Wjec a2 biology student unit guide unit by4 metabolism, microbiology and homeostasis

Tai Lieu Chat Luong


STUDENT UNIT GUIDE

WJEC A2 Biology Unit BY4
Metabolism, Microbiology and
­Homeostasis
Andy Clarke


I would like to thank Alex Cook and Phil Evans for their help and advice in writing this book.
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Contents
Getting the most from this book����������������������������������������������������������������������������������������������������������� 4
About this book����������������������������������������������������������������������������������������������������������������������������������������� 5

Content Guidance
Energy and living things������������������������������������������������������������������������������������������������������������������������������� 6
Respiration���������������������������������������������������������������������������������������������������������������������������������������������������� 7
Photosynthesis�������������������������������������������������������������������������������������������������������������������������������������������� 16
Microbiology����������������������������������������������������������������������������������������������������������������������������������������������� 24
Populations�������������������������������������������������������������������������������������������������������������������������������������������������� 33
Excretion����������������������������������������������������������������������������������������������������������������������������������������������������� 41
The nervous system������������������������������������������������������������������������������������������������������������������������������������ 51
Responses in plants������������������������������������������������������������������������������������������������������������������������������������ 65

Questions & Answers
Q1 ATP and respiration������������������������������������������������������������������������������������������������������������������������������ 71

Q2 Respiration�������������������������������������������������������������������������������������������������������������������������������������������� 73
Q3 Photosynthesis�������������������������������������������������������������������������������������������������������������������������������������� 75
Q4 Microbiology����������������������������������������������������������������������������������������������������������������������������������������� 78
Q5 Populations������������������������������������������������������������������������������������������������������������������������������������������� 81
Q6 The kidney�������������������������������������������������������������������������������������������������������������������������������������������� 83
Q7 The nervous system������������������������������������������������������������������������������������������������������������������������������ 86
Q8 The nitrogen cycle�������������������������������������������������������������������������������������������������������������������������������� 89
Knowledge check answers�������������������������������������������������������������������������������������������������������������������� 91
Index����������������������������������������������������������������������������������������������������������������������������������������������������������� 93


Getting the most from this book
Examiner tips
Advice from the examiner on key points in the
text to help you learn and recall unit content,
avoid pitfalls, and polish your exam technique in
order to boost your grade.

Knowledge check
Rapid-fire questions throughout the Content
Guidance section to check your understanding.

Summary

Knowledge check answers
1 Turn to the back of the book for the Knowledge
check answers.

Summaries
l

Each core topic is rounded off by a
bullet-list summary for quick-check
reference of what you need to know.

Questions & Answers
The nitrogen cycle

Exam-style questions

Question

8

Question 8 The nitrogen cycle
Describe the nitrogen cycle. Include the form that nitrogen takes in each part and the role of bacteria
(giving names wherever possible). Any diagrams included in your answer must be fully annotated.
Total: 10 marks

Examiner comments
on the questions
Tips on what you
need to do to gain full

The last question on every WJEC exam paper is an essay-style question worth 10 marks.
There are always two alternatives and you are required to answer one. Although the subject
matter of the questions will differ, on the whole these questions are testing recall with
understanding (AO1). Therefore, if you have revised the whole of the unit and are well prepared
you should gain most of the marks on this type of question. You may include diagrams within
your answer and you are strongly advised to do this. Biology is a visual subject and your notes

will probably contain many diagrams to help you understand the biology. You will not gain any
credit for just drawing a diagram. However, if you annotate it then the annotations will gain
credit. Drawing diagrams will also help you to construct a coherent answer.

icon

.

Sample student
answers

When plants and animals die decomposers b release ammonia into the soil. c

l

The ammonia is then converted into nitrates by bacteria. d

l

The plants can then absorb the nitrates to make more proteins. e

l

Other bacteria change nitrates into nitrogen gas f which enters the atmosphere. g

l

Some plants, such as peas, can absorb the nitrogen directly. h

each answer would be

awarded in the exam and

3/10 marks awarded The diagram of the nitrogen cycle is incomplete and there are
six statements about the cycle, demonstrating a lack of preparation. a , c g These points gain
marks for correctly identifying the locations of different forms of nitrogenous compound. b, d,
e, f There is no reference made to any of the processes involved (putrefaction, nitrification,
denitrification and nitrogen fixation) or to the names of the bacteria involved. h This statement is
incorrect and shows a lack of understanding.

then read the examiner
comments (preceded by
the icon

Student B
Plan:

N2
NO3–

) following

each student answer.

Plants

NO2–
NH4+

Animals

Decomposers

Essay:
Plants absorb nitrates from the soil a to provide a source of nitrogen for the synthesis
of amino acids and proteins. b Animals consume the plants, digest the proteins into
amino acids, which they then use to make proteins.

Unit BY4: Metabolism, Microbiology and Homeostasis

4

Find out how many marks

plants and animals. a

then look at the student
each set of questions.

answers

Nitrogen is an important element and is found in proteins and nucleic acids in

l

Practise the questions,
answers that follow

on sample student

Student A

l

marks, indicated by the

Examiner commentary

89

WJEC A2 Biology


About this book
This guide will help you to prepare for BY4, the examination for WJEC A2 Biology
Unit  4: Metabolism, Microbiology and Homeostasis. Your understanding of
many of the principles in Unit 1 may be re-examined here as well.

