll adapted to their environment so natural selection acts to maintain their characteristics. The periods of sudden change that occasionally occ ur, may correspond wi th rapid environmental change, caused fo r example by vo lcanic erupt ions or meteor impacts. New adaptatio ns wo uld be necessary to cope wi th changed enviro nmental conditio ns, hence strong directio nal selection and rapid evolutio n. This view of the pace of evo lution is called punctuated equilibrium .

TRANSIENT POLYMORPHISMS A pop ulatio n in w hic h there are two alle les of a gene in the gene poo l is polymorphic. If one allele is gradually replacin g the other the popu lation shows transient polymorphism. The peppered moth, Biston betularia, is an examp le of this. In bot h Britain and the Un ited States, melanic forms were discove red in the 19th century (carbonaria and swettaria) . Both of these forms are due to dom inant alleles of a gene that affects wing co lour. These domin ant alle les increased in frequency in some areas, w here air pollution caused natural selection to favour moths wi th dark wings .

CONVERGENT EVOLUTION Livin g organisms often fi nd the same solutio ns to partic ular physio logica l prob lems. If natural selection acts in the same way , in different parts of the wo rld, species can become remarkably similar, despite not being closely related. This is called convergent evolution . It is the converse, in many ways, of adaptive radi ation . Instead of closely-related species show ing striking differences, unrelated species show striking simi larities. Cacti and euphorbias are examples of this. The photograp hs below show a cactus from the south-west USA and a euphorbia from Madagascar.

In many areas the domi nant alleles then decreased in frequency in the second half of the 20th century. This was because there had been cont rol of air poll utio n and the cleaner air meant that natural selection favou red the lighter coloured moths. The dom inant alleles for darker w ings wi ll probably reduce to very low frequencies in areas w here there is clean air.

BALANCED POLYMORPHISMS Someti mes two alle les of gene can persist indefinitely in the gene pool of a popul ation. It is not therefore a transient polymorphism and instead is called balanced pol ymorphism . The most thoro ughly researched example of a balanced polymorphism is sickle cell anemia (see page 23). • Individu als with the genotype H&AH&A do not develop sick le cell anemia but are susceptib le to malaria. • Individuals wi th the genotype Hb5Hb5 are resistant to malaria, but develop severe sick le cell anemia. • Heterozygous indi vid uals (H&A Hb5) do not develop sickle cell anemia and are resistant to malaria. They are therefore the best adapted in areas w here malaria is found. Both of the alle les of the hemoglobin gene therefore tend to persist in malarial areas. The sick le cell alle le has increased in frequency to high levels in some of these areas. In parts of Africa, as many as 40% of the pop ulation are carrie rs of the sickle cell allele, so show resistance to malaria.

Ocotillo (a cactus) from south-west USA

Allaudia (a euphorbia) from Madagascar

Evolution 125

Human origins

HUMANS AS PRIMATES

Ardipithecus ramidus (4 .4 mill ion years)

The prim ates are an o rde r of mammals, incl ud ing apes, mon keys, tarsiers and lemurs. They we re given this name because they we re co nsidered to be the highest orde r of ani mals. Hum ans are classif ied as prim ates, because they have the anatom ica l features that are characteristic of this order: • Grasping limbs, w it h lon g f ingers and a separated opp osable thumb. • M obil e arms, w ith sho ulder jo ints allowing m ove ment in thr ee pl anes and the bon es of the shoulde r gird le allowing w eight to be transferred via the arms. • Stereoscop ic visio n, with fo rwa rd facin g eyes on a fl attened face, giv ing ove rlapping fields of view . • Skull modified fo r upright posture.

Onl y fragments of skulls and other bon es have been found so far. They suggest c haracters intermed iate betwee n chim panzees and A ustralop ithecus : - small numb ers of large molars, like chimps - inci sors slightly smaller than those of chi mps - canines blunt and proj ectin g less than tho se of ch imps - fo ramen magnu m (hole th rough w hich spi nal co rd enters the skull) furth er fo rw ard than in apes, suggesti ng A rdipithecus was at least partiall y bi pedal.

The unavoidable co ncl usio n, so shoc king w hen it was first draw n, is that hum ans evo lved from other primate spec ies. There has been a huge research effort to try to fi nd out how this occurr ed.

Australopithec us afarensis (4 to 2.5 mil lion years)

tall lower jaw fairly large molars

Australopithec us africanus (3 to <2.5 million years)

TRENDS IN HOMINID FOSSILS Hom in ids are memb ers of the fam ily Hominidae - the family that incl udes humans. A notable feature of th is fam ily is wa lking on tw o legs - bip edalism. Homo sap iens is currently the o nly species of hominid but ot her species existed in the past. At var io us stages in hom inid evo lutio n, several species almost certainly co-ex isted, fo r example Homo sapie ns w ith Homo neanderthalensis. M any hom inid fossils have been fo und, dated, and assigned to a species. These fossils show evo luti onary trends: • includ ing inc reasing adaptat io n to bipedalism • increasing brain size in relation to body size.

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126 Evolution

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Human evolution

TRACING HUMAN EVOLUTION

HOMINID DIETS AND BRAIN SIZE

O ur understandi ng of human evo lutio n is based mostly on fossils and the hominid fossil record co ntains many gaps. It is not unu sual fo r the fossil reco rd of a group of orga nisms to be inco mpl ete. O nly a tiny pro portion of animal bodi es becom e fossilized. It is far mo re usual for animal bod ies to be eaten by detriti vores, decomp osed by bacteria o r broken down chemica lly . O rganic acids in decomposing material react w ith alkali in bones and teeth, for example. Homin id fossils co nsist o nly of bon es and teeth. These remain s have been preserved w here dr y sed iments have qui ck ly cove red them and have remain ed und isturbed.

The brains of early homini ds (Australopithecus) we re only sli ghtly larger in relation to body size than the brains of apes. The powerful jaw s and teeth of A ustralopithecus indi cate a main ly vegetarian di et.

Because the hom inid fossil record is incomp lete, it is far from clear how the different species of hom inid are related . Ma ny detail s of human evolutionary origins are also uncertain. Di scoveries of small numbers of fossils can cause major changes in the prevailing theories. For example, there have been recent finds of an Australopithecus species, w ith characteristics betw een those of Ardipithec us ram idus and Australopithecus afarensis. Dati ng of fossils of the three species from the Afar district of Ethiopia suggests that they did not co-exist, but instead they form an evolutionary lineage. As w ith most theories about human evo lution, this has been disputed!

Abo ut 2 .5 million years ago Africa became much coo ler and d rier. Savannah grassland replaced fo rest. This change of habi tat may have prompted the evo lutio n of the first species of Homo, w ith the development of increasingly sophisticated too ls and a change to a d iet that included meat obta ined by hunt ing and killing large ani mals. Th is change in di et cor respo nds w ith the start of the increase in brain size of hom ini ds. Th is w as due to continued rapid brain growt h after birth . In apes and earl ier hom inids, brain growth slows after bi rth. The corre lat ion betwee n the change in die t and the increases in brain size can be exp lai ned in two w ays:

1. Eating meat increases the supply of protein, fat and energy in the di et, making it possible fo r the grow th of larger brains. 2. Catc hing and killi ng prey on the savannas is more di ffic ult than gathering plant food s, so natural select io n wi ll have favoured homi nid s w ith larger brains and greater intelli gence.

DATING FOSSILS To place fossils into a sequence it is necessary to know their dates. Fossils, or the rocks containing fossils, can be dated using radioisotopes - radioactive isotopes of chemical elements. Wh en an atom of a radioi sotope decays, it changes into another isotop e and gives off radiation . The rate of decay varies between different radioisotopes and is expressed as the half-life.

The half-life is the time taken for the radioactivity to fa ll to half of its original leve l. The graph below shows a decay curve for radi oi sotop es.

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The two radioisotopes that are most com mo nly used are 14C and 4oK. In radiocarbon dating the percentage of surv iv ing 14Catoms in the samp le is measured. In potassium- argon datin g, the prop ort ions of parent 40K atoms and daughter 40Ar atoms are measured. In both methods the age in half-li ves can then be deduced from the decay curve. The half- life of 14C is 57 30 years so it is usefu l for datin g samples that are betwee n one thou sand and one hundred thousand years o ld . The half­ life of 4oK is 1250 mi ll io n years so it is useful fo r datin g samples older than 10 0 000 years.

GENETIC AND CULTURAL EVOLUTION The large brai ns of Homo sapiens and ot her species of Hom o all ow much to be learned, both during the long period of child hood and during adu lthood. Language, too l mak ing skills, huntin g techn iques, method s of agric ulture, reli gio n, art and many ot her for ms of behaviour are passed on from one generation of a tribe or othe r group to the next by teachin g and learning. These thin gs are the culture of the group. New methods, in vent ions o r customs can be in co rporated into w hat is passed o n. This is called cultural evolution and is diffe rent from the type of evo lutio n that i nvo lves natural selection betwee n in herited differences - genet ic evolution . • Cultural evo lutio n does not in vol ve changes in alle le frequenc ies in the gene poo l. • Changes due to cultural evo lution can happen du rin g one human li fetim e, w hereas genetic evo lutio n happens ov e r generations, so cultural can be much more rapid than genetic evo lutio n. • Cultural evo lutio n invo lves characteristics acquired du ring a person 's life (nurture) w hereas geneti c evo lutio n involves characteristics that are inherited (nature). In the recent evo lut io n of hum ans, cultural evo lution has been ve ry important and has been respon sible for most of the changes in the lives of humans ove r the last few thou sand years. This is muc h too short a period for genetic evo lutio n to cause much change. A lso some aspects of cultural evo lutio n, for exam ple the deve lopme nt of medi cin e, have reduced natural selectio n between di fferent genetic types and therefore genetic evo lutio n.

Evolution 127

The Hardy-Weinberg principle

THE HARDY-WEINBERG EQUATION

HARDY-WEINBERG CALCULATIONS

Evolut io n invo lves changes in allele frequency, so it is a useful skill to be able to do calculatio ns invo lving allele frequencies. The Hardy- W einberg equation is often used for thi s. If there are tw o alleles of a gene in a population, the frequency of the alleles in the popu lation is usually represented by the letters p and q. The total frequency of the alleles in the popu lation is 1.0, so

The Hardy- W einberg equation can be used in calculatio ns if certai n assumptio ns can be made : • that there is random mati ng in the pop ulat ion • natural selectio n does not cause higher mortalit y of indi vid uals w ith one allele than the other • there is no mutatio n • the populatio n is not very small • there is no immigratio n or emigra tio n. If these assumptio ns are co rrect, the po pulation is said to be in Hardy-Weinb erg equi libriu m and the equatio n is valid for that populat io n.

p + q = 1. If there is random matin g in a popul ation, the chance of inherit ing two co pies of the first of the two alle les is p x p. The chance of in heritin g tw o copies of the second of the tw o alle les is q x q. The expec ted frequency of the two homozygous genotypes is therefo re rl- and q2. The expected frequency of the heterozygous genotype is 2pq . The sum of all of these frequencies is 1. p2 + 2pq + q2

=1

Thi s is calle d the Hardy-Weinberg equati on. It is represented by the figure below .

p

p

q

pq

1. Example of calculating phenotype frequencies A n experimental plot of pea plants is established by sow ing seeds of pure breed ing tall and dwa rf variet ies, in a ratio of three tall to one dwa rf. The plants are allowed to produ ce and disperse seeds natu rally. The co nd itio ns on the plot ensure that all the ass umptions fo r the Hardy-Weinb erg equatio n are satisf ied. W hat proporti on s of tall and dwarf pea plants are expected after several generatio ns? Genotypes of pu re-breed ing varieties are TT and tt Frequency of T (p) is 0.75 Frequency of t (q) is 0.25 Frequency of dw arf plants (tt) = q2 = 0.25 2 = 0.0625 Frequency of tall plants = 1 - q2 = 1 - 0.0625 = 0.9375 This frequency co uld also be calculated as rl- + 2pq

2. Example of calculating all ele fr equencies The gene that contro ls t he ability to taste phenylthiocarbamid e (PTC) has two alle les.

q

pq

Occas io nally it is possible to test w hether the proportio ns of genoty pes in a populati on f it this equatio n. Both allele frequencies and genotype frequencies must be know n. The table below shows the results of a survey of the M N blood group gene in a Japanese town. The tw o alleles of this gene are co-dom inant. A llele frequencies in the parental generatio n

M alle le: p = 0.52 5

N allele: q = 0.475

Genotype frequencies in the offspr ing

MM MN NN

Predicted p2 = 0.276 2pq = 0.499 q2 = 0.225

Actual 0.274 0.502 0.224

Abi lity to taste PTC is due to the dom inant allele (D and

non -tasting is due to the recessive alle le (t).

1600 peopl e w ere tested in a survey.

461 were no n-tasters - a frequency of 0.288 .

Their genoty pe was hom ozygo us recessive (t t).

If q = frequency of t alle le, q2 = 0.288 so q = 0.537

If P = frequency of T alle le, p = (1 - q) = 0.4 63

3. Example of calculating genoty pe frequ enci es Cystic fib rosis is a genetic di sease caused by recessive alleles of a chlo ride channel gene. M ore than 27000 peop le in Scot land, no ne of w ho m had cystic fibr osis, were screened to see if they we re carriers of an allele for cysti c fib rosis. From t he frequency of carriers, the allele frequencies in the population co uld be deduced: Frequency of nor mal allele = p = 0.9776

Frequency of cystic fi brosis alle le = q = 0.0224

Wh en these peop le have chi ld ren, the chance of their child being homozygous fo r the cystic fibrosis alle le is q2 = (0.0224)2 = 0.000502

The results of the survey show that the actual genotypes fit those predicted by the Hardy-Wei nberg equatio n very cl osely. The populat io n therefore follow s the Hard y-Weinberg Principle.

This is equivalent to about one child in 1900 w ith cystic fib rosis. The chance of their chi ld being a carrier is 2pq

= 2(0.9776

x 0.0224)

= 0.0438

Thi s is equivalent to abo ut o ne chi ld in 23 being a carrier.

128 Evolution

Classification and phylogeny

REASONS FOR CLASSIFICATION

-

Classificatio n in bio logy is arranging li ving organisms into groups. There are many advantages: • Species ident ificat ion - it is easier to fi nd out to w hi ch species an organism belo ngs with organisms classified rather t han forming a disorgan ized catalogue . • Predictive valu e - if several members of a group have a characteristic , another species in this group w ill probably also have this characteristic. • Evolutionary links - species that are in the same group probab ly share characterist ics because they have evo lved from a common ancesto r, so the cl assification of grou ps can be used to predict how they evo lved. These are advantages of a natural cl assificatio n - one that matches the evo luti onary origi ns of the species in the group . Artificia l classif icatio n systems sometimes help with species identification, but have no other value. An example of an artificia l classifi cation is putti ng insects, bird s and bats into one group because they fly. The w ings of these ani mals are examp les of analogous st ructures - structu res with a common fun ction , but a d ifferent evo lutionary ori gin . Natu ral classification is based o n homologous st ructures - structures that have a common evo lutionary orig in, even if their function is differe nt. The pentadactyl limb (see page 125) is an examples of a homologous structure in mamma ls. Organisms with homol ogous structu res shou ld be classified in the same group because they must have commo n ancestry, even if they look superfici ally d ifferent.

Hy lobates syndactylus (siamang)

(w hi

ba tes conc olor heeked gibbon) Hylobates klossi Kloss's gibbon)

Hylobates lar (w hite eaded gibbon)

r'o ngo pygmaeu s (orang-utan)

Pan troglod ytes (co rnrn: n chimpanzee) -

Pan pani scus (pygmy chimpanzee) '­

Hom o sapiens (human) Corilla gorilla (gorilla)

BIOCHEMISTRY AND COMMON ANCESTRY There are remarkable simi larities betwe en living organisms in their bioc hemistry. • A ll use DNA (o r RNA) as their genetic material. • A ll use the same universal genetic code, with only a few insignifi cant variatio ns. • Al l use the same 20 amino aci ds in their proteins . • A ll use left, and not right-h anded amino acids. The simil arities in ami no acid compositio n are striking because many ot her amino acids, in bot h left and right­ handed versions, were available w hen life evolv ed, according to Miller and U rey's experim ents. These bio chemica l simi larities suggest very strongly that all organisms have evo lved from a common ancestor, which had all of these characteristics.

PHYLOGENY AND BIOCHEMISTRY Tracin g evolutionary links and origins is called phyl ogeny. The phylogeny of many group s has been studied by comp aring the structure of a protein or othe r biochem ical that they contain . Usual ly the results match the existing classification of the group. The di agram (above right) shows the results of a study based o n DNA seque nces.

VARIATION AND EVOLUTIONARY CLOCKS D ifferences in the base sequence of DNA and therefore in the amino acid sequence of protei ns, accumu late gradually over lo ng periods of time . There is evide nce that differe nces accumulate at a roughly co nstant rate. They can therefore be used as an evo luti o nary clo ck . The number of differe nces in amino acid sequence can be used to deduce how long ago species split from a co mmo n ancestor. For example, mito chondr ial DNA from three humans and four related primates has been completely sequenced. From the differences in base sequence, a hypothetical phylogeny has been constructed, show n (below ). Usi ng the numbers of differences in base sequence as an evo luti onary clock, these appro ximate dates for splits betwee n groups have been deduced : 70 000 years ago, Europeans-Japanese split 140 000 years ago, Afr ican-European/Japanese split about 5 mil lio n years ago, human-ch impanzees split. Phylo genetic tre e for humans and clo sely relat ed apes ~ E u ro p ean

~

Chimpanzees and gorill as are currently in a family with orang-utans, but shou ld prob ably be placed in the same fami ly as humans, acco rdin g to this DNA evidence.

I

---

~

I

I

y

L - Japanese African Common chimpanzee

,

Pygmy chimpanzee Gori lla Orang-utan

Evolution 129

Cladistics

CLADES, CLADOGRAMS AND CLADISTICS

CLADOGRAMS AND CLASSIFICATION

The tree di agrams shown on the previous page started to be produ ced in the second half of the 20th century. Neither t he data on base o r ami no acid sequences no r the powerful co mputers needed to analyse the data we re available before then. The di agrams use branch ing poin ts, or nodes, to show groups of o rganisms w hic h are related, and therefor e presumably had co mmo n ancestry. These groups are called clades, from the Greek wor d klados - a branch .

The classif icat io n of many groups has been re-examin ed using c1 adograms. In many cases, c1 adograms have co nfirmed existing cl assification s. Thi s is not surprising as both traditi onal classification and clad ist ics are attempti ng to refl ect phylogenetic relati on ships - the evo lutio nary origins of groups of livi ng o rganisms. Cladogra ms can be difficul t to recon ci le w ith traditional cl assification s, because the nodes can occu r at any po int. It can therefo re seem rather arbitrary how the hierarchy of taxa is fitted to the clades. In some cases, cl adistics suggests radicall y different phyl ogenies. Should the existing classificatio ns be tru sted in these cases, or the new ones based o n cl adisti cs? The strength of clad istics is that the co mparisons betw een o rganisms are object ive, based, as they are, on mo lecular di fferences. The wea kness is th at these mol ecul ar differences are analysed on the basis of prob abili ties. Occas ionally imp robable events occu r, maki ng the analyses wro ng. So, although cladistics should not be treated as infallible, in many cases it can st imulate a reint erpretation of the data o n w hich traditional cl assification s have been based.

A clade is a group o f organisms that evolved from a comm on ances tor. Clades can be large groups, with a common ancestor far back

in evo lutio n, o r smaller groups w ith a more recent commo n

ancestor.

The tree di agrams show ing cl ades are called c1adograms.

Cladograms have been used to re-evaluate the classification

of many groups of o rganisms. The method s used are very

di fferent from procedures traditi on all y used by taxonomi sts,

so a new name has been given to this type of cl assification ­

cladistics.

Cladistics is a method o f classification o f living organisms based on the construction and analysis o f cladograms.

CONSTRUCTING CLADOGRAMS The co nstructio n of c1 adograms usuall y invol ves extremely comp licated calculations that are don e by powerful co mputers. The aim is to wo rk out how the d ifferences in base or amino acid sequence could have evo lved w ith the smallest number of mutation s. Thi s is called parsimon y analysis and although it does not prove how evo lutio n did occ ur, it gives the most likely course. A simpl er method of co nstructing a c1 adogram is given here. The amino acid sequence of hemoglob in has been com pared in many vertebrates. The table (below ) shows the numb ers of differences in the ami no acid sequence of ten vertebrates. The data in this table, and the detail s of w hat the ami no aci d differences are, has been used to co nstruct the c1 adogram below . A tim e scale has been incl uded by cali brating the rate of change in the amino aci d sequences. By co mpar ing the table and the c1adog ram, it is possibl e to deduce how a c1adog ram can be co nstructed from numbers of d ifferences in base or ami no acid sequence. A simple c1 adogram co uld also be co nstructed using inform ation about the form (mo rpho logy) of o rganisms. Numbers of differences in the amino acid sequence of hemoglobin in ten vertebrates Elephant Platypus Ostrich Human ---26 40 43 45 Elephant ---45 Platypus- - ­ 54 Ostrich

Starling 41 48 52 26 Starling

Crocodi le Lungfish 47 83 50 84 51 89 36 91 47 91 Crocodi le- ­ 85 Lungfish

Phylogenetic tree diagram for ten vertebrates I

I

I

I

I

I

60

50

40

30

20

10

80

40

-

-----1

'--­

----1 I

I

400

130 Evolution

290

200

140

Coelacanth 70 72 74 75 77 78 90

Goldfish 68 63 70 68 67 70 94

Shark 71 74 76 73 70 77 86

Coelacanth- ­

83 78 Goldfish - - - 88

EXAM QUESTIONS ON OPTION D - EVOLUTION 0 1 The scatte rgram below sho w s th e relation ship between brain size and tot al body mass in species of mamm al. Prim ate species are shown as so lid c ircle s and other specie s of mam mal as open circ les.

c o

humans

\

0 0

o·

~ C1l U

. 0

0

'" on

.2


N

'v;

c '§ co

• primates o other mammals

Body mass (log scale) [Source: CU P, Encyclopaedia 01 Human Evolution,]

a) Using the data in the scatte rgram, (i) state the relatio nship between body mass and brain size in mam mals

n

(ii) co mpare the brain size in relati on to bod y mass of p rim ates with that of other mam mals

[2J

(iii) exp lai n brief ly how the scatte rgram ca n be int erpreted to show that human brains are larger than those of other pr imates.

[2J

b) Increases in brain siz e in relatio n to bod y mass could be du e either to increases in brain size or decreases in bod y mass. Suggest one advantage to pr im ates of redu ced bod y mass.

[1]

0 2 The fi gu re below sho ws the base sequence of part of a hemoglobi n gene in four species of mam mal. Human

TGA CAA GAA CA - GTT AG AG - TGTC CGA

O rang utan

TCA CGA GAACA - GTT AGA G -TGTC CGA

Lemu r

TAA CG A TAA CAG GAT AGA G - T ATC TGA

Rabbit

TGG TGA TAACAA GAC A GA GATATC CGA

a) Calc ulate the number of diffe rences betwee n base sequence of (i) hu mans and orang utans (ii) hu mans and lemu rs (iii) humans and rabbits (iv) orang utans and lem urs (v) ora ng utans and rabbits [6]

(vi) lemurs and rabbits b) Using the di fferences in base sequence betw een the fo ur mamma l species, construct a c1 adogram .

[4J

0 3 In Africa, south of the Sahara and north of the Zam bezi , the sick le ce ll allele Hb , is very co m mon. In some ethn ic gro ups th e proportion of newb orn babi es that are homozygous recessive can be as high as 0.053 (5.3% ). These babi es suffer from sick le ce ll anem ia. a) Calculate the frequency of th e sic kle ce ll allele in these ethn ic groups.

[2]

b) Calcu late the percentage of the po pulatio n th at are car riers of the sickle ce ll allele.

n

c) O utline th e reason s for the high frequency of the sic kle ce ll alle le in these ethnic gro ups, despite the serio us consequences of sick le ce ll anem ia.

[2]

18 Questions - Evolution 131

16 Stimulus and response REFLEXES

NATURAL SELECTION AND RESPONSES

O ne of the basic activities of the nervou s system is the coord ination of rapid responses to st imuli, includ ing reflexes.

Ani mal respon ses can be altered by natural selection if they are genetica ll y programmed and affect the ani mal's chances of survival and reproduction. Offspring inherit successful types of response from their parents. Sometimes the environment of an animal species changes and natural selecti on may then favour a different type of response. Tw o examples related to global warming are given here, but there are many others from all around the wo rld. 1. Migration in Sylvia atricapilla (blackcap) This bi rd breeds in the early summer across much of central and no rthern Europ e. It then migrates to w armer areas befo re th e w inter. U ntil recentl y, popul ations in Germany mi grated to Spain or other M edit erranean areas. Recent studies have show n a chan ge in migratio n pattern, w ith 10% of the birds migrating to the UK. Experim ents w ith eggs have shown t hat the directi on of migration is genet ically programm ed and inh erited. The blackcaps th at migrate from Germany to the U K for t he w inter instincti vely tend to fly west, w hereas those sti ll mi grati ng to Spain tend to fly southw est.

A stim ulus is a change in the environment, eithe r internal or external, that is detected by a receptor and elicits a response. A response is a change in an organism, produced by a

stim ulus.

A reflex is a rapid un conscious response to a stim ulus. A ltho ugh t hey are the simp lest type of coo rdination, reflexes invol ve a precise pathw ay of neuron s, with at least thr ee synapses. The pathw ay is called a reflex arc. An examp le of a reflex is pu ll ing away the hand after touching a hot obje ct ­ this is called the pain w ithdrawa l reflex. The reflex arc that coo rd inates t his is show n in the diagram (below) . Reflex arcs invo lve these five parts: • receptors - to detect a stimulus; receptors can be sensory cells or nerve end ings of sensory neuron s • sensory neurons - to receive messages across synapses, from receptors and carry them to the central nervou s system (spinal co rd or brain) • relay neurons - to receive messages, across synapses, from sensory neuron s, and pass them to the moto r neurons that can cause an appropri ate response • motor neurons - to receive messages, across synapses, from relay neuron s and carry them to an effector • effectors - to carry out a respo nse after receiving a message from a moto r neuro n; effectors can be muscles, wh ich respo nd by contracti ng, or glands, w hich respond by secreting.

2. Timing of breeding in Parus major (great tit) Parus major breeds in spring o r early summer throughout much of Europe. The tim ing of egg laying is genetica lly determin ed. Day length is used to determine the ti me of year. Recent stud ies in the Netherl ands have shown that the mean date of egg layin g is becoming earlier. Adults that breed earlier enjoy greater reprodu cti ve success. Thi s is due to the earlier opening of leaves o n decid uous trees and an earl ier peak in the bio mass of invertebrates feedi ng on tree leaves. These invertebrates are the main food that ad ults co lle ct and feed to off spring.

Components of a reflex arc

o00nerve fibre of sensory

neuron

receptor cells or nerve endings sensing pain

relay neuron

cell body of sensory neuron in the dorsal root ganglion

nerve fibre

of motor ~ neuron ~ ~

"::=t+= ::=

effector (muscle

that pulis hand

away from

pain when

it contracts)

white matter

grey matter

spinal cord

132 Neurobiology and behaviour

Perception of stimuli

DIVERSITY OF SENSORY RECEPTORS Hum ans have a di versity of types of receptor and so can perceive a w ide range of stimuli .

Type

Stimulus

Example

Mec hanorecepto rs

Mechanical energy in the form of sound w aves Movements due to pressure or gravity

Hair cells in the cochlea of the ear Pressure receptor cells in the skin

Chemo rece pto rs

Chemical substances di ssol ved in w ater (tongue) Chemical substances as vapours in the air (nose)

Receptor cells in the tongue Nerve end ings in the nose

Therm orecept ors

Temperature

Nerve endi ngs in skin detect w arm or co ld

Photorecept or s

Electromagneti c radi ation, usual ly in the form of light

Rod and cone cells in the eye

Stru ctu re of th e human ea r

pinna

bones of skuII

I musclesattached

bones of middle ear

parts of inner ear concerned wit h balance

I

!

!

/

ear drum

'I

outer ear round w indow

PERCEPTION OF SOUND 1. Ear drum

3. Oval wind ow

Wh en sound w aves reach the eardrum at the end of the outer ear, they make it vibrate. The vibrati o n consists of rapid movements of the eardrum, tow ards and awa y from the midd le ear. The role of the eardrum is to pick up sound vibrations fro m the air and transmit them to the midd le ear.

This is a membranou s structure, like the eard rum. It transm its sound w aves to the flu id filli ng the cochlea. This fluid is incom pressible, so a second membranou s w indow is needed, called the round wi ndow. W hen the oval wi ndow moves tow ards the coc hlea, the round w indow moves away from it, so the fluid in the coc hlea can vibr ate freely, with its vo lume remain ing co nstant.

2. Bones of the middle ear There is a series of very small bon es in the midd le ear, called ossicl es. Each ossicle tou ches the next one. The first ossicl e is attached to the eardrum and the third one is attac hed to the o va l w indow. The ossic les' role is to transmit sound w aves fro m the eard rum to the ov al w indow . They also act as levers, reducing the amplitude of the w aves, but increasing their force, w hic h amplifies sounds by about 20 tim es. The ov al w indow's small size, comp ared w ith the eardrum, helps wi th amplification. M uscles attached to the ossicl es prot ect the ear from loud sounds, by co ntracting to damp down vibrations in the ossicles.

4. Hair ce lls in th e co chlea The cochlea co nsists of a tub e, wou nd to form a spira l shape. W ith in the tube are membranes, with receptors called hair cells attached. These cells have hair bundl es, w hich stretch from one of the membr anes to another. Wh en the sound waves pass thro ugh the fluid in the cochlea, the hair bund les vibrate. Because of gradual variations in the w idth and thickness of the membranes, different frequencies of sound can be d isti nguished, because each hair bund le o nly reson ates w ith particular frequenci es. Wh en the hair bundle s vib rate, the hair cells send messages across synapses and o n to the brain vi a the audi tory nerve.

