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978-0-521-17691-0 - Biology Unit 2 for CAPE ® Examinations

Myda Ramesar, Mary Jones and Geoff Jones
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Contents
Introduction iv 7 Homeostasis and hormonal
1 Photosynthesis and ATP synthesis 1 action 140
An overview of photosynthesis 1 Coordinating cell activities 140
Leaf structure and function 2 Homeostasis 140
Chloroplast structure and function 4 The mammalian endocrine system 141
Factors affecting the rate of photosynthesis 9 Plant growth regulators 150
Limiting factors and crop production 12 8 The kidney, excretion and
2 Cellular respiration and ATP osmoregulation 161
synthesis 21 Excretion 161
ATP 21 The kidneys 162
Glycolysis 22 Osmoregulation 169
The link reaction 24 Using urine for diagnosis 172
The Krebs cycle 25 9 Nervous coordination 179
Oxidative phosphorylation 26 The human nervous system 179
How much ATP? 28 Neurones 179
Structure and function in mitochondria 29 Transmission of nerve impulses 182
Anaerobic respiration 30 Synapses 187
Respiratory substrates 32
10 Health and disease 199
Measuring the rate of aerobic respiration 33
What is health? 199
3 Energy flow and nutrient cycling 42 Acquired immune deficiency syndrome 201
Some terms used in ecology 42 Diabetes mellitus 206
Food chains and food webs 44 Cancer 208
Energy flow through an ecosystem 47
11 Immunology 221
Cycling matter in ecosystems 51
Parasites and pathogens 221
4 Ecological systems, biodiversity The immune response 221
and conservation 62 Antibodies 231
Biotic and abiotic factors 62 How immunity develops 231
Biodiversity 67 Monoclonal antibodies 234
Conservation 71
12 Social and preventative medicine 244
5 Transport in plants 84 Diet and health 244
Plant transport systems 84 Exercise and health 255
Uptake of ions 85 Infectious diseases 260
Water transport 85
13 Substance abuse 269
Transport in phloem 95
Legal and illegal drugs 269
6 The circulatory system of Drug dependency 269
mammals 110 Alcohol 270
Transport in mammals 110 Smoking 274
The mammalian heart 110
SAQ answers 284
Blood vessels 120
Blood 125
Glossary 299
Index 311
Acknowledgements 316
iii

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Myda Ramesar, Mary Jones and Geoff Jones
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Chapter 1
Photosynthesis and ATP synthesis
By the end of this chapter you should be able to:
a describe the structure of a dicotyledonous d outline the essential stages of the Calvin
leaf, a palisade cell and a chloroplast, relating cycle involving the light-independent fixation
these structures to their roles in the process of of carbon dioxide;
photosynthesis;
e discuss the concept of limiting factors in
b make drawings from prepared slides of a photosynthesis;
transverse section of a dicotyledonous leaf
and a palisade cell; f discuss the extent to which knowledge of
limiting factors can be used to improve plant
c explain the process of photophosphorylation; productivity.

Humans, like all animals and fungi, are trapped energy from these molecules and convert
heterotrophs. This means that we need to eat it into a form that their cells can use. This process
food containing organic molecules, especially is called respiration, and it involves oxidation of
carbohydrates, fats and proteins. These organic the energy-containing organic substances, forming
molecules are our only source of energy. another energy-containing substance called ATP.
Plants, however, do not need to take in any Every cell has to make its own ATP. You can find
organic molecules at all. They obtain their energy out more about ATP in Chapter 2.
from sunlight. They can use this energy to build
their own organic molecules for themselves, An overview of photosynthesis
using simple inorganic substances. They first Photosynthesis happens in several different
produce carbohydrates from carbon dioxide and kinds of organisms, not only plants. There are
water, by photosynthesis. They can then use these many kinds of bacteria that can photosynthesise.
carbohydrates, plus inorganic ions such as nitrate, Photosynthesis also takes place in
phosphate and magnesium, to manufacture all the phytoplankton, tiny organisms that float in the
organic molecules that they need. Organisms that upper layers of the sea and lakes. Here, though,
feed in this way – self-sufficient, not needing any we will concentrate on photosynthesis in green
organic molecules that another organism has made plants, which takes place in the chloroplasts of
– are autotrophs. several plant tissues, especially the palisade
So heterotrophs depend on autotrophs for mesophyll and spongy mesophyll tissues of leaves
the supply of organic molecules on which they (Figure 1.1). This photosynthesis is the ultimate
feed. Some heterotrophs feed directly on plants, source of almost all of our food.
while others feed further along a food chain. But The overall equation for photosynthesis is:
eventually all of an animal’s or fungus’s 6CO + 6H O C H O + 6O
food
can be traced back to plants, and the energy of 2 2
6
12 6 2