Content Guidance
The Content Guidance section covers all the concepts you need to understand
and  facts you need to know for the BY4 exam. It also includes examiner tips and
knowledge checks to help you prepare for BY4.
The order in which topics appear in the guide follows the order of the specification
with the exception of the detail of chemiosmosis, which is included in respiration and
photosynthesis, rather than with ATP.
The concepts in each topic are presented first followed by details of the processes
and  adaptations of the various structures involved. You are advised to familiarise
yourself with the key ideas before attempting to learn the associated facts.
The A2 biology course is more demanding than AS and includes stretch-andchallenge and synoptic aspects.
Stretch and challenge: At A2 you have to develop a greater understanding of biological
concepts and demonstrate a greater ability to apply your knowledge and understanding
(AO2). The Content Guidance section contains boxes detailing investigations carried

out on particular aspects of biology. The specification does not require you to know the
details of these investigations, but they will give you an idea of the sort of information
you could be provided with to assess AO2.
Synoptic element: You need to start piecing together the topics you have studied so
far and try to see the links between them; this is the synoptic element. In Unit BY1
you learnt the ‘core concepts’ in biology — the fundamentals of biochemistry and cell
biology. This knowledge underpins all aspects of A2 biology. To ensure you have a
good understanding of Unit BY4 it is essential that you revisit these concepts. Synoptic
links are highlighted throughout the Content Guidance section.

Questions and Answers
This section will help you to:
l

familiarise yourself with the question styles you can expect in the unit test

l

understand what the examiners mean by terms such as ‘describe’ and ‘explain’

l

interpret the question material — especially any data that the examiners give you

l

write concise answers to the questions that the examiners set

It would be impossible to give examples of every kind of question in one book, but
these should give you a flavour of what to expect. Two students, Student A and Student

B, attempt each question in this section. Their answers, along with the examiner
comments, should help you to see what you need to do to score a good mark — and
how you can easily not score a mark even if you understand the biology.

Unit BY4: Metabolism, Microbiology and H
­ omeostasis

5


Content Guidance
Energy and living things
Key concepts you must understand
l Most energy available to living organisms is derived directly or indirectly from

the sun.
l Autotrophic organisms (e.g. plants) convert light energy into chemical energy

during photosynthesis. This chemical energy is locked up within organic molecules.
l All organisms, both autotrophic and heterotrophic, break down these organic

molecules during respiration to produce adenosine triphosphate (ATP).
l ATP is the only source of immediate energy within the cell for processes such

as active transport, muscle contraction and the synthesis of organic molecules,
such as proteins.
l ATP is often referred to as the ‘universal energy currency’ because it transfers

energy for biochemical reactions in the cells of all living organisms.

Examiner tip
Synoptic link to BY1: In
Unit BY1 you studied the
structure of nucleotides
and the functions of nucleic
acids. Revisiting these
topics will help you with
aspects of energy transfer.

Adenosine triphosphate (ATP)
The structure of ATP is shown in Figure 1. It is a free RNA nucleotide consisting of a ribose
sugar, the base adenine and three phosphate groups (adenosine = ribose + adenine).
NH2

Adenine
N
H

C

C

N

C
C

N
C
N

6

O

O H2C
H

Ribose

Examiner tip
Make sure that you get
the name right. You
could be given a diagram
similar to Figure 1 and
asked to name it or label
it. Many students get this
wrong by labelling the
base adenosine, or calling
the molecule adenine
triphosphate or adenosine
triosephosphate.

H

H
OH

P
O

H

H

O

O
O

P

O
O

O

P

O

O

Phosphate groups

OH

Figure 1 A molecule of ATP

As energy is released when ATP is hydrolysed to adenosine diphosphate (ADP) and

inorganic phosphate (P i), it is an exergonic reaction (see Figure 2). This reaction is
catalysed by the enzyme ATPase and involves the removal of the terminal phosphate
group. The reaction is always coupled with an energy-requiring reaction (endergonic
reaction) so that energy is transferred.
ATP acts as an energy carrier and is suited to its function because:
l

the molecule is soluble and can be transported within the cell (but cannot leave the
cell), transferring chemical energy to energy-requiring processes

WJEC A2 Biology


Respiration
the hydrolysis of ATP releases small quantities of energy (30.6 kJ mol−1) that are
matched closely to the energy required in the coupled reaction
l

the energy is transferred quickly as the hydrolysis of ATP requires only one enzyme

ATP

Energy from
respiration or
photons of light

Energy for
cellular work

ADP + P i

Figure 2 The interconversion of ATP, ADP and P i

ATP is reformed from ADP and P i by a condensation reaction. This requires the input of
energy, i.e. it is an endergonic reaction. The energy required can come from cellular
respiration or from the transduction of light energy during photosynthesis. This
reaction is catalysed by the enzyme ATP synthase (also known as ATP synthetase).

After studying this topic you should be able to:
l understand the importance of chemical energy in
biological processes

l

Examiner tip
The ‘law of conservation of
energy’ states that energy
can neither be created
nor destroyed. However,
energy can be converted
from one form to
another. When answering
questions relating to the
hydrolysis of ATP, you
must refer to energy being
released. You will not gain
credit for stating that
energy is produced.
Knowledge check 1
(a) Give three examples
of cellular activities that

require ATP.
(b)Describe three
advantages of ATP
for its function as the
universal source of
energy.

recognise the structure of ATP and describe its role
as an energy carrier and its use in the liberation of
energy for cellular activity

Summary

l

Respiration
Key concepts you must understand
l Respiration is a process that occurs within the cells of all living organisms.

It can be represented by the following simple chemical equation:
C6H12O6 + 6O2

6CO2 + 6H 2O

l Respiration releases chemical energy from the oxidation of organic molecules,

such as glucose, to synthesise ATP.
l There are three ways in which molecules can be oxidised or reduced:

Oxidation

Reduction

1

Gaining oxygen

Losing oxygen

2

Losing hydrogen

Gaining hydrogen

3

Losing electrons (e−)

Gaining electrons (e−)

Unit BY4: Metabolism, Microbiology and H
­ omeostasis

Examiner tip
In biology it is more helpful
to think about oxidation in
terms of loss of hydrogen
and loss of electrons and
reduction in terms of gain

of hydrogen and electrons.
7


Content Guidance
l Oxidation and reduction reactions always take place together because as one

molecule is oxidised another molecule is reduced. These chemical reactions are
called redox reactions.
l Figure 3 represents a typical step in the respiratory pathway. Note that the

coenzyme (NAD) is reduced as the organic molecule is oxidised.
NAD

Reduced
NAD
Oxidised
organic molecule

Organic molecule

Figure 3 Oxidation of an organic molecule coupled with the reduction of a coenzyme

l The oxidation reactions involved in respiration are exergonic. The energy

released from the organic molecules is used to reduce the coenzymes NAD and
FAD, as these reactions are coupled. During each oxidation reaction a small