Neurobiology and behaviour 133

Vision in humans

PHOTORECEPTORS The photo recepto rs of the eye are contained in the retin a. The figures (right) show the structure of the eye and the structure of the retina. There are two types of photoreceptor ce ll - rod ce lls and co ne ce lls. These cell types bot h absorb light and then transmit messages to the brain, via the optic nerve. They are different in these ways : 1. Rod ce lls are more sensit ive to light than co ne cells, so they functio n better in dim light. Rod ce lls beco me bleached in bright light, but co ne cells funct io n we ll. 2. Rod cells abso rb all w avelengths of visible light, so they give monochrome vision , w hereas there are th ree types of co ne cell, sensitive to red, green and blue li ght, w hic h give co lou r visio n. 3. Groups of up to tw o hund red rod cells pass impu lses to the same sensory neuron of the opt ic nerve, w hereas many co ne cells have their own indi vi du al neuron th rou gh w hic h messages can be sent to the brain . Cone cells therefo re giv e greater visual acuity th an rod cell s. 4. Rod cells are more w idely di spersed through the retina so they give a w ider f ield of v isio n, w hereas co ne cells are very co ncentrated near the fovea, givi ng one acute area of the field of vi sion.

The Herm an grid illusion

••••• ••••• ••••• ••••• •••••

The grid (above) is a famo us example of an optica l illusion . Grey areas appear at the intersecti ons of the w hite lines, w hic h are not real. If all of the grid is cov ered up apart f rom o ne w hite line, the grey areas d isappear. This ill usion can be explained in terms of the processing of visual stimuli.

134 Neurobiology and behaviour

Struct ure of th e eye (in hor izontal sectio n) lens

sclera

aqueous

humour

choroid

pupil

retina

iris

fovea blin d spot

conjunctiva

cornea

vitreous humour

optic nerve

direction of light

'-r---J

I

nerve fibres of ganglio n cells

PROCESSING OF VISUAL STIMULI Betw een the percepti on of photons of light and imp ulses reachin g the brai n, there are a series of stages of processing of visual stimuli.

1. Con ver gence Bipolar cells in the retin a co mbine the imp ulses from groups of rod or co ne cells and pass them on to ganglio n cell s (sensory neuro ns of the optic nerve).

2. Edge enhancem ent Eac h ganglio n ce ll is st imulated w hen l ight fa ll s on a sma ll c irc ular area of ret in a ca lle d t he recept ive f ie ld . There are tw o types of gang lio n ce ll . In o ne typ e, the gang lio n is stim ulated if li ght fa lls o n th e ce nt re of th e recept ive fiel d, but th is st imulat io n is redu ced if li ght also falls o n the periph ery. In th e ot her typ e, l ight fall ing o n th e periphery of th e recept ive fi eld stim ulates th e ganglio n ce ll, but t hi s st imulat io n is redu ced if l ight also fa lls o n t he ce ntre. Bot h typ es of gang lio n ce ll are th erefore mor e st imulated if the edge of l ight/ dark areas is wit hin th e receptive field . W hite areas of t he Herman grid look w hi ter if th ey are next to a blac k area.

Contralat eral processing The left and right optic nerves meet at a structure ca lled the optic chiasma. Here all the neuro ns that are carry ing impulses from the half of the retina nearest to the nose cross ove r to the opposite optic nerve. As a result the left optic nerve carries informatio n from the right half of the field of vision and vice versa. Th is al lows the brain to deduce di stances and sizes.

Innate and learned behaviour

INNATE BEHAVIOUR IN INVERTEBRATES Most behaviour in invertebrates is innate, not learned. Innate behaviour is sometimes called instinctive. It develops independently of the environmental context. In contrast, learned behaviour develops as a result of experience. Innate behaviour can be investigated by simple experiments with invertebrates, for example chemotaxis in Planaria (flatworms). A taxis is a movernent towards or away from a directional stimulus. If Planaria are placed in a shallow dish with small pieces of food in part of the dish, they usually move towards the food. Other variables need to be kept constant, for example the amount of light in different parts of the dish. Also, in behaviour experiments like this, results should be quantitative, not rnerely descriptive. For example, a line could be drawn across the middle of the dish to mark the halves of the dish with and without food. The numbers of Planaria in each half of the dish could be recorded each minute during the experi ment. The graph (right) shows the results of an experiment, using slaters (wood Iice), to investigate a behaviou I' pattern called kinesis. Kinesis is response to a non-directional stimulus, in which the rate of rnovement or the rate of turning depends on the level of the stimulus, but the direction of movement is not affected.

LEARNED BEHAVIOUR AND SURVIVAL In diverse and changeable environments, animals can improve their chances of survival by learning new behaviour patterns. Examples: • Some chimpanzees learn to catch termites by poking sticks

into termite mounds.

• Birds learn to avoid eating orange and black striped

cinnabar moth caterpillars, after associating their

colouration and unpleasant taste.

• Many bird species learn to take avoiding action when they

hear alarm calls warning them of a predator.

• Foxes learn to avoid touching electric fences after receiving an electric shock. • In Britain, hedgehogs have learned to run across busy roads, instead of rolling up into a ball.

PAVLOV AND CONDITIONING IN DOGS Ivan Pavlov investigated the salivation reflex in dogs. He observed that his dogs secreted saliva when they saw or tasted food. The sight or taste of meat is called the unconditioned stimulus and the secretion of saliva is called the unconditioned response. Pavlov then gave the dogs a neutral stimu Ius, such as the sound of a ringing bell or ticking metronome, before he gave the unconditioned stimulus - the sight or taste of food. He found that after repeating this procedure for a few days, the dogs started to secrete saliva before they had received the unconditioned stimulus. The sound of the bell or the metronome is called the conditioned stimulus and the secretion of saliva before the uncond itioned stimu Ius is the conditioned response. The dogs had learned to associate two external stimuli - the sound of a bell or metronome and the arrival of food. This is caIIed conditioning - an alteration in the behaviour of an anirnal as a result of the association of external stimuli.

Quantitative investigation of kinesis in slaters (woodlice)

70

350

g

300r

60

(

r

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1

1 ~ber of turnings

250

35

30

2

50 ~

25 +-' Vl

·E

~ ~

Q3 200 20

Q. tJl

Q)

E 150

Q3

15 ?fi

...0

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Q)

'E '0

~

E

:::::i

z

100 30

I

1

501

\

~

-110

~

-.J5

I

20 10 20 30 40 50 60 70 80 90 100%0 Relative humidity The graph shows that as humidity rises, the movement of the slaters is less and although the number of turns per hour is less, the number per metre moved is more. Slaters often congregate in small, humid spaces, increasing their chances of survival and reproduction.

DEVELOPMENT OF BIRDSONG Birdsong is an interesting example of behaviour, because it has been shown in some species to be partly innate and partly learned. The chaffinch (Fringi//a coe/ebs) is an example. Male chaffinches use their song to keep other rnales out of their territory and to attract females. The song varies a little between males, allowing identification of individuals. It also has recognizable features to show that it is a chaffinch singing. The figures (below) show the normal song of a male, reared where he cou Id hear the song of adu It chaffi nches, and the song of male that was reared in isolation in a soundproof box. The song of the bird reared in isolation had some features of the normal song, including the correct length and number of notes, which must have been innate. However, there is a narrower range of frequencies, and fewer distinctive phases. These must be learned from other chaffinches. ~

(a) a normal chaffinch song

j: ~,~~~,~,\~

~8

l

a ~ ~ u ~

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8

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0.5 1.0 1.5 2.0 time / sec (b) a song from a bird reared in isolation

6

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0.5

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2.0 time / sec

Neurobiology and behaviour 135

Neurotransmitters and synapses

EXCITATORY AND INHIBITORY SYNAPSES A lt hough there is a w ide variety of synapses in th e nervou s system, especia lly the brain, there are tw o main types.

Electro n micrograph show ing adjacent neur ons co nta ining vesicles of differ ent neur otransmitters

Excitat ory synapses This type of synapse wa s describ ed in page 52. The neurotr ansmitt er released by the presynapt ic neuron causes sodium ion s o r other positiv ely charged ions to enter the postsynaptic neuro n, hel pin g to depo larize it and cause an actio n potentia l. Postsyn apti c transmission is therefore exc ited (stimulated).

Inhibitor y synapses In these synapses, the neurotr ansmitt er released by the presyn apti c neuron causes negatively charged chlo ride ion s to move into the postsyn apt ic neuron, increasing its polari zation. This effect, called hyp erpolarization , makes it more diff icult to depol arize a neuron suff icie nt ly to cause an actio n potential. Postsynapt ic transmission is therefo re inhibited. The electron mi crograph (above right) show s adjacen t neurons co ntaini ng different neurotransmitt ers. The graphs below show the effects of exc itato ry and inhibitor y neurotransmitters on the membran e pote ntial of a postsynaptic neuron .

DECISION-MAKING IN THE CNS action potential in presynaptic neuron

- 70

5

10

15

excitatory post­ synaptic potential

-7 (H

-

--'

- 7lJ-t- -

<,

/

inhibitory post­ synaptic potentia,I _--­

O ne of the fundamental roles of the brain and spinal co rd is deci sion-m akin g. This can be a simple process, as in a reflex, or much more co mp licated, fo r examp le w hen choosing a partner. Synapses are the sites at w hic h deci sion s are made. On e pulse of exci tato ry neurotransmitter, released w hen an actio n po tential reach es the end of a postsynaptic neuron, is unl ikely to be eno ugh to cause postsynaptic transmission . A rapid sequence of pul ses of neurotransmitter is needed . These co uld co me from the same presyn apti c neuron, or mo re likely from a number of different ones. Thi s is possible because postsynaptic neuron s have synapses w it h more than o ne pre­ synaptic neuron e, sometimes w ith hundreds. W here many presynaptic neurons fo rm synapses w ith a postsynapti c neuron, some of these synapseswi ll be excitatory and others w il l be inhibitory. The effects of exci tatory neurot ransmitters may be cancelled out if an inhibito ry neurotransmitter is also being released. Wh ether an action potenti al is initi ated in the postsynaptic neuron is therefore decid ed by the summation of messages from all of these synapses. In this way, deci sions can be made by the central nervous system. The fi gure (below) shows a postsyn aptic motor neuron and some of its associated presynapti c neurons.

Synapses between many neurons and one motor neuron

fir( summation of excitatory postsynaptic potentials

-70

5

10 15 time / mill iseconds

136 Neurobiology and behaviour

Neurons forming synapses wit h a motor neuron. c--- --'==------.. The propagation of an impulse is /'~:----~'--- s t im u lated by the neurotransmitter in some synapses and inhibited by the neurotransmitter in other synapses.

Psychoactive drugs

EXCITATORY AND INHIBITORY DRUGS

ADDICTION TO PSYCHOACTIVE DRUGS

Drugs are chemical substances that are ingested, injected, inhaled or put into the body in some other way, to cause a change in the functioning of the body. Psychoactive drugs affect the brai n and personal ity. Most psychoactive drugs affect the functioning of the brain by disrupting synaptic transmission. Excitatory drugs work either by promoting transmission at excitatory synapses or inhibiting transmission at inhibitory synapses. Inhibitory drugs do the opposite.

The causes of addiction to psychoactive drugs have been widely studied, because of the physical and social damage that addictions can cause. Three factors increase levels of addiction, especially when they are combined.

Examples of psychoactive drugs Excitatory

Inhibitory

nicotine

benzodiazepines

cocaine

alcohol

arnphetam ines

THC

Psychoactive drugs can affect synaptic transmission in a variety of ways: • Some psychoactive drugs have a chemical structure sirnilar to a neurotransmitter and so bind to receptors for that neurotransmitter in postsynaptic membranes. They block the receptors, preventing the neurotransmitter from having its usual effect. • Other psychoactive drugs with a chemical structure similar to a neurotransmitter have the same effect as the neu rotransrn itter. However, un like the neu rotransm itter, they are not broken down so when they bind to the receptor the effect is much longer lasting. • Some psychoactive drugs interfere with the breakdown of neurotransmitters in synapses or its reabsorption into the presynaptic neuron and so prolong the effect of neu rotransm itters.

1. Dopamine secretion The first factor affecting whether addiction develops is the drug itself. Some drugs are addictive and some are not. A feature of many addictive drugs is that transmission is stimulated at synapses using dopamine as a neurotransmitter. These synapses are involved in the reward pathway, which gives us feelings of well-being and pleasure (see the example of cocaine below). Users of addictive drugs find it very difficult to stop, because they have become dependent on the feelings that dopamine promotes.

2. Genetic predisposition Even with many drugs that are potentially addictive, not everyone becomes an addict. Addictions, especially alcoholism, are much comrnoner in some families than others. This suggests that genes can make some people predisposed. Researchers are now trying to identify the genes that are involved.

3. Social factors It is sti II not certai n that a person who is genetically predisposed to develop addictions will do so when exposed to an addictive drug. Social factors can either prevent or encou rage it. Cultural traditions, peer pressure, poverty and social deprivation, traumatic life experiences and rnental health problems all increase the chances of an addiction developing.

EFFECTS OF COCAINE AND THC 1. Cocaine Cocaine is an excitatory psychoactive drug. It stimu lates transmission at synapses in the brain that use dopamine as a neurotransmitter. Cocaine binds to membrane proteins that pump dopamine back into the presynaptic neuron. It blocks these transporters, causing a build-up of dopamine in the synapse. The synapses that use doparnine as a neurotransmitter are responsible for pleasurable feelings that we get during certain activities, for example eating or having sex. Because cocaine causes continuous transmission at these synapses, it gives feelings of euphoria that are not related to any particular activity. It also causes users to have increased energy, alertness and tal kativeness. Cocaine is highly addictive and is a widely abused drug. Tissue taken frorn the brains of cocaine users after death had lower than normal levels of dopamine, suggesting that the body adapts to cocaine use by reducing secretion. This would explain cocaine-induced depression. Crack is a form of cocaine that forms a vapour when it is heated. It can therefore be inhaled and absorbed very rapidly and gives very intense effects. These cause greater addiction and overdose problems than other forms of cocaine.

2. THC (tetrahydrocannabinol) Cannabis contains a mixture of chemicals, but one of them called THC causes rnost of its psychoactive effects. THC affects transmission at an unusual type of synapse, where the postsynaptic neuron can release a signalling chemical that binds to receptors in the membrane of the presynaptic neuron. It is not yet certain what these signalling chemicals are. THC also binds, giving thern their name - cannabinoid receptors. When THC binds to cannabinoid receptors, it blocks the release of excitatory neurotransmitter. THC is therefore an inhibitory psychoactive drug. Cannabinoid receptors are found in synapses in various parts of the brain, including the cerebellum, hippocampus and cerebral hemispheres. Users make various claims about the effects of THC, most of which are not backed up by any evidence. There is good evidence for disruption of psychomotor behaviour so it is not safe to drive vehicles or operate machinery. Short-term memory impairment, intoxication and stimulation of appetite are other effects.

Neurobiology and behaviour 137

The human brain

FUNCTIONS OF PARTS OF THE BRAIN The brain is made up of parts, each of w hich has a d istincti ve structure and carries out speci fic funct ions. The struct ure of the brain is shown in the d iagram (right). The parts labell ed in the diagram have these funct ions:

Structure and functio n of parts of the brain

Cerebral hemispheres

~~§~~~$~2~---

Hypothalamus

M edull a oblongata - co ntrols auto mat ic and hom eostatic activities, such as swallow ing and vo miting, di gestio n, breathin g and heart activity

Cerebellu m

Cerebe llum - coor d inates unconsciou s funct ions suc h as balance and movements, incl udin g hand-eye coord inatio n. Hypothalamus - maintain s homeostasis using both the nervous and endocr ine systems; produces the hormo nes t hat are secreted by the posterio r pit uitary gland; sends releasing factors to stim ulate horm one secretio n by t he anterio r pituitary gland Pituitary gland - posterior lobe stores and secretes horm ones produ ced by the hypoth alamu s; anterio r lob e produ ces and secretes horm ones th at regul ate many body functio ns

--tt1 L.1-<"------ --t'---­

'---H-HHt -+ I - - -­

-

MeduIIa oblongata

Pituitary gland

Cerebral hemispheres - receives im pulses from the eye, ear, nose and tongue; acts as the integratin g centre fo r highe r co mplex funct io ns, including learning, memo ry, emotio ns and co nsciousness.

THE PUPIL REFLEX AND BRAIN DEATH INVESTIGATING BRAIN FUNCTION Vario us techniq ues have been used to fi nd o ut w hat the fun cti on of each part of the brain is. 1. Animal experiments M any ex perime nts have been perfo rmed o n animals, includ ing pr imates, often invo lv ing surgica l procedures ­ parts of the skul l have to be removed to get acce ss to the brai n. The anima l must be kept alive so th at the brain is stil l f unct io ning. Experi mental proc edur es are ca rried o ut o n th e brai n and the effec ts o n t he animal are t hen o bserved, either during the operat io n o r afterw ards. M any scientists have et hica l o bj ect io ns to these experiments as th e animals may ex perience som e suffe ring and are often sacrif iced .

2. l esions Accide nts, strokes and tumours can damage specific parts of the brain . The damaged areas are called lesion s and from them, the locatio n of partic ular brain functio ns can be deduced . For example, lesion s in Broca' s area in the left cerebral hemi sphere cause dysphasia - inab ility to speak, but readin g and wr iting are sti ll possible. The craving-ce ntre of the brain w as fir st ident ifi ed from the case of a man w ho lost the desire to smo ke cigarettes, after a stroke damaged a region in his brain called the insula. 3. Functional magnetic resonance imaging Funct io nal magnetic resonance imagin g (fM RI) is a technique for determini ng w hic h parts of the brain are activated by specific tho ught processes . Active parts of the brain receive increased bloo d fl ow , w hic h fM RI records. The expe rimental subjec t is placed in the scanner and a high­ resoluti on scan of the brain is taken. A series of low ­ resoluti on scans is then taken, w hi le the subjec t is being given a stimulus. The scans show w hic h parts of the brai n are activated du ring the response to the stimulus. A n example of fMR I is shown (right). It indicates acti vity in the visual co rtex.

138 Neurobiology and behaviou r

If a bri ght light shines into one eye, the pupils of both eyes co nstrict. Thi s is called the pupi l reflex. Photo recepto r cells in the retina detect the light stim ulus. Nerve impulses are sent in sensory neurons of the optic nerve to t he brain. The medu lla oblo ngata (brain stem) processes the im pulses and then sends impu lses to ci rcu lar muscle fib res in the iris of t he eye. These muscle fib res contract, causing the pup il to co nstr ict. In the past, w hen a vital organ of the bod y ceased to function, the w hole body wo uld rapidl y d ie. Advances in medicin e now allow the rest of the body to be kept alive w hen certain o rgans are not fun ct ionin g. So meti mes an o rgan of the bod y recov ers after a tim e and the pati ent can enjoy a good quality of life again. If a patient is in a com a (pro longed unconsci ousness) because of damage to the cerebral hemispheres, recovery may be possible. However, damage to the medulla oblongata is much more serio us and recovery cannot be expected. Doctor s therefo re use tests of brain stem functio n to decide w hether to try to preserve a patient's life. The pup il ref lex is often used. If an uncon sci ous patient 's pup ils do not co nstrict w hen a li ght is shone into the eye, thi s suggests that they have injuries serious enough to have caused brai n death.

Brain and behaviour

UNCONSCIOUS COORDINATION

FORAGING BEHAVIOUR

The part of the ne rvou s system that is used to con tro l internal processes unconsci ou sly is called the auto nomic nervou s system. Impulses are sent from the brain through the two parts of this system - the parasympa thetic and sympathetic systems. Three of the processes controlled by these tw o systems are outlined in the table (below ).

Wh en animals search for foo d, they are foraging. Research has show n that animals opt imize foo d intake by their fo raging behaviou r. Tw o exam ples of this are descri bed here.

Organ

Parasympathetic system

Sympat het ic system

Heart

Heart rate is slowed as the bod y is relaxed and less blood flow is needed.

Heart rate speeds up so that more bloo d can be pumped to the muscles.

Blood flow to the gut

Blood vesse ls are d ilated, in creasing blood flow to the gut.

Bloo d ve ssels are co nstricted, decreasing blood flo w to the gut.

Iris of the eye

Circular muscle fib res co ntract, so the pu piI constricts to protect the retina.

Radial muscles co ntract, di lati ng the pupil to g ive a better image.

PERCEPTION OF PAIN Pain recepto rs are located in the ski n and ot her organs. They co nsist of free ne rv e endi ngs, w hic h perceive mechanical, thermal o r chemical stim uli. Impu lses are sent from these pain receptors to sensory areas of the cerebral cortex, causing feeli ngs of pai n. These feelings are necessary to allow us to kno w w hen o ur body is being damaged, so t hat we can take avo idin g act ion - pain w ithdrawa l refl exes fo r exa mple. H o w ev er , pa in sometimes becomes excess iv e or stops us fro m concentrat ing o n impo rtant act iv ities. In th ese sit uations, th e pitui tary gland releases en dorphins. The endo rphins are carried in the bl ood to the br ain . They bind to receptor s in the membranes of neuro ns that send pai n signa ls and blo ck the release of a neurotr ansmitt er th at is used to transmi t the pain sign als w it hi n the brain .

Endorp hin s are secreted during stressful times, after inj uries and eve n durin g physica l exe rci se such as run nin g.

M ale red deer fi ghting (rutting) in th e fall

1. Bluegill sunf ish (Lep om is macr och iru s) These fish li ve in ponds, w here th ey prey on small invertebrates, incl uding Dap hnia. W hen there is a low density of prey, bluegill sunfish consume all sizes of them. At medi um prey densities, bluegill sunfish co nsume only prey of moderate o r larger sizes. At high prey densiti es they mostly consume large prey, plus some of med ium size. Consumi ng small numbers of large prey takes less energy than large numbers of small prey, hence the preference fo r large prey. At low prey densities, smaller prey have to be eaten as w ell , to get eno ugh food in total. 2. Starli ngs (Sturn us vulgaris) Starli ngs are birds that feed their you ng mainly on crane-fly larvae, w hic h they obtain by probi ng into so il w ith their beak. Starlin gs beco me less effic ient at probing for larvae, as the num ber of larvae they are holdin g in their beaks increases. The few er journ eys back to the nest, the less tim e and energy is used in transpo rting the larvae to the offspring. The optimum number of larvae for starli ngs to catc h and carry back to the nest depends on the di stance between the fo raging area and the nest. As the distance increases, the optimum num ber of larvae also inc reases. When starli ngs have been observed, th e number of larvae actually caught and transported has been found to be very close to the theoreti cal opti mum.

RHYTHMICAL BEHAVIOUR PATTERNS M any animals show rhythm ical patterns in behaviou r. These usually follow either a diurnal (daily) or an annual (yearly) cycle. On e example of each is given here. There are longer cycles, for examp le the 13 and 17-year reproductive cycles of cicadas. 1. Moonrats Like many mammals, moonrats (Echinosorex gy m nura) are nocturnal. They live in Asia, in lowl and forests includ ing mangroves. Their excelle nt sense of smell helps th em to fo rage at night w hen much of their prey is active - insects and other invertebrates. They are less vu lnerable to predat io n at night and in the day they rest in hol es amo ng tree roots o r in holl ow logs, w here they are unlikely to be di scovered. 2. Red deer Reproducti on fo llo w s an annual cycl e in red deer (Cervus elap hus). M ales and females are only sexually active in the fall (autumn). M ales fight to establish domi nance ov er groups of females (figure, left) w it h w hom they mate. The adva ntage is that if the females start gestatio n in the fall, the offsprin g are born in spri ng. Most foo d is available in spri ng and summer fo r feed ing the offsp ri ng, so th is type of season breeding giv es the offspri ng the greatest chance of su rv iv al. In the fall , males try to take possession of as large a group of females as they can and mate w ith them w hen they co me into oestrus.

Neurobiology and behaviour 139

Evolution of animal behaviour

SOCIAL ORGANIZATION

EVOLUTION OF ALTRUISTIC BEHAVIOUR

Some anima ls live in co lo nies w ith clear socia l o rganizatio n. Two examples are describ ed here: 1. Hone y bees live in co lo nies consisti ng of up to sixty thou sand indi viduals. The co lo ny acts like a super­ organism that lives or d ies together, and can reproduce to for m extra co lo nies by swarming. There are three castes of honey bee, each of w hich has di fferent tasks. The single queen bee is no rmally the only member of the co lo ny to lay eggs. The wo rker bees do all the j obs that are needed to maintain the co lo ny. The drones do nothing to help the co lo ny to survive, but if they successfully mate w it h vi rgi n queens they spread the genes of the co lony to new co lo nies. Wo rkers eject d rones from the co lo ny at the end of the season in w hich virgin queens are available. The table below summarizes the tasks of the three castes.

A dicti o nary definit ion of altruism is simply ' unselfish behavio ur'. In Bio logy it has come to mean something mo re speci fic - altruism is defined as actio ns that in crease anot her individ ual's lifet ime nu mber of offspri ng at a cost to one's ow n survival and reproduction. Parental care is therefore not altruism. There has been much d iscussio n about the evo lutio n of altruistic behavio ur. We might expect natural selectio n always to be against behavi our that reduces the chances of surviva l and reproducti on, yet there are some we ll -know n examples of altruistic behavio ur.

Caste

Gender

Tasks

Q ueen

Fertil e female

Layi ng eggs. Produci ng a pherom one to control the activities of wo rkers.

Drone

Fertile male

M ating w ith virgin females.

Worker

Inferti le female

Collecting nectar and po llen. Converting po llen into honey. Secreti ng wax and using it to bui ld the comb. Feeding and looking after larvae. Guard ing the hive.

Wa ggle dance of honey bees

1. Non-breeding naked mol e rats The tasks of non -breeding workers in a naked mo le rat co lo ny are described (left). These tasks allo w the breeding male and female in the co lon y to reprod uce successfully. The evolutio n of this type of altruism, sometimes called kin selectio n, is easy to explain. The mo le rats in a colo ny are all genetically related, so altho ugh the wo rkers are helping to rear offspring that are not their own, they are help ing to ensure the surviva l of their ow n genes. 2. Blood sharing in vam pire bats This behavi ou r was investigated in a pop ulatio n of vampire bats in Costa Rica. They live in groups and feed at night by suck ing blood from larger animals. If o ne of the bats in the group fails to feed for more than two co nsecutive nights it may di e of starvation. However, bats that have fed successfulIy regurgitate blood for a bat that has fai led to feed. Tests have show n that this is done w hether the two bats are genetically related or not. This is called recip rocal altruism because the bat that don ates food to a hungry bat may in the future receive blood w hen it is hungry. There is an advantage for the w ho le group, because the benefit of receivi ng blood w hen starving is greater than the cost of don ating blood after feeding we ll.

EVOLUTION OF EXAGERRATED TRAITS

2. Naked mole rat s (H eterocephal us glaber) li ve in colonies of up to 80 ind ividu als, in bu rrow systems in parts of East Af rica. O ne dominant female mol e rat acts li ke a queen bee. She is the only female in the co mmunity to reprodu ce, mating w ith o ne of the males in the co lo ny. Three other castes of mo le rat help her. • ' Frequent wo rkers' dig the tun nels and bring food. • ' Infrequent wo rkers' are larger and occasionally help w ith heavier tasks. • ' No n-workers' live in the central nest, keepin g the

breedi ng female and her young offsp ring war m and

defending the co lo ny if it is attacked.

The large and complex bu rrow systems could probably not be co nstructed or defended w ithout social o rganizatio n. A co lo ny of social organisms is someti mes co nsidered to be one super-organism. Either the co lo ny as a w hole survives and reproduces to form new co lo nies or it does not. Natural select io n therefore exists at the level of the co lony .

140 Neurobiology and behaviour

Some species of ani mal have characteristics or behaviour patterns that seem to be developed excessively. The long and brightly colou red tail feathers of a peacock are an examp le. These are on ly used during courtship, to try to attract a female. At other tim es, the tail feathers wi ll be an encumbrance, hi ndering rapid moveme nt, especially durin g attacks by predators. This may be the explanati on for the evo lut io n of an exaggerated trait: any indi vidu al that survives, despite the exaggerated trait, must be well -adapted in other ways and so is a good mate to choose.

EXAM QUESTIONS ON OPTION E - NEUROBIOLOGY AND BEHAVIOUR inactive adenylyl cycl ase

E1 O do rants are substances whi ch can be detected by chemoreceptors in the nose. M any different odo rants can be detected but each chemoreceptor cell is sensit ive to only one type. The di agrams (right) show the mechanism used in the chemoreceptor. a) Deduce wh ich part of the mech anism is different in chemoreceptor cells that are sensitive to di fferent odor ants.

calcium channel (closed)

calcium-dependent chloridechanne\ (closed)

-+

[2]

b) Wh en the odorant binds to the receptor protein, the receptor protein starts activating G protein. Using the data show n in the di agrams outli ne the effects at activated G protein. m

receptor protein /

G-protein odorant

T/l

active adenylyl cy ~ lase

c) Predict the effect of entry of calcium ions and exit of chlo ride io ns on the chemo receptor cell. [1] activated G-protein [Source of data : Gold et al, Nat ure, (1997), 385 , page 677 ]

E2 a) State w hich type of receptor is found in the eye.

[1]

b) Outli ne the neural pathway involv ed in th e pupil ref lex.

[2J

c) State how this reflex can be used to find out the co nditi on of the central nervou s system,

[l J

E3 The electron mi crographs (centre and right) show the structur e of hair cells in the coc hlea. The scanning electron mic rograph (centre) shows two cells, each sitting in the cup-shaped upper surface of a Di eter's cell.

/

a) Suggest a fun ction for the strut-like proje ction

from th e Di eter' s cells, [1]

b) Percept ion of sound depends on movement of

the hair s (stereoci lia) that proj ect from the

upper surface of the hair cells.

(i) Describ e the group of stereoci lia proj ectin g

from one hair cell. [3]

(ii) Calcu late the length of the longest

stereoci li um. The scale bar is 5 urn

lo ng.

[lJ

(iii)Explain how the stereocili a of hair cells

that perceive high and low frequency

sound s would differ. [1]

c) There are two types of hair cell in the coch lea,

inn er and outer. The hair cell s show n in the

mi crographs are outer hair cells. They do not

pass impu lses di rectly to neurones, but act like

cel lular pistons, lengthening and shortening at

the same frequency as the sound that they

perceive.