sunlight. The xylem tissues of roots, stems and leaf

In this chapter, we will look in detail at how vascular bundles bring water to the
plants transfer energy from sunlight to chemical photosynthesising cells of the leaf. The carbon
energy in organic molecules. In Chapter 2, we dioxide diffuses into the leaf through stomata, the
will see how all living organisms can then release tiny holes usually found in the lower epidermis of
the the leaf. It then 1

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Myda Ramesar, Mary Jones and Geoff Jones
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Chapter 1: Photosynthesis and ATP synthesis

palisade mesophyll
spongy mesophyll
midrib vascular bundle lamina

upper epidermisxylem phloem

cuticle

upper epidermis

stoma
palisade mesophyll

veins spongy mesophyll

lower epidermis

lower epidermis

guard cellstomachloroplastair space

Figure 1.1 The structure of a leaf.

diffuses through air spaces and into mesophyll

cells and finally into chloroplasts, where •betheable to absorb carbon dioxide and dispose of
waste product, oxygen;
photosynthesis takes place.
•have a water supply and be able to export
manufactured carbohydrate to the rest of the
Leaf structure and function plant.
The leaf has a broad, thin lamina, a midrib and a The large surface area and thinness of the lamina
network of veins. allows it to absorb a lot of light. Its thinness
It may also have a leaf stalk (petiole). Figure minimises the length of the diffusion pathway
1.2 is a photomicrograph of a section of a typical for gaseous exchange. The arrangement of leaves
leaf from a mesophyte – that is, a plant adapted for on the plant (the leaf mosaic) helps the plant to
normal terrestrial conditions (it is adapted neither absorb as much light as possible.
for living in water nor for withstanding excessive The upper epidermis is made of thin, flat,
drought). transparent cells which allow light through to the
To perform its function the leaf must: cells of the mesophyll below, where photosynthesis

• contain chlorophyll and other photosynthetic

pigments arranged in such a way that they can
takes place. A waxy transparent cuticle, which
is secreted by the epidermal cells, provides a
absorb light; watertight layer preventing water loss other than
through the stomata, which can be closed in dry

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Myda Ramesar, Mary Jones and Geoff Jones
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Chapter 1: Photosynthesis and ATP synthesis

a b
cuticle
upper epidermis

palisade mesophyll

cytoplasm
vascular bundle (vein) vacuolemesophyll
nucleuscell
chloropast

spongy mesophyll

air space

lower epidermis

guard cell
stoma

Figure 1.2 a Photomicrograph of a TS of a leaf (t 300), b drawing of part of a.

conditions. The cuticle and epidermis together turgidity of these guard cells cause them to change
form a protective layer against shape so that they open and close the pore. When
microorganisms and some insects. the guard cells gain water, the pore opens; as they
The structure of the lower epidermis is similar lose water it closes. Guard cells have unevenly
to that of the upper, except that most mesophytes thickened cell walls. The wall adjacent to the pore
have many stomata in the lower epidermis. (Some is very thick, whilst the wall furthest from the
have a few stomata in the upper epidermis also.) pore is thin. Bundles of cellulose microfibrils
Stomata are the pores in the epidermis through are arranged as hoops around each guard cell
which diffusion of gases occurs, including carbon and, as the cell becomes turgid, these hoops
dioxide. Each stoma is bounded by two sausage- ensure that the cell mostly increases in length
shaped guard cells (Figure 1.3). Changes in the and not
diameter. Since the ends of the two guard cells are
stoma closed joined and the thin outer wall bends more readily
stoma open than the thick inner one, the guard cells become
curved. This makes the pore between the cells
open.
chloroplasts
Guard cells gain and lose water by osmosis. A
decrease in water potential is needed before water
can enter the cells by osmosis. This is achieved by
guard cells
the active removal of hydrogen ions, using energy
from ATP, and then intake of potassium ions
thickthin
(indirect active transport).
cell wallcell wall An electron micrograph and a drawing of
a palisade cell is shown in Unit 1 on page
41.
Figure 1.3 Photomicrograph of stomata and Figure 1.4 shows a photomicrograph of palisade
guard cells in Tradescantia leaf epidermis (t cells. The palisade mesophyll is the main site of
2000). 3
photosynthesis, as there are more chloroplasts per
cell than in the spongy mesophyll.