Examiner tip
Synoptic link to BY1:

Respiration is a series
of enzyme-catalysed
reactions. Therefore
factors that affect
enzymes affect the
rate of respiration. The
most important factor
influencing the rate of
respiration is temperature.

quantity of energy is, in effect, transferred to these coenzymes.
l During glycolysis, the link reaction and Krebs cycle, organic molecules are

repeatedly oxidised and therefore most of the energy contained within glucose is
transferred to the reduced coenzymes NADH 2 and FADH 2. When the coenzymes
are re-oxidised the stored energy is used to synthesise ATP via oxidative
phosphorylation.
l The series of oxidation reactions in respiration brings about the gradual release

of chemical energy from organic molecules in a series of small steps (as opposed
to combustion which is the uncontrolled release of energy in a single step).
l Aerobic respiration occurs in the presence of oxygen. Respiration that takes

place in the absence of oxygen is called anaerobic respiration.

Aerobic respiration
Mitochondria are present in all eukaryotic cells and they are involved in synthesis
of ATP during aerobic respiration. Figure 4 shows the structure of a mitochondrion.
The organelle is composed of a double membrane enclosing a fluid-filled matrix. The
inner membrane is highly folded to form cristae. This increases the surface area for

the synthesis of ATP.
Cristae

Outer
membrane

Matrix

Inner
membrane
Figure 4 Structure of a mitochondrion

Figure 5 shows the location of the four stages of respiration. ATP is synthesised
mainly in the mitochondria.

8

WJEC A2 Biology


Respiration
Glycolysis

The link reaction
Krebs cycle
(formation of
acetyl coenzyme A)

Electron transport
chain

Glucose

Acetyl
coenzyme
A

Krebs
cycle

Electron
transport and
chemiosmosis

2 ATP

34 ATP

Pyruvate

2 ATP

Figure 5 Outline of the stages of aerobic respiration

Glycolysis (splitting of glucose)
Glycolysis occurs in the cytoplasm — this is where the enzymes for glycolysis are
located. The main stages in the pathway are shown in Figure 6.
Glucose
6C
2 ATP

2 ADP
Hexose bisphosphate
6C

2 × triose phosphate
3C
2 NAD

4 ADP + Pi

2 NADH2

4 ATP
2 × pyruvate
3C

Figure 6 The steps involved in glycolysis
l

Step 1: Two molecules of ATP are required for the phosphorylation of glucose to
produce hexose bisphosphate. The energy from the hydrolysis of ATP activates
glucose and makes the molecule more reactive.

l

Step 2: Hexose bisphosphate is split (lysis) producing two molecules of triose
phosphate.

Unit BY4: Metabolism, Microbiology and H
­ omeostasis

9


Content Guidance
Dehydrogenation
reactions involve the
removal of hydrogen
from a molecule.
They are catalysed by
dehydrogenase enzymes.
Substrate-level
phosphorylation
involves the synthesis of
ATP using energy released
from the breakdown of
a high-energy substrate
molecule.

l

Step 3: Triose phosphate (TP) is oxidised via a dehydrogenation reaction
into pyruvate. The hydrogen removed is used to reduce the coenzyme NAD to
reduced NAD (NADH 2). This reaction is exergonic, and the energy released is used
to synthesise four ATP molecules by substrate-level phosphorylation.

Glycolysis results in a net gain of two ATP molecules (two ATP molecules are used
initially and four ATP molecules are synthesised).

The link reaction

Glycolysis links to the Krebs cycle via the link reaction (Figure 7). It takes place in the
mitochondrial matrix (where the enzymes involved in the link reaction are found).
Pyruvate
3C

Knowledge check 2

NAD
CO2

Why is glycolysis referred
to as being anaerobic?

NADH2
Acetate
2C
Acetyl CoA
2C
Coenzyme A
Figure 7 The link reaction

Decarboxylation
reactions involve the
removal of a carboxyl
group from a molecule
resulting in the production
of CO2. They are catalysed
by decarboxylase enzymes.
Examiner tip
It is important that you

can state the precise
locations within the cell
where the different stages
of respiration occur. You
will not gain any credit
for stating that the link
reaction and Krebs
cycle take place in the
‘mitochondria’ or in the
‘matrix’. You must say
‘mitochondrial matrix’.

Specific carrier proteins contained in the outer mitochondrial membrane transport
pyruvate into the matrix. (Note that there are no glucose carrier proteins.) The
pyruvate undergoes oxidative decarboxylation to form acetate (a 2C molecule).
This involves:
l

the removal of hydrogen (oxidation) to reduce the coenzyme NAD

l

the removal of a carboxyl group (decarboxylation) to form carbon dioxide

The acetate combines with coenzyme A to form acetyl coenzyme A.
Two molecules of pyruvate enter the link reaction, so the reactions shown in
Figures 7 and 8 represent only one-half of the reactions for the complete oxidation of
one molecule of glucose.

Krebs cycle

The Krebs cycle occurs in the mitochondrial matrix (this is where the correct
enzymes are located). It involves a series of decarboxylation reactions and
dehydrogenation reactions. Carbon dioxide, ATP and reduced coenzymes are
produced (see Figure 8).
Acetyl coenzyme A releases acetate (2C), which then combines with a 4C acid to
form a 6C acid. This 6C acid is broken down in a series of oxidative decarboxylation
reactions that regenerate the 4C acid. These reactions involve:
l

the loss of hydrogen (dehydrogenation/oxidation) and the loss of carbon dioxide
(decarboxylation)

10

WJEC A2 Biology


Respiration
Acetyl CoA
2C

Examiner tip
Figure 8 shows the
names of some of the
intermediate molecules
involved in the Krebs cycle.
They may appear in the
exam, but you are not
expected to know them.
What is important is that

you understand what is
produced when these
molecules are recycled.