(i) Suggest how the acti on of outer hair cells

[21

helps in hearin g. (ii) Deduce, from the structure of the hair cell

shown in the transmissi on electron

micrograph (right), where energy is expended

to shorten and lengthen the cell. [2]

IB Questions - Neurobiology and behaviour 141

17 Classification of microbes

CLASSIFICATION IN THREE DOMAINS A system of classification of living organisms into five kingdoms was deve lo ped in the second half of t he 20th century. Biologists mostly accepted it. In this cl assificatio n, all pro karyotes were placed in one kingdo m and euka ryotes in fo ur kingdoms. How ever, w hen the base sequence of nucleic aci ds was compared, two very di fferent groups of prokaryotes were identified. These groups are as d ifferent from each other as from eukaryotes. A higher grade of taxonomi c group w as needed to reflect th is, now cal led a doma in. Three dom ains have been described : • A rchaea • Eubacteria • Eukaryota. The o riginal evidence for th is came from base sequences of ribosomal RNA, w hich is found in all organisms and evo lves slowly, so it is suitabl e fo r studying the earl iest evo lutiona ry events. More evidence has since been obtained fro m gene sequenci ng stud ies. The table (right) shows the fundam ental d ifferences that also ju stify the new cl assification . A n explanation of intr on s is given in page 61. The figur e (below) shows the classification of livi ng organisms into three domai ns. Names of groups w ithi n each domai n have been om itted.

DISTINGUISHING THE THREE DOMAINS

Signi fic ant characters that are useful in distinguishing betw een t he t hree domain s

.s

'" ..c .'" ~

<.I


t

t

'" '0 >­

..c

'"

..:.:

u.l

u.l

:::l

. '"

:::l

A re cell w alls made of pepti dog lycan?

None

A ll

No ne

What are the bo nds in memb rane lipids?

Ether

Ester

Ester

Wh at size are riboso mes?

70S

70S

80S

Do most genes contain introns ?

No

No

Yes

How many species have histone proteins?

A few

I None

A ll

CELL WALLS IN EUBACTERIA Eubacteria

Cell wa l l structure varies in the Eubacteri a. There are two main types of structure, whi ch are show n in the d iagrams (below) . Eubacteri a w it h the structure show n in the upper di agram are called Gram-positive, as they are stai ned pu rple by Gram stain, w hereas Eubacteri a wi th the structure show n in the low er dia gram are Gram-negative, as they stain less intensive ly and appear red. Gram-posit ive Eubacteria

Archaea

Eukaryota

HABITATS OF ARCHAEA The Archaea are very diverse in thei r metabo lism and this helps them to thri ve in a very wid e d iversity of habitats, includ ing some of the more extreme in the wor ld. • Halophiles li ve in habitats with a very high salt content - at least 1.5 mo l drrr' and ofte n much higher. These co ncentratio ns are found in saline lakes such as the Dead Sea. • Therm ophiles li ve in very hot habitats, up to 100 °C in some cases. Examples of these habitats are hot springs in vo lcanic areas and geothermally heated regions of the sea f loo r, includ ing hydrothermal vents known as black smokers. • Me t hanogens live in anaerobic habitats w here organic matter is available. Examp les are swamps and w aterlogged soils, in the gut of cattle and other rumin ants and in dumps of organic w aste created by humans.

142 Microbes and biotechnology

plasma

membrane

of phospho­

lipids and

proteins

thick layer of peptido­ glycan

Gram-negati ve Eubacteria thin layer peptido­ glycan

\ ~l--- of

plasma membrane of phospho­ lipids and proteins

t

inside

outer layer of lipopoly­ saccharide and protein

t

outside

Diversity of microbes

SHAPE IN EUBACTERIA

STRUCTURE OF VIRUSES

The cells of Eubacteri a vary co nsiderably in shape . They can be spher ica l, rod-shaped, spiral, or co mma shaped , for example.

M ost bio logists do not co nsider v iruses to be liv ing organisms.

Instead, t hey are regarded as genetic struct ures that can

reprodu ce using the cell s of a li v ing o rganism. Every v irus has

a sma ll num ber of genes composed of nucl eic aci d,

sur rounded by a prot ei n coat. The coat is called the capsid.

Apart from this, there are few sim ilarit ies in structure. Vir uses

probabl y are di verse in structure because they evo lved

repeated ly, rather than all evo lv ing from a single ancestral

virus.

There are three key di fferences in virus struct ure:

cocci s p~ er ig l bacteria 0

<;;I

0

Q

0

o

0

0

00

spirilla SPi/ral_Shaped bacteria

bacilli

vibrios

::::~J~~ShaP.•:..•.e. d

mdo'h" O '"'"

G

single cocci (e.g. Pneumo coccus)

(e.g. Spirillum )

-; .·

1 . Is the capsid enveloped? In many v iruses, the capsid is naked - it is the outer layer. In ot her v iruses, there is a lipid bilayer outside the capsid. These are called enve lo ped viruses.

(e.g. Vibri o cho lerae, causes cholera)

single bacilli (e.g. Escherichi a co li)

A ltho ugh bacteri a can exist as single cells, some spec ies can also fo rm aggregates - gro ups of ce lls lin ked together. For example, layers of bacteria called biofil ms can for m o n rock s or ot her surfaces. The cells jo int ly secrete adhesive po lysaccharides, stic king the cells to the surface and to each other. Single cells co uld not produ ce eno ugh of the po lysaccharid e for efficient adhesio n. The bacterium Streptococcus muta ns fo rms biofilms on teeth, w hic h are calle d plaque and can cause dental decay .

2. Are the genes DNA or RN A? The genes in some v iruses are com posed of D NA w hereas in others they are RNA . 3 . Are the genes single or double-strand ed? The genes of viruses can be either single stran ded or doubl e stranded, w hether they are co m posed of DNA or RNA .

DIVERSITY OF MICROSCOPIC EUKARYOTES A ny li v ing o rganism that is too small to see wi th the naked eye is micro sco pic. There are many types of mi croscop ic eukaryote, w hic h are very diverse in their modes of nutriti on, their mod es of loco motio n and w hether they have cell wa lls, chlo roplasts and cilia or flagell a. Five typ es are described below . CELL STRUCTUREAN D LOCOMOTIO N j

r Has a cell wa ll but no method of locomotion

I Cell ulose cell wall nucleus

1

r

Chitin cell wall

Flagellu m for locomotion

nucl eus

nucleus

1 No cell wall but has a method of locomotion 1 Cili a for locomotion nucleus

1 Amoeboid movement (like a phagocyte) nucleus

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Autotrophic o photosynthesis using a chloro plast o needs onIy Iight and inorganic compounds

Heterotrophic o saprotrophic - absorbs sugar and other small molecules

Heterotrophi c and autotrophic o photosynthesis using chloroplasts
Heterotrophic o ingests living and dead organic matter by endocytosis

Heterotrophic o ingests li ving and dead organic matter by endocytosis

AUTOTROPHIC NUTRITION

HETEROTRO PHIC

NUTRITION

Microbes and biotechnology 143

The nitrogen cycle

ECOLOGICAL ROLES OF MICROBES

NITRATE FERTILIZERS AND RIVERS

M icrob es are ve ry var ied in their metabo lism and so can have many d ifferent ro les in eco systems. For example, some microbes are produc ers. Other mi crobes are decomposers. M icrobes can also be nitro gen fixers in ecosystems.

A lthoug h nitrate is an essential nutr ient fo r plants, its eco logica l effects in rivers can be detr imental. 1. N itrate ion s are solu ble and are leached from soils very easily if excessive amo unts are app lied to crops. If phosphate and other minerals also reach a high co ncent ratio n, a river beco mes eutrophic. 2 . The eutrophicatio n causes algae to proliferate. Ni trate from fert ilize rs sometimes causes an excessive growt h of algae, called an algal bloom . Som e of the algae are depri ved of light and die. 3. Bacteria decom pose the dead algae. The bacteria create an increased biochemical oxygen demand and so cause deo xygenation of the wate r. 4. Low oxygen levels ki ll fish and ot her aquatic animals. The graph (below) shows the results of an experiment in w hic h a lake was ferti li zed w ith nitrates every year starting in 1969 . The density of algae was estimated by measuring chlo rop hyll co ncentrat ion in the wate r. Befo re the experiment, the con centratio n was below 5 ug drrr-' throughou t the year.

MICROBES AND THE NITROGEN CYCLE M any mi crobes, includin g nitrogen f ixers, have rol es in the nitrogen cycle . The w ho le cycle is show n in the di agram (below).

1. Nitrogen fixation Free-liv ing Azotobacter and Rhiz obium living mutu alistically in root nodu les both fi x nitr ogen. N itr ogen fi xation is conversio n of nitrogen from the atmosphere into ammo nia, using energy from ATP.

2. Nitrification The co nversio n of ammo nia to nitrate (nitrificatio n) invo lves tw o types of soil bacteria. N itrosomonas co nve rts ammo nia to nitrite and N itrobacter co nve rt nitr ite to nitrate. N itrifi cati on happens very rapid ly, as long as soils are we ll aerated w ith abundant supplies of oxyge n.

3 . D enitrificati on N itrate is somet imes co nve rted into nitrogen in a type of anaerob ic respiratio n. This process is called denitrificat ion as it reduces nitrate levels in soils. Pseud om onas denitrificans is an examp le of a bacterium that carries out denit rification . N itrate is broken dow n w hen it is used as a terminal electron accepto r in respirati on instead of oxygen. Anaerobic soi ls therefore enco urage denitr ificatio n. Bad d rainage and wa terlogg ing are a frequent cause of anaerob ic co ndit io ns in soi ls.

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144 Microbes and biotechnology

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Sewage treatment and methane generation

SEWAGE IN RIVERS

USING MICROBES IN SEWAGE TREATMENT

Raw sewage ofte n contai ns pat hogens. If it is released into rivers, and peop le drink water from the river or swi m in it, they may become infected w it h the pathoge ns. Raw sewage also has ecologica l effects on rive rs, shown in the figu re (below) .

1. Trickle filter beds Rotating boom Decomposers digest organic matter

Rock fragments with a large surface area on wh ich microbes grow

Nitrifying bacteria convert ammonia to nitrates

Releaseof raw sewage

inflow of raw sewage 2. Reed beds gravel or other solid substrate

Saprotrophic bacteria feed on organic matter in the sewage - the bacteria use up large amounts of oxygen so the sewage creates a high bioc hemical oxygen demand.

reeds

Decomposers break down organic matter, releasing ammon ia and Nitrifying bacteria convert mine ral ions ammonia to nitrites and nitrates

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Denitrifyi ng bacteria convert nitrates to nitrogen

METHANE GENERATION The water may be deoxygenated, ki lling fish.

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Decompositio n of the organic matter resuIts in release of ammonia and phosphate. Ammo nia is converted to nitrate. High nitrate and phosphate levels (eutrophicat ion) stimulate algal growt h.

Biomass already provides large amo unts of fue l, in the fo rm of wood, crop residues and dri ed manure. Me thods now ex ist fo r co nverti ng biomass into fue ls that are more co nvenient to use, such as ethanol and methane. Methane is sometimes called marsh gas, beca use it is natu rall y produced by mi crobes in anaerobic co nditions. These con ditions are recreated in bioreactors used fo r methane generation. A variety of types of organ ic matter can be the feedstock, incl uding manure from farm anima ls and cellu lose, The feedstock is loaded into the bioreactor w here anaerobic co nditio ns enco urage the growth of three gro ups of natur all y occurring bacte ria. The first group convert organic matter into organ ic acids and alco ho l. The second group convert o rganic acids and alco ho l into carbo n diox ide, hyd rogen and acetate . The third gro up of bacte ria are the methanogenic archaea - they produce methane from carbon diox ide, hyd rogen and acetate. Carbo n diox ide + hydrogen COz + 4H z Acetate CH 3COO H

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methane + water

CH 4 + 2H zO

met hane + carbo n d ioxide

CH 4 + COz

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Photosynthesis by algae increases oxygen levels in the water.

Assuming that an excessivealgal bloom does not develop, the river then recovers from the sewage pollution, usually many kilometres downstream.

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Ii ,>P,.. ~~ Digested slurry used as ferti lizer on fields or gardens Partition (retains coarse slurr y)

Microbes and biotechnology 145

Microbes and biotechnology

GENE THERAPY

RISKS OF GENE THERAPY

Gene therapy is the treatment of genetic di sease by altering the genotype. In the case of a di sease caused by a recessive allele, a fully functio nal domin ant alle le must be inserted into defective cells. The situatio n is more co mplex w ith genetic di seases caused by do minant alleles - expressio n of the defec tive gene must be prevented and a functioning allele may also need to be inserted. There are tw o stages in the life cycle w hen gene therapy co uld be attempted: 1. Somatic-cell therapy - body ce lls are altered, w hich do not develop into gametes. Ofte n very large num bers of cells wi ll need to be altered , and altho ugh the genetic disease may be cured in the treated ind iv id ual, it can still be passed on to offspri ng. 2. Germ-line therapy - sperm or egg ce lls are treated (or ce lls that w ill d iv ide to prod uce sperm or egg cells). The disease shou ld be com pletely absent in offspring fo rmed using the gametes, but the parent in w hic h the d isease has been d iagnosed still has the disease.

Most attempts at gene therapy so far have not been successful and the hopes of patients and their families have been raised and then d isappoi nted . There have also been cases w here the treatme nt has harmed the patients. One examp le of this invo lved a tria l of gene therapy for SCiD using retroviruses, in a group of ten ch ild ren in France. Two of t he c hi ldre n deve loped leukemi a. The viral vecto r had inserted DNA into a cancer-ca using gene and activa ted it. Adenoviruses are possib le alternative viral vectors , as they do not insert thei r genes into host cell chromosomes, so should not activate the cance r-causing genes.

VIRAL VECTORS IN GENE THERAPY Viruses have had millions of years to evo lve efficient mechani sms fo r entering mamma lia n cells and del ivering genes to them. They sometimes also incorporate these genes into the host cell's chromoso mes. Viruses are therefo re obv io us candida tes fo r the gene de live ry system, needed in gene therapy. Mod if ied vi ruses must be produced co ntaining the desired gene, w hic h w ill infect target cells but not repl icate to fo rm more vir us particles. A modified vir us that is used in this w ay is ca lled a vector. The most w idely used virus vectors are retrov iruses. O ne exam ple of thei r use is in the t reatment of SCiD (severe com bined immuno-deficiency), a genetic disease that is due to the lack of an enzyme ca lled ADA. A famous early case involved a baby called A nd rew : Gene therapy for SCi D

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Genetic screening before birth shows that Andrew hasSCiD

The allele that codes for ADA is obtained. This gene is inserted into a retrovir us

Blood removed from Andrew's placenta and umbili cal cord immediately after birth contains stem cells. These are extracted from the blood

Retroviruses are mixed wi th the stem cells. They enter them and insert the gene into the stem cells' chromosomes

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USE OF REVERSE TRANSCRIPTASE IN MOLECULAR BIOLOGY Retroviruses, suc h as H IV, are viruses that use RNA as their genetic material. They co ntai n an enzy me that cata lyses the pro duction of DNA from RNA. This enzy me is called reverse transcriptase. Retrov iruses use it to make a DNA copy of their RNA genes, after they have entered a host cell. The DNA copy beco mes inserted into the host cell's chromosomes . Molec ular bio logists use reverse transcriptase to make cop ies of t he genes that they use in gene transfer. 1. Cells that are transcribi ng the require d gene are obtai ned and mRNA transcripts are ext racted. 2. Single-stranded DNA copies of the m RNA are made using reverse transcriptase. This is ca lled eDNA. 3. DNA po lymerase is used to co nvert the single-stranded DNA into double-stranded DNA, producing genes that can be transferred into anot her organism . The fig ure (below) is a summa ry of the proced ure. The genes prod uced contai n no introns, so if they are transferred to bacte ria, w hic h do not ed it out intro ns, the correct protein w ill nonetheless be prod uced. Production of eDNA f rom mRNA

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For four years T-cells (w hite blood cells), produced by the stem cells, made ADA enzymes, using the ADA gene. After four years more treatment was needed.

146 Microbes and biotechnology

Reverse transcriptase breaks dow n the strand of RNA

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Microbes and food production

SACCHAROMYCES AND BREWING

SACCHAROMYCES AND BAKING

Beer, w ine and other alco ho lic drink s are brew ed using yeasts h om the genus Saccharom yces.'Whe n oxygen \s absent, the yeast switches to anaerobic cell respirati on and excretes the ethano l and carbo n di oxid e produ ced in this process.

Yeast is used in bakin g bread. It is mix ed into the dou gh b e\ore b aK\ng. 1he yeast oroouces ethano\ ana carbon dioxid e by anaerobic cell respiration . The carbon dio xid e form s bubbl es w ithin the dough, makin g the dou gh rise - it increases in volume. This makes the dou gh less dense - it is leavened. Wh en the dou gh is baked most of the ethano l evaporates and the carbon dio xid e bubbl es give the bread a li ght texture, w hich makes it more appetizing.

An aerobi c cell respiration is also called fermentation . D uring fermentatio n, t he ethano l concentratio n of the fluid around the yeast cells can rise to approxi mately 15% by volume, before it becomes tox ic to the yeast and the fermentation ends. Most of the carbon dio xid e bubbles out into the atmosphere.

1. Wine production Grapes are crushed to make ju ice, w hich is pl aced into large vessels, or vats. Yeast cells are naturally present on the grapes and they grow and divid e in the jui ce. Sometimes selected varieties of yeast are added. W ithin a few days, all of the oxygen in the jui ce is used up and the yeast cells respire anaerobically from then onw ards. The fermentation ends w hen the sugar in the jui ce has been used up or w hen the ethano l content reaches 15%. The jui ce has then becom e w ine.

TRADITIONAL FOOD PRESERVATIVES There are many ways of preservin g foods. All of them w or k by preventin g the grow th of microbes in the food . Several tradition al methods involve adding chemicals to the food.

1. Acids Vin egar, containing ethano ic acid, can be used to preserve foods, because microbes cannot grow at low pH . Yoghurt is made w hen bacteria convert lactose in milk to lacti c acid . This reduces the pH of the milk , preventing the growth of most microbes and therefore preservin g the milk as yoghurt.

2. Beer production

2. Salt

Starch, rather than sugars, are the feedstock for beer produ ction. Yeast cannot ferment starch, so there must be an extra stage in t he produ ction process. Barley seeds are we tted and allowe d to start germinat ing. Am ylase is produ ced in th e germi nating seeds. The amylase can convert starch to maltose. The barley seeds are dri ed after a few days to kill them and preserve the amylase. The dried, semi-germi nated barley seeds are called malted barley. Beer produ ction involves mixin g malted barley, w ith oth er sources of starch, and a selected variety of yeast into wa ter in a vat. Hops are added as fl avouring. Amyl ase from the malted barley di gests starch, to release maltose, w hic h the yeast converts to ethano l by anaerobic cell respirati on .

If salt, usuall y sodium c hlo ride, is added to food s, to c reate a high salt concentratio n, mi crobes cannot grow in the food and it is preserved. An y microbes in the food are kill ed because water is drawn out of them by osmosis.

3. Sugar Honey is naturall y preserved, because of its high sugar content. If honey is properly ripened, no microbes can grow in it, because the sugar is so concentrated. As wi th salt, water is drawn , by osmosis, out of any microbes in honey, killin g them. If enough sugar is added to a food then it is also preserved. Jam is an example of a food preserved by high sugar co ncentrati ons.

PRODUCTION OF SOY SAUCE

FOOD POISONING

The traditional method of producing soy sauce takes about six month s and invol ves a fungus, Aspergillus.

Some mi crob es that are found in food produ ce tox ins, w hich are harmful to human health . This is called food poi sonin g. On e of the co mmonest form s is caused by certain strains of

1. Soya beans are coo ked and are mi xed w ith ground roasted w heat grains. 2. The mi xtur e is ino cul ated w ith Aspergillus, which grows rapi d ly ove r the soya and w heat. 3. After a few days, the mi xtu re is transferred to vats and salt solutio n is added. 4. The mi xtu re is left in the vats for about six months, during w hich tim e the Aspergillus ferments the starch and prot ein s into alco hol, organic acids, sugars and ami no acids. 5. Soy sauce is the liquid produ ced by pressing the mi xtur e extracted from the vats at the end of the fermentatio n. It is a complex combination of sweet, salty, sour and unami flavours. Its traditio nal use is in ori ental coo king, but it is now used w idely thro ughout the wor ld.

Staphylococcus aureus. Symptoms If food co ntaining the toxin is eaten, nausea, vomiti ng and di arrhoea develop w ith a few hou rs.

Method of transmission If food is co ntaminated w ith the pathogenic strains of S. aureus during handling and the food is stored above 4 °C, the bacteri a multipl y and produ ce harmful toxin s. A w ide variety of foods can carry the bacteria and therefore toxin s: poultry, meat, eggs, salads, puddings, sauces and bakery produ cts co ntaining cream.

Treatment The main aim of treatment is to repl ace substances lost in d iarrhoea. O ral rehydrati on fluids are used, w hich are dilute so lutio ns of min eral ions, includin g sod ium and c hlo ride, together w ith a littl e sugar and some flavou rin g to make it palatable. Intravenous fluid s are o nly given w hen vomitin g prevents rehydration . Ant ib iot ics are not norm ally used as the bod y cl ears the infection w ithout them.

Microbes and biotechnology 147

Metabolism of microbes

SOURCES OF ENERGY AND CARBON Mi crob es, especia lly prokaryotes, are much mo re varied in their metabo lism than larger organisms. They can be divided into groups accord ing to t heir sour ces of two essent ial thin gs ­ energy and carbo n. The table (right) summariz es the di fferences. Phot oautotrophs - organisms that use li ght energy to generate ATP and to prod uce o rganic co mpo unds from inorganic substances. Examp le - An abaen a (show n in the diagram below )

SOURC EOF CARBON Inorganic Organic -C0 2 compounds

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Photoautotrophs

Photoheterotrophs

Chemoautotrophs

Chemoheterotrophs

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Chemoh eterot roph s - o rganisms that use energy from chemical reactions to generate ATP and that use organic compounds made by other o rganisms. Examp le - Lactob acillus (a bacterium used to make yogurt) Plants are almost all photoautotrophs and most animals are chemo heterotro phs.

Structure of a cyanobacterium

y photosynthetic cells

y nitrogen-fixing cell

photosynthetic membranes

USE OF BACTERIA IN BIOREMEDIATION M icrob es can someti mes be used to clean up po llutio n of soil o r water. This is called bioremediation. The bacteri a may break the po ll utant down into harml ess substances o r may remove it from the enviro nment by co ncentrating it w ithin the mi crobi al cells. Usuall y the bacterium is already present in th e envi ronment, but it may need to be stimu lated by applicatio ns of nutri ents, such as nitrate o r phosphate ferti lizer. Fou r examples of bioremediation are given here. 1. Oil spills in water Crude o il co ntains a w ide variety of chem ical compo unds, many of wh ich have very harmfu l effects w hen released into the environment. M any different mi crob es are able to ox id ize hyd rocarbo ns in oil spill s, and so help in bioremedi ation . The numb ers of these mi crobe s increase naturally on the surface of the o il, but even so, it can take months for most of a spi llage to di sappear and some hydrocarbons are very resistant to microb ial decom position . App lication of inorganic fertilizer can speed up the process of bioremedi ation .

148 Microbes and biotechnology

2. Selenium polluti on Comp ounds of the metal selenium so metimes pol lute soils or w ater. Various bacteria absorb selenate ion s (SeO/ - and SeO/ - ) and ox id ize t hem to metalli c seleni um, w hich is much less toxic. 3. Pesticide polluti on A w ide variety of c hemical substances have been develop ed for use as pestici des. W hen these substances are used, residu es may be left in the soil or elsewhere in the environ ment. These resid ues gradually di sappear but the t ime taken fo r this to happen varies fro m a few days up to fo ur o r mo re years. This depends on how easy it is for microbes to break down the pesticid e. 4. Sol vent pollution Chlo rinated solvents, for example chloro form, are often found as po ll utants of groundwate r - w ater percol ating thro ugh soil and rock . There are a few groups of bacteria that dech lor inate these solvents in anaerobic cond itio ns, co nverting them into much less toxi c substances.

Microbes and disease LIFE CYCLE OF THE INFLUENZA VIRUS

ENDOTOXINS AND EXOTOXINS

Influen za is cau sed by an e nve lope d virus, w ith sing le-s tranded RNA as its gen eti c materi al. • It bi nds to glyco protei ns on the surface of th e ce lls in the linin g of th e upper resp iratory tract. • It is th en tak en into th ese ce lls by e ndocytos is. • O nce ins ide the host ce lls, the vira l RNA is rep licat ed a nd ca ps id prote ins are synthesized usin g th e ribosom es of th e ho st ce ll. • New influen za viru ses a re asse mb led from th e RNA and prot ein s. • Th e host ce ll is bur st o pe n. This is ca lled lysis. The influen za viruse s a re re leased , e nve lope d in membran e from th e ho st ce ll's plasm a membran e . • The viruse s th at have bee n re leased go o n to invade ot he r host ce lls, spr eadin g th e infection . This type of life cycle , w he re a vi rus tak es o ve r a host ce ll, uses it to reprodu ce a nd th en bursts it open a nd kills it, is ca lled a lytic life cycle .

Ma ny pathogen s harm the ir hosts by producin g toxins. In so me cas es th e to xin is a prot ein th at is re le ased by th e pat hogen - this is a n exotoxi n . Ma ny exotox ins are high ly toxic o r eve n fata l, for exam ple, th e bacte rium th at ca use s c ho lera rel eas es a prot ein th at perforates the membran es of ce lls in the intestin e . This ca uses loss of fluid from th e wa ll of the intest ine a nd extreme ly seve re di arrh oea . Exoto xin s ca n mov e throu gh th e body of th e host a nd ca use dam age away from th e a rea of infection . Another type of toxin is prese nt in th e o uter membran e of gra m-negative bacte ria . The toxic part of the membra ne is lipo pol ysacch a ride a nd becau se it is part of th e struc ture of the bacterium , it is an endo tox in . Th e tox icity of e ndo tox ins is no t grea t, b ut they ca use feve r a nd ac he s, w h ich exotox ins usuall y do not.

ACTION OF ANTIBIOTICS

TYPES OF BACTERIAL INFECTION

Antibiotics are c he m ica l substa nces produced by microb es th at kill or in hibit the grow th of ot he r micro bes. Th e ir d isco very a nd use is o ne of th e triumph s of modern me di ci ne , revo lut ion izi ng the treatm e nt of bacter ial diseases. Antibi otics a ll interfer e w ith so me aspect of microbi a l metab olism. Most of th em ac t aga inst bacte ria, by o ne of th ese mec hani sms :

Ther e a re two main typ es of bacter ial infect ion :

1. Inhibiting of cell wa ll synt hes is - pen ic illin a nd so me oth er antibiotic s inh ibit e nz ymes tha t a re invol ved in th e sy nthes is of th e bact er ia l ce ll wa ll 2. Inhibitin g pr ot ein sy nt hesis - e rythrom yc in, stre pto myci n a nd so me othe r a nt ibio tics block o ne of th e stages in bacteri a l protein sy nthe sis 3. Inhi biting nucl eic aci d synt hesis - rifampin a nd so me oth er antibiotics blo ck th e sy nthes is of RNA by RNA po lym erase

in bacteria Antib iotics can safe ly be ingested becau se these processes a re sufficie ntly different in hum an cells for th em not to be blo cked .

1. Extr acellul ar bacter ial inf ecti on Som e pat hogeni c bact eri a invade th e bo dy a nd rem ain in th e inter cellu lar spaces, usin g th e nut rients th e re . Exampl e : Streptococcus This gro up of bacteri a most co mmo nly infe ct s th e upper respir atory tract. Streptococcus ce lls so met imes fo rm a n outer covering, ca lled a caps ule, w hic h he lps them to resist the antibo dies in hum an tissue s. 2 . Intracellul ar ba ct eri al infection Som e pathogen ic bacte ria inva de the bod y of th e ho st a nd e nte r its ce lls, re lying o n the met abo lism of th e host ce lls for so me processes. Examp le : Chlamydia Small den se Chlamydia ce lls are a ble to survive o utside ho st ce lls, but not grow o r d ivide . W he n they mak e co ntac t with a

host cell, the y are taken in by endoc ytosis. Once inside they c ha nge into larger ac tive ce lls, whi c h use ATP a nd o ther substa nces produced by th e host, fo r growth a nd reproduction . Eventua lly these ac tive ce lls become sma lle r a nd den ser and are re leased . They may th e n be d ispe rsed and e nte r othe r host ce lls.

CONTROLLING MICROBIAL GROWTH 1. Irradi ation - io nizing radi ation , for exa mp le ga mma radi ation, ca n be used to kill m icrob es in food , includ ing path ogen ic bacte ria a nd th ose that ca use food spoi lage . Free rad icals form ed by th e irradi ation may a lte r flavour, but not as mu ch as w ith heating. Som e bacteria ca n survive irradi ation e .g. Clostridium bo tulinum. Irradi ated foo ds do not become radioactive, but som e co nsumers a re still re lucta nt to bu y th em . 2 . Past eurizati on - m ilk ca n co nta in pa thoge ns, incl udi ng the bacteri a t hat ca use tub er culosis. Past euri zat ion kills a ll path ogen s a nd most bacte ria caus ing de cay. A typ ica l meth od invo lves heatin g the m ilk to at least n oe for 15 sec o nds , fo llowed by rapid coolin g. Lon ger periods of heatin g o r higher temperatures ste rilize the milk, preve ntin g decay mor e effect ive ly, but a lte ring the flavou r of the milk , so pasteu rizati on is often preferr ed to sterilizatio n .

3 . Ant iseptics - c he m ica l substa nces th at kill o r prevent the grow th of bacter ia o n th e skin o r in wound s, helping to prevent infect ion. Antise ptics ca n be used o n th e surface of living tissues bec au se th ey a re not ve ry toxic to tissu e a nd there is little or no abso rptio n. Ho wever , th ey would be harmful if tak e n intern a lly. They ca nno t th erefor e be used in food s, a nd th ey wo uld a lso taste unp leas ant. 4 . Disin fect ants - che mica l substa nces that kill or prevent th e growth of microb es o n no n- living surfaces. The y ca n be used to ste rilize medi ca l eq uipme nt, surfaces used in food preparation a nd man y othe r place s wh ere microbia l growth m ust be prevented . Effe ctive disinfectants a re high ly toxic to microbes, but th e dis ad vantage of this is that they are too toxic to be used on o r in livin g tissues, o r in food s.