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Myda Ramesar, Mary Jones and Geoff Jones
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Chapter 1: Photosynthesis and ATP synthesis

occurs in the spongy mesophyll only at high light

intensities. The irregular packing of the cells
upper epidermis
and the large air spaces thus produced provide a
large surface area of moist cell wall for gaseous
palisade cell exchange.
The veins in the leaf help to support the large
surface area of the leaf. They contain xylem,
chloroplasts
which brings in the water necessary for
photosynthesis and for cell turgor, and phloem,
which takes the products of photosynthesis to
other parts of the plant.
nucleus
vacuole Chloroplast structure and function
The equation on page 1 is a simplification of
photosynthesis. In reality photosynthesis is a
complex metabolic pathway – a series of reactions
Figure 1.4 Photomicrograph of palisade cells linked to each other in numerous steps, many of
(t 600). which are catalysed by enzymes. These reactions
take place in two stages. The first is the light-
Palisade cells show several adaptations for light dependent stage, and this is followed by the light-
absorption. independent stage. Both of these stages take place

• They are long cylinders arranged at right-angles

to the upper epidermis. This reduces the number
inside chloroplasts within cells of the leaves and
often stems of plants (Figure 1.5).
of light-absorbing cross walls in the upper part Figure 1.6 shows the structure of a typical
of the leaf so that as much light as possible can chloroplast. Each cell in a photosynthesising tissue
reach the chloroplasts. may have ten or even 100 chloroplasts inside it.

• The cells have a large vacuole with a thin

peripheral layer of cytoplasm. This restricts the
A chloroplast is surrounded by two membranes,
forming an envelope. There are more membranes
chloroplasts to a layer near the outside of the inside the chloroplast, which are arranged so
cell where light can reach them most easily. that they enclose fluid-filled sacs between them.

• The chloroplasts can be moved (by proteins in

the cytoplasm, as they cannot move themselves)
The membranes are called lamellae and the fluid-

within the cells, to absorb the most light or to

protect the chloroplasts from excessive light light
plant cell
intensities.
The palisade cells also show adaptations for
gaseous exchange.

• The cylindrical cells pack together with long,

narrow air spaces between them. This gives a
chloroplast

large surface area of contact between cell and H2 O light-dependent stage O2

air.

• The cell walls are thin, so that gases can

diffuse through them more easily.
CO2 light-independent stage

Spongy mesophyll is mainly adapted as a surface

C6H12O6
for the exchange of carbon dioxide and oxygen.
The cells contain chloroplasts, but in smaller
numbers than in palisade cells. Photosynthesis Figure 1.5 The stages of photosynthesis.
4

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Myda Ramesar, Mary Jones and Geoff Jones
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Chapter 1: Photosynthesis and ATP synthesis

filled sacs are thylakoids. In some parts of the

Electron micrograph of a chloroplast
chloroplasts, the thylakoids are stacked up like
a pile of pancakes, and these stacks are called
grana. The ‘background material’ inside the
chloroplast is called the stroma.
starch grain
Embedded tightly in the membranes inside
ribosome stroma the chloroplast are several different kinds of
granum photosynthetic pigments. These are coloured
substances that absorb energy from certain
lamella lipid droplet
chloroplast envelopewavelengths (colours) of light. The most abundant
pigment is chlorophyll, which comes in two
forms, chlorophyll a and chlorophyll b.
The stacked membranes have a large surface
area and so their photosynthetic pigments can
capture light very efficiently. The transformation
of light energy into chemical energy is carried
out by other chemicals in the membranes closely
associated with the photosynthetic pigments. The
membranes not only hold chemicals allowing them
to function correctly, but also create the thylakoid
(× 20 000)
spaces. The space inside each thylakoid, the
thylakoid lumen, is needed for the accumulation of
Diagram of a chloroplast
outer membrane hydrogen ions, H+, used in the production of ATP
chloroplast envelope
ribosomes (see page 7 and Chapter 2).
inner membrane
starch grain Chloroplasts often contain starch grains,
lipid droplet because starch is the form in which plants store the
carbohydrate that they make by photosynthesis.
They also contain ribosomes and their own small
circular strand of DNA. (You may remember that
chloroplasts are thought to have evolved from
bacteria that first invaded eukaryotic cells over a
thousand million years ago.)
lamella
thylakoid
SAQ
granum stroma 1 List the features of a chloroplast that aid
Electron micrograph of part of a chloroplast
lamellaegranumstromathylakoid photosynthesis.
ribosome