Coenzyme A

(Oxaloacetate)
4C

(Citrate)
6C

FADH2

NAD

FAD

CO2

CO2

NADH2

2 NADH2
2 NAD

(Ketoglutarate)
5C

ATP

Knowledge check 3

ADP + Pi

Explain why carbon
dioxide is not produced
when glucose is added to
a preparation of isolated
mitochondria.

Figure 8 The steps involved in the Krebs cycle
l

the reduction of the coenzymes NAD and FAD to NADH 2 and FADH 2

l

the production of ATP from ADP and P i by substrate-level phosphorylation

The electron transport chain (ETC)
The electron transport chain involves a chain of electron carriers located on the inner
mitochondrial membrane (cristae). The cristae have a large surface area so there
are more electron carriers, which increases ATP synthesis. The reduced coenzymes,
NADH 2 and FADH 2, produced during glycolysis, the link reaction and the Krebs cycle
act as a source of electrons and protons.
Figure 9 shows the electron carriers at progressively lower energy levels. As electrons
pass along the chain of carriers in a series of redox reactions, they release energy. This
energy is used to synthesise ATP by oxidative phosphorylation. Oxygen is the

terminal electron acceptor. It combines with protons (H+) and electrons (e−) and is
reduced to water.

Oxidative
phosphorylation
involves the synthesis of
ATP using energy released
from redox reactions.

ADP + Pi
Potential energy level

NADH2
Carrier 2
NAD
Reduced
carrier 2

ADP + Pi
Reduced
carrier 3

ADP + Pi
Carrier 4
H2O

Carrier 3

ATP

Reduced
carrier 4

ATP
ATP

O2

Figure 9 The electron transport chain

Unit BY4: Metabolism, Microbiology and H
­ omeostasis

11


Content Guidance
Figure 9 shows that for each NADH 2 entering the chain three ATP molecules are
produced; each FADH 2 only generates two ATP molecules.

Chemiosmotic theory of oxidative phosphorylation
Figure 10 shows how ATP is synthesised during oxidative phosphorylation:
l

The energy released from the electrons during the redox reactions is used to pump
protons (H+) from the matrix through the inner mitochondrial membrane into the
intermembrane space.

l

The protons accumulate so that steep concentration and electrochemical gradients
are established across the inner mitochondrial membrane.

l

The inner membrane is impermeable to protons, so they can only diffuse back into
the matrix via the stalked particles, which consist of a chemiosmotic channel
protein attached to the enzyme ATP synthase.

l

The flow of protons through the ATP synthase provides the energy required to
produce ATP from ADP and P i.

Outer membrane
H+

Examiner tip
Synoptic links to BY1:
In Unit 1 you learnt that
cyanide is a respiratory
inhibitor. It is a noncompetitive inhibitor
of the enzyme cytochrome
oxidase, which is
associated with the final
proton pump in the
electron transport chain.
When cyanide attaches to
the enzyme the electron
transport chain cannot

function and oxidative
phosphorylation cannot
occur.
Knowledge check 4
Describe the role of
oxygen in aerobic
respiration.

Intermembrane
space

H+

H+

H+

H+
H

+

H+

H+

H+
H+

H+

Electron carrier

H+

Proton pump
−

e
Inner membrane

e−

ATP synthase
NADH2
NAD + H+

FADH2
FAD + H+

Matrix

ADP + Pi

ATP

O2 + 2H+

H2O

Figure 10 Electron transport chain and chemiosmosis

Each molecule of NADH 2 entering the chain results in three ATP molecules being
synthesised as three proton pumps are involved. Each molecule of FADH 2 results in
two ATP molecules being synthesised as only two proton pumps are involved.

Summary of aerobic respiration
Aerobic respiration involves the oxidation of glucose via a series of dehydrogenation
reactions (see Figure 11). Table 1 on p. 14 shows a summary of the molecules involved
and the location of the different stages in aerobic respiration.
Table 2 on p. 14 shows the number of ATP molecules produced via substrate-level
phosphorylation and oxidative phosphorylation. The complete oxidation of one
molecule of glucose can produce a maximum of 38 molecules of ATP:
l

Four molecules of ATP (two from glycolysis and two from the Krebs cycle) are
produced by substrate-level phosphorylation.

l

12

Thirty-four molecules of ATP are produced by oxidative phosphorylation.

WJEC A2 Biology


Respiration
Glucose (6C)
ATP

Glycogen

Starch
(plants)

ADP
Glucose phosphate (6C)
ATP
ADP
Hexose bisphosphate (6C)
Triose phosphate (3C)

Triose phosphate (3C)

2ADP

NAD
Reduced
NAD

2ATP
Glucose

pyruvate = glycolysis
Pyruvate

NAD

Pyruvate

Reduced
NAD

acetyl coA = link reaction

Coenzyme A

CO 2

Acetyl coenzyme A

Reduced
NAD

Oxaloacetate (4C)

Coenzyme A

Citrate (6C)
NAD

NAD

Reduced
NAD

Krebs cycle

CO 2
Reduced

FAD
FAD

NAD

ATP ADP + Pi

CO 2

Reduced
NAD

Reduced hydrogen carriers
(reduced NAD and FAD are oxidised)
Oxygen
Water

Oxidative phosphorylation
ATP

ADP + Pi

Figure 11 Summary of aerobic respiration

Unit BY4: Metabolism, Microbiology and H
­ omeostasis

Examiner tip
On an exam paper, the
reduced forms of NAD

and FAD are likely to
be written as reduced
NAD and reduced FAD
respectively (as in Figure
11). When answering
questions it is perfectly
acceptable to use NADH2
or NADH + H+ and
FADH2 or FADH + H+.