Microbes and biotechnology 149

Epidemiology

EPIDEMICS AND PANDEMICS '

TRANSMISSION OF PATHOGENS

Epidemiology is the study of the occurrence, distribution and control of diseases.

On e of the main probl ems in the life of a pathogen is how to reach a new host and gain entry to the body. There are various possibl e methods. • Contact - contagio us diseases are transmitted w hen an uninfected person tou ches an infected person as the pathogen can enter the bod y throu gh the skin. • Cuts - pathogens enter the body w hen the skin is cut or pun ctur ed by any objec t th at is co ntaminated w ith pathogens. • Droplets - diseases of the ventilation system can be transmitted w hen an infected person coughs or sneezes out dropl ets cont aining patho gens, w hich are breathed in by an unin fected person. • Food or water - pathogens in cont amin ated food o r water enter the bod y throu gh the soft gut wa ll. • Sexual intercourse - sexually transmitted di seases gain entry throu gh the soft mucous membr anes of the penis and vagi na during sexual intercourse. • Insects - blood-sucking insects inject their mouthparts thou gh the skin and can transmit patho gens that are sucked o ut in the blood of an infected person.

There is an epidemic w hen the numb er of cases of a di sease in a region is unu suall y high. There is a pandemic w hen an epidemic has spread very wide ly, to affect a large geographic area, suc h as a cont inent. Example: the Asian flu pandemic of 1957 Occurrence: pandemic s of influ enza occur irregularly, but usuall y at intervals of several decades. An epidemic began in February 1957 , spread into a pandemi c and reached its peak in O ctob er 1957, w ith 22 million new cases in two weeks, decl ining from then on w ards. Distribution: the new strain of influ enza virus that caused the pandemi c first appeared in M ainl and China, spread ing to Hon g Kong and then throu ghout the w orld by air and sea routes. Control: clearly, there was no effective control of the pandemic in 1957 . Wh en new strains of influ enza virus appear, vacci nes are still not immediately available, because developm ent and manufacture takes months. There we re no effective antiviral dru gs available and there are still no drugs that are as effective as antibiotics for bacterial di seases. If a dangerous new strain of influenza is identifie d early enough, attempts can be made to prevent its spread by isolating all infected people, but this di d not happen in 1957.

MALARIA 300-5 00 mill ion peopl e per year becom e ill as a result of malari a, wi th more than a million deaths, makin g it one of the w or ld' s most devastating diseases.

Cause A proto zoan parasite called Plasmodium is the cause. After enteri ng the bod y, it first invades and reprodu ces inside liver cell s and then changes into a d ifferent form, w hich targets red blood cells. In the most severe form of malaria, the parasite fo ll ows a 48-hou r cycle of invadi ng red blood cells, growing and reprodu cin g inside them and bu rst ing out into the blood plasma.

Effects The w orst symptoms occ ur w hile the parasites are cir cul ating in the blood pl asma: fever, shiverin g, sweating, headache, general body pain and sto mach upsets. In severe cases the attac ks can becom e progressively more serious. Capi llar ies are blocked by parasiti zed red bloo d cells and bu rst causing anemia and wides pread damage to o rgans inclu din g the brain. Death may then fo llow . Transmission The parasite cannot by itself get from the body of on e human host to another. It uses an insect vecto r - female Anopheles mosquitoes, w hich feed on human blood . If the mosquitoes ingest blood from a person w ith malari a, the malarial parasites survive and reprodu ce inside the stomach and then spread to the salivary glands. Wh en the mosquito next feeds, usually on a different person, it first inj ects saliva th at cont ains Plasmodium into the person, infecting them w ith malaria if they do not already have it.

150 Microbes and biotechnology

SPONGIFORM ENCEPHALOPATHIES These are serious, incurable diseases of mammals. The best­ kno wn examples are scrapie in sheep, BSE in cattle and Creutzfeld-Jacob di sease (CJD) in hum ans. In each case the tissues of the brain are gradually brok en down , giving a spongy appearance and causing premature aging, dementia and eventually death. Spongiform encephalopathies are infectious , but the nature of the infectio us agent is puzzlin g. • Enzymes that d igest D NA and RNA do not affect it. • It is very heat stable and is not easily damaged by ion izin g radiation . • It cannot therefore be a livin g organism. • It is affected by chemic al treatments that denature protein s. Research has led to a protein of 254 amino aci ds, now called prion protein or PrP. There are two form s of PrP, the norm al for m, Prpc, w hic h is found o n the surface of neuron s and Prpsc, found in d iseased brain tissue. Accord ing to the prion hypoth esis, Prpc is co nverted into Prpsc by a conform ation al change and Prpsc causes thi s change. So, if any Prpsc is present in the brain , it w ill cause mor e and more to be produced by a sort of positive feed back. Brain cells attempt to di gest it using protease, but part of the Prpsc molecul e resists digestion and the resultin g prot ein fi bri ls accumulate in brain cells, presumably causing sympto ms of the d isease. Experim ents have show n th at w hen experimental animals are inocul ated w ith Prpsc spo ngifo rm encephalo pathies deve lo p. Ho w ever, not all observatio ns can be accounted fo r by the prion hypoth esis. It does not exp lain how rapid ly the di fferent forms of the d isease progress, including sporadic CjD and variant Cj D in hum ans. No other hypoth esis seems plausibl e thou gh, so research is focu sing on modifi cation s to the prion hypoth esis.

EXAM QUESTIONS ON OPTION F - MICROBES AND BIOTECHNOLOGY F1 The graph below shows some of the effects of di scharge of raw sewage int o a river . vo

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bacteria

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algae and photosynthetic bacteria

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input of sewage a) Explain the decrease in oxyge n co ncentratio n downstre am of th e inp ut of raw sew age.

[2J

b) Explain the increase in ammo nia and phosphate co ncentratio n down stream of the input of raw sewage.

[2]

c) Explain w hy th e max imum co ncentration of nitr ate is down stream of the maximum co ncentration of ammo nia.

[2J

d) Expl ain the increase in the numbers of algae and photosynth etic bacteria shown in the graph.

[2]

e) Suggest reasons for the decrease in numbers of bacteria, dow nstream of the part of the river w here there is the maximum numb er of bacteria.

[2]

F2 Reverse transcriptase is an enzy me found on ly in cells infected by certain viru ses. a) Outline the process catalysed by thi s enzy me.

[2J

b) (i) State th e name of the group of viru ses that co ntain the gene for thi s enzy me.

tn [1]

(ii) State one example of a virus from th is group. c) Explain bri efly w hy the enzy me is a usefu l tool for mol ecu lar bio logists.

[3]

F3 The electro n mi crograph (right) show s adenoviruses, at a magnification of x120 000. Ad enovi ruses cause the co mmo n co ld in hum ans. a) (i) State the name of the out er layer of th ese viruses, visible in the electro n mi crograph.

[1]

(ii ) State wh at materi al is cont ained inside t his o uter layer of the viruses. [1 J b) Outlin e how adenov iruses co uld be used in gene therapy.

f2l

c) Explain w hether adenoviruses are intracellul ar or extracellular in their mode of infecti on .

[2]

18 Questions - Microbes and biotechnology 151

18

OPTION G - ECOLOGY AND CONSERVATION

Distribution of plants and animals DISTRIBUTION OF PLANT SPECIES

DISTRIBUTION OF ANIMAL SPECIES

The di stributi on of a species is the range of places th at it inh abits. The di stribution of pl ants is closely linked to t he levels of abiotic factors in the environment. The main abiotic factors are temperature, water, light, soil pH , salinity and mineral nutrients. Avicennia ge rm inans, for example, is a tree found in mangrove swamps o n the coast of Mexi co . It grows w here the climate is hot and the soi ls are waterlogged and anaerobic, w ith high levels of salinity, a pH clo se to neutral and high levels of min eral nutri ents. Few pl ants can grow in these co nditions, but Avicenn ia germinans thr ives. Sometimes the Distribution of AsperuJa di stribution of a plant cynanchica (Squinancy Wort) specie s shows w hat co nd itions a plant prefers. The fi gure shows the distr ibuti on of Asperula cynanchica in Britain and Ireland . It is found in areas w ith alkali ne so ils form ed fro m chalk or lim estone rock . It is absent fro m co lder north ern areas even w here the soils are alkali ne.

The d istribut ion of animal species is affected by both abiot ic and bioti c facto rs. • Temperature - external temperatures affect all animals, especial ly those th at do not maint ain co nstant internal body temperatures. Extremes of temperature require specia l adaptations, so onl y some species can survive them. • Water - animals vary in the amount of water th at they require. Some animals are aquatic and must have water to live in and at the other extreme some animals including desert rats are adapted to survive in arid areas w here they are unlikely ever to drink water. • Breeding sites - all species of animals breed at some stage in their life cycle. Many species need a speci al type of site and can only live in areas w here these sites are available. For example, mosquitoes need stagnant water for egg laying. • Food supply - many animal speci es are adapted to feed on specific foods and can onl y live in areas w here these foods are obt ainable. For example, blu e w hales feed mainly o n krill and so co ngregate in areas of the ocean w here krill is abundant. • Territory - so me species of animal establish and defend territories, either for feedin g or breedin g. This tends to give the spec ies an even rather th an a clumped di stribution . Pair s of tawn y owl s defend a single territory t hroughout their ad ult liv es.

RANDOM SAMPLING USING QUADRATS

Random sampling using quadrats

A sampl e is a part of a popul ation , part of an area or some other w hole thing, chosen to illustrate wh at the w ho le popul ation, area o r other thing is lik e. For example, a sample of a popul ation is some ind ivid uals in the popul ati on but not all of them.

1. Mark out gridlines along two edges of the area.

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In a random sample, every individual in a population has an equal chance of being selected. Random sampling of pl ant population s invo lves count ing numb ers in small, randoml y located parts of the total area. The sampl e areas are usuall y square and are marked o ut using frames called quadrats. A method for random sampling, using qu adrats, is show n in the fi gure (right).

TRANSECTS AND DISTRIBUTIONS An alternative to random samp li ng is to investigate pl ant or animal di stribut ions alo ng a lin e marked out across a site. The lin e is called a transec t. Transects are particul arly useful w hen there is a gradi ent in an abiotic variable. For example, if the soil in a vall ey is much wetter in the bottom of the valley than up the sides, a transect across the vall ey can be used to investigate thi s and the di stribu tion s of pl ant and animal species that are co rrelated w it h the variatio n in soil moi sture content. Transects can be used to investi gate plant and animal d istributi ons on seashores. The transect should be laid out at right angles to the high tid e and low tide lin es, so that it follow s the gradie nt in time of inund ation by sea w ater and tim e of exposure to air.

2. Use a calculator or tables to generate two random

numbers, to use as co-ordinates and place a quadrat on the

ground wit h its corner at these co-ordinates

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3. Count how many individuals there are inside the quadrat

of the plant population being studied. Repeat stages 2 and 3

as many times as possible.

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4. Measure the total size of the area occupied by the

population, in square metres.

5. Calculate the mean number of plants per quadrat. Then calculate the estimated population size using this equation: mean number per quadrat x total area population size = -------';-----'';---,----­ area of each quadrat

152 Ecology and conservation

Niches and interactions

THE NICHE CONCEPT

FUNDAMENTAL AND REALIZED NICHES

Stud ies of the d istributio ns of organisms and of interacti on s betw een o rganisms show that there are many di fferent ways of existing in an ecosystem. The mode of existence of a species in an ecosystem is its eco logica l ni che. The niche includ es:

The niche that a species co uld occupy is often smalle r than the niche that the species actually occ upies. These potential and actual niches are call ed the fundamental niche and the realized niche of the species. Differences betw een the fundamental and realized niches are due to competitio n.

• Habitat - w here the species lives in the ecosystem. • Nutrition - how the species obtains its food. • Relationships - t he interactio ns wi th other species in the ecosystem.

O ther species prevent a species from occupying part of its fundamental niche by out-co mpeting o r by excl ud ing it in some other way .

If tw o species have a similar niche, they w ill compete in the overlapping parts of the niche, for example for breedi ng sites o r fo r food. Because they do not compete in other w ays, they w ill usually be able to coexist. However, if two species in an ecosystem have exactly the same niche they w ill compete in all aspects of their life and one of the tw o species wi ll inevitably prove to be the superio r competitor. This species w il l cause the disappearance of the other species from the ecosystem.

The fundame ntal niche of a spe cies is its potential mode of ex istence, given the adaptations o f the species. The realiz ed niche of a species is its actual mode of ex istence, which results from its adaptations and competition from other species. . Competitive excl usion happens w hen a speci es is unable to occ upy any part of its fundamental nic he in an area, so it has no realized niche in that area.

The principle that only one species can occupy a niche in an ecosystem is called the competitive exclusion principle .

INTERACTIONS BETWEEN SPECIES A ll living organisms are affected by the acti vities of ot her livi ng organisms. A situat io n in w hich tw o species affect each other is call ed an interaction . The tabl e below shows a classificat io n of interacti ons.

Interacti on

Terrest rial example

Marine exampl e

Herbivory - a primary co nsumer feedi ng on a plant or other producer. The prod ucer's growt h affects food availa bility for th e herbivore.

The beetle Epitrix atropae feeds only on leaves of Atropa belladonna, often causing seve re damage to them. To most other organisms the leaves are highly toxi c.

A lgae grow ing o n rocks in shallow seas are often heavily grazed. For example, a snail Lacuna pallida feeds on the brow n seaweed Fucus serratus on rocky shores in Europe.

Predation - a consumer feeding o n anot her co nsumer. The numbers and behavio ur of the prey affect the predato r.

The Canada lynx is a predator of the Arctic hare. Changes in the numbers of hares (up or down ) are fo llo wed by similar changes in lyn x num bers.

Bonitos feed on anchovetas in the Pacific Oc ean west of Peru. W hen the anchoveta popu latio n crashed in the 1970s starving bo nitos were found, wi th completely empty stomachs.

Parasitism - a parasite is an organism that li ves o n o r in a host and obtains food from it. The host is always harmed by the parasite.

The ti ck Ixodes scapularis is a parasite of deer and of w hite-footed mi ce in northeast USA. The ti ck feeds by sucking blood from its hosts and therefore wea kens them.

O rganisms that cause infectiou s di seases are all parasites. Fo r example, Sph ingomonas bacteria cause a di sease in elliptical star corals on the Florida reef.

Competition - tw o species using the same resour ce compete if the amo unt of the resource used by each species reduces the amo unt available to the other species.

Dou glas Fir and W estern Heml ock grow together in mi xed forests in O regon and other states in northwest USA, co mpeting w it h each other for li ght, w ater and minerals.

Speci es of coral co mpete w it h each other on coral reefs. Pocillop ora damicornis competes w ith many other cor als, including Pavona varians, w hich benefit w hen predators feed on

Pocillopora dam icornis. Mutuali sm - mutualists are members of different species that live together in a close relatio nship, from w hich both benefit.

Usnea subfloridana and other li chens co nsist of a fungus and an alga grow ing mut ualist icall y. The alga suppl ies food s made by photosynthesis and the fungus absorbs mineral ion s.

The clea ner wrasse is a small fish of warm trop ical seasthat cleans parasites from the gills and bod y of larger fish such as ret icul ate damsel fishes. The cleaner benefits because the parasites that it removes are its foo d.

Ecology and conservation 153

Biomass and trophic levels

MEASURING BIOMASS

CONSTRUCTING PYRAMIDS OF ENERGY

Eco logists often use a measure ca lled biom ass.

Pyramids show the energy f low th rou gh each trop hic level in an ecosystem. To constr uct a pyra mid of energy, energy fl ow throu gh each species in the ecosystem must be measured . In each troph ic level the energy f low through all species is added up.

Bioma ss is the total dry mass of organic matter in organisms or eco systems. For example, if an eco log ist wa nted to compare the amo unts of o rganisms in each trophi c level in an ecosystem, biom ass mi ght be used . M easurin g biomass is a destruct ive techn iqu e, so the samp les used are as small as possible.

Method 1. Representative sampl es of al l living o rgani sms in the ecosystem are co llected, fo r example from randomly positioned qu adrats. 2. The organisms are sorted into trop hic levels. 3. The organi sms are dri ed, by bein g placed in an oven at

60-80°C. 4 . The mass of o rganisms in each trophic level is measured using an electronic balance.

5. Dr y ing and measuring the mass may be repeated to c heck that samp les we re co mpletely d ry.

DIFFICULTIES WITH TROPHIC LEVELS Sorting organisms into trophi c levels can cause co nsiderable di ffi cu lti es. Thi s is because many species exist partly in o ne trophic level and partly in anot her. The fo llowi ng examp les illu strate th is. • Euglena, a uni cellular orga nism fo und in po nds, has c hlo rop lasts and photosynthesizes, but it also feeds heterorophicall y by endocytos is. • Chimpanzees main ly feed on fru it and ot her plant matter, but they also sometimes eat termit es and even larger animals such as monk eys, so they are bot h fi rst and second co nsumers. • Herrin g are second co nsumers w hen they feed on Calanus (a cope pod) and other first co nsumers but they are thi rd co nsumers w hen they feed on sand eels and other second co nsumers. • Oysters (Ostrea species) and many other filter feeders co nsume bot h ultraplanktoni c producers and mi croplanktoni c consumers, so they are first and second consumers. They also consume dead organic matter, so they are also detriti vores. It is di ffi cu lt to decid e into w hic h trophi c level these types of organism should be classif ied. O ne practi cal so lutio n is to classify each species acco rd ing to its main food source.

NUMBERS AND BIOMASS OF ORGANISMS IN HIGHER TROPHIC LEVELS Pyramid s of energy show that there are large losses of energy at each trop hic level. Reasons for losses of energy are explai ned on page 41 . Losses of energy in ecosystems are acco mpanied by losses of biom ass. Respir ation is an examp le of a process in w hic h bot h energy and biom ass are lost. Wh en glucose or anot her respiratory substrate is ox idi zed in respirati on , energy from the gluco se is released fo r use in the ce ll and is then lost as heat. The mass of the glucose does not disappear - it passes into the carbon d iox ide and wa ter that are produ ced in respiration . Wh en

154 Ecology and conservation

The lo west bar of a py ramid of energy is the total amo unt of energy that flows th rough the producers in the ecosystem . This is also called gross pro duction.

Cross production is the total amount of organic m atter produced by plants in an ecosystem. Gross producti on and all the other energy fl ows in a pyra mid are measured in ki lojou les of energy per square metre per year (k] m-2 year"). Gross produ ction does not have to be measured d irectl y, as it can be calcu lated from net production and plant respirati on.

Net production is the amo unt of gross production in an eco system rem aining after sub tracting the amo unt used by plants in respiration. gross prod uction = plant respiration

+ net pro ductio n

Exa mple - an old field com m unity in Michigan, USA. net prod ucti on = 20.79 x 10 3 k] m-2 vear ' plant respiration = 3.68 x 10 3 kj m-2 vear' gross prod uct ion = (20.79 + 3.68) x 10 3 k] m-2 vear' = 24 .47 x 10 3 k] m-2 year' The upp er bars of a py rami d of energy are the total amo unts of energy th at flo w throu gh the variou s groups of co nsumers. This is the amo unt of energy in the food that the co nsumers ingest. The data below was obtained from an Arcti c tundra ecosystem on Devon Island in northern Canada. Trophi c level Producers

Energy f low (k] m-2 year:")

4925

Primary co nsumers

24

Second ary co nsumers

4

Thi s data can be used to co nstruct a py ramid of energy. Each bar of the pyramid should be draw n to the same scale and labelled w ith the trophic level.

these waste produ cts are exc reted, biom ass is lost. As a result of respiration and other processes, both energy and bio mass are lost at each stage in a foo d chai n. The energy co ntent per gram of foo d does not decrease alo ng a food chain. If anything, the foo d eaten by the higher trop hic levels is richer in energy per gram than that eaten by low er trophic levels. However, the total biom ass of foo d available to higher troph ic levels is very small. It cannot suppo rt large numb ers of o rganisms, especi ally if these organi sms need to be large to over power their prey. Hi gher trophi c levels therefore usually co ntain very small numbers of large organi sms, wi th a low tot al biomass per un it area.

Succession and biomes

ECOLOGICAL SUCCESSION

BIOMES AND BIOSPHERE

A n eco logica l successio n is a series of changes to an ecosystem, caused by co mplex interactio ns betw een the community of li vi ng organisms and the abiotic environment. Tw o types of successio n are recognized: Primary succession starts in an environment w here livi ng organisms have not previo usly existed, for example a new island, created by vo lcanic activity. Secondary succession occ urs in areas w here an ecosystem is present, but is replaced by other ecosystems, because of a change in co nditions. For example, abandoned farmland developing into forest. Du rin g an eco logical successio n, the co mmunity causes the abio tic environment to change. As a result, some species di e out and others join the co mmunity . A lthough the co mmunity may continue to c hange in this w ay for hundreds of years, eventually a stable community develops, called the cl imax co mmun ity. The changes to the abioti c environment dur ing ecological successio ns vary, but some often occ ur. • The amount of organic matter in the soil increases as o rganic matter released by plants and other o rganisms accumulates. • The soil becomes deeper as organic matter helps to bind mi neral matter together. • The soil structure improves as the organic matter content rises, increasing the amount of water that can be retained and the rate at wh ich excess water drains throug h. • Soil erosio n is reduced by the bindi ng actio n of the roots of larger plants. • The amounts of mi neral recycli ng increases, as the soil can hold larger amo unts and more minerals are held in the increasing biom ass of the community.

Ecol ogical successio n usuall y stop s w hen a stable ecosystem develop s that contains a group of organisms called the cl im ax co mmuni ty. Di fferent types of ecosystem develop in d ifferent parts of the w orld . A type of ecosystem is called a biome .

AN EXAMPLE OF PRIMARY SUCCESSION

MAJOR BIOMES OF THE WORLD

O n t he slopes of Vol can O sorno, in southern Chile, there are large areas of bare vo lcanic ash, released duri ng recent eruptio ns of the vo lcano. Adj acent areas show the stages in an eco logica l successio n. • M osses spread over the ash, eventually forming a complete cover. • Small herbs jo in the mosses. • Shrubs, including Pernettya, Eucryphia and Emb othrium, enter the community and gradually replace the herbs and mosses. • Trees, inclu ding Nothofagus, gradually spread to replace the shrubs w it h dense fo rest.

Rainfall and temperature are the two main factors that determ ine w hat typ e of ecosystem develo ps in an area, and therefo re w hat the distributi on of bio mes arou nd the wo rld is. The c1imograph below show s the relatio nship betwee n the levels of these tw o facto rs and the types of biome. The characterist ics of six major bio mes are descr ibed below . The biomes of the wo rld together make up the bio sphere. It is now wel l know n that the ecosystems and bi omes of the wo rld functio n as one overall ecological system; so the biosphere is the thin layer of interdependent and interrelated ecosystems and bio mes that cover the Earth.

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500 1000 1500 2000 2500 3000 3500 4 000 4500 rainfall / mm year:'

Desert

Rainfall very low ; wa rm to very hot days and co ld nights.

Very few plants, some stor ing water and some grow ing qu ickly after rain .

Grassland

Rainfall low ; w arm or hot summers and co ld w inters.

Dom inated by grasses and other herbs that can w ithstand grazing.

Shrubland

Coo l wet w inters and hot dry summers, often w ith fires.

D rought-resistant shrubs dom inate, often w ith evergreen fo liage.

Temp erate deciduous forest

M oderate rainfall w ith wa rm summers and cool w inters.

Trees th at shed th eir leaves in the w inter do m inate w ith shrubs and herbs beneath.

Tropical rainforest

Rainfall high to very high and hot o r very hot in all seasons.

A huge d iversity of pl ants: tall evergreen trees, smaller trees, shrubs and herbs.

Tundra

Very low temperatures; littl e precipitation mostl y as snow .

Very small trees, a few herbs, mosses and li chens are present.

A stage in succession to forest on Volcan Osorno

Ecology and conservation 155

Biodiversity and rainforests

BIODIVERSITY

RAIN FOREST CONSERVATION

The w or d biod iversity w as only invented in 1986. It is an abbrevia tio n of ' bio log ica l di versity' and enco mpasses the d iversity of ecosy stems o n Earth, the di versity of specie s w ithi n them, and the genetic di versity of each spec ies. O ne of the main tasks of eco log ists is co nservatio n of the w orld 's bi od iversity .

A ll of the wo rld's bi om es m ust be co nserved, but trop ical rain forests have been part icul arly th reatened recently and there are many reasons fo r strenuo us effo rts to co nserve them .

THE SIMPSON DIVERSITY INDEX It is sometimes useful to have an overall measure of species ric hness in an ecosystem. The Simpso n index is one of th e most co mmo nly used. M eth od 1. Use a random sam pling tec hnique to search for o rganisms in the ecosystem. 2. Identify each of the orga nisms found . 3. Co unt the to tal num ber of ind iv idu als of each species. 4 . Calc ulate the index (D).

Economic reason s New com mo di ties, for examp le medi cin es or materials, may be found in rainforest speci es. o New crop plants or farm animals co uld be developed from rainfo rest spec ies or ex isting varieties co uld be improved using thei r genes. o Ecoto urism cou ld prov ide conside rable incom e. o

Ecological reasons Rain fo rests fi x large amounts of carbo n dioxid e and, wi thout them, the greenho use effect and globa l wa rming wo uld probab ly be more severe. o D amage to rainforests can have widespread effects including soi l ero sion , sil ting up of rivers, f loodi ng and even changes to wea ther patterns. o

Ethical reasons

D = N (N - 1) ~ n (n - 1)

Every species has a right to life, regardl ess of w hether it is useful to hum ans or not. o The w ild life of rain forests has cultural imp ortance to the ind igeno us hum an popu lation s and it is therefor e wro ng to destroy it. o It wo uld be w ro ng to deprive hum ans of the future the ric h experiences th at the Earth 's biod iversity provid e to us. o

N = tot al numb er of organisms n = numb er of indiv idu als per species Example O rganisms w ere fou nd and id entified in the River Enni ngdalselva in a part of Swe de n w here some lakes and rivers have been affected by acid rai n. Six sites in the riv er w ere chosen random ly and kick sampling w as used at each site alo ng a 10m transect. Nets w ith a 25 cm x 25 cm opening and 0.5 mm mesh we re used . The results are shown in the tab le below. Group

Species

Name

Ephemerida

Oixa species

Mayfly larva

Rain forests have species in them that are beauti ful and give us great enjoyment. o Painters, w riters and co m posers have been and co ntinue to be inspired by rainforests. o

8

Odonata

Tipu fa species

Dragonfl y larva

5

Trich op ter a

Species unidentified

Caddisfly larva

4

Plecoptera

Nemoura variegata

Stonefly larva

4

Hemiptera

Gerris species

Pond skater

3

Isopoda

Asell us aquaticus

Water louse

2

Acari

Arrhenurus species

Water mite

Platyhelminth

Oendocoefum fact.

Flatworm

4

Platyhelminth

Ougesia species

Flatworm

3

Hirundi nea

Species unidentified

Leach

O ligochaeta

Lumbricufides

Annelid worm

2

Gastropoda

Lymnaea species

Snail

4

Bivalvia

Margaritifer

Pearl mussel

D = 42 (42 -1) = 12.3 140 The high diversity index suggests that the river has not been damaged by aci d rai n, o r any other disturbance. This fits in w ith observation s of a thr ivi ng salm on pop ulatio n in the riv er. If the Simpson divers ity index w as calcu lated for another river in the same area, or a river in the same biom e elsewh ere in th e w or ld, the eco logical health of these rivers co uld be compared with River Enni ngdalselva. This wo uld help to assessw hether co nservati on measures w ere needed in any of the rivers. It would also allow rivers w it h high biodi versity to be identified and given appro priate co nservatio n status, fo r examp le as nature reserves.

156 Ecology and conservation

Aesth et ic reaso ns

BIOMAGNIFICATION Som e po ll utants are absorbed into living o rgani sms and accumu late because they are not effic ient ly exc reted . W hen a predator co nsumes prey co ntaining the pol lut ant and absorbs it, the level in the body of the predator rises and can reach levels much higher than those in the bodi es of its prey. Th is increase is calle d bi om agni fi cat ion and it can happen at each stage in the foo d chain. Biom agnifi catio n is the p rocess by w hic h chem ica l substances beco me mor e concentrated at each trop hic level. Polych lor in ated bipheny ls (PCBs) are chemica ls that w ere used as insu lators in elect rica l devi ces and as flame­ retardants. It was shown as long ago as 1953 that mod erate do ses ki lled experimental rats, but manufact ure co nt inued unt il the 1970s. PCBs have escaped into the environme nt and are now detectable thr ou ghout the w or ld . They are bot h persistent and hi ghly toxi c. Bioaccu mul ation facto rs (BAF) for PCBs vary co nsiderably. Examples are give n below .

Pathway

BAF

So il to earthworm Fish to bird or mamm al W ater to f ish W ater to shell fish

10 90 50000 10 000 000

Impacts of humans on ecosystems

IMPACTS OF ALIEN SPECIES A n alien species is a type of organism that hum ans have introdu ced to an area w here it does not naturally occ ur. A lien species are someti mes very invasive and cause co nside rable ecologica l damage. For examp le, the f loati ng fern, Salvinia molesta, has damaged many lakes in the trop ics and sub­ tropi cs. It grows rapidl y, doubli ng the num ber of leaves in about two weeks, spreading ove r the wa ter surface and elim inating native pl ant species by interspecific competition . it has been contro lled by introdu ci ng anoth er alien species­ salvi ni a weevil (Cyrtobag us salviniae), w hich feeds on the fl oating fern. This is an example of biological control.