Photosynthetic pigments
lipid droplet A pigment is a substance whose molecules
absorb some wavelengths (colours) of light, but
not others. The wavelengths it does not absorb
are either reflected or transmitted through the
substance. These unabsorbed wavelengths reach
(× 36 500)
our eyes, so we see the pigment in these colours.
The majority of the pigments in a chloroplast
Figure 1.6 The structure of a chloroplast. are chlorophyll a and chlorophyll b (Figure 1.7).
5

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Myda Ramesar, Mary Jones and Geoff Jones
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Chapter 1: Photosynthesis and ATP synthesis

–CH3in chlorophyll a SAQ

–CHO in chlorophyll b 2 a Use Figure 1.8 to explain why
chlorophyll looks green.
b What colour are carotenoids?

The light-dependent stage

This stage of photosynthesis takes place on the
thylakoids inside the chloroplast. It involves the
absorption of light energy by chlorophyll, and the
use of that energy and the products from splitting
water to make ATP and reduced NADP.
Figure 1.7 A chlorophyll molecule.
Photosystems
These are the primary pigments.. Both types of The chlorophyll molecules are arranged in
chlorophyll absorb similar wavelengths of light, clusters called photosystems in the thylakoid
but chlorophyll a absorbs slightly longer membranes (Figure 1.9). Each photosystem spans
wavelengths than chlorophyll b. This can be the membrane, and contains protein molecules
shown in a graph called an absorption spectrum and pigment molecules. Energy is captured from
(Figure 1.8).
Figure Light
1.9 energy
A photosystem
is absorbed in
by achlorophyll
thylakoid a molecules at the reactio
membrane showing photoactivation of chlorophyll.
Key
chlorophyll a
chlorophyll b light energy
carotene The energy is passed from one molecule to ano

Chlorophyll emits a high-energ

Light

400 500 600 700

Wavelength of light / nm e−

e−
Figure 1.8 Absorption spectra for chlorophyll
and carotene. H2 O

O2
Other pigments found in chloroplasts include thylakoid membrane
carotenoids, such as carotene and xanthophylls.
These absorb a wide range of short wavelength A low-energy electrona photosystem – replaces the high-including
light, including more blue-green light than the carotenoids
chlorophylls. They are accessory pigments. They
help by absorbing wavelengths of light that would
otherwise not be used by the plant. They pass on
some of this energy to chlorophyll. They probably
also help to protect chlorophyll from damage by
very intense light.
6

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Chapter 1: Photosynthesis and ATP synthesis

photons of light that hit the photosystem, and leaves the chlorophyll molecules completely. The
is funnelled down to a pair of molecules at the electron is then passed along the chain of electron
reaction centre of the photosystem complex. carriers. The energy from the electron is used to
There are two different sorts of photosystem, make ATP. The electron, now having lost its
PSI and PSII, both with a small number of extra energy, eventually returns to chlorophyll a
molecules of chlorophyll a at the reaction centre. in PSI.