13


Content Guidance
Knowledge check 5

Table 1 Molecules involved and the location of the different stages in aerobic respiration

Apart from oxygen and
carbon dioxide, name:

Stage in
respiration

Precise location in Molecules
the cell
required

Molecules
produced

(a) two molecules that
show a net movement
into a mitochondrion

Glycolysis

Cytoplasm

Pyruvate, ATP,
NADH2

Link reaction

Mitochondrial matrix Pyruvate, NAD

Acetyl CoA,
NADH2 , CO2

Krebs cycle

Mitochondrial matrix Acetyl CoA, ADP
and Pi, NAD, FAD

CO2 , ATP, NADH2 ,
FADH2

Electron
transport chain

Inner mitochondrial
membrane/cristae

NAD and FAD, ATP,
Water

(b)two molecules that
show a net movement
out of a mitochondrion

NADH2 and FADH2 ,
ADP and Pi, Oxygen

Table 2 The ATP tally

Knowledge check 6
Explain what would
happen to the production
of ATP in an organism if:

Glucose, ATP, ADP
and Pi, NAD

Stages in aerobic
respiration

(Net) number of molecules produced per glucose molecule
NADH

FADH

ATP

Glycolysis

2

0

2

(a) its body temperature
rose slightly

Link reaction

2

0

0

(b)there was a reduced
concentration of
enzymes in the
mitochondrial matrix

Krebs cycle

6

2

2

Electron transport
chain

The NADH2 and FADH2 supply the energy
required to synthesise ATP:
● The oxidation of 1 NADH results in 3 ATP
2
being synthesised
● The oxidation of 1 FADH results in 2 ATP
2
being synthesised

34

Anaerobic respiration
Anaerobic respiration takes place in the cytoplasm of cells and occurs in the absence
of oxygen. It is the incomplete breakdown of glucose. Without oxygen the electron
transport chain cannot occur and NADH 2 and FADH 2 are not oxidised. NAD and
FAD become limiting factors (i.e. they run out) and therefore the dehydrogenation
reactions of the Krebs cycle and the link reaction can no longer occur. Glycolysis
continues because the pyruvate enters a different pathway and is reduced, therefore
oxidising NADH 2. The pyruvate is converted to lactate in animals and ethanol in
plants and fungi.
Figure 12 shows the anaerobic pathway in animals. Pyruvate is reduced by NADH 2 to
form lactate. This recycles the NAD, which is then reused to oxidise triose phosphate,

allowing ATP to be synthesised.
Figure 13 shows the anaerobic pathway in plants and fungi. Pyruvate undergoes
a decarboxylation reaction producing ethanal and carbon dioxide. The ethanal is
then reduced by NADH 2 to form ethanol. This recycles NAD, which is then reused to
oxidise triose phosphate.

14

WJEC A2 Biology


Respiration
2 × Triose phosphate (3C)
4ADP
4ATP

2×
NAD

2H

2 × Reduced
NAD

2 × Pyruvate (3C)

2 × Lactate (3C)

Figure 12 Anaerobic respiration in animals

2 × Triose phosphate (3C)

Knowledge check 7

4ADP

State the name of the
molecule that acts as the
terminal electron acceptor
in the following processes:

2×
NAD

2H

4ATP

2 × Reduced
NAD
2 × Pyruvate (3C)

2 × Ethanal
(2C)

2 × Ethanol
(2C)

2CO 2
Figure 13 Anaerobic respiration in plants and fungi

(a) aerobic respiration
(b)anaerobic respiration in
a muscle cell
(c) anaerobic respiration in
yeast

Comparison of energy yields
Not all the energy of the glucose molecule is transferred to ATP. There is a loss of
energy as heat energy.
Aerobic respiration involves the complete breakdown of glucose to carbon dioxide
and water. It produces 38 molecules of ATP per molecule of glucose. It is about
40% efficient.
Anaerobic respiration involves the incomplete breakdown of glucose and produces
two molecules of ATP per molecule of glucose. It is about 2% efficient. Energy still
remains locked up in lactate/ethanol.

Alternative respiratory substrates
Under certain circumstances fats and proteins may be used as respiratory substrates.
Individuals are able to survive for long periods without food because they can use
their reserves of carbohydrate, fat and protein:
l

Glycerol is converted into triose phosphate and enters glycolysis. Long-chain fatty
acid molecules are split into 2C fragments, which enter the pathways as acetyl
coenzyme A.

l

When a person is starving, tissue protein used as a source of energy. It is hydrolysed

into its constituent amino acids, which are deaminated (NH 2 groups are removed).
This leaves an organic acid that can enter the Krebs cycle.

Unit BY4: Metabolism, Microbiology and H
­ omeostasis

Examiner tip
All organic molecules can
be respired, but glucose
is the main respiratory
substrate. Most questions
on respiration use glucose
as the starting point.

15


Content Guidance
Summary

After studying this topic you should be able to:
l understand that all living organisms carry out
respiration to provide energy in their cells
l describe the process of glycolysis and the
production of pyruvate, ATP and reduced NAD
l describe the formation of acetyl coenzyme A during
the link reaction
l describe the Krebs cycle and the production of ATP,
reduced NAD and reduced FAD with release of
carbon dioxide

l explain the role of reduced NAD (and reduced
FAD) as a source of electrons and protons for the
electron transport system

define the terms dehydrogenation, decarboxylation,
substrate-level phosphorylation and oxidative
phosphorylation
l explain the synthesis of ATP by means of a flow
of protons through the enzyme ATP synthase by
chemiosmosis
l describe and explain the breakdown of glucose
under aerobic and anaerobic conditions
l state how many molecules of ATP are produced in
each of the four stages of respiration
l understand that all organic molecules can be used
as respiratory substrates and describe how lipids
and amino acids are utilised
l

Photosynthesis
Examiner tip
Most of life on Earth
is dependent upon
photosynthesis:
l It converts light energy
into chemical energy
that can be used by
other organisms.
l It provides a source
of complex organic

molecules for
heterotrophic organisms.
l It releases oxygen which
is necessary for aerobic
respiration.