Salvinia m olesta was deliberate ly transported around the wor ld as an aquari um o r pond plant. A lien species have also been introduced acc identally. For example, three species of rat we re introduced to the mai nland of New Zealand duri ng the 19th century. They caused many species of bird to d isappear from the mai nland. This is calle d species extinction. Some of these bird s were able to survive on islands that remained free of rats. Until the 1950s, Big South Cape Island in th e far south of New Zealand remained rat-free and was a haven for many rare bird s. Three types we re, by then, found nowh ere else: South Island sadd leback, Stewart Island snipe and Stead's bush w ren. South Island Saddleback

In the mid-1950s black rats (Rattus rattus) reached Big South Cape Island. Their numbers rose exponentially and by 1964 there were huge num bers on th e island. They attacked eggs, you ng bird s in nests and even adult bird s, wh ich w ere not behaviour all y adapted to resist them. Thi s is an examp le of alien species causing damage by predation . It became obv ious that human interventi on was needed to save the three rarestspecies of bird . Ecologists from the New Zealand W ildlife Service trapped as many of the remain ing indiv iduals as they could. O nly two Stewart island snipe we re trapped and they died soon after, so this species became ext inct. N ine Stead's bush w rens we re trapped and transferred to another island that was still rat-free. Unfortunately they failed to breed and gradually died out, so'this species also became extinct. Forty-one South Island saddlebacks we re caught and transferred to two other rat-free islands. They survived and bred and were eventually distrib uted to other islands. In the 1980s they we re re-introduced to Little Barrier Island after another alien species had been eli minated - w ild cats. The South Island saddlebac k was the first species of bird to be saved fro m extinctio n by human interventi on. Its future for the moment seems rel atively secure.

Islands in the far south of New Zealand

Stead's bush wren

r

South Island of

New Zealand is

20km to the north

OZONE AND ULTRA-VIOLET RADIATION Ultra-vi ol et radi ation has very damaging effects on living organisms and biol ogical produ ctivity. • • • •

It increases mut atio n rates, by causing damage to DN A. It can cause cancers, especially of the skin. It causes severe sunburn and cataracts of the eye. It redu ces photosynthesis rates in pl ants and algae and so affects food chains.

The amou nt of damaging ultr a-viol et rad iation reachi ng the Earth's surface wo uld be much greater w ithout the ozo ne layer in the atmosphere. Ozone absorbs shortwave rad iation, especia lly ultr a-viol et. At low altitudes in the atmosphere, the concentratio n of ozo ne is usuall y about 0.0 1 ppm, but at 20-50 km above the Earth' s surface, in the stratosphere, ozo ne is much more concentrated - about 1-1 Oppm . This is the ozo ne layer.

Measurements of ozo ne concentratio ns in the stratosphere have show n th at there has been dep letio n throughout the wo rld. Since the 1980 s an ozo ne ' ho le' has appeared over the A ntarctic every year between September and October, wh ich persists for several month s. CFCs are the mai n cause of ozo ne depletio n. They are chemica l co mpounds manufactur ed by hum ans and released into the atmosphere. U ltra-vio let light causes CFCs to d issociate and release atoms of chlo rine. These chlorine atoms are highl y reactive and cause comp lex reaction s in whi ch ozone is con verted to oxygen. The reacti ons form a cyc le, with the chlo rine atoms being released again, so that they can go on to cause the destructi on of more ozo ne. O ne chl orin e atom can potentially cause th e destruction of hund reds of thousands of ozo ne mol ecul es.

Ecology and conservation 157

Conservation IN-SITU CONSERVATION METHODS

ACTIVE MANAGEMENT TECHNIQUES

The best place to co nserve a species is in its own habit at. Thi s is ca lled in situ conservatio n. M any terrestri al and marin e natur e reserves have been established for thi s purpose, but ot her areas can also be important, incl udi ng farmland and gardens.

Some pri stine nature reserves can be left in their natural state, but often hum ans have caused changes and acti ve management is therefo re needed to ensure the surv ival of rare o r endangered species. The Hin ew ai Reserve in the South Island of New Zealand is a good examp le of limited, but effect ive, management. Va lleys that had been cl eared of nativ e forest to becom e farm land have been allowed to revert to native fo rest, by secondary successio n. Acti ve co nservatio n measures have included th e cull ing of goats. They are an alien speci es and damage nativ e plants by grazing. Native plants are now re-establ ishin g at H inew ai at an amazing rate.

In situ conservatio n has several adva ntages. • • • •

Species remain adapted to thei r habitats. Greater genetic diversity can be co nserved . An imals maintain natura l behaviour patterns. Speci es interact w ith each other, hel ping to co nserve the w hole ecosystem.

The size and shape of nature reserves affects their conservation value. The di stributi on of ecosystems withi n a natur e reserve is also imp ortant. These are the biogeographi cal feat ures of a nature reserve. Large nature reserves usually promote co nservat io n of biodiversity mor e effect ively than small ones. The eco logy of the edges of ecosystems is different f rom the central areas, due to edge effects. An example of an edge effect is the egg-lay ing habits of the cowbird of the w estern Un ited States. It feeds in open areas on insects disturbed by large grazing mamm als, but it lays its eggs in the nests of songbirds, near the edges of forests. Fragmentation of forests has led to a co nsiderable inc rease in cowbird popul ati on s and the nest parasit ism due to them, because of the increase in forest edge. W here a habitat is fragmented, w ild life co rrido rs can be very valuable in allowing organisms to move between different areas, for example tunn els under busy roads.

MONITORING ENVIRONMENTAL CHANGE Problems in natural ecosystems are detected qu ickl y if there is frequent environmental mon itorin g. Abi oti c factors can be measured direct ly, but another usefu l technique is the use of living organisms to detect changes. Ind icato r species are very useful, as they need particul ar enviro nmental conditions and therefore show w hat the co nditio ns in an ecosystem are. Lichens are valuable indica tor species because their to lerance of sulphur di oxide varies considerably from the most tolerant to the least tolerant species. Indi cator species are also often used to assess poll ution levels in aquatic ecosystems. Stonefly, mayfly and caddisfly larvae (below) requ ire unpo lluted, we ll­ oxygenated wa ter. Other aquatic species, incl uding chironomid mid ge larvae, rat-tailed maggot larvae and tubifex w orm s, indica te low oxygen levels and excessive levels of suspended organic matter, from untreated sewage for example. Ind icator species in aquatic ecosyste ms Indicators of high

EX-SITU CONSERVATION METHODS Despite the adva ntages of in situ co nservat io n, it is not always enough to ensure the surviva l of a species. • Some speci es becom e so rare that it is not safe to leave them unprotected in the w ild . • Sometimes destructi on of a natural habit at makes it essential to remove threatened species from it.

~O"'

158 Ecology and conservation

O"-::J'no",

5tonefly nymph (up to 30mm)

Chiron omid (bloodw orm: a midge larva) (up to 20mm)

M ayfl y larva (up to 15mm)

Rat-tail ed maggot larva (up to 55mm incl uding tube)

In these situatio ns ex situ measures are needed. 1. Capt ive br eedin g - some or all memb ers of a speci es are caught and moved to a zoo , wh ere they are encouraged to breed. Wh en numb ers are high eno ugh, some are return ed to the w ild to re-establ ish a natur al populatio n. An exam ple of a species help ed by captive breedin g is the Haw aii an kestrel. 2. Bot anic gardens:- sites w here many di fferent species of plants are culti vated, either in greenhouses or in the ope n. O ne of the largest, the Royal Botanic Ga rde ns of Kew , has more th an 50000 of the world' s 250 000 kno wn species in its co llect io n. 3. Seed bank s - seeds are kept in co ld sto rage at - 1OQC to - 20Q C. Seeds of most species remain vi able for mor e than a hundred years in these conditions. Ot her specie s that are not as lon g lasting can be germinated and grow n to prod uce rep lacement seed befor e vi abilit y is lost. The Kew Mi llenn ium Seed Bank w ill eventually hol d seed of 25000 endangered species.

Indi cators of low

~ r): · -

.~kF, <'! ~

.

" " "

Caddisfl y larva (up to 30mm)

~

~

Tubifex (sludge wor m) (up to 40mm)

To obtain an ove rall env ironmental assessment of a riv er or other ecosystems, a biotic inde x can be calculated. There are various method s, whi ch usuall y invo lve mu lti plyin g the numb er of individuals of each indi cator species by its po llution to lerance rati ng. An abundance of tol erant species gives a low ove rall sco re and an abunda nce of int o lerant species gives a high score.

Population ecology

ESTIMATING ANIMAL POPULATION SIZES

r-STRATEGIES AND K-STRATEGIES

It is usually impossible to count every individual in a popul ation . Instead an accurate estimate is made. Ecol og ists often need to measure the size of a popu lation . T nere are many rnern oos 'or maKin g estim ates popul ation size. The capture- mark- release-recapt ure meth od is suitable for ani mals that move around and are di ffi cult to find .

Liv ing organisms differ great ly in their life cycl es and their patterns of reprodu cti on . As a result, there are different patterns of popul ati on grow th. Natural select io n can cause th ese ch
0'

Strategies for an unstable environment

CAPTURE-MARK-RELEASE-RECAPTURE METHOD 1. Capture as many individuals as possible in the

area occupied by the animal population,

using netting, trapping or careful searching

In an unstable environment, life exp ectancy is very short and few individua ls survive long enough to reprodu ce even once. The po pulatio n of a spec ies in these env iro nmental condit io ns is unlik ely ever to becom e large enou gh for density-dependent factor s such as co mpet itio n to becom e im port ant. The most successful species use r-strategies: • o nly growi ng to a small body size, whi ch can be qui ck ly reached • maturing early, so reprodu cti on happens wh ile still young • reprodu cin g once only, with all available energy and resources devoted to it • prod uci ng many offspring, wi th a relatively small body size • givi ng offspring littl e or no parental care.

2. M ark each indiv idual, without making them more visible to predators. e.g. marking the inside of the snail shell w ith a dot of non-toxic paint.

If all or most offspring survi ved and reached reproductive maturity, there wo uld be exponential population growt h and probably over -populatio n. W ith r-strategists thi s is ver)' unlikel)' because the chance of survival of their offspring is so small . Exampl es of r-strategists Eschschoftzia cal ifom ic a (Califo rnian popp y) Lemmu s lemmus (lemming) Clup ea harengus (herring)

Strategies for a stable environment 3. Release all the marked individuals and allow them to settle back into their habitat.

c:~. L---£..

~~--.

~~

_J:.~>

~ .- ".1. , -~

. •

4. Recapture as many indivi duals as possible and count how many are marked and how many unmarked. . ",

.~" ;"

'•.'Ii :

•.1 _ .1:..

~ ~ ~ ~I ~ ~ -~ 'lifi'.o..I ~

_II. .

24 marked

";d~&b.;~.iG~~~

16 unmarked

5. Calculate the estimated population size by using the Lincoln index: population size = n1 x nz

n3 n1 = number caught and marked initi ally

nz = total number caught on the second occasion

In a stable environme nt, life expectancy is much lo nger and many indi vidual s w ill survive lo ng enou gh to reprodu ce repeatedly. The popu lation of a species in these environmental co nditions is likely to becom e large eno ugh for density-dependent factors such as competitio n to become important. The most successful species use K-strat egies: • grow ing to a large body size, w hich is an advantage in intra-spec ific com petition • maturing late, with reprodu cti on not beginning until an individual is rel atively o ld • reproducin g mor e than once and sometimes many tim es du rin g the extended life-span • producin g few offspring, w ith a relatively large body size • giv ing much parental care to offspring. Larger numbers of small offspring would make a higher rate of

pop ulation grow th possible. With K-strategists, rapid

populatio n grow th is unlikely ever to continue for long,

because it w ill lead to intense co mpetitio n. Small offspring, o r

offspring that are not nurtur ed by their parents, are unlikely to

co mpete effectively enough to reach adu ltho od.

Examples of K-strategists

Q uercus petraea (sess ile oak tree)

Loxodon ta africana (Afri can elephant)

Oermo chel ys coriacea (leatherback turt le)

n3 = number of marked individuals recaptured

Ecology and conservation 159

Fish conservation and species extinctions

SUSTAINABLE YIELDS OF FISH

ESTIMATING SIZES OF FISH STOCKS

W ild populatio ns of fish are an importa nt food source fo r many human pop ulatio ns. They are a renew able resour ce - a resou rce that need never run out, if it is used in a sustainable way . A renew able resou rce is constantly replaced or replenished, in the case of fi sh by them reprodu cin g and grow ing.

It is very difficult to estimate the size of commercia l fish stocks accurately . Thi s is because fish cannot be seen f rom above the wate r surface and many species move around rapidl y o r are not distrib uted evenly, so random sampling methods are ineffective. The usual method of est imati ng stocks invo lves co llecting data on fish catc hes. The num bers of fish of each age are cou nted and an age distr ib ut ion for the pop ulat io n is obtai ned. Survivors hip curves and spawning rates can then be ded uced, from wh ich esti mates of the total stoc k can be made. However there are great uncertainties, fo r examp le w hat proportio n of the total populatio n has been caught. Capture-mark-release- recapture methods have been used, with fish marked using internal or external tagging. This method can wo rk we ll in lakes, but it is less successful in the ope n sea. By the time the marked fish have mixed back into the ove rall populatio n by migratio n, the proport io n of marked fish that can ever be recaptured is too smal l for accurate estimates of the size of the stock. Other method s of estimatio n of fish stocks have been used in specific situatio ns. Echo sounders can be used to measure the size of shoals of fish, or even single fish in some cases. The fish must not be swim ming too deeply and trawl s must also be used for calib ration and to check w hich species offish has been detected by the echolocat ion. No ne of these methods can estimate stoc ks with anythi ng approachi ng certai nty and, as a result, di sputes between the fishing indu stry and conservation agencies abo ut stocks are very co mmo n.

Sustainab le use of renew able resource means harvesting at a rate that avo ids a decl ine in the resource. This is particul arly im po rtant w ith fish popul ation s. If they are over-ex ploite d and the num bers of adult fish fall below a cr itical level, spaw ni ng fai ls. The disastrous co llapse in the Peruvian anchoveta fishery is an example of thi s. Indu stri al scale explo itatio n of the anchoveta began in 194 0 and grew at a rapid rate until 1973, w hen the annual catc h dropped from 12 mill ion tonn es to zero. The fall in anchoveta egg production in the years preceding the pop ulatio n crash is show n in the graph below . An EI Ni no event was partly respon sibl e, but ove r-fishi ng w as also a major facto r. Graph showing a collapse in anchoveta egg production 6000 <11

Q.

E

:Jl Qj

Q.

CD '" CD

U.J

5000 400 0 30 00 2000 1000 0

W ith fisheries, sustai nable use means not catc hing fish faster than the stocks can replenish themselves. The maximum sustainable yield is the largest amo unt that can be harvested wi thout a declin e in stocks. One of the aims of research into fisheries is to determin e wh at the maximum sustainable yie ld of particular fisheries is. Internation al co-o peratio n is then usuall y needed to ensure that th is yield is not exceeded.

INTERNATIONAL CONSERVATION OF FISH International measures are needed to promote fish co nservatio n because most fish live in internatio nal wa ters, wh ere ships from any cou ntry can catch fish. Var io us measures w ould help. • Monito ring of stoc ks and of reprodu ction rates. • Q uotas for catc hes of species with low stocks . • Closed seasons in w hich fishing is not allowed, especially during the breedi ng season. • Excl usio n zones in w hic h fishi ng is banned. • M o ratori a on catc hi ng endangered species. • M inimum net sizes, so.that immature fish are not caught. • Banning of d rift nets, w hich catc h many di fferent species of fi sh indi scrimin ately. Some of these measures have been used already in parts of the wo rld, w ith lim ited success. Enforcement -is very di ffi cult and relies on a level of internat io nal trust and co -operatio n th at is not always seen.

160 Ecology and conservation

EXTINCTION OF SPECIES W hen the last members of a species die, the species beco mes exti nct. The rate of species extinctio ns is probably at an all­ time high at the moment, as a result of human activities. There are unfortun ately many exti nct species from w hic h to select examp les for study, including the passenger pigeo n and the do do. The example described here is the Caro li na parakeet, Conuropsis carolinensis. These brightl y co loured parrots (rig ht) were once common in forests to the east of the Mississipp i, from New York to Florida, feeding on seeds of trees and herbs: Clearance of forests reduced their habitat and they started to feed o n c rops. Farmers ki lled many of them. Others were caught to obtain feat hers, which we re used to make fashio nable women's clothing . They we re also trapped and kept as pets. By 1900 there we re no Caroli na parakeets in the wi ld and the last specimen d ied in Ci ncinnati Z oo in 1918.

EXAM QUESTIONS ON OPTION G - ECOLOGY AND CONSERVATION Gl Food chains are d ifficult to study in natural ecosystems, so a group of eco logists set up co mmun it ies in cu lture vessels. They used them to investigate the effects of varying nutrient co ncent ratio ns. In all of the vessels an aquatic bacterium , Serratia tnetcescens, was present. Three co ncentratio ns of the nutri ents on wh ich S. m arcescens feeds we re used. In some of the cu ltures Colpidium striatum, a predator of S. mercescens, was added. In some of these cultures Didinium nasutum, a predator of C. striatum, was added . The cultu res therefore each had one, two or three trophic levels. The populatio n density of S. m arcescen s at the end of the experi ment is shown in the bar chart below.

1000000

c

.9

'5 ---0

~~

100000

'" ~ U Q,j -

iDS o o

::J

.... u

~'O .

I

merc esce ns only

s. marcescens and C. striatum S. marcescens and C. striatum and O. nasutum

,I

I

(j)

::: ~

10000

0­

>-0

> c: c:

~

f---­

0;j) .":::

-

CJ ::J ~~

s W~

1000

======

======

= =

.~ - ..0

~E

= =

-

o ::J c:

Q..

-

100

75

5

1000

Nutrient level/mg litre- 1 [Source: Kaunzinger, Nature (1998), 395, pages 495-496]

a) (i) Explain the effect of the nutrient co ncent ration on the popu latio n density of S. marcescen s.

[1]

(ii) Explain the effect of t he presence of C. striatum on the po pul ation density of S. marcescens .

[1]

(iii) Explain the effect of the presence of D. nasutum o n the popu lation density of S. marcescens.

[2]

b) In the culture wi th the lowest nutrient level D. nasutum eventuall y died out but C. striatum survive d. Explain the reason s for D. nasutum dy ing out.

[2]

c) Using the results of this investigatio n, predict a relationship betwee n nutrient level s and length of food chain in natura l ecosystems.

[1 ]

G2 a) Explain how indicato r species may be used.

[2]

b) O ut li ne two ex situ methods of conservatio n of endangered species.

[2]

G3 The graph below shows inputs of mercury from the UK to marine waters and flow rates of rivers, betwee n 1990

and 2004 , as a percentage of levels in 1990.

160 140

-- ---- --- Riverine flow rate

- - - mercury

I

I ,

,

I

,

I

(j)

120

::J

~ 100

o

~

...,

--_!_<~ ~-~-~ -~ ~:. ~-~ . _::>.,,< ~ ~-~~/ ::

/ ,'0__ _ /

,

\

/

"

..- \

\\

_.:'\ /'

80

'0 60 ~

o

40 20

oj 1990

' "1994

1992

,

,

1996 1998 year

,

2000

[

2002

-,

2004

a) State the trend in mercury in puts from the U K to marine waters.

[1]

b) Using the data in the graph, deduce the reason s for fluctuations, from year to year, in mercury in puts.

[2]

c) Biom agni ficati on of mercur y can occ ur in marine ecosystems. Suggest two co nsequences of biomag nification of mercur y in ecosystems.

.

,.

Ecology and conservation - IB Questions 16 "!

Hormonal control

HORMONES Hormones are chemica l messengers, secreted by endoc rine glands directl y into the blood . The blo od carries them to target ce lls. w here they elici t a response. A w ide range of chemica l substances is used as hormones in hum ans: Steroids e.g. estrogen, pro gesteron e, testosteron e Peptides e.g. insul in, ADH, FSH, LH Tyrosine derivatives e.g. thyrox in

Structures of the hypothalamus and pituitary gland Cell bodies of neurosecretory cells in two hypothalamic nuclei (other nuclei indicated by dotted lines)

Neurosecretory ceIIs w ith nerve endings on the surface of blood capillaries _--------- --- ---- ------

HYPOTH ALAM US (area inside dashes)

1_

C,\\

.>:

... i

MODE OF ACTION OF HORMONES Hormones do not all w ork in the same way. There are tw o main types of mechanism. 1. Steroid horm ones enter target cells by passing throu gh the plasma membr ane. They bind to receptor prot eins in the cytoplasm of target ce lls, to fo rm a hormon e-receptor complex. This co mplex acts as a regul ator of gene transcription , by binding to specific genes. Transcr iption of some genes is promoted; other genes are inhibited. In th is way steroi d hormon es co ntro l w hether or not particul ar enzymes or other proteins are synthesized. They therefore can help to co ntro l the activ ity and developm ent of target cells. 2. Peptid e horm on es do not enter ce lls. Instead they bind to receptor s in the pl asma memb rane of target cells. The bindin g of the hormon e causes the release of a second ary messenger insid e the cell. The secondary messenger causes a change to the activi t ies of the cell, usuall y by act ivating or inhibiting an enzy me.

HYPOTHALAMUS AND PITUITARY GLAND The hypoth alamu s is a small part of the brain th at links the nervou s and endocr ine systems. It co ntrols hormon e secretio n by the pituitary gland located below it (show n in the figure, above right ). The anterio r and posterior lob es of the pitu itary gland are co nt rolled in a d ifferent way by the hypoth alamus: Anterior pituitary - neurosecretory cells in the hypoth alamus secrete ho rmon es, called releasing hormon es, into capillaries in the hypoth alamu s. These capillaries join to form a blood vessel that lead to the capillaries in the anterio r pituitary. Thi s vessel is a port al vein - an unusual type of blood vessel that carries blood directl y from one capillary netw ork to another. The releasing horm on es st imulate the anterior pituitary to secrete hormones. For example, G nRH stimulates the release of FSH and LH . Posterior pituitary - neuro secreto ry cells in the posterior pituitary synthesize horm on es, pass them via axons to nerve end ings in the posterior pituitary and contro l their secretio n. The secretion of ADH is controlled in thi s w ay (see right ).

162 Further human physiology

Nerve tracts containing axons of neurosecretory cells

Portal vesse l, Network of link ing two capiIlaries capi lIary receiving networks hormones from neurosecretory cells

Netwo rk of capillari es that release hypothalamic hormones and absorb anterior pituitary hormones

Nerve endingsof neurosecretory cells secreting hormones into capillaries (not show n) POSTERIOR LOBE O F PITUITARY GLAND

ANTERIO R LOBEOF PITUITARYGLAND

CONTROL OF ADH SECRETION Neurosec reto ry ce lls in the supra-optic nucl eus of the hypoth alamus synthesize A D H, transpo rt it down their axons and store it in nerve end ings in the posterio r pituitary gland . O smorece pto r ce lls in the hypoth alamu s monitor the co ncentrat ion of the blood pl asma. If the plasma becom es too concentrated, impulses are passed to the ADH-secretin g neurosecretory cells, w hic h convey the impulses to their nerve endi ngs in the posterior pitu itary. The impul ses sti mulate release of A D H into the blo od from the sto res in the nerve end ings. ADH causes a reduction in the concentratio n of the blood pl asma, by stimulati ng the kidn ey to produ ce hypertonic urin e (see page 102). If the osmorece pto r cells detect that the co ncentratio n of blo od pl asma is too low , the neuro secretory ce lls are not stimul ated to release A D H and the blood ADH level rapidl y drops , allowing larger vo lumes of dilute hypotonic urine to be exc reted .

Secretion of digestive juices

SUMMARY OF DIGESTION

CONTROL OF GASTRIC JUICE SECRETION

Food is digested as it passes along th e alimentary canal, from the mouth to the anus. Longit udi nal and ci rcular mu scle fibr es in the w all of the alimentary canal contract and relax, squeezing the food and breaking up large so lid lumps. D igestive j uices, contai ning enzymes, are mixed w ith th e food . The enzy mes di gest proteins, nucl eic aci ds, starch and other macro molecu les. Di gestive jui ces are secreted by the saliva ry glands, by glands in the wa ll of the sto mach and by t he pancreas. These are all examples of exocrine glands.

The control of di gestive j uice secretio n invol ves both nerves and hormones. The contro l of gastric j uice secretion is described here as an example. Before food reaches the stomach, gastric jui ce is already being secreted, as a result of a ref lex actio n. The sight or smell of food stimu lates the brain to send nerve impul ses to exocri ne gland cells i n th e wa ll of the stomach . Th e gland cells start to secrete gast ric juice in respo nse. Mu ch more gastric juice is secreted w hen food enters the stomach. The food is detected by tou ch receptors and chemo receptors in the linin g of the sto mach and by stretc h recepto rs in the stomach wa ll. Impulses are sent from these recepto rs to the brain, w hich sends more nerve impulses to the exocrine gland cell s. W hen food is in the stomach, impulses are also sent to endoc rine gland cells in the stomach lining that secrete a hormone called gastrin. Gastrin is carried to the exocrine gland cells in the stomach w all, w here it stim ulates them to increase the secretio n of hydrochloric acid. This causes the pH of the food that has entered the stomach to fall to about pH 3.0.

Some macromo lecules cannot be d igested by humans, fo r example cellulose. The enzy me cellulase digests cellulose, but humans lack the gene that cod es for this enzy me, and so cannot make it. U ndigested cellulose is an important part of d ietary fibre, w hic h has beneficial effects o n the d igestive system.

EXOCRINE GLANDS The secretory cells in an exocr ine gland are in a layer that is

only one cell thi ck . The total area of the layer of secretory

cells can be very large because of invaginatio n and

branch ing. The digestive jui ce is released from the cells by

exocy tosis. It is then d ischarged from the gland by travell ing

alo ng ducts. O ne group of secretory cells, cl ustered around

the end of a duct, is called an acinus .

The ducts and acini in part of the pancreas that secretes

panc reatic j uice are show n below .

Structure of exocrine gland tissue in the pancreas

one acinus

MEMBRANE-BOUND DIGESTIVE ENZYMES Enzymes secreted by exocrine gland cells become mixed w ith the food in the alimentary canal and carry out all the init ial stages of digestion . How ever, some of the enzymes that complete the process of di gestion wo rk in a different w ay. They are produced by the wa ll of the small intestine, but are not secreted. Instead, these enzymes remain in the plasma membranes of cells on the surface of t he villi (epithelium cells). The active sites of the enzymes are exposed to the food in the small intestine. They can di gest their substrates and the products of d igestion can then immediately be absorbed. Epithelium cells tend to be lost from the tips of villi by abrasio n, but t he memb rane-bound enzymes continue to wo rk as they becom e mixed into the food in the small intestine. Electron micrograph of an exocrine gland cell in the pancreas (X 6000 ). The cent ral regio n of one cell is show n incl udi ng the nucl eus.

basement membrane wall of duct

EXOCRINE GLAND CELLS Exocrine gland cell s have distinctive features. • O ne or tw o prominent nucleoli inside the nucleus, for producti o n of riboso me subunits. • A n extensive "area of rough endop lasmic reticul um, for protein synthesis. • Go lgi apparatuses for processing proteins. • M any large vesicles, sometimes called sec reto ry granules, for storage of the substances being secreted and transport of them to the plasma membra ne. The vesicl es are usually densely stained because of the concentratio n of proteins. • M itochondria, to provid e ATP for protein synthesis and other cell act ivities. The figure (right) is an electron micrograph of a pancreas cell and show s these disti nctive features.

Further human physiology 163

Digestive enzymes

SOURCES OF DIGESTIVE ENZYMES

DIGESTION OF LIPIDS

Food co ntains many different types of substance that have to be digested before they can be absorbed. D igestion therefore invo lves many different enzymes, secreted by exoc rine glands. The table allows the co ntents of saliva, gastric j uice and pancreati c ju ice to be co mpared - there are both sim ilar ities and differences.

The di gesti on of lipids poses special problems, because they are insolub le in water. Foods and the di gestive ju ices added to th em are mainly composed of w ater. In the ali mentary canal, li pids in foods melt and form liquid droplets. Because of their insol ubil ity, these drop lets tend to coa lesce to form larger droplets. Lipase is w ater-so lub le so it does not enter the lipid drop lets, but its active site is hyd rophobic (shown on page 68) and hydro lyses lipid s on the surface of drop lets. The dropl ets gradually decrease in size as the li pid s o n their surface are digested. However, food does not remain in the alimentary canal lo ng enough for large droplets to be digested co mpletely. Bile helps to ove rcome thi s probl em. It contai ns substances called bile salts, w hich are natu ral detergents. Bi le salt mo lecules have a hyd rophobic end and a hydroph ili c end. They are therefore attracted to both water and lipids and coat lipid drop lets, causing them to break up into smaller dropl ets. This process is called emulsificat io n. Bile is secreted by the liver and stored in the gall bladder. W hen it is di scharged into the small intestine it emulsifies lipids, w hich speeds up their di gestion, because many small drop lets have a larger total surface area, accessible to lipase, than one large d roplet of the same vo lume. With the help of bi le, lipids can be co mpletely di gested in the small intestine.

Cont ent

Di gestive ju ic e

Source

saliva

salivary glands

- salivary amylase - mucus

gastric juice

glands in sto mach wa ll

- pepsinogen - hydrochloric acid - mucus

pancreatic juice

pancreas

-

pancreatic amy lase pancreatic lipase phospholipase trypsinogen carboxy peptidase HC0 3 ions (alkaline)

Pepsin and trypsi n are potenti all y very harmfu l to the

exoc rine gland cells that secrete them. They are therefore

secreted as inactiv e precur sors, called pepsinogen and

tr ypsinogen. Pepsinogen is activa ted by hyd rochlori c acid,

whi ch co nverts it into pepsin. Di fferent cells in the wa ll of

the stomach secrete pepsinogen and hyd rochl o ric acid

(below) . Pepsinogen is therefore o nly activated after it has

been secreted. An enzy me, enterokinase, w hich is secreted

by t he lin ing of the small intestine, activates trypsinogen.

Acti vation therefore only happens w hen trypsinogen enters

the small intestine.

Structure of th e sto mach wall pits epitheli um

cells in neck --1----l---l~

of gastric gland

(secrete mucus)

oxyntic cells --+---+---4~

(secrete

hydrochloric

acid)

peptic cel l s - -(secrete

pepsinogen)

-+----J,;:1DJ

164 Further human physiology

THE EFFECTS OF HELICOBACTER PYLORI Heli cobacter py lori is an acid-to lerant bacterium that infects the lining of the sto mach. There is evidence that it causes several d iseases of the stomac h.