Photophosphorylation Non-cyclic photophosphorylation

Photophosphorylation means ‘phosphorylation This process involves both kinds of photosystem.
using light’. It refers to the production of ATP, by It results not only in the production of ATP, but
combining a phosphate group with ADP, using also of reduced NADP.
energy that originally came from light: Light hitting either PSI or PSII causes electrons
ADP + phosphate ATP to be emitted. The electrons from PSII pass down
Photophosphorylation happens when an electron the electron carrier chain, generating ATP by
is passed along a series of electron carriers, photophosphorylation. However, instead of going
forming an electron transport chain in the thylakoid back to PSII, the electrons instead replace the
membranes. The electron starts off with a lot of electrons lost from PSI.
energy, and it gradually loses some of it as it The phosphorylation of ADP to ATP
moves from one carrier to the next. The energy is involves the movement of H+ across the
used to cause a phosphate group to react with thylakoid membrane. This process also occurs in
ADP. respiration and is described in detail in Chapter
2.
Cyclic photophosphorylation The electrons emitted from PSI are not used to
This process involves only PSI, not PSII. It results make ATP. Instead, they help to reduce NADP.
in the formation of ATP, but not reduced NADP For this to happen, hydrogen ions are required.
(Figure 1.10). These come from another event that happens when
Light is absorbed by PSI and the energy passed light hits PSII. PSII contains an enzyme that splits
on to electrons in the chlorophyll a molecules at water when it is activated by light. The reaction is
the reaction centre. In each chlorophyll a called photolysis:
molecule, one of the electrons becomes so 2H2O 4H+ + 4e− + O2
energetic that it The hydrogen ions are taken up by NADP, forming
reduced NADP. The electrons replace the ones
high-energy electron
that were emitted from PSII when light hit it.
ADP + Pi The oxygen diffuses out of the chloroplast and
e−
eventually out of the leaf, as an excretory product.

ATP
The Z-scheme
electron carriers
The Z-scheme is simply a way of summarising
photosyste

what happens to electrons during the light-

energy

light absorbed dependent reactions. It is a kind of graph, with the

e− y-axis indicating the ‘energy level’ of the electron
(Figure 1.11).
Start at the bottom left, where light hits
e−
photosystem II. The red vertical line going up
Key shows the increase in the energy level of electrons
change in energy of electrons as they
movement of electrons between electron are emitted from this photosystem. You
carriers
can also see where these electrons came from – the
splitting of water molecules. (In fact, it probably
Figure 1.10 Cyclic photophosphorylation. isn’t the same electrons – but the electrons from
the 7

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Chapter 1: Photosynthesis and ATP synthesis

high-energy electron
high-energy electron e−

chain of electron carriers e.g. ferredoxin

ADP + P i
e−

ATP photosyste
oxidised NADP + H+
energy

photosystem

light absorbed
e−
reduced NADP
chain of electron carriers
e.g. cytochrome
H2 O e−

light absorbed Key

e− change in energy of electrons movement of electrons between electron c
O2 H+

Figure 1.11 The Z-scheme, summarising non-cyclic photophosphorylation.

water replace the ones that are emitted from the

The light-independent stage
photosystem.)
Now the ATP and reduced NADP that have been
If you keep following the vertical line
formed in the light-dependent stage are used
showing the increasing energy in the electrons,
to help to produce carbohydrates from carbon
you arrive at a point where it starts a steep dive
dioxide. These events take place in the stroma
downwards.
of the chloroplast. The cyclic series of reactions is
This shows the electrons losing their energy as
known as the Calvin cycle (Figure 1.12).
they pass along the electron carrier chain.
The chloroplast stroma contains an enzyme
Eventually they arrive at photosystem I.
called rubisco (its full name is ribulose
You can then track the movement of the
bisphosphate carboxylase). This is thought to
electrons to a higher energy level when PSI is hit
be the most abundant enzyme in the world. Its
by light, before they fall back downwards as they
function is to catalyse the reaction in which carbon
lose energy and become part of a reduced NADP
dioxide combines with a substance called RuBP
molecule.

SAQ
3 Copy and complete the table to compare cyclic (If a box in a particular row is not applicable,
and non-cyclic photophosphorylation. write n/a.)
Cyclic Non-cyclic
photophosphorylation photophosphorylation
Is PSI involved?
Is PSII involved?
Where does PSI obtain replacement electrons from?
Where does PSII obtain replacement electrons from?
Is ATP made?
Is reduced NADP made?
8

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Chapter 1: Photosynthesis and ATP synthesis

carbon dioxide (1C)

carboxylation of RuBP (carbon fixation)
rubisco
ribulose bisphosphate, RuBP (5C)

intermediate (6C)
ADP
regeneration of RuBP by Calvin cycle

phosphorylation
ATP glycerate
3-phosphate, GP (3C)
triose phosphate (3C)

This is used to make glucose, sucrose

triose and other carbohydrates.
phosphate reduction
of GPreduced NADP
ATP

oxidised NADP ADP + P i

Figure 1.12 The Calvin cycle.