Key concepts you must understand
l Green plants are autotrophic organisms that, during photosynthesis, synthesise

complex organic molecules from simple inorganic molecules using light energy.
Photosynthesis can be represented by the following simple chemical equation:
6CO2 + 6H 2O

C6H12O6 + 6O2

l During photosynthesis light energy is converted into chemical energy in the

form of organic molecules.
l Photosynthesis takes place in the chloroplasts of plant cells. The main site of

photosynthesis is the palisade tissue of the leaf.
l Chloroplasts are surrounded by a double membrane that encloses a fluid-filled

stroma (see Figure 14). Within the stroma is a series of flattened membranebound sacs called thylakoids, which form stacks called grana. These thylakoid
membranes provide a very large surface area for the absorption of light energy.
l There are two main stages in photosynthesis: the light-dependent stage and

the light-independent stage. In the light-dependent stage:
–Photosynthetic pigments (e.g. chlorophyll) absorb light energy, which results

Photophosphorylation
involves the synthesis of
ATP using light energy.

in the loss of electrons. The electrons are transferred to an electron acceptor.
–The energy absorbed by the electrons is then released via a series of redox
reactions and used to synthesise ATP from ADP and P i (photophosphorylation)
and to reduce the coenzyme NADP to NADPH 2.
–Light energy is converted into chemical energy within the organic molecules
ATP and NADPH 2.

16

WJEC A2 Biology


Photosynthesis
Outer membrane
Inner membrane

Chloroplast envelope
Lipid droplet

Intergranal lamella
Thylakoid

Stroma
Granum

Examiner tip

Synoptic link to BY1:
Starch grains are found
in chloroplasts. Within
the stroma molecules
of glucose undergo
condensation reactions to
form starch. Therefore,
there must be an enzyme
in the stroma that catalyses
these reactions.

Starch grain
DNA

70S ribosomes

Cytosol
Figure 14 The structure of a chloroplast

l The light-independent stage involves a series of enzyme-catalysed reactions in

which carbon dioxide is reduced to form a carbohydrate. This requires NADPH 2
and energy released from the hydrolysis of ATP.
l Figure 15 shows an overview of the two main stages in photosynthesis occurring

within a chloroplast.

Light energy

H2O

Light-dependent stage
ADP + Pi

CO2

ATP

O2

NADP NADPH2

Light-independent stage

CHO
(carbohydrate)

Figure 15 Outline of the stages of photosynthesis

Photosynthetic pigments
There are several photosynthetic pigments found in plants. They can be divided
into two main groups, the chlorophylls and the carotenoids. The function of the
pigments is to absorb light energy, thereby converting it into chemical energy.
Chromatography can be used to separate out the leaf pigments so that they can be
identified.

Unit BY4: Metabolism, Microbiology and H
­ omeostasis

17

Content Guidance

Absorption and action spectra
The absorption spectrum (Figure 16a) shows the percentage of light absorbed by a
particular pigment at different wavelengths of light. The action spectrum (Figure 16b)
shows the rate of photosynthesis at different wavelengths of light. Since the two graphs
show a similar trend, it suggests that these pigments are those responsible for the
absorption of the wavelengths of light used in photosynthesis.

Rate of photosynthesis

(b)

Percentage absorbance

(a)

Chlorophyll b
Carotenoids
Chlorophyll a

400

500

600

700

400

500

Wavelength of light/nm

600

700

Wavelength of light/nm

Figure 16 (a) Absorption spectra for photosynthetic pigments;
(b) The action spectrum for photosynthesis

Examiner tip
At A2 you are expected
to use the correct
terminology when
answering questions. You
will not gain credit for
vague statements such as
‘chlorophyll absorbs light’
or ‘chlorophyll absorbs
blue–violet light’. You
must refer to chlorophyll
absorbing either light
energy or wavelengths
of light in the blue–violet

region of the spectrum.

From the absorption spectrum it can be seen that:
l

chlorophyll molecules absorb wavelengths of light in the blue–violet and red
regions of the visible spectrum

l

the peak absorptions for chlorophyll a and chlorophyll b differ slightly

l

the carotenoids (e.g. xanthophyll and carotene) absorb wavelengths of light in the
blue–violet region

Photosystems
It can be seen from Figure 17 that the photosynthetic pigments are arranged in
clusters embedded in the thylakoid membranes of the chloroplasts. These clusters
are known as photosystems. A photosystem consists of an antenna complex and a
reaction centre (see Figure 18).
In a photosystem, chlorophyll a is the main photosynthetic pigment and is found
in the reaction centre. Chlorophyll b and the carotenoids are accessory pigments
found in the antenna complex. The molecules in the complex are arranged so as to
channel light energy to the reaction centre.
There are two types of photosystem:
l

In photosystem I, the reaction centre is called P700 as it contains a chlorophyll a

molecule with a maximum absorption at a wavelength of 700 nm.

l

In photosystem II, the reaction centre is called P680 as it contains a chlorophyll
a molecule with a maximum absorption at a wavelength of 680 nm.

18

WJEC A2 Biology


Photosynthesis
(a)

Knowledge check 8

Outer
membrane

Intermembrane
space

Inner
membrane

Explain the advantage to a
plant of having chloroplasts
that contain several
different light-absorbing

pigments.

Stroma

(b)

Thylakoid lumen
Granum
(stack of
thylakoids)

Thylakoid

Lamellae

Knowledge check 9
Explain why plants appear
green.

(c)
Cluster of pigment molecules
embedded in membrane (see Figure 18)
Thylakoid membrane
Stroma

Examiner tip
Synoptic link to BY1: In
BY1, you learnt about the
structure of chloroplasts
and mitochondria. You

may be given electron
micrographs or drawings
of these organelles and
asked to identify structures
or to indicate where the
stages of photosynthesis or
respiration occur.