1. Stomach ulcers These are areas of damage to the lin ing of the stomach. O ld medical textbooks state that they are caused by excessive secretio n of gastric j uice , containi ng acid. There is now strong evidence t hat infect io n of the sto mach w ith H. py lori is a more signif icant factor than gastric aci d. • Ant acid treatments may relieve the symptoms of ulc ers for a w hile, but not permanentl y. • A ntimicro bia l treatments that eliminate H. py lori infection cure ulc ers o n a lon g-term basis. • H. py lori infecti on is strongly associated with the presence of stomac h ulcers. • Vo lunt ary infect ion w ith the bacterium has show n that it can cause gastrit is, w hich often leads to ulcerati on. • Abo ut half of the H. p ylori strains isol ated from patients wi th sto mach disease produ ce toxin s that cause infla mmatio n - and patients infected with these strains tend to have the most severe ulceration . • Proteases and other enzy mes that are released by H . py lori damage the stomach lin ing. 2. Stomac h cancer Stom ach cancer is the growth of tum our s in the wal l of the sto mach. As w ith sto mach ulcers, a far higher percentage of patients w ith stomach cancer are infected w ith H. pyl ori than the general popu lation . H. py lor i infect ion is associated with redu ced vita mi n C concentratio n in gastric j uice. This wi ll increase the c hance of a tumour fo rming, but further research is needed to establish a causal link between H . p ylori infection and stomach cancer.

Absorption of digested foods

STRUCTURE OF THE ILEUM Digested food s are abso rbed in the small intestine, mainly in the latte r part, ca lled the ileum . The tissue laye rs of the wall of the ileum are show n in the transverse sec tion be low (left). These tissue layers are visible in the light micrograph of the ile um be low (right).

Tran sverse sect io n of ileum

Micro graph of ileum in longitudinal section (x 40) longitudinal muscle layer

villi

circular muscle layer

VILLUS EPITHELIUM CELLS Digested fo od s a re abso rbe d by villi In the ileum. The st ruc ture of a villus is shown o n page 4 7. The o ute r laye r of ce lls wh ere a bso rptio n oc c urs is the e pithe lium. The figure (right) is e lect ro n mic rograp h of e p ithe lium ce lls, show ing the structura l featu res t hat are typica l of this ce ll type . The plasm a membranes of adjacent ce lls a re firm ly linked togeth er ne a r the free su rface by struc tures ca lled tight junctions. These structures prevent mo lecu les from lea king betwee n the e p ithe lium ce lls. To be abso rbed, di gested food s have to pass throu gh the p lasma membra ne of the e pit hel ium ce lls, and abso rpt ion ca n the refo re be ca refu lly co ntro lled . The table be low desc ribes the mech an isms used to abso rb foods a nd the struct ura l features used in these mec han isms.

Micrograph of villus epithelium cell s (x 25 00) __ .;-.y . "lI.~ , ~ "",

JIo:O;W

l!!"~#i

Som e mate ria ls a re not abso rbed, inclu din g ce llu lose , ligni n, bile pigmen ts, bacter ia and a brade d intest inal ce lls. The y are the refore egested in the feces .

Relationship s betw een st ructur e a nd function in villu s epithelium cell s Structural feature

Function

Microv illi - prot rusio ns of the free surface of the p lasma me mbran e into the lume n of the ile um; abo ut 1urn lo ng and Oil urn w ide .

Mic rovilli great ly increase the surface area of plasm a memb ran e exposed to th e d igested food in the ile um. This increases the rate of a bso rptio n of foo ds by d iffusion . Lip id s, and othe r foods th at ca n pass eas ily thro ugh the hyd ro pho bic ce ntre of the plasma membran e of the epithel ium ce lls, are abso rbed by simpl e diffu sion . Fructose a nd so me ot her hydro p hilic food substa nces at a low co nce ntration inside bod y ce lls a re abso rbed by facilitated diffu sion . Ther e is a stee p e no ug h co nce ntration grad ient fo r abso rpt ion of these substa nces by d iffusion , but they need ass ista nce to pass thr ough the plasma membrane. Ch ann e l pro te ins hel p them to cross the hyd rophobi c ce ntre of the me mb ra ne.

Mitoc hondria - ther e a re man y mitoc hond ria sca tte red thro ugh the cyto plasm.

Mito chond ria prod uce the ATP that is need ed for abso rption of substa nces by active tra nsport. Pump proteins in the plasm a membrane of the mic rovi lli ca rry o ut the active transport. G lucose, a mino acid s and miner a l io ns incl ud ing sod ium, ca lcium and iron a re abso rbed in th is way.

Pinocytic ves icle s - ther e a re man y sma ll ves icles, es pecia lly near the mic rovilli.

Pinocyt ic vesicles a re form ed by endocytosis. Eac h ves icle co nta ins a sma ll drop let of fluid from the lumen of the ile um. The memb ra nes of these ves icles are fo rmed fro m the p lasm a mem b ran e a nd so co nta in c ha nne ls for faci litated d iffusion and pu mps for ac tive tran sport . Digested food s ca n be a bso rbed from the vesicle s into the cyto p lasm.

Further human physiology 165

Liver

BLOOD FLOW THROUGH THE LIVER

ROLES OF THE LIVER

The li ver is the largest organ in the human abdo men. It contai ns huge numbers of cells call ed hepatocytes, w hic h carry out many vital processes. The liver is supplied w it h blood by two vessels - the hepatic portal vein and the hepatic art ery. O ne vessel, the hepatic vein, carries bloo d away . The blood bro ught by the hepati c po rtal vein is deoxygenated, because it has already flowe d thro ugh the wa ll of the stomach or the intestines. The level of nutr ients in this bloo d varies considerably, depend ing on the amo unt of di gested food th at is being absorbed. O ne of the main funct io ns of the li ver is to regulate levels of nutrients befo re the blood f lows on to the rest of the body. Excessively high levels of glucose and other nutrients wo uld cause damage to the organs of the bod y, especially the brain. Inside the liver, the hepatic port al vein d ivides up into vessels called sinusoids. These vessels are w ider th an normal capillaries, w ith wa lls that are more po rous. The wa lls consist of a single layer of very thin cells. There are many pores or gaps betw een the cells but no basement membr ane. Bloo d flowi ng alo ng the sinusoids is therefore in close contact w ith the surro und ing hepatocytes. The hepatic artery supp lies the liver wi th oxyge nated blood from the left side of the heart via the aorta. Branches of the hepatic artery jo in the sinusoids at vario us poin ts along their length, provi di ng the hepatocytes w ith the oxygen that they need for aerob ic cell respiration. The sinusoids drain into w ider vessels that are branches of the hepati c vein. Blood from the liver is carried by the hepatic vei n to the right side of the heart via the infer io r vena cava. The fig ure (below) shows the relatio nshi ps betw een blood vessels in li ver ti ssue.

Nutrient storage and regulati on Wh en certain nutri ents are in excess in the blood, hepatocytes absorb and store them, releasing them w hen they are at too Iow a level. For example, w hen the bloo d glucose level is too high, insulin stimu lates hepatocytes to absorb glucose and conve rt it to glycogen for storage. W hen the blood glucose level is too low , glucagon stimulates hepatocytes to break down glycogen and releaseglucose into the blood . Iron, retinol (vitamin A) and calcife rol (vitamin D) are also stored in the liver w hen they are in surplus and released w hen there is a deficit in the blood .

St ructur e of a sinusoid in th e li ver

Breakdown of erythrocytes Erythrocytes, also called red blood cel ls, have a fairly short lifespan of about 120 days. The plasma membrane becomes fragile and eventually ruptures, releasing the hemoglobin into the blood plasma. The hemoglobin is absorbed by phagocytosis, chiefly in the liver. Some of the cells in the wa lls of the sinusoids are phagocytic, called Kupff er cells. Inside these cells the hemoglobin is split into heme groups and glob ins. The globi ns are hydrolysed to amino acids, which are released into the blood. Iron is removed from the heme groups, to leave a yellow coloured substance called bil e pigment or bi li rubin . The iron and the bile pigment are released into the blood . Mu ch of the iron is carried to bone marrow , to be used in production of hemoglobi n for new red blood cells. The bi le pigment is used for bil e producti on in the liver . Glo bins

~

A mi no acids

Hemoglob in /

<, Heme groups

Iro n < B'I ' I e pigment

Synt hesis of plasma proteins The rou gh endoplasmic reticulu m of hepatocytes produces 90% of the protei ns in blood plasma, incl ud ing all of the albumin and f ibrinogen. Synt hesis of cho lesterol A lthough some cholestero l is absorbed fro m food in the intestine, a larger quantit y is synthesized each day by hepatocytes. hepatocytes

lumen of sinusoid

Det oxific ati on Hepatocytes absorb toxic substances from bloo d and convert them by chem ica l reaction s into non-toxic or less toxi c substances.

LIVER DAMAGE FROM ALCOHOL ABUSE Kupffer cell branch of hepatic vein

f

166 Further human physiology

Liver cells absorb alco ho l and co nvert it into ot her substances to detox ify it. Excessive consu mption of alco ho l th erefor e damages liver cells mor e th an most other parts of the body. Fatty deposits bu i ld up, w hic h can cause hepat it is. A lco ho lic hepat iti s is inf lamm at ion of t he liver, ofte n associated wi th nausea and ja und ice . If this is persistent (c hro nic), fo r examp le after ten or more years of heavy d rinki ng, it can cause ci rrhosis - no rmal liver t issue is grad ually replaced by scar ti ssue. Live r cells gradually die and are not repl aced, so liver fu ncti on becom es inc reasing ly poo r and eve nt ually deat h can result f rom liver fai lure.

Cardiac cycle

EVENTS OF THE CARDIAC CYCLE

Contractio n of the chambers of the heart is ca lled systole and relaxat ion is calle d dia stole.

The sequence of actio ns occ urring repeatedl y in a beating heart is called the cardiac cycle . The cardiac cy cle is descr ibed briefl y on page 48. The figure below shows the pressure and vo lume changes in the left atrium, left ventricle and aorta, duri ng tw o cycles. It also show s electric cur rents (electrocard iogram) and sounds (phonoca rd iogram)

1. Atrial systole The cardiac cycle begin s w ith the co ntraction of the w all of the atrium. Th is happens wh en the ventricle is already 70% fu ll. The co ntractio n of the atrium pumps more bloo d into the ventricl e, fi ll ing it to its maximum capaci ty before the start of ventricul ar systol e.

genera\eo 'Dy \ne 'Dea\\'i'\%nean.. aortic aortic valve atrioventricular valve open valve open open ,.....--0-----.

•

2. Ventricular systole Contractio n of the ventricle wall causes a rapid increase in pressure insid e the ventric le. This causes the clo sure of the atrio-ventric ular valve, wi th resulting vibratio ns in the valve and adj acent w alls of the heart. These vibration s are the fir st heart sound . The pressure in the ventricle rapid ly rises above the pressure in the aorta, causing the aortic (semi-lunar) valve to open. Blood can then be pumped from the ventricle into the aorta, raising the aortic bl ood pressure and decreasing the volu me of blood in the ventr icl e to a mi nimum . W hi le the ventricle is contracti ng, the atrium is relaxin g and blood enters it fro m the pu lmona ry veins.

..----..

120

R

® T

electrocardiogram

@ phonocardiogram

CONTROL OF THE HEART BEAT Heart muscle cells are sti mulated to co ntract by electr ica l impu lses. Interconnecti ons between adjace nt cells all ow impu lses to spread th rough the wa ll of the heart, stimu lating it to co ntract. A small region in the wa ll of the right atrium init iates each impu lse (right). This region is called the SA node (sinoatrial node) and acts as the pacemaker of the heart. Impu lses in it iated by the SA node spread out in all d irecti ons throu gh the wa lls of the atria, but are prevented from spreading direct ly into the wa ll s of the ventr icles by a layer of fibrous tissue. Instead, im pulses have to travel to the ventricle s vi a a second node, call ed the AV node (atrioventricular nod e). Thi s node is posit ioned in the w all of the right atrium, cl ose to the jun ction between the atria and ventricles. Impulses reach the A V node 0.03 seconds after being emitted from the SA node. There is a delay of 0.09 seco nds before impulses pass on from the AV node, w hic h gives the atria time to pump blood into the ventricles before the ventricles co ntract. Impu Ises are sent from the AV node alo ng tw o bu nd les of co nducting fibres that pass throu gh the septum betw een the left and right ventricles, to the base of the heart. Narrower co nducti ng fibres branch out fro m these bund les and carry impu lses to all parts of the wa ll s of the ventricles, causing almost simultaneo us contraction throu ghout the ventricles. The effects of nerves and horm ones on the heart beat rate are descri bed on page 48.

3. Ventricular dia stol e Relaxation of the ventricle w all causes pressure in the ventr icl e to fall below the pressure in the aorta. The sem i­ lunar valve therefore closes, with the resulti ng vibrations that are the cause of the second heart sound . W hen the pressure in the ventricle falls below the pressure in the atrium, the atrio­ ventric ular valve opens and blood that has accumulated in the atrium flow s into the ventricle causing a rapid rise in ventric ular vo lum e. With both the atrium and the ventricle relaxed, blood co ntinues to drain from the pulm onary veins through the atrium into the ventricle until by the end of the cycle it is about 70% full.

Structures involved in th e contro l of the heart beat

sympathetic nerve (accelerates heart)

"

wall of right ventricle

I

branches of conducting fibres

Numbers represent the time taken for impu lses from the pacemaker to reach different parts of the heart wall

Further human physiology 167

Coronary heart disease

ATHEROSCLEROSIS

FACTORS AFFECTING THE RISK OF CHD

Atherosclerosis is a degenerative di sease of large and medium sized arteries. Phagocytes are attracted to sites of damage to the in ner lin ing of the arteries. The phagocytes release growth factors that st imulate the muscle and fib rous tissues in the artery w all to thicken. LDL may penetrate the damaged areas and release cho lesterol, w hich can buil d up to form large deposits. The grow th of wa ll ti ssue and accumulatio n of cho lesterol cause the artery wa ll to bul ge inw ards, reducin g or even preventing the fl ow of blo od. The thickened wa ll loses its elasticity and calci um salts are so metimes deposited in it, making it hard.

Atheroscle rosis and co ronary thromb osis are together know n as co ro nary heart di sease (CH D). The rates of CH D vary w idely between co untries.

The fi gure (below) shows a healthy coron ary artery and another that shows signs of atherosclerosis.

smooth inner lining of endothelium cells

Country New Zealand United States Germany

Sweden

Australia

Italy

Spain

France i=-=~=::::J -----' Japan

10 10

males I females

-f=;=;.....,.--.--~~--r-~~---.~~,......,~~..--1

o

50

100 150 200 250 Deaths per 100,000 population

M uch research has been don e to try to identify factors that increase the risk of CHD. The fo llo w ing factors all increase the statistical risk: • Increasing age • Being male rather than female • Havi ng a famil y history of CH D outer layer of artery

unobstructed lumen

Structure of an artery showing atherosclerosis

thickened lining

of artery

blood clot

layer of elastic and muscle fibres

outer layer of artery

CORONARY THROMBOSIS The rough inner surface of atheroscle rotic arteries tends to cause blood clots to form. The for mation of clots is called thrombo sis. The w all of the heart is supplied w ith blood by the coronary arteries. If a bloo d clot blo cks one of these arteries, part of the wa ll of the heart is deprived of its supply of oxygen. The cells in this part of the w all are unable to respire and so stop contract ing. Thi s is either called myocardi al infarcti on or a heart attack. Someti mes small, uncoo rdin ated co ntractio ns co ntinue. These are called fib rill atio ns, but they do not pump blood effectively.

168 Further human physiology

These three factors are not influ enced by a person' s lifestyle, but some of lifestyle facto rs th at increase the risk are: • Obesity • Physical inactivi ty • Hi gh blood pressure • Tob acco smo king The effect of d iet is more equivocal. There is some evidence for di etary factor s increasing the risk of CHD : • Trans fat - positively co rrelated with CHD rates and the data is difficult to explain in any way other than that trans fats cause CH D • Saturated fat intake - posit ively co rrelated w ith CHD rates in some countries, but evidence of a causal li nk is lacking. • Cho lesterol intake - redu cin g d ietary cho lestero l tends to redu ce blood cho lesterol levels slig htly , and there is a positive co rrelat io n between blood cho lesterol levels and CH D, but it is a w eaker co rrelatio n than w ith saturated fat, and again the causal lin k is not proven. Cholesterol in blood can be part of both low-density and high-density li popr otein (LDL and HDL). W hereas high LDL levels are associated with an increased risk of CH D, high HDL levels are associated with a reduced risk. Thi s is because HD L is used to remove cho lesterol from tissues. The levels of LDL, H DL and saturated fats in the bl ood are not so lely due to diet - genetic factor s are also imp ort ant. This may explain w hy some pop ulatio ns co nsume large quantiti es of cho lestero l and saturated fats and yet have extremely low CHD rates - the M aasai of Kenya for example. Finall y, there have been claims that some facto rs reduce the risk of CHD . An example is cis-unsaturated fatty acid int ake. These fatty aci ds are fo und in o live o il and may explain low CH D rates in M editerranean countries. How ever, more evidence is needed before a causal link is established.

Oxygen transport

Oxyge n is transpo rted from the lungs to respiri ng tissues by hemoglob in in red blood cells. Hemoglobin is a prote in that is highly adapted to its fu nctio n.

OXYGEN DISSOCIATION CURVES If air w ith the normal oxyge n co ntent is bubb led throug h a sample of blood, oxygen binds to the hemoglobin unti l almost all of the hemoglo bin mo lecules have four oxygen mo lecu les bo und. The hemoglobin is nearly 100% saturated. If air w ith a low oxygen co ntent is then bubbled through, some of the oxyge n dissociates from the hemoglobin , reducing its percentage sat uration. The oxygen co ntent of the air is measured as a partial pressure. Partial p ressures are the pressures exerted by each of the gases in a m ix ture of gases. The percentage saturation of hemoglobin w ith oxyge n at each partial pressure of oxygen is show n on an oxyge n dissociatio n curve . The fig ure (below) shows the oxygen di ssociation curves of hemoglobin and myoglob in. M yoglobin is a protein consist ing of one globi n and one heme group that is used to store oxygen in muscles. The oxygen curve for myoglobi n is to the left of t he curve for adult hemoglobin because myoglobi n has a higher affinity for oxygen. At mod erate partial pressures of oxyge n, adult hemoglob in releases oxyge n and myoglobin bind s it. M yoglobin only releases its oxyge n wh en the parti al pressure of oxyge n in the muscle is very low . The release of oxyge n from myoglob in delays the onset of anaerobic respiration in muscles durin g vigorous exercise. The dissoci ati on c urves for myoglobin and hemoglob in have different shapes. The curve for hemoglobin is S-shaped and that for myog lo bi n is not. M yoglob in co nsists of one heme group attached to a glo bin, w hereas hemoglobin has four heme groups, each attached to d ifferent globins that interact w ith each ot her. As oxygen mo lecu les di ssoci ate from hemoglobi n, confo rmational changes occ ur, w hich make it easier for other oxyge n mo lecul es to dissociate. Bloo d co ntaining adult hemoglobi n therefore releases large amo unts of oxygen over a narrow range of oxygen parti al pressures, corresponding to th e conditio ns norm all y found in respir ing ti ssues. O xygen di ssociation curves of hemoglobin and myoglobin

0.0

90

1myog l~> •••••·

>X

o

..r:

.~ c: :0

, ,

80

,

I ' hemoglobin

·· · a 50 ·· s 40 ··· ·· 30 · '" ··· · 20 · · 2 · 10 · ·· E Q)

.s:

Q)

Q)

I

normal range of oxygen partial pressures in tissues

Q)

CL

0

75

~..r: ~

::::

~ 3:

p(C0 2 )

50

'" c: Q) . ­

=6 kPa

0.0.0 ~ ..Q

~ ~

25

2 E Q) Q)

CL ..r:

o

I L..-=""

5

10

15

Partial pressure of oxygen/ kPa

FETAL HEMOGLOBIN The hemoglobin in the red blood cells of a fetus is slightly di fferent in amino acid sequence fro m adult hemoglobin . The f igure (below) shows that it has greater aff inity for oxygen and so, in the placenta, the oxygen that di ssociates fro m adult hemoglobin binds to fetal hemoglobin, w hich only releases it once it enters the tissues of the fetus. O xygen di ssociati on curves of adult and fetal hemo globin _

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THE BOHR SHIFT The release of oxyge n by hemoglob in in respi ring ti ssues is promoted by an effect called the Bohr shift. Hemoglobin' s affinity for oxyge n is reduced as the partial pressure of carbo n dioxide inc reases (below). Respiring tissues have high parti al pressures of carbo n di oxide, so oxyge n tends to di ssoci ate. The lungs have low er partial pressures of carbo n di oxide, so oxyge n tends to bind to hemoglobin.

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The partial pressure of oxyge n at high altitude is lower than at sea level. Hemoglobin may not beco me fully saturated as it passes through the lungs, so tissues of the body may not be adeq uate ly supp lied w ith oxy gen. A condit io n call ed mou ntain sickness can develop, w it h muscular weakness, rapid pul se, nausea and headaches. This can be avoi ded by ascending gradually to allow the body to accl imatize to high altitude. Dur ing accli matizatio n the venti latio n rate increases . Extra red blood cells are produ ced, increasing the hemog lobin co ntent of the blood. Mu scles produ ce more myoglobin and develop a denser capi l lary netw ork. These changes help to supply the bod y w ith eno ugh oxyge n. Some peop le w ho are native to high altitu de show other adaptat ions, includi ng a high lung capacity with a large surface area fo r gas exc hange, larger tid al volum es and hemoglobin w it h an increased affinity for oxyge n.

Further human physiology 169

Carbon dioxide transport

Carbon di oxid e is prod uced by aerobic respiration in ce lls and then eit her di ffu ses di rectl y into capi llaries or into t issue fl uid that is draw n into cap illaries. Carbon dioxide is carr ied by the blood to the lun gs in three d iffe rent ways . A small amo unt (7%) is carried d issolved in t he pl asma. The remain der is eit her conve rted to hydrogen carbo nate ions or binds to hemoglobin.

CONVERSION TO HYDROGEN CARBONATE IONS Carbon dioxide can be co nverted into hydrogen carbonate ions within a fractio n of a second of entering the blood . Abo ut 70% of carbo n diox ide is carried in this way . Afte r diffusing into red blood cells, carbo n diox ide co mb ines w ith wa ter to for m carbon ic acid. This reaction is catalysed by carbo nic anhydrase. Carbo nic acid rapid ly d issociates into hydrogen carbonate and hydrogen ion s. The hydrogen carbonate io ns move out of the red blood cells by faci litated diffusion. A carrier protein is used t hat simultaneously moves a chlor ide ion into the red blood cell. This is called the chloride shift and prevents the balance of charges across the memb rane from being altered . The fig ure (below) shows the reactions that prod uce hydrogen carbonate ions and the chlo ride shift. The hydr ogen io ns that dissociate from carbo nic acid bind to hemoglobi n in the red blood cells, preventi ng an excessive change in pH. This is called pH buffering. Plasma protein s also act as pH buffers in blood .

plasma

THE EFFECT OF EXERCISE ON VENTILATION Du ring vigoro us exerc ise, the energy dema nds of the body can increase by over ten times. The rate of aerob ic respi ratio n in muscles ri ses so there is an increase in the amount of CO 2 entering the bloo d and the co ncentrat io n rises. Thi s redu ces the pH of the bl ood and is rapid ly detected by cells in the wal ls of arter ies, w hic h mo nitor bloo d pH and co ncentratio ns of oxyge n and carbon dioxide in the blood. These cells are called chemosensor s. The chemosensors send nerve im pu lses to the parts of the medull a of the brain that control the venti lation rate, called the br eathing centres. The breathi ng centres also mo nitor blood pH and carbo n dioxide conce ntratio n. If the concentration of carbo n di oxid e in the blood ri ses and the blood pH falls below its normal level of pH 7.4 , the breath ing centres increase t he rate of inspiration and expiration. This is done by send ing nerve impu lses to the diaphragm and intercostal muscl es, causing them to inc rease the rate at w hic h they co ntract and rel ax. The increase in the venti latio n rate hel ps to remove from the body the CO 2 pro duced in aerob ic cell respiration. It also help s to increase the rate of oxyge n uptake, w hic h allows aerob ic cell respiration to cont inue in the muscles and it hel ps to repay the oxygen debt after anaerobic ce ll respiration. After exercise, the level of CO 2 in the blood falls, the pH of the blood ri ses and the breathing centres cause the venti lation rate to decrease. The figure (below) shows the relatio nship between blood pH, partia l pressure of carbon dioxide in blood and venti latio n rate. Effect of vary ing blood pH and CO 2 level on the vent ilat ion rate 11

red blood cell

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In respirin g tissues, carbo n dioxide binds reversibl y to hemoglobin , to fo rm carbam ino hemog lob in. In the lun gs, carb aminohemo globin d issociates and the carbon d iox ide is released. Between 15% and 25% of carbo n dioxide is carrie d in this way. The binding of carbon dioxide and hydrogen ions to hemoglobin lowers its affinity for oxyge n. This causes the Boh r shift (page 169).

7.6 7.5 7.4 7.3 7.2 7.1 7.0 6.9

170 Further human physiology

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ASTHMA Duri ng asthma attacks the muscl es in the wa ll of the bronc hi co ntract excessively, narrowi ng the bronchi. Ve nti lation is a struggle and gas exc hange is reduced . Asthma is an allergic reaction, often to house dust mites, but sometimes also to poll en, pets and some fu ngi. Acco rdi ng to a recent t heory, li ving in very clea n hom es increases the risk. W it hout eno ugh pathogens to fig ht, the immune system starts to react against harml ess substances, causing allergies to develop.

EXAM QUESTIONS ON OPTION H - FURTHER HUMAN PHYSIOLOGY H1 The bacterium Helicobacter pylori infects the lining of the stomach. A survey was done using patients who had complained of pain or discomfort in their digestive system. The lining of their oesophagus, stomach and duodenum (upper part of the small intestine) was examined using an endoscope and the patients' blood was tested for the presence of antibodies against

H. pylori. The table below show the results of the survey.

Antibodies against H. pylori present (number of patients)

Antibodies against H. pylori absent (number of patients)

Normal

51

82

Oesophagus inflamed

11

25

Stomach ulcer

15

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a) Explain why the researchers tested for antibodies against H. pylori in the blood of the patients.

[2]

b) Discuss the evidence from the survey results for H. pylori as a cause of stomach ulcers and stomach cancer.

[3]

c) (i) Compare the results for inflammation of the oesophagus and the duodenum.

[2]

(ii) Suggest a reason for the difference in the results.

[2]

H2 a) Outline how the atria of the heart are stimulated to contract.

[2]

b) Explain the origin of the heart sounds.

[2]

H3 V E is the total volume of air expired from the lungs per minute. The graph below shows the relationship between V E and the carbon dioxide content of the inspired air. I

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c) Predict the effect on V E of increasing the carbon dioxide concentration of inspired air above 7 0/0.

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Further human physiology - 18 Questions 171

D urin g the IB Bio logy co urse, yo ur teacher wi ll help you to imp rove yo ur skills in plannin g and perform ing investigati ons. W hen yo ur teacher thi nks that yo u are ready, your ski lls wi ll be assessed. This w ill be done dur ing lesso ns at your schoo l, so it is called internal assessment (IA). Exams that are sent off to an examiner are called external assessment. In IB Bio logy, 24% of the marks are for IA. A ltho ugh yo ur teacher w ill help yo u as much as possible, yo u cannot be given hi gher marks than you deserve, because samples of wo rk from yo ur schoo l are checked to see w hether they have been marked to the right standard. This is called external mod eratio n. You must therefore demon strate high levels of skill to gain high marks in IA. Five skills are assessed in IA - these are calle d the IA criteria. They are Design; Data co llectio n and processing; Concl usio n and evaluatio n; M anipu lative skills; Person al skil ls. Each of these cr iteria is divided into three aspects. Fo r each aspect, yo ur teacher w ill decid e wh ether you deserve a mark of 2 (for meeti ng thi s aspect of the criterio n ful ly), 1 (for meeti ng it partially) or 0 (fo r not meeting it at all) . The maxim um mark fo r a criterio n is therefore 6. The first three cr iteria are assessed on at least tw o occasio ns and yo ur highest tw o scores are selected. There w ill be o ne ove rall assessment of yo ur manip ulat ive skills, to ref lect the skil l level that you have reached during the course. There w ill be one overall assessment of person al skills. This wi ll be done duri ng t he Group 4 proj ect - the co-operative science proj ect that yo u participate in, at some stage during the course. The maximum possib le mark for IA is therefore 48 (2 x 6 for the f irst three cri teria and 1 x 6 for the last two criteria). The co mments below explain how to improve yo ur level of skill in each of the five cr iteria. IA criterion

Guidance

Design

1. The first aspect of design is choosing a probl em or research quest io n to investi gate. You are expected to pick one factor to vary in an expe riment. This is the independent variab le and it is expected to affect the level of another variable, called the dependent variable. You are also expected to identify other variables that co uld affect the independent variable and therefore must be kept co nstant. These are calle d controlled variables. For example, if you delib erately vary temperature, the activ ity of an enzyme w ill vary, but pH, enzy me co ncentratio n and substrate concentratio n must be kept constant. 2. The second aspect of design is planning how to manipu late the level of the ind ependent variable, and how to keep the levels of all the co ntrolled variables co nstant. 3. The third aspect of design is the detailed planning of the method. This inclu des deci di ng on the range of the ind ependent variable and also the method for preci se and accurate measurement of the dependent variable. You must also deci de how many measurements you need to make. O ne measurement may sometimes be eno ugh, but yo u can only calculate the standard deviation if you repeat measurements to give a sample of at least fi ve for each level of the ind ependent variable.