(ribulose bisphosphate). SAQ

RuBP molecules each contain five atoms 4 Suggest what happens to the ADP,
of carbon. The reaction with carbon dioxide inorganic phosphate and NADP that are
therefore produces a six-carbon molecule, formed during the Calvin cycle.
but
this immediately splits to form two three-carbon
molecules. This three-carbon substance is Factors affecting the rate of
glycerate 3-phosphate, usually known as GP. An photosynthesis
alternative name is phosphoglyceric acid (PGA). Photosynthesis requires several inputs. It needs
Now the two products of the light-dependent raw materials in the form of carbon dioxide and
stages come into play. The reduced NADP and the water, and energy in the form of sunlight. The
ATP are used to provide energy and phosphate light-independent stage also requires a reasonably
groups, which change the GP into a three-carbon high temperature, because the rates of reactions
sugar called triose phosphate (TP or GALP). are affected by the kinetic energy of the
This is the first carbohydrate that is made in molecules involved.
photosynthesis. If any of these requirements is in short supply,
There are many possible fates of the triose it can limit the rate at which the reactions of
phosphate. Five-sixths of it are used to regenerate photosynthesis are able to take place.
RuBP. The remainder can be converted into other
carbohydrates. For example, two triose phosphates Light intensity
can combine to produce a hexose phosphate Light provides the energy that drives the light-
molecule. From these, glucose, fructose, sucrose, dependent reactions, so it is obvious that when
starch and cellulose can be formed. there is no light, there is no photosynthesis. If
The triose phosphate can also be used to make we provide a plant with more light, then it will
lipids and amino acids. For amino acid production, photosynthesise faster.
nitrogen needs to be added, which plants obtain However, this can only happen up to a point.
from the soil in the form of nitrate ions or We would eventually reach a light intensity
ammonium ions. where, if we give the plant more light, its rate
9

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Chapter 1: Photosynthesis and ATP synthesis

of photosynthesis does not change. We can say outside, providing the diffusion gradient that keeps
that ‘light saturation’ has occurred. Some other it moving into the leaf.
factor, such as the availability of carbon dioxide Carbon dioxide concentration is often a limiting
or the quantity of chlorophyll in the plant’s factor for photosynthesis. If we give plants extra
leaves, is preventing the rate of photosynthesis carbon dioxide, they can photosynthesise faster.
from continuing to increase. Figure 1.14 shows the relationship between carbon
This relationship is shown in Figure 1.13. Over dioxide concentration and rate of photosynthesis.
the first part of the curve, we can see that rate Figure 1.15 shows the effect of carbon dioxide at
of photosynthesis does indeed increase as light different light intensities.
intensity increases. For these light intensities,
light is a limiting factor. The light intensity is
limiting the rate of photosynthesis. If we give the
plant more light, then it will photosynthesise
faster.
But, from point X onwards, increasing the
light intensity has no effect on the rate of
photosynthesis. Along this part of the curve,
Rate of

light is no longer a limiting factor. Something

else is. It is most likely to be the carbon dioxide
concentration. 0
Carbon dioxide concentration
X
Figure 1.14 The effect of carbon dioxide on rate
of photosynthesis.
Light is not a limiting factor.

at high light intensity

Rate of

Light is a limiting factor. at low light intensity

Rate of

0
Light intensity
0
Figure 1.13 The effect of light intensity on the Carbon dioxide concentration

rate of photosynthesis. Figure 1.15 The effect of carbon dioxide

concentration on the rate of photosynthesis at
Carbon dioxide concentration different light intensities.
The concentration of carbon dioxide in the air
is very low, only about 0.04%. Yet this SAQ
substance is needed for the formation of every 5 a Over which part of the curve in Figure
organic molecule inside every living thing on 1.14 is carbon dioxide a limiting factor
Earth. for photosynthesis?
Plants absorb carbon dioxide into their leaves b Suggest why the curve flattens out at
by diffusion through the stomata. During daylight, high levels of CO2.
carbon dioxide is used in the Calvin cycle in the
chloroplasts, so the concentration of carbon
dioxide inside the leaf is even lower than in the air
10

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