Figure 17 (a) The structure of a chloroplast; (b) A section through
a single thylakoid; (c) Pigments in a thylakoid membrane

Knowledge check 10
Light energy
Transfer of energy

State exactly where
in the chloroplast you
would expect to find
photosystems.

Knowledge check 11
Antenna complex

Accessory
pigments

Reaction centre
(chlorophyll a)
Figure 18 A photosystem

Unit BY4: Metabolism, Microbiology and H
­ omeostasis

Photosystems contain
several pigments. State
the location of the
following pigments within a
photosystem:
(a)chlorophyll a
(b)chlorophyll b

19


Content Guidance
Examiner tip
NADP is the coenzyme
involved in photosynthesis.
Do not confuse it with
NAD, which is involved
in respiration. Remember
that the letter ‘p’ occurs
in both NADP and
photosynthesis.

The light-dependent stage
The light-dependent stage involves the formation of ATP by photophosphorylation
and the reduction of the coenzyme NADP. These events are summarised in a diagram,
known as the ‘Z-scheme’ shown in Figure 19.
Electron acceptor

Electron carrier

2e−

6
NADPH2
5

4
Potential energy level

2e−
2

2e−

NADP

3

2e−
ADP + Pi
ATP
1

P680

Photosystem I

P700

Photosystem II

2e−

H2 O

Light energy

2H+

Light energy
1/ O
2 2

Figure 19 The light-dependent stage (the ‘Z-scheme’)

(1) Photosynthetic pigments in the antenna complex of photosystem II absorb light
energy. The energy is transferred to the reaction centre where it excites two
electrons in the chlorophyll a molecule.
(2) The excited electrons are boosted to a higher energy level. They leave the
chlorophyll a molecule and are received by an electron acceptor.
(3) The electrons are passed along the electron transport chain (ETC) in a series of
redox reactions to photosystem I, which is at a lower energy level. The energy lost by
the electrons is used to convert ADP and P i to ATP — this is photophosphorylation.
(4) Light absorbed by photosystem I boosts two electrons from the chlorophyll a
molecule in the reaction centre to an even higher energy level. The electrons are

Examiner tip
The electrons lost from

the chlorophyll a molecule
in photosystem I are used
to reduce NADP. These
electrons are replaced
by those lost by the
chlorophyll a molecule in
photosystem II, which are
in turn replaced by those
lost by the water molecule
during photolysis.

received by another electron acceptor.
(5) Electrons (from the chlorophyll a molecule) and H+ (from the photolysis of water)
are used to reduce NADP (the final electron acceptor) to NADPH 2.

Photolysis of water
This occurs at stage 1 of the light-dependent reaction. The electrons removed from
the chlorophyll a molecule in photosystem II are replaced by electrons (e−) from a
water molecule. The loss of electrons from the water molecule causes it to dissociate
into protons (H+) and oxygen — this is known as photolysis.

Chemiosmotic theory of photophosphorylation
Figure 20 shows how ATP is synthesised during non-cyclic photophosphorylation. As
the electrons pass along the electron transport chain they lose energy. This energy
is used to pump protons (H+) from the stroma, across the thylakoid membrane and

20

WJEC A2 Biology

Photosynthesis
into the thylakoid space. The protons accumulate so that steep concentration and
electrochemical gradients are established between the thylakoid space and the
stroma. These gradients are also maintained by:
l

the photolysis of water, which occurs in the thylakoid space and increases the H+

l

the reduction of NADP, which occurs in the stroma and decreases the H+ concentration

concentration
The protons (H+) diffuse back into the stroma through the chemiosmotic protein
channels where the enzyme ATP synthase is located. The flow of protons through
ATP synthase provides the energy required to produce ATP from ADP and P i.

H

+

H+

H+

H+
H

H+

1/ O
2 2

H+

+

Thylakoid space
+

H

2H+

H+

H+

H2O
−

−

e

e
PS II
+

H
Light energy
P680

Electron carrier

e−

e−

Thylakoid
membrane

Proton pump

H+

Light energy
P700

e−
PS I
NADPH2
NADP + 2H+
Stroma

ATP synthase
ATP
ADP + Pi

Figure 20 Chemiosmosis and non-cyclic photophosphorylation

Electrons from the chlorophyll a molecules in photosystem I are used to reduce NADP
and are replaced indirectly by electrons from the photolysis of water. This is known
as non-cyclic phosphorylation and is represented by stages 1 to 5 in Figure 19.
You can see from Figure 19 that the electron acceptor at stage 4 is at the highest energy
state. It is possible for some of these excited electrons to return to the chlorophyll a
molecule in photosystem I via the electron transport chain. This is known as cyclic
phosphorylation and is represented by stages 4, 6 and 3 in Figure 19.
Cyclic and non-cyclic photophosphorylation are compared in Table 3.
Table 3 Cyclic and non-cyclic photophosphorylation

Feature

Cyclic
photophosphorylation

Non-cyclic
photophosphorylation

Photosystems involved

I only

I and II

Photolysis of water

No

Yes

Electron donor

Chlorophyll a in
photosystem I

Chlorophyll a in
photosystem I

Terminal electron acceptor

Chlorophyll a in
photosystem I

NADP

Products

ATP

ATP, NAPH2 and oxygen

Unit BY4: Metabolism, Microbiology and H
­ omeostasis

21


Content Guidance

Examiner tip
Balancing the equation:

The light-independent stage (Calvin cycle)

6CO2 + 6H2O →
C6H12O6 + 6O2

The light-independent reactions take place in the stroma of the chloroplast because

For every molecule of
CO2 that enters the Calvin
cycle two molecules of
triose phosphate (TP) are
produced. Six molecules
of CO2 entering the cycle
results in the production of
12 molecules of TP of which
two molecules leave the
cycle and combine to form
one molecule of glucose.