Dat a coll ection and proce ssing

1. The first aspect is recordin g results of an experiment - the results are calle d raw data. Usually the raw data is quantit ative - measurements w it h S.1. units. Record these measurements as accurately as possib le using a results table that yo u have produced yo urself, either handw ritten, o r w ord-proce ssed. Show every result that yo u obtained, not j ust the mean results. A ll the results should be given to the same number of decim al places. The co lumn headings o n results tables should show both the quantity being measured and the S.1. units. W hen yo u are being assessed for this aspect, yo u should show the size of the uncertainty w ith each result. For example, the time given by a stopwatc h might be plus or minus 10 mi lli second s, or w ith a ruler it might o nly be possib le to measure lengths to plus or minu s 0.5 mm . 2. To satisfy the second aspect you must process the raw data in some way. This mi ght invo lve calculat ing the mean, o r a percentage. Processing of raw data makes it suitable for plottin g on a graph. A n example of this is calcu lati ng the percentage mass change of samples of potato, placed in different salt so lutio ns. 3. The third aspect of thi s cr iterio n invol ves presenti ng the processed data as a graph or other appropriate chart, chosen by you. Remember these rules for graphs: • put the independent variable on th e x-axis and the dependent variable on the y-axis • choose an appropriate scale for the x-axis and the y-axi s so that the graph is a suit able size • label bot h the axes and remember to incl ude units (fo r example, mass/ grams) • plot the data points accurately and jo in the m w it h a best-fit curve o r straight line • if you have calculated mean results, plot these rather than individu al results • error bars are could be added to show the range of uncertainty above and below each po int - there are several ways of doin g this, but the most usual is to show the standard error. (Standard error = standard deviati on di vid ed by the square root of the sample size).

172

Conclusion and evaluation

1. The first aspect of this criterion is drawing valid conclusions frorn the data that you obtained. These questions can be used as prompts. What trends or patterns are shown by the data? What relationship is there between the independent and dependent variables? Your graph should give you the evidence for the relationship. If you calculated mean results, is there a significant difference between the means? What is the explanation for the observed relationships or differences between means? 2. The next task is commenting on the design of the investigation and the experimental methods used. You should list all of the weaknesses, including measurements not being precise enough, results being inaccurate because of errors, or allocation of time to the various parts of the investigation not being appropriate. For each weakness in the investigation, you must assess how significantly it affected the results. The process of identifying weaknesses and assessing their impact is called evaluation. 3. The third aspect of this criterion is explaining what could be done to improve the investigation, if it was done again. You must be specific - for instance, it is not enough to say that more precise measurements should be made; you must explain how more precise measurements could be made.

Manipulative skills

1. By the time that your teacher assesses your manipulative skills, you must have shown that you can follow instructions safely and accurately, even with cornplicated laboratory practical work. Be sensible about asking for help from your teacher. Try to work out what to do yourself. But, if you have not been given full enough instructions or are worried about the safety of the proced ure, ask for hel p. 2. During the course, your teacher should give the opportunity to learn how to use a wide range of techniques and equipment. By the time your skills are assessed you should be competent in all these techniques. Work in a careful and systematic way - arrange your apparatus tidily and do not waste time, but work without rushing. 3. You should always know about any potential risks in the procedure that you are following. You should never put yourself or others in the laboratory at risk of accident or injury.

Personal skills

1. You will be assessed on your approach to the co-operative science project (Group 4 project). You are expected to show self-motivation and follow through the project until it is completed. Obviously, you will not satisfy this aspect if your teachers have to encourage you to persevere with the project! 2. Scientists often work in teams, so the ability to co-operate with others is important. During the Group 4 project, you must show that you can collaborate with others, by cornrnunicating effectively and working co-operatively. You should ask yourself these questions: Are you only interested in your own views or do you ask for the views of others? To satisfy this aspect you must exchange ideas with others and help to combine them so that the tearn completes a task more effectively than anyone individual could. 3. You rnay be asked to complete a self-evaluation forrn, to allow this aspect of personal skill to be assessed. You are expected to show a realistic awareness of your own strengths and weaknesses. You are also expected to explain what you have learned from the Group 4 project.

173

GUIDANCE FOR STUDENTS WORKING ON EXTENDED ESSAYS IN BIOLOGY

M any IB students choose a biol ogical research qu esti on fo r their extended essay. There are unlimited oppo rtunities fo r novel and interesting work because of the di versity of li fe. M any excellent Biol ogy extended essays are wr itten each year. Every essay is an indi vidu al effo rt and there is no fo rmula for w riting the perfect essay. The steps shown below are intended to help you to avo id some co mmo n faults, w ithout preventin g you from w riting the essay that yo u wa nt to w rite. Whil e you are wo rking on the essay, yo ur most im port ant resour ce wi ll be the teacher w ho is supervising yo u. If you need hel p at any stage, f ix a tim e to talk thin gs ove r. You should make sure that yo ur supervisor always know s w hat yo u are doi ng - discuss how thin gs are go ing as frequent ly as possibl e. If yo u don't, yo u co uld waste a lot of tim e on an unprodu ctiv e approac h to the wo rk. Remem ber two important maxim s: 'things take time' and ' if somethi ng can go wro ng it wi ll' . Assume from the start that you' ll have to do a second run of any experiments or observations and allow time fo r thi s. Start wo rk as soon as possible and then yo u w il l have ti me to produ ce the finest essay that you can. You can also earn extra points towa rds yo ur diploma.

Planning and data collection

Choose a suitable topic

Pick the field of biol ogy that interests you most and gradually narrow down to one small section of it. You must choose a truly biol ogical topi c - o ne that invol ves li ving organisms and interacti on s betw een them . It must be a topic in w hic h yo u can have a personal inpu t - this isn't easy w ith some topics, for example diagnosis and treatment of di seases, so these are best avoide d.

Choose an approac h

There are tw o main types of approac h. 1. Doi ng expe riments/ mak ing careful observatio ns. 2. Searchi ng in books, journ als o r on the internet fo r relevant data. M ost of the best essays co mbine both app roaches. If yo u cannot design and do experiments in your chosen topic, reconsider yo ur choice of to pic!

Do some preli minary wo rk

Try out some expe riments - thi s should allow you to find out w hether your approac h is lik ely to be successful. Avo id experiments that cause unnecessary risks, suffering to anim als or env ironmental damage. Do some backgroun d readin g and take careful notes of im port ant relevant info rmat io n. Prel imi nary wo rk should get yo u thin kin g and asking questions abo ut your topi c.

Formul ate a research questi on

Thi s should be a question wo rth asking - not one with an obvio us answer. It should be narrow enough to be fully answered in a 4000-w ord essay, based on 40 hour s' wo rk. It is best stated as a questio n, w hic h can be used to develop a hypoth esis - a prediction that yo u are going to test. It is abso lutely vi tal at this stage to talk to yo ur main help eryour teacher.

Plan your methods

If yo u are fol low ing adv ice give n earl ier, yo u w ill be designin g experi ments or pl annin g how to make careful observatio ns. A lthough yo u may use some standard protoco ls, there should ideall y be a person al input to the exper imental design, even if you are wo rki ng in a research laborator y. You must show that you understa nd the theor y behind any methods that you use, and the li mitations and uncertainties involved - if you do not then the methods are too complex!

Co llect the data that yo u need

Rememb er the thin gs that you have been taught w hen planning exper iments fo r Internal Assess ment - variab les must be co ntro lle d and repeats are needed to allow yo u to assess the reli ability of yo ur data. If yo u aren't doin g your own experiments, you must obta in the publi shed results of experiments, not j ust the co ncl usio ns that we re drawn fro m these experimenta l results.

174

Writing up your essay

Write an introduction

This can be quite brief. There is no need to include large arnounts of background material, especially if it is straightforward biology. Instead, say why the topic is worth writing about and give the background inforrnation that is needed to understand the essay. The introduction should make it clear how and why you have chosen your research question. You should, of course, state your research question precisely, either in italics or bold type.

Describe your methods

This section shouldn't be very long - if it is then your methods were probably too complex. Explain clearly and fully what you did and why. You should include enough detail to allow your experiments to be repeated. Make clear how the experiments tested your hypothesis or gave the evidence needed to answer the research question. Explain the limitations and uncertainties that were caused by the methods that you used.

Display your results

Use clear tables or other formats to display the data that you have obtained - the results of your experiments. You only need to put raw data into an appendix if you have huge amounts of it. Use graphs or other charts to display the most significant features of the data, for example mean results. If you are using data frorn other scientists, you should display and manipulate it in an original way.

Analyse your data

This should be a long and detailed section of the essay. You should discuss whether the data is reliable - were the repeats close? do the results show a consistent trend? What confidence level do statistical tests show? Were there errors or uncertainties that had an impact on your results? Then use your understanding of the topic to discuss possible explanations for any trends, with reasons for rejecting or accepting thern.

Draw your conclusions

Only a short section is needed here. It should not include new information or views different from those expressed in earlier sections of the essay. Instead, you should surn up what answer you have found to your research question or whether your hypothesis is . supported or undermined. Your conclusions should be based only on the data that you have obtained and analysed. You should make it clear what the unresolved issues are, and suggest how they could be investigated.

Write an abstract

You must summarize your whole essay in 300 words. You must include your research question clearly, how you investigated it and what conclusion you reached. The usual purpose of an abstract is to give the reader a quick irnpression of the contents of a long article so that he or she can decide whether it is worth reading or not! Obviously your essay will be well worth reading!

Add the finishing touches

You now need to write a contents page and a bibliography. The contents page lists the sections of the essay with the number of the page on which each section begins. The bibliography is a numbered list of the published sources that you used. You should put a reference in the text of your essay, in the form of a superscript number, wherever you have used information from these sources. Proof-read your essay to check for spelling or grammatical mistakes.

1

7 ~ 1\0.1

GUIDANCE FOR STUDENTS PREPARING FOR FINAL EXAMS

If yo u want to do we l l in your fin al exams, yo u mu st prepare for them very carefull y in the weeks beforehand. The most imp ort ant task is to memorize all the facts that you have been taught. For a high grade, you w ill need a comprehensive knowl edge of them. Y ou will need to spend many hours on revision and find tacti cs that w ork fo r you. You should also practi se answe ring exam questio ns. You can use the qu estion s at the end of topics in thi s book, after you have revi sed each topi c. You r teacher should also give yo u some past exam papers to try. There are thr ee sty les of qu estion in IB Biol ogy exams. • Multiple choice questions - These are question s w here you choose one of four possible answe rs. Read all of them before choosi ng o ne. If yo u cannot decid e on one answer, try to eliminate answe rs that are obvio usly wron g to narrow down the possibil iti es. Leave diffi cul t questions until you have answered the straightfo rwa rd ones. Give an answe r to eve ry question­ marks are not deducted for wron g answe rs. • Structured questions - These question s are broken up into small sect io ns, each of whi ch you answe r in the space or on the lin es provided. If you run out of space, conti nue your answer elsewhere on the paper - it w il l be marked as lon g as yo u indi cate cl early w hat you have don e. The num ber of marks for each sectio n is indi cated and thi s helps show you how detail ed your answer needs to be. Some structured questio ns invo lve data analysis. Look throu gh the data question s in thi s book to see some of the w ays in w hich data can be presented. You should always study the data very carefull y before answe ring the questions, fo r example the scales and labelling on the axes of graphs. If there are calculatio ns, remember to show yo ur w orking and give units with your answe r, for example grams o r mill imetres. • Free response questions - These questions requir e long and detailed answers on lin ed paper. You can decide w hat sty le of answer to give. Usually continuous prose is best, but sometimes ideas can be show n o n a table or on a carefully annotated di agram. There may be a choice of free response question. Read the w hole of each question before making your choice. There w ill be marks for the quality of constructio n of your answe r. If the question is divid ed up into secti ons (a), (b) and so on, yo u must answer it in these sections. Try to express your ideas clearly so that the examiner understands wh at you mean. Plan out your answer on scrap paper, so that you arrange your ideas in a logical sequence and do not inclu de irrelevant material. As with all questions, you must wr ite legibly or the examiner may not be able to mark your w ork. This may mean that you have to wri te more slowl y than normal. If you do revi se carefull y and build up a co mprehensive knowledge of the facts on the syllabus you sho uld fi nd many of the

questions straightforwar d. This is because, in IB Biol ogy exams, 50% of the marks are for simple factual recall . These qu estions

w ill start w ith w ords lik e list, state, outline o r describe. The other 50% of the marks invol ve mo re than simpl e factu al recall­

they invol ve express ing ideas that are more complex o r invol ve using yo ur know ledge to devel op an answe r th at yo u probably

haven't been taught.

The wor d at the start of each question tells you wh at to do . These w ord s are therefore called command term s.

Explain- Sometim es thi s invol ves giving the mechanism behind somethi ng - ofte n a logical chain of eve nts, each o ne causing

the next. Thi s is a 'how' sort of exp lanation. A key wo rd is oft en 'therefo re'. Sometimes it invol ves giving th e reason s or causes

for something. Thi s is a 'why' sort of explanatio n. A key word is ofte n ' because'.

Discuss - There w on't be a simple straightforward answe r to these questions. Sometime s your answe r should include arguments

fo r and against something. Try to give a balanced account. Sometim es yo ur answe r should co nsist of a series of alternative

hypotheses - you could indicate how likely each one is but yo u don 't need to make a final choice .

Suggest - Don 't expect to have been taught the answer to these questio ns. Use yo ur ove rall biol ogical understandin g to find

answers - as long as they are possible, they w ill get a mark.

Compare - Thi s type of question inv olves assessing how similar or different two or more thin gs are. You cannot do thi s by

describin g the thin gs separately. Every point that you make should be a similarity or a difference. There may be mo re simi larities

or more di fferences - all of them are relevant.

Distinguish - Thi s is simil ar to a co mpare question, except that o nly di fferences need to be includ ed in yo ur answer. The key

word in thi s type of question is ofte n 'w hereas' .

In both co mpare and di stinguish question s a table is ofte n the best way to arrange your answer . Use the columns of the table for

the thin gs th at yo u are comparing and the row s for the ind iv idual similarities o r differences.

Evaluate - Thi s usuall y i nvo lves assess ing the value, imp ortance o r effects of something. You mi ght have to assess how useful

a techniqu e is, or how useful a model is in helping to explain something. You mi ght have to assess the expected impacts of

something o n the environment. Wh atev er it is that yo u are evaluati ng, you wi ll probably have to use yo ur jud gement in

comp osing yo ur answer.

There are other co mmand terms that are used in qu estion s, but they are more straightfo rwa rd and you are unli kely to have

d iffic ulty in und erstandin g w hat sort of answer to give.

176

TOPICS 1 AND 2 STATISTICAL ANALYSIS AND CELLS 1 (a) X = rough endop lasmic reticulum Y = mit ochondri a (b) nuclear membrane is the curved structure o n the left-hand side (c) proteins because there is rough endo plasmic reticu lum wi th ribosomes whi ch make prot ein; ATP because there are many mit ochondria which make ATP. 2 (a)(i) phospho lipid (ii) head is hydro phili c and tails are hyd rophobic (b)(i) II is integral (ii) any tw o of : III is a pump protein; transfers specific substances; uses energy from ATP to move substance against the concentratio n gradient. 3 (a)(i) 12.4 ; %; (ii) 5.22 (b)(i) positiv e; co rrelatio n; (ii) does not prove obesity causes high blood pressure; co rrelat ion does not establish a causal relat ionship; high blood pressure may be caused by something else that also caused obesity;

TOPIC 3 THE CHEMISTRY OF LIFE 1 (a)(i) DN A (ii) DNA (iii) RNA (b) experimental error (c)(i) DNA is doub le stranded; A pairs with T and C pairs with G; one base in each pair is therefore A o r G, so A + G = 50%; (ii) any tw o of A = T; C = G; C + G = 50% ; A + G / C + G = 1.00 (d)(i) influenza virus (ii) RNA co ntains uracil instead of thymi ne; single stranded so amo unts of G and C not equal. 2 (a)(i) CO 2 concentratio n fall s in the light and rises in the dark; (ii) CO 2 concentratio n fall s wh en it is w armer and rises w hen it is coo ler; (b) CO 2 co ncentratio n is mo re closely related to light intensity; wh en there is a temporary dark period during the thir d day but it stays wa rm pH drop s so CO 2 co ncentrat io n rises; (c)(i) respiration produ ci ng CO 2 ; (ii) photosynthesis causing CO 2 uptake; 3 (a) radical/variable porti on of the ami no acid (b) C - N bo nd; 0 = linked to C and H- linked to N (c) 70S ribo somes in prokaryotes vs. 80S ribosomes in eukaryotes; free rib osomes in prokaryotes vs. rib osomes sometimes linked to rou gh endo plasmic reticulum in eukaryotes.

TOPIC 4 GENETICS 1 (a) a group ind iv idual must be genotype ii because it is due to a recessive alle le; B group indiv idual in generatio n 2 must be IBi because t he parent that w as blood gro up A cou ld not have passed o n IB; B group indivi dual in generatio n 3 must have been IBi group parent must have passed o n i; because the (b) parents could have been group 0 ; parents could have been group A w ith genotype IAi; parents could have been group B with genotype IBi (c) blood transfusio n. 2 (a) C' C' CW CW and C' CW (b) The allele fo r red fl owers is do m inant in peas but co dominant in Mirabilis (c) gametes C' and CW; genotypes C' C' C' CW CW C' and CW CW; phenoty pes red pink pink and w hit e, respectiv ely. 3 (a) a group of organisms w ith identical genotypes (b) nucleus removed from a cell in an adult organism; nucl eus removed from an egg cell and replaced with the nucleus fro m the adult animal (cHi) fragments had moved dow n; larger fragments are nearer the top and move more slow ly; (ii) culture cells have the same profile as udder cells as they have the same pattern of bands; Do ll y's blood cells have the same profi le as the udd er/c ulture cells as they have the same pattern of bands; Doll y was cl oned fro m the udder cel ls; sheep 1-1 2 are genetica lly different;

a

TOPIC 5 ECOLOGY AND EVOLUTION 1 (a) sigmoi d/S-shaped (b)(i) li ne reach ing a plateau by year 8 (ii ) any tw o of : food supp ly; predatio n; breed ing sites; d isease (c)(i) populatio n wo uld have reached carry ing capacity mor e quickly (ii) carry ing capacit y wo uld have been the same. 2 (a) I = secondary co nsumers II = prim ary consumers III = produ cers (b) chemic al energy (c) arrow from the sun to box III (d) any two of : arrows represent energy losses; heat produced because energy transform ation s are never 100% effic ient;

energy not passed along the food chain to another organism.

3 (a) methane causes an increase in the Earth's temperature by the greenhouse effect; temperature only increases as a result of an increase in atmospheric met hane; methane emissio ns to the atmosphere must be greater than losses (b) methane emission is a natural process, e.g. swamps and marshes; hum ans cause methane emissio n, e.g. coa l burni ng/cattle and sheep/ rice paddies; most emissio ns are caused by humans/hum ans have increased emissio ns co nsiderably (c) any three of : drain swamps and marshes; reduce cattle and sheep farm ing; stop grow ing rice in paddies; control releases of natural gas; reduce burning of coal; prevent forest fi res/burning of bi omass.

TOPIC 6 HUMAN HEALTH AND PHYSIOLOGY 1 (a) Tb is higher than Ta ; Tb is co nstant w hereas Ta is decreasing (b) heat absorbed from the enviro nment; heat generated by cell respir ation (c) acti ve during darkness because it maintains co nstant high body temperature as a result of cell respir ation. 2 (a)(i) ingesti on of pathogens (ii) in blood; in bod y tissues (b) to allow the produc tio n of many di fferent types of antibody ; to fight many d ifferent diseases. 3 (a) I = trachea II = bronchi o les (b) maintains co ncent ratio n grad ients of oxyge n and CO 2 betwee n air in alveo li and blood; ensures rapid diffu sion/gaseou s exchange (c) alveo lus w all consisti ng of very thi n cells; blood cap illa ries adjace nt to alveo lus; bron chio le connected to alveo lus; diameter of alveo lus indica ted;

TOPIC 7 NUCLEIC ACIDS AND PROTEINS 1 (a)(i) higher than 40 °C; init ial rate was faster; then reaction stopped due to denaturation (ii) lower temperature than 40 °C because the rate is slowe r; 30 "C because the rate is half that at 40 °C (b)(i) curve drawn above the curve W (similar to curve Y) (ii) curve drawn above the curve W; gradient of curve decreasing markedly w ith time show ing increasing inhibition as the

substrate concentratio n falls.

2 (a) 3' term inal is deoxyribose/ri bose to w hich a nucleot ide can be lin ked; 5' termin al is phosphate group to w hic h a nucl eotide can be linked (b) A ny 3 of : pur ines and pyrim id ines are both bases; both are part of nucleot ides; A and G are puri nes and C and T are pyri midines; purin es can only pair w ith pyrim idin es in DNA; pu rines have tw o rings and purines only one ring (c) An y 5 of : DNA is transcribed; mRNA is translated; RNA is produced by t ranscripti on; po lypepti des are produ ced by

translat io n; transcription is do ne by RNA pol ymerase; translatio n is do ne by ribosomes;

177

3 (a) globular (b) number and sequence of amino acids (c)(i) X is a beta pleated sheet and Y is alpha helix (ii) hydrogen bonding (d) any two of: tertiary structure determines the enzyme's shape; determines the active site's shape; makes the enzyme substrate specific; shape ensures that when the substrate binds it is distorted/induced fit.

TOPIC 8 CELL RESPIRATION AND PHOTOSYNTHESIS 1 (a) Any two of: double membrane; cristae/infoldings of inner membrane; ovoid shape; (b) double outer membrane shown; inner membrane shown folded in to form a crista (c)(i) label indicating the matrix (ii) label indicating the inner membrane/cristae (iii) label indicating the cytoplasm outside the mitochondria. 2 (a) peaks in the red and blue sections of the spectrum; minimum in the green section at about half of maximal rate (b) action and absorption spectra are closely correlated; because pigments absorb the Iight energy used in photosynthesis; the more light absorbed at a wavelength the more photosynthesis. 3 (a) oxidative phosphorylation and photophosphorylation (b) barrier to proton movement; allows a proton gradient to develop; location of ATP synthase; (c) plasma membrane;

TOPIC 9 PLANT SCIENCE 1 (a)(i) more Pfr (ii) more Pfr (b)Pir slowly reverts to PI' in darkness; timing is based on the amount of conversion; (c) Pir promotes flowering in long-day plants; and inhibits it in short-day plants; 2 (a) Any three of: parallel versus net-I ike veins; vascu lar bundles distributed through stem versus in a ring; one versus two cotyledons; floral organs in 3s versus in 4s or 5s; unbranched versus branched roots; (b) apical meristem increases length of the stem; lateral meristem increases width of stem; (c) monocots cannot thicken their stems; cannot grow into large trees; less opportunity of branching; 3 (a)(i) 6 pm to 6 am/sunset to sunrise (ii) 6 am to 4.30 pm (b) CAM plant is the xerophyte because it opens its stomata at night; less water loss during cooler conditions in the night (c)(i) partial closure between 11 am and 12 am; followed by reopening (ii) plant needs to limit transpiration during the hottest part of the day.

TOPIC 10 GENETICS 1 (a) polygenic (b) AaBb; blue-flowered (c) all gametes shown with one allele of each gene only; four homozygous genotypes shown AABB AAbb aaBB and aabb; four double heterozygous genotypes shown AaBb; eight other genotypes shown AABb AAbB aaBb aabB AaBB aABB Aabb and aAbb; all sixteen phenotypes indicated (d) 9 blue 3 red and 4 white (e) gene A converts white to red and gene B converts red to blue. 2 reassortment of genes into different combinations from those of the parents (b) black body long wing; grey body vestigial wing (c) genes are linked/found on the same chromosome; parental combinations are kept together; unless there is a cross-over between the genes (d) any two of: find which chromosome a gene is located on; identify all of the genes in a linkage group; estimate how far apart the loci of genes on a chromosome are. 3 (a) first; prophase; (b)(i) four chromatids (ii) five chiasmata; (c) breakage of chromatids; rejoining of non-sister chromatids; exchange of material between chromatids;

TOPIC 11 HUMAN HEALTH AND PHYSIOLOGY 1 (a) excretion is removal from the body of waste products; waste products of metabolism (b) Any two of: protein in blood plasma but not urine; glucose in blood but not in urine; higher concentration of urea/waste products of metabolism in urine than blood plasma; composition of urine is more variable than blood plasma (c) loop of Henle makes medulla hypotonic by raising sodium/mineral ion concentration; allows production of hypertonic urine (d) basement membrane of glomeru lus/fi Itration slits; 2 (a)(i) actin (ii) regions II and III (b)(i) II would increase in length (ii) I and III would increase in length. 3 (a) Any four of: both contain a haploid nucleus; both have a plasma membrane; the sperm has a tail but the egg does not; the egg has much more cytoplasm; mitochondria in sperm are helical but in eggs are ovoid; the egg has cortical granules but the sperm does not; (b) stimulates gametogenesis in both men and women; promotes development of follicles in women and primary sperrnatocvtes in men; stimulates estrogen secretion in women but not testosterone in men; (c) both stimulate the development of the corpus luteum; both stimulate the secretion of progesterone; before fertilization by LH and after fertilization by HCG;

OPTION A - HUMAN NUTRITION AND HEALTH 1 (a)(i) 24.3 (ii) 22.6 (b)(i) 24.2 and 22.5 (ii) values are very close (c) below 18.5 is underweight; 25-30 is overweight; above 30 is obese; 2 (a)(i) monounsaturated fatty acids have one double bond and polyunsaturated have more than one; (ii) trans fatty acids have hydrogen bonded to different sides of double bonded carbon atoms versus cis fatty acids have hydrogen bonded to the same side; (b) saturated fatty acids are linked with increased blood cholesterol; cholesterol/saturated fatty acids are linked with atheroma; correlation between saturated fat intake and CH D; 3 (a) one mark for any two of: protein; fats; carbohydrate; minerals; vitamins; water; (b) Any three of: human milk contains the ideal combination of nutrients for human babies; breast-feeding helps with bonding; breast milk contains antibodies; human milk does not cause allergies (c) milk production from cattle involves separating calves from their mothers when they are very young; also involves slaughter of calves/young cattle;

178

OPTION B - PHYSIOLOGY OF EXERCISE 1 (a) hurnans store less oxygen per kg of body tissue (b) Any three of: both store most in blood; seal stores a higher proportion in blood than human; smallest proportion stored in lung of seal but muscle of human; human stores higher proportion in lung than seal; seal stores higher proportion in muscle than human (c) any three of: size of muscle; ratio of fast and slow fibres; concentration of myoglobin in muscle; arnount of blood in muscle. 2 (a) thin actin and thick myosin filaments shown; actin filaments attached to Z discs; actin filaments interdigitating with myosin; (b) ATP provides energy; for myosin heads; to detach from actin and recock (c) cardiac output is higher when muscles are

contracti ng;

3 (a) two; (b) discs bulge; soft pulpy core of disc is protruding; (c) (white matter of) spinal cord; (d) abnormal neck movements; heavy loads;

OPTION C - CELLS AND ENERGY 1 (a) CO 2 concentration (b)(i) temperature; rate of photosynthesis rises as temperature rises; (ii) temperature controls the rate of photosynthesis between 35 and 40°C; but is not the factor nearest to its minirnum level/is supra-optimal (c) light is the limiting factor at low light intensity; temperature therefore does not affect the rate of photosynthesis. 2 (a) (i) malonate inhibits succinate dehydogenase/other example (ii) copper/mercury/silver ions/other example; (b) similarity: both types of inhibitor reduce the rate of catalysis; difference between competitive and non-competitive: inhibitor structure similar to substrate vs. not similar/inhibitor binds to active site vs. binds elsewhere. 3 (a) pyruvate; acetyl group; (b) both are CO 2 ; (c) NADH + H+ (d) Krebs cycle;

OPTION D - EVOLUTION 1 (a)(i) positive correlation (ii) any two of: prirnate brains are larger in relation to body mass; but there is much variation; largest primates have relatively small brains (iii) any two of: scattergram shows that human brain has the largest size; primates with a larger body mass have a smaller brain; human brain mass is furthest above the line of best fit (b) easier to climb trees/speed of movement/less food needed. 2 (a)(i) 2 (ii) 6 (iii) 9 (iv) 6 (v) 10 (vi) 7 (b) c1adogram with four species; first split between rabbit and other three species; second split between lemur and other two species; final split between humans and orang utans; 3 (a) p2 + 2pq + q2 = 1 and q2 is the frequency of homozygous recessives; frequency = 0.23/23% (b) 35% (c) carriers have increased resistance to malaria; selective advantage over homozygous dominants so the sickle cell allele survives.

OPTION E - NEUROBIOLOGY AND BEHAVIOUR 1 (a) receptor protein; each receptor protein's shape is complementary to a specific odorant; (b) Any three of: G protein activates the enzyme adenylyl cyclase; enzyme converts ATP to CAJVIP; CAMP causes calcium channel to open; calcium causes chloride channel to open (c) membrane of chemoreceptor cell depolarizes/action potential created/chemoreceptor cell passes an impulse to a sensory neuron. 2 (a) photoreceptors (b) in sensory neurons from the retina to the brain; in motor neurons frorn the brain to the circular muscle

fibres in the iris (c) no response when a light is shone into eye of unconscious patient indicates damage to the brainstem.

3 (a) supporting the hair cells/reticular larnina; (b)(i) three rows; srnall medium and longer stereocilia; arranged in a W shape;

(ii) 1.2 urn: (iii) longer perceive lower frequency sounds; (c)(i) amplifies sounds; for the inner hair cells to perceive more easily; (ii) in the plasma membrane; mitochondria close to the edge of the cell;

OPTION F - MICROBES AND BIOTECHNOLOGY 1 (a) bacteria numbers increase; bacteria use oxygen in aerobic cell respiration; (b) bacteria decompose raw sewage; ammonia and phosphate are released during decornposition; (c) ammonia is converted to nitrate; by nitrifying bacteria; (d) eutrophication; nutrients stimulate growth of photosynthetic bacteria/algae; (e) bacteria consumed by other organisms;

raw sewage has all been decomposed;

2 (a) synthesis of DNNcDNA; from RNA (b)(i) retroviruses (ii) HIV (c) any three of: mRNA can be obtained quite easily; genes can be hard to find; gene consisting of DNA can be made from RNA; no introns in the gene using reverse transcriptase; gene can be inserted into other organisms; cDNNprobes can be used to locate other genes; 3 (a)(i) protein coat/capsid (ii) nucleic acid/genes; (b) insert gene into viral DNA; virus acts as a vector for the gene; (c) intracellular; all viruses rely on a host cell for most of their processes;

OPTION G- ECOLOGY AND CONSERVATION 1 (a)(i) S. marcescens feeds on the nutrients so more grow at high nutrient levels (ii)C. striatum reduce the numbers by predation (iii) O. nasutum increases the numbers because it feeds on C. striatum; which reduces the predation of S. marcescens (b) low popu lation of S. marcescens at low nutrient levels; therefore very tow levels of C. striatum on which O. nastum feeds (c) longer food chain with higher nutrient levels. 2 (a) indicator species need particular environmental conditions; can be used to give a measure of polJution levels/levels of an environmental variable (b) any two of: captive breeding and release of endangered species; growth of endangered plants in botanic gardens; storage of frozen seeds of endangered species in seed banks. 3 (a) mercury inputs reduced; (b) increases/decreases when river flow rates rise/fall; high rainfall leaches more mercury out; (c) death of organisms in higher trophic levels; toxic effects for humans consuming fish from higher trophic levels: _

179

OPTION H - FURTI-IER HUMAN PHYSIOLOGY 1 (a) H. pylori is implicated as a cause of stomach ulcers/cancer; antibodies show that the patient has been infected with H. pylori; (b) Any two of: incidence of stomach ulcers and cancer is higher in patients who had been infected with H. pylori; all patients with stomach cancer had been infected with H. pylori; some patients with stomach ulcers had not been infected so there must be alternative causes; correlation does not prove causation; (c)(i) higher incidence of duodenal inflammation in patients who had been infected; higher incidence of oesophagus inflammation in patients who had not been infected; (ii) H. pylori infects the stomach; toxins produced by H. pylori will pass on to the duodenum, not back to the oesophagus; 2 (a) SAN/pacemaker sends out a signal; signal spreads out through the walls of the atria (b) any two of: lub dup sounds made when valves close; closing valve causes vibration of blood in ventricle; rushing sounds due to flow of blood. 3 (a) V E increases as carbon dioxide concentration increases; greater increases in V E with successive increases in carbon dioxide concentration; (b) increases in carbon dioxide concentration in inspired air increase the blood concentration; detected by chemosensors in aorta/carotid artery; impulses sent to ventilation centre of brain/medulla; (c) further increases in V E; until maximal V E is reached;

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1 1 1 1 2 2

2.1.1 2.1.2 2.1.3 2.104 2.1.5 2.1.6 2.1.7 2.1.8 2.1.9 2.1.10 2.2.1 2.2.2 2.2.3 2.204 2.3 .1 2.3 .2 2.3 .3 2.304 2.3.5 2.3 .6 204.1 204.2 204.3 204 04 204.5 204.6 204.7 204 .8 2.5 .1 2.5.2 2.5.3 2.504 2.5.5 2.5.6

3 3 3 5 5 5 3 4 4 4 6 6 6 6 7 7 7 7 7 10 8 8 8 9 9 10 10 10 11 11 1 11 11 11

3.1.1 3.1.2 3.1.3 3.104 3.1.5 3.1.6 3.2.1 3.2.2 3.2.3 3.204 3.2.5 3.2.6 3.2.7 3.3 .1 3.3 .2 3.3 .3 3.304 3.3 .5 304 .1 304 .2 304.3 3.5.1 3.5.2 3.5.3 3.504 3.5.5 3.6.1 3.6.2 3.6.3 3.604 3.6.5 3.7.1 3.7.2 3.7.3 . . 3.704 3.8.1 3.8.2 3.8.3 3.804

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Page A.S. 6.1.3 6.104 6.1.5 6.1.6 6.1.7 6.2.1 6.2.2 6.2.3 6.204 6.2.5 6.2.6 6.2.7 6.3 .1 6.3 .2 6.3.3 6.304 6.3.5 6.3 .6 6.3.7 6.3.8 604.1 604.2 604.3 60404 604.5 6.5.1 6.5.2 6.5.3 6.504 6.5.5 6.5.6 6.5.7 6.5.8 6.5 .9 6.5.10 6.5.11 6.5.12 6.6.1 6.6.2 6.6.3 6.604 6.6.5 6.6.6

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7.1.1 7.1.2 7.1.3 7.104 7.1.5 7.2.1 7.2.2 7.2.3 7.3.1 7.3.2 7.3.3 7.304 704.1 704.2 704.3 70404 704 .5 704.6 704.7 7.5.1 7.5.2 7.5.3 7.504 7.6.1 7.6 .2 7.6 .3 7 .604 7.6.5

60 61 61 61 61 60 60 61 62 62 62 61 63 63 65 64 63 64,65 63 66, 67 68 68 68 71 69 69 70 70

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23 23 23 23 24 24 24 25 25 25 25 26-29 26 27 27 28 28 28 28 28 28 26-28 27,29 30 30 30 30 30 32 31 31 31 31 32 32 32

5.1.1 5.1.2 5.1.3 5.104 5.1.5 5.1.6 5. 1.7 5.1.8 5.1.9 5.1.10 5.1.1 1 5.1.12 5.1.13 5.1.14 5.2.1 5.2.2 5.2.3 5.204 5.2.5 5.2.6 5.3.1 5.3.2 5.3.3 ' 5.304 504. 1 504.2 504.3 50404 5 04 .5 504.6 504.7 504 .8 5.5.1 5.5.2 5.5.3 5.504 5.5.5

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123 F.1.9 144

123 F.2.1 144

123 F.2.2 144

123 F.2.3 144

124 F.2.4 124 F.2.5 144,1 45

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125 F.3.1 146

125 F.3.2 146

125 F.3.3 146

127 F.3A 146

127 F.3.5 142

127 FA.l 14 7

126 FA.2 14 7

126 FA.3 14 7

126 FAA 148

127 F.5.1 148

127 F.5.2 148

127 F.5.3 148

127 F.5A 148

128 F.5.5 150

128 F.6.1 149

128 F.6.2 149

129 F.6.3 149

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129 F.6.6 149

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130 F.6.1O 130 G.l .l 152

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132 G .1A 153

132 G.1.5 153

132 G.l.6 153

133 G.l .7 153

134 G.l .8 154

134 G.l .9 154

134 G.1.10 154

134 G.2. 1 154

133 G.2 .2 154

133 G.2.3 154

135 G .2A 154

135 G.2.5 155

135 G.2.6 155

135 G.2.7 155

135 G.2.8 155

135 G.2.9 155

136 G.2.10 155

136 G.2.11 156

137 G.3.1 156

137 G.3.2 156

137 G.3.3 157

137 G.3A 157

138 G.3.5 157

138 G.3.6 156

138 G.3.7 156

139 G.3.8 157

138 G.3.9 15 7

138 G.3.lO 157

139 G.3.11 158

140 G A. l

Page

GA .2 GA.3 GA A GA .5 GA .6 G.5 .1 G .5.2 G.5.3 G .5A G.5.5 G.5.6

160

158

158

158

158

159

159

159

160

160

160

H.l .l H.1.2 H.1.3 H.1A H.l.5 H.2.1 H.2.2 H.2.3 H.2A H.2.5 H.2.6 H.2.7 H.2.8 H.2.9 H.3.1 H.3.2 H.3.3 H.3A HA.l HA.2 HA.3 HA A HA .5 HA .6 HA.7 H.5.1 H.5.2 H.5.3 H.5A H.5.5 H.6.1 H.6.2 H.6.3 H.6A H.6.5 H.6.6 H.6.7

162

162

162

162

162

163

163

164

163

163

163

164

164

164

165

165

165

165

166

166

166

166

166

166

166

167

167

167

168

168

169

170

169

170

170

170

169

181

Index

A

abiotic factors 152

ABO blood groups 27

abscisic acid 83

absorption of food 165

absorptio n spectrum 77

acety l coe nzy me A 74

acrosome react ion 106

actin 100

actio n potenti al 53

act ion spectrum 77

activatio n energy 69

active immunity 97

active management 158

active sites 18, 69 , 70

active transport 9, 84

adaptation 38

adaptive rad iatio n 125

addiction 13 7

adenine 60

adenosine triphosphate 20

ADH 10 2, 16 2

adrenalin 48

aerobic cell respiration 20, 75, 11 7

AIDS 50

albinism 29

alco hol 137

alco ho l abuse 166

algal bloo ms 144, 145

ali en species 15 7

al lele frequencies 123, 128

alle les 23, 26

allopatric speciatio n 124

allostery 71

alpha heli x 66

altitude 169

altruism 140

alveo li 51

ami no acids 14, 62 , 66, 67

amino ac ids in food 11

amnioce ntesis 25 , 10 7

Amoeba 143

amphetamines 137

amy lase 14 7

Anabaena 148

anabo li c steroids 11 6

anaerobic cell respir ation 20 , 74, 117

analogous structures 129

angiospermop hytes 35

animal cells 7

ani mal experiments 138

annelida 35

anorexia nervosa 113

anterio r pituitary 162

anthrax 98

.antibiotic resistance 39

antib iotics 49, 149

antibod ies 49 , 50, 96, 9 7

anticodo n 17, 63

anti-diuretic hormone 102, 162

antigens 49, 96

antisense strand 62

antiseptics 149

apica l meristems 87

appetite control 112

archaea 142, 145

Ardipithecus 126, 12 7

182

arteries 48

arterio les 55

arthropoda 35

Asian flu 150

BSE 150

Bt maize 3 1

bulbs 86

buoyancy 15

Asp ergillus 147

assim ilatio n 4 7

asthma 170

atheroscle rosis 168

atmosphere 123

ATP 20, 73, 78

ATP synthase 75

ATP synthesis 74, 75

ATPase 75

A ustralopithec us 126, 127

autonom ic nervous system 137

autosoma l lin kage 92

autotrophs 4 1

auxin 87

AV (atrioventric ular) node 167

B

bacteria 6, 49, 14 2

bacterial infecti on 149

base pairi ng 16, 60, 62

base substi tutio n 23

B-cell s 96

beer prod uction 14 7

bees 140

behavioural iso latio n 124

benzod iazep ines 13 7

beta pleated sheets 66

bi le 166

bi le salts 164

binom ial system 34

biochemical oxyg en demand 144

biodiversity 156

bi ofi lms 143

bi ogas 14 5

biogeographi cal features 158

biolog ical co ntro l 15 7

biom agnif ication 156

biom ass 2 1, 154

bi omes 155

bioreactor s 14 5

bio remed iati on 148

biosphere 155

biotic factors 152

bioti c i ndex 158

bi pedalism 126

bi rdso ng 135

birth 107

bladder 56

blood 48

bloo d clotting 98

blood gro ups 2 7

BO D 144

body mass in dex 112

body temperature 55

Bohr shift 169

bo nes 99

botani c gardens 158

bovin e spongifo rm encephalopathy 150

brain size 127

bread makin g 14 7

breast-feeding 113

bryophytes 35

C

calc ium 14, 52

Calvi n cycl e 79

CAM pl ants 83

cambium 87

cancer 11

cannabis 137

capi lla ries 48, 55

capsid 14 3

captive breedi ng 158

capture-mark-release method 159

carbam ino hemoglobin 170

carbohydrates 15

carbohydrates in food 112

carbon cycle 43

carbon di oxide transport 1 70

carbon fixatio n 21, 43 , 79

carbonic anhydrase 170

cardiac cyc le 167

card iac o utput 119

card iov ascular systems 119

Caroli na parakeet 160

carriers 28

carrying capacity 36

cartil age 99

eD NA 146

cell divisio n 11, 20, 73, 74

cell theory 3

cell wa lls 6, 7, 142

ce ll s 3, 10, 15, 114

central nervou s system 52 , 136

centrioles 11

centrom ere 23

cerebell um 138

cerebral hemispheres 138

. CFCs 15 7

channels 8

CHD 11 1, 114, 168

chem iosmosis 75, 78

chemoautotrophs 148

chemoheterotrop hs 148

chemosensors 170

c hiasmata 93

chi ldbirth 10 7

Chlamydia 149

Chiarella 143

c hlor ide shift 170

chlorophy ll 21, 77, 78

chloroplasts 7, 79,80, 12 3

cho lesterol 114, 166, 168

chorion 108

chorionic vill us samp li ng 25

chromatids 23

chromosomes 23

c irrhosis 166

CJD 150

cl ade 130

cl adistics 130

c1adog rams 130

class 35

classification 3, 129, 130, 14 2

c limograph 155

cl inical obesity 112

clo nal selection 97

cl one 32

clo ning 32

clotti ng 98

cnidaria 35

CNS 52, 136

coca ine 137

coc hlea 133

codominance 27, 90

co-dominant alleles 27, 28

codons 17, 62

collagen 68

co lour blindness 28

comb ustio n 43

communities 40

competition 153

competit ive excl usio n 153

competitive inhib ition 70

condensatio n reacti ons 15

co nditio ning 135

cone cells 134

co niferophytes 35

co nifers 35

co njugated proteins 67

conservatio n 156, 158

consumers 41, 42

continuous variation 91

convergent evo lution 125

copulation 107

cornea 134

coronary heart disease 111, 114, 168

coronary thrombosis 168

corpus luteum 57, 104

correlation 2

co rtical reacti on 106

creatine phosphate 117

creation of life 122

Creutzfeld-Jacob disease 150

cristae 76

crossing over 92, 93

cultural evo lution 126

cyanobacteria 148

cyc lic photoph osphorylation 81

cystic fib rosis 128

cytokinesis 11

cytoplasm 3, 6, 7

cytosine 60

D

Darw in 38

decarboxylation 74

decision making 136

deficiency di seases 110

denaturation 18

denitrifi cation 144, 145

deoxyr ibonucl eic acid 16

depolarization 53

desert 155

detoxifi cation 166

detrivores 41

di abetes 55, 113

diaphragm 51

dicoty ledons 86

die tary fib re 114

di etary supplementatio n 110

diets 110

differentiation 3, 4

diffusion 9

digestion 47, 163

di gestion 163

di gestive enzy mes 163, 164

di gestive j uices 163

dihybrid crosses 89, 90

d iplo id 24

disaccharides 15

disease 49, 50

disinfectants 149

dislocation of joint s 119

distribution of animals 152

distributi on of plants 152

disulfide bri dges 66

div ersity index 156

DNA 16, 60

DN A fingerpri nting 30

DNA polym erase 60

DNA profi lin g 30

DNA repl ication 16

Do lly the sheep 32

domains 142

domin ant alleles 16

dopamine 137

Down syndrome 25

drugs 137

drugs in sport 116

E ear 133

eco logical effi ciency 42

eco logical niches 153

eco logica l succession 155

eco logy 43

ecosystems 43

effector s 132

egestion 47

egg cell 104, 105

eggs in the di et 114

elbow 99

electron transport chain 75

elements 14

embryos 58

emergent properties 3

emulsification of fats 164

end product inhibition 71

endocri ne system 54

endocy tosis 10, 165

endoplasmic reticulu m 7, 10

endorphins 139

endosymbiotic theory 123

endotoxins 149

energy 20

energy effic iency 42

energy flow 41

energy in food 112

energy losses 41, 42

energy pyramids 42, 154

energy requirements 112

energy sto rage 15

enviro nmental monito ring 158

enzyme in hibition 70, 71

enzyme specificity 18

enzymes 18, 19, 69

epidemics 150

epistasis 90

epithelium 165

EPa 119

ER 7

error bars 1

erythrocytes 49

erythropo ietin 119

estimating fi sh stocks 160

estrogen 57, 108

ethano l 20

eubacteria 142, 143

Eug lena 143

eukaryotes 7, 61, 142

eutro phicatio n 144, 145

evo lutio n 37, 38, 39, 125, 127

evolutio nary c locks 129

ex situ co nservation 158

exagerrated traits 140

exci tatory drugs 137

excitato ry synapses 136

excretion 101, 102

exercise and ventilatio n 170

exergonic reacti ons 69

exocrine glands 163

exocy tosis 10

exons 61

exotoxi ns 149

extracellular inf ections 149

extracellular material 3, 10

eye 134

F F, hybrids 16

faci litated diffusion 9

family 35

fast and slow muscle 116

fatty acids 14, 111

ferns 35

ferti li zation 58, 85, 106, 107

fetal develop ment 107

fetal hemoglobin 169

fibre 114

fibrinogen 98

fibrous proteins 68

filicinophytes 35

fish conservatio n 160

fish stocks 160

fish yields 160

fitness 116

flagell a 6, 143

flatw orms 35

fl owering 87

flowers 85,86

flui d mosaic model 8

fM RI1 38

fol licl e 56,57, 104

foo d chains 40

food mi les 114

food poi sonin g 147

food preservation 147

food we bs 42

for aging behavi our 139

forensics 30

fossil fuels 43

fossilization 126, 127

fossils 37

fructose 15

FSH 56, 57, 58

functional magnetic resonance im aging 138

fundamental niches 153

G gametogenesis 103, 104, 105

gas exchange 51, 169

gastric ju ice 164

gel electrophoresis 30

gender 28

gene interact ion 90

183

gene linkage 92, 93

gene mutation 23

gene pools 123, 128

gene therapy 146

genes 18,23

genetic code 17, 62

genetic diseases 23, 29

genetic evolution 127

genetic modification 31

genetic variation 24

genome 23

genotype 16

genus 34

geographical isolation 124

germ ination 85

gerrn-l ine therapy 146

giberellin 85

glands 163

global warming 44

globular proteins 68

glomerulus 101

glucagon 55

glucose 14, 15, 55

glycerides 15

glycerol 14

glycogen 7, 15, 117

glycolysis 73

glycoproteins 8, 10

GM031

goitre 110

Golgi apparatus 7, 10

gradualism 125

Gram stain 142

grassland 155

greenhouse effect 44

gross production 154

guanine 60

guard cells 83

H

Haber process 144

habitat 45

haemoglobin 67, 68, 166, 169, 170

half-life 125

haloph iles 142

haploid 24

Hardy-Weinberg equation 128

Hardy-Weinberg principle 128

HCG 58, 108

hearing 133

heart 48, 119, 167

heart action 167

heart attacks 168

heart beat 167

heart rate 119

helicase 60

Helicobacter pylori 164

helper T-cells 96

hemoglobin 67,68, 166, 169, 170

hemophilia 28

hepatic blood vessels 166

hepatocytes 166

herbivory 153

heterotrophs 41

heterozygous 16

hip joint 99

histone 61

HIV 50,146

homeostasis 54, 55

hominids 126, 127

Homo 126,127

1'84

homologous 24

homologous structures 129

homozygous 16

honey 114

honey bees 140

hormones 8, 162

human ancestors 126, 127

human classification 127, 129

human diets 110

human evolution 126, 127

human genome project 32

human impacts 45

human milk 113

human origins 126, 127

human reproduction 103

hybridoma cells 98

hydrogen bonds 13, 16, 60

hydrogen carbonate 170

hydrolysis reactions 15

hypothalamus 55, 112, 138, 162

I

IDD (iodine deficiency disorder) 110

identification 34

ileum 165

immunization 97

immunity 97

immunoglobins 68

in situ conservation 158

in vitro fertilization 58

independent assortment 89, 92

indicator species 158

induced fit hypothesis 69

infections 49, 149

infertility 58

influenza 149

inhibitors 70, 71

inhibitory drugs 137

inhibitory synapses 136

initiation of translation 65

injuries in sport 119

innate behaviour 135

inoculation 97

inorganic compounds 14

insect pollination 85

instinct 135

insulin 31, 55

international conservation 160

interphase 11

interspecific competition 157

intervertebral discs 119, 120

intestines 47

intracellular infections 149

intramolecular bonding 66

introns 61

iodine 110

iris 134, 139

iron 14

IVF 58

J joints 99

K karyotypes 24, 25

keys 34

kidney structure 101

kinesis 135

Krebs cycle 74

K-strategies 159

L lactase 19

lactate 20, 117

lactic acid 20, 117

lactose 15, 19

lateral meristems 87

LDL 168

learned behaviour 135

leaves 83, 86

leptin 112

lesions 138

leu kocytes 49

LH 56,57 ligaments 99, 119

ligase 60

light-dependent reactions 77, 78

light-independent reactions 77, 79

limiting factors 81

link reaction 74

linkage 92

lipase 68

lipid digestion 164

lipids 15

lipids in food 112, 114

liver 55, 166

liver cell 7

Iiver damage 166

loop of Henle 102

lung capacity 118

lungs 51

lymphocyte 49,50 Iysosomes 7

lytic life cycles 149

M

macroevolution 126

macrophages 96

magnification 5

malaria 98, 150

malnutrition 111

maltose 85

management of wildlife reserves 158

mean 1

meat in the diet 114

medulla oblongata 138

meiosis 24, 92, 93, 94

melanisim 39

membrane proteins 8, 68

membranes 8

Mendel 16, 89

menstrual cycle 57

menstruation 57

meristems 87

metabolic pathways 71

metabolism 71

methane generation 145

methanogens 142

microevolution 127

m icrometres 5

microvilli 47, 102, 108, 165

migration 132

milk113,114 Miller and Urey 122

mineral absorption 84

mineral elements 14

mineral ion uptake 84

minerals in food 110

mitochondria 7, 74, 75, 76, 123

mitosis 11

mollusca 35

monitoring environments 158

mo noclo nal antibodies 98

monocotyl edon s 86

mo nohy brid crosses 16

monosaccharid es 15

mosses 35

motor neuron s 52, 132

mucous membranes 49

mul ti cellul ar 3

multi ple alle les 27

muscle 99, 100

muscle co ntraction 100

muscle fatigue 117

muscul ar dystroph y 29

mutation 23, 29

mutu ali sm 153

myofibril s 99

myoglob in 116, 117, 169

myometrium 108

myosin 68, 100

N

NAD 73

NA DP 78

naked mol e rats 140

natu ral selectio n 38,39, 132

nature reserves 158

negative feedback 54, 55

nephron s 10 1, 102

nerve impul se 53

nerves 52

nervou s system 52, 54

net produ cti on 154

neuron 52, 132

neurotransmitters 52, 136

niches 153

nicotine 137

nitrates in wa ter 144,1 45

nitri fi cation 144

nit rifyin g bacteria 145, 148

nitr ogen 14

nitrogen cycl e 144

nitr ogen fixation 144

nom encl ature 34

non- com petitiv e inh ibiti on 70

non-di sjunction 25

norm al distributi on 1

nose 133

nucl eoid 6

nucl eosomes 61

nucl eotides 16, 60

nucl eus 3

nutri ent cycles 43

nutri tion 110

o obesity 112, 168

oestrogen (estrogen) 57, 108

o il spi lls 148

Okazaki fragments 60

omega-3 fatty acids 111

oocy te 104

ooge nesis 104, 105, 106

order 35

organic compounds 14

origi n of cells 123

ori gin of life 122

osmoregulat ion 101, 102

osmosis 9, 84

ovary 56, 104

ov ulatio n 56, 57

ox idatio n reacti on s 73

oxidat ive phosphoryl ation 75

oxyge n debt 11 7

oxygen dissoci ation 169

oxyge n transport 169

ozo ne 157

p pacema ker 48

pain 137

painkill ers 137

pancreas 55, 163

pancreatic juice 164

pandemics 150

Paramecium 143

parasiti sm 153

parasymp athetic system 137

parti al pressure 169

passive immunity 97

passive transport 9

pasteuriz ation 149

pathogen transm ission 150

pathogens 49

Pavl ov 135

peR 30

peacocks 140

pedigree charts 27, 29

penis 56

pepsinogen 164

peptid e bo nds 15, 63

pepti de hormones 162

peptide lin kage 15, 63

perform ance enhancing substances 116

pesticides 148

pH 19

phagocyte 49

phenotyp e 16

phenyl ketonuria 111

phl oem 83, 84

phosphol ipid s 8

phosphoru s 14

photoa utotrophs 148

photoheterotrophs 148

photo lysis 21, 78

photoperiod ism 87

photophosphoryl ation 77, 78

photoreceptors 134

photosynthesis 21, 77, 83

pho tosystems 78

phototropi sm 87

phyl ogeny 127, 129, 130

phylum 35

phytochrome 87

pigments 77

pil i 6, 138, 162

pl acenta 107, 108

plant cel ls 4, 7

pla nt reprodu ct ion 85

plants 35

plasma (blood) 49

plasma ce lls 96

plasma membrane 3, 6

plasma proteins 166

plasmids 31

platelets 49, 98

pl atyhelm in ths 35

pol arity 13

po lli natio n 85

pollu tion 145

po lygenic inheritance 91

po lyme rase chain react ion 30

po lymo rphism 125, 126

po lypeptides 15, 17, 64, 67

polyploi dy 124

pol ysaccharides 15

pol ysomes 64

popul ati on dy namics 36

popul ati on growth curves 36

popul ation s 36

pori fera 35

positive feedback 107

posterior pitui tary 162

postsynaptic potentials 136

pre-bi otic Earth 122

predation 153, 157

pregnancy 107, 108

pr imary structure 67

prim ary succession 155

prim ates 127, 129

prio ns 150

producers 40

progesterone 57, 108

pro karyotes 6, 61, 123

prostheti c gro ups 67

protease 164

protein defi ci ency 111

prot ein di gestion 164

protein fun cti on s 68

protein structure 66, 67

protei n synthesis 64

prote ins 8

proteins in food 112

prothrom bin 98

protobi onts 123

psychoacti ve dru gs 137

puberty 56

pubic hair 56

pumps 8, 10

punctu ated equil ibrium 125

Punnett grid 26, 89

pupil 134, 138

pupil reflex 138

purin es 60

pyramid s of energy 42, 154

pyrim idines 60

pyruvate 20,73,74

Q quadrats 152

R

rainfall 155

rain forests 156

random sampling 152

realized niches 153

receptors 132, 133, 134

recessive alle les 16

recom bin ation 92, 93

recycl ing 43

red bloo d cells 49

reduction reacti ons 73

reed beds 145

reflex arc 132

reflexes 132, 135

relay neurons 52, 132

repetiti ve sequences 6 1

repli cation 16, 60, 61

repol arization 53

reprodu ctive systems 56

respiration 20, 73, 74

restin g potenti al 53

restricti on enzy mes 31

retin a 134

retrovi ruses 146

reverse transcriptase 146

Rhiz obium 144

04 k~

1,, ­

rhythmical behaviour 139

ribonucleic acid 17, 122

ribose 14

ribosomes 6, 7, 63, 64

ribulose bisphosphate 79

rickets 110

risk 110

river pollution 145

RNA 17,122 RNA polymerase 62

rod cells 134

roots 84, 86

rough endoplasmic reticulum 7, 10

r-strategies 159

rubisco 79

RuBP 79

S SA (sinoatrial) node 167

Saccharomyces 143, 147

saliva 164

saprotrophs 41, 43

sarcolemma 99

sarcomeres 99, 100

satellite DNA 30

saturated fatty acids 111, 114, 168

scale bars 5

SCID146

scrapie 150

scurvy 110

secondary structure 66, 67

secondary succession 155

seed banks 158

seed dispersal 85

seedlings 85

seeds 85

segmented worms 35

segregation 16

selective re-absorption 102

selenium 148

semen 105

seminiferous tubules 103

sense strand 62

sensory neurons 52, 132

sensory receptors 132, 133, 134

severe combined immunodeficiency

disease 146

sewage 145

sex chromosomes 28

sex determination 28

sex drive 56

sex linkage 28, 90

sexual reproduction 39, 56

shrubland 155

sickle cell anemia 23

sieve tubes 84

sigmoid growth curves 36

significance (statistical) 1

simple reflexes 132

Simpson diversity index 156

sinusoids 166

size 5

skeletal muscle 100

skin cancer 110, 157

skin colour 91

skulls 126

slipped disc 119

smoking 168

social behaviour 140

sodium 14

somatic-line therapy 146

186

sound perception 133

soy sauce 147

speciation 124

species 34, 124

species extinction 160

specificity of enzymes 18

speed 116

sperm (spermatozoa) 103, 1 OS, 106

spermatogenesis 103, 105, 106

spinal cord 132

spinal reflexes 132

sponges 35

spongiform encephalopathy 150

sprains 119

stamina 116

standard deviation 1

starch 7

statistical tests 1

stem cells 4

stems 84,86

steroid hormones 162

stomach 47, 164

stomach cancer 164

stomach uleers 164

stop codons 62, 65

striated muscle 99

stroke volume 119

substrate concentration 19

substrates 18

sucrose 15

sulphur 14

sunlight 41

surface areas 5

sweat 55

sympathetic nerve 167

sympathetic system 137

sympatric speciation 124

synapses 52, 136

T

t test 2

taxis 135

T-cells 96

temperate deciduous forest 155

temperature 19

tendons 99

tendrils 86

termination of translation 65

tertiary structu re 67

test crosses 29, 93

testes 56, 103

testosterone 56, 103

THC (tetrahydrocannabinol) 137

therapeutic cloning 32

thermoph i les 142

thrombin 98

thylakoids 78

thymine 60

tidal volume 118

tongue 133

torn muscles 119

training 118, 119

trans fats 111, 168

transcription 17, 62

transects 152

transfer RNA 63, 64, 65

transgenic organisms 31

translation 17, 63, 64

translocation 84

transmission of pathogens 150

transm itter 52

transpiration 83, 84

trickle fi Iter beds 145

tRNA 63,64,65

trophic levels 40, 154

tropical rainforest 155

trypsinogen 164

tubers 86

tumours 11

tundra 155

U

ultra-violet radiation 157

ultrafiltration 101

umbilical cord 4,108,

unconscious coordination 139

unicellular 3

units 5

unsaturated fatty acids 111

uracil 17

urinel0l, 102

V

vaccination 97

vacuoles 7

vagina 56

vagus nerve 167

variant CJD 150

variation 24, 38

vasopressin (ADH) 102

vegan diets 114

vegetarian diets 114

veins 48

ventilation 51, 118

ventilation rate 118, 170

vesicles 10, 52

villi 47, 165

virus vectors 146

viruses 5, 49, 143, 146, 149

visual stimu Ii 134

vital capacity 118

vitamin C 110

vitamin D 110

vitamins 110

V0 2 117

W Wallace 38

warming up 118

water 13

water uptake 84

wildlife reserves 158

wine production 147

withdrawal reflex 132

x

X chromosomes 28

xerophytes 83

xylem 84

y Y chromosomes 28

yoghurt 147, 149

z Z line 100

zona pellucida 105