NADPH 2 (from the light-dependent stage) are used to reduce carbon dioxide to triose

Examiner tip
Synoptic links to BY1:
Plants require magnesium
to synthesise chlorophyll.
Magnesium deficiency leads
to chlorosis and death.

Plants also require nitrogen
to synthesise amino acids
and nucleic acids from triose
phosphate. Plants obtain
their nitrogen as nitrates
(NO3−) or ammonium ions
(NH4+) from the soil. (This
is also a synoptic link to the
nitrogen cycle.)

this is where the enzymes involved are located. During these reactions ATP and
phosphate (a 3C carbohydrate). Figure 21 shows the main stages in the Calvin cycle.
CO2

1
Ribulose bisphosphate
5C

2×glycerate phosphate
3C

NADPH2
NADP

2

ATP

3

ADP

5

ATP

Triose phosphate
3C

6

1

Glucose and other
carbohydrates

ADP + Pi
6

Amino acids
and proteins

Triose phosphate
3C
4

Lipids

Figure 21 The steps involved in the light-independent stage (the Calvin cycle)

(1) Carbon dioxide combines with ribulose bisphosphate (RuBP) to form two molecules
of glycerate-3-phosphate (GP), which is the first product of photosynthesis. This
reaction is a carboxylation (addition of carbon dioxide) reaction and is catalysed
by the enzyme Rubisco (ribulose bisphosphate carboxylase). As carbon dioxide
is converted from an inorganic form into an organic molecule the process is also
referred to as carbon fixation.
(2) NADPH 2 is used to reduce the two molecules of glycerate-3-phosphate into two

Knowledge check 12
Name the two products
from the light-dependent
stage of photosynthesis
that are required for the
Calvin cycle.

22

molecules of triose phosphate (TP). The hydrolysis of ATP provides the energy for
this reaction.
(3) Most of the TP (five out of six molecules) is converted by a series of reactions into
RuBP. ATP supplies the phosphate and energy required.
(4) Some of the TP (one of six molecules) is converted rapidly to glucose and other
carbohydrates, amino acids, lipids and nucleic acids.

WJEC A2 Biology


Photosynthesis
Investigating photosynthesis: Calvin’s lollipop
Melvin Calvin was an American biochemist who investigated the pathway by which

carbon dioxide is converted into organic compounds during photosynthesis. A
suspension of the unicellular alga Chlorella was placed in a flattened glass vessel that
was called the ‘lollipop’ (see Figure 22a). The suspension of Chlorella was supplied
with radioactive carbon dioxide. The lollipop was illuminated and the algae allowed
to photosynthesise. As the Chlorella photosynthesised, the radioactive carbon
dioxide was ‘fixed’ and incorporated into organic molecules (the intermediate
compounds), which became radioactive. At specific time intervals samples of the
Chlorella were released into boiling alcohol. This denatured enzymes, killed the
Chlorella and stopped the light-independent reactions at a particular point in time.
Compounds that the radioactive carbon had reached at a particular moment were
determined by chromatography and autoradiography (see Figure 22b). The order
in which each compound is produced was found by identifying the molecules and
analysing the results. From these results Calvin discovered the metabolic pathway
that is now known as the light-independent stage of photosynthesis.
(a)

Suspension of
algal cells
Light

Syringe for
injecting
radioactive
carbon
dioxide

Rapid
action
tap
Hot

alcohol
(b)

Autoradiogram produced after
5 seconds of photosynthesis

Autoradiogram produced after
15 seconds of photosynthesis
Aspartic
acid

Sugar
phosphates

Glycerate-3phosphate
Triose
phosphate

Sugar
diphosphates
Original position
of extract

Original position
of extract

Figure 22 (a) Calvin’s lollipop; (b) autoradiograms showing the
different molecules synthesised during Calvin’s experiments

Unit BY4: Metabolism, Microbiology and H

­ omeostasis

23


Content Guidance
Summary

After studying this topic you should be able to:
l understand that chloroplasts are transducers that
convert light energy into the chemical energy of ATP
l describe the absorption of various wavelengths of
light by chlorophyll and associated pigments and
describe the relationship between absorption and
action spectra
l describe both the arrangement of photosynthetic
pigments within photosystems and energy transfer
to reaction centres
l describe the processes of cyclic and non-cyclic
photophosphorylation (light-dependent stage)
including:
– the source of electrons for the electron
transport chain
– photolysis of water as a source of electrons for
photosystem II

– the reduction of NADP by the addition of
electrons and protons
l explain the synthesis of ATP by means of a flow
of protons through the enzyme ATP synthase by

chemiosmosis
l describe the reactions occurring in the lightindependent stage including:
– the role of NADPH2 as a source of reducing
power and ATP as a source of energy for the
reactions
– the uptake of carbon dioxide and the role of
Rubisco
– the fate of triose phosphate
l describe the role of magnesium and nitrogen in
plant metabolism

Microbiology
Key concepts you must understand
l Microbiology is the study of organisms that are too small to be seen with the

naked eye.
l For thousands of years people have been manipulating microorganisms to produce

various foods and drinks including bread, cheese, yoghurt, beer and wine.
l With increased knowledge and understanding of microorganisms, modern

biotechnology is used to produce other useful products, such as enzymes and
antibiotics.
l Genetic engineering has given the potential to produce a wide range of products

including human proteins such as insulin.
l To produce useful products such as new antibiotics it is necessary to be able to:

– culture microorganisms in the laboratory
–have an understanding of a microorganism’s metabolism to provide the

optimum conditions for growth and the conditions necessary for the
production of the useful product.

Examiner tip
Synoptic links to BY1:
Look back at your notes on
BY1 and construct a table
to compare the structure
of a prokaryotic cell with a
eukaryotic cell.

24

Bacterial classification
Bacteria are classified by the shape of their cells their reaction to the Gram stain.

Classification by shape
There are three main types of bacteria as classified by shape (see Figure 23). The
shape of the bacteria is due to their rigid cell wall, which has a unique structure.

WJEC A2 Biology