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Cambridge
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Biology
Second edition
CJ Clegg
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Cambridge
International
AS & A Level
Biology
Second edition
C J Clegg
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Contents
Contents
Introduction
AS LEVEL
1 Cell structure
1.1 The microscope in cell studies
1.2 Cells as the basic units of living organisms
2 Biological molecules
2.1 Testing for biological molecules
2.2 Carbohydrates and lipids
2.3 Proteins
2.4 Water
3 Enzymes
3.1 Mode of action of enzymes
3.2 Factors that affect enzyme action
4 Cell membranes and transport
4.1 Fluid mosaic membranes
4.2 Movement of substances into and out of cells
5 The mitotic cell cycle
5.1 Replication and division of nuclei and cells
5.2 Chromosome behaviour in mitosis
6 Nucleic acids and protein synthesis
6.1 Structure of nucleic acids and replication of DNA
6.2 Protein synthesis
7 Transport in plants
7.1 Structure of transport tissues
7.2 Transport mechanisms
8 Transport in mammals
8.1 The circulatory system
8.2 Transport of oxygen and carbon dioxide
8.3 The heart
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9 Gas exchange and smoking
9.1 The gas exchange system
10 Infectious disease
10.1 Infectious diseases
10.2 Antibiotics
11 Immunity
11.1 The immune system
11.2 Antibodies and vaccination
A LEVEL
12 Energy and respiration
12.1 Energy
12.2 Respiration
13 Photosynthesis
13.1 Photosynthesis as an energy transfer process
13.2 Investigation of limiting factors
14 Homeostasis
14.1 Homeostasis in mammals
14.2 Homeostasis in plants
15 Control and co-ordination
15.1 Control and co-ordination in mammals
15.2 Control and co-ordination in plants
16 Inherited change
16.1 Passage of information from parent to offspring
16.2 The roles of genes in determining the phenotype
16.3 Gene control
17 Selection and evolution
17.1 Variation
17.2 Natural and artificial selection
17.3 Evolution
18 Classification, biodiversity and conservation
18.1 Classification
18.2 Biodiversity
18.3 Conservation
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Contents
19 Genetic technology
19.1 Principles of genetic technology
19.2 Genetic technology applied to medicine
19.3 Genetically modified organisms in agriculture
Answers
Index
Acknowledgements
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AS Level
3
There are many
opportunities in this
topic for students to gain
experience of carrying out
practical investigations and
analysing and interpreting
their results.
3.1 Mode of action of enzymes
Enzymes are essential for
life to exist. Their mode of
action and the factors that
affect their activity are
explored in this topic. Prior
knowledge for this topic
is an understanding that
an enzyme is a biological
catalyst that increases
the rate of a reaction and
remains unchanged when
the reaction is complete.
Enzymes
Learning Outcomes
By the end of this topic, you should be able to:
3.1.1 state that enzymes are globular proteins that catalyse reactions
inside cells (intracellular enzymes) or are secreted to catalyse
reactions outside cells (extracellular enzymes)
3.1.2 explain the mode of action of enzymes in terms of an active site,
enzyme-substrate complex, lowering of activation energy and
enzyme specificity, including the lock-and-key hypothesis and the
induced-fit hypothesis
3.1.3 investigate the progress of enzyme-catalysed reactions by
measuring rates of formation of products using catalase and rates
of disappearance of substrate using amylase
3.1 Mode of action of enzymes
There are many different enzymes, each one specific to a particular reaction.
This specificity is the key to understanding the efficient functioning of cells
and living organisms.
Introducing enzymes and their role in metabolism
Enzymes are globular proteins that catalyse the many thousands of metabolic
reactions taking place within cells and organisms. Metabolism is the name we
give to these chemical reactions of life. The molecules involved are collectively
called metabolites. Many of these metabolites are made in organisms. Other
metabolites have been imported from the environment, such as from food
substances taken in, water and the gases carbon dioxide and oxygen.
Metabolism actually consists of chains (linear sequences) and cycles of enzymecatalysed reactions, such as we see in respiration, photosynthesis, protein
synthesis and many other pathways. These reactions may be classified as one
of just two types, according to whether they involve the build-up or breakdown
of organic molecules:
» In anabolic reactions, larger molecules are built up from smaller molecules.
Examples of anabolism are the synthesis of proteins from amino acids and
the synthesis of polysaccharides from simple sugars.
» In catabolic reactions, larger molecules are broken down. Examples of
catabolism are the digestion of complex foods and the breakdown of sugar in
respiration (Figure 3.1).
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3
synthesis of complex
molecules used in growth
and development and in
metabolic processes,
e.g. proteins,
polysaccharides,
lipids, hormones, growth
factors, haemoglobin,
chlorophyll
3 Enzymes
anabolism:
energy-requiring
reactions, i.e.
endergonic
reactions
nutrients
sugars,
amino acids,
fatty acids,
i.e. smaller
organic
molecules
catabolism
energy-releasing
reactions,
i.e. exergonic
reactions
release of simple
substances,
e.g. small inorganic
molecules, CO2, H2O,
mineral ions
▲ Figure 3.1 Metabolism:
an overview
Enzymes as globular proteins
In Topic 2 we saw that the tertiary structure of globular proteins is typically
spherical. In these molecules their linear chain of amino acids (primary
structure) is precisely folded and held in a globular, three-dimensional shape
containing a-helices and b-sheets. Also, the R-groups of the amino acids
present on the exterior of the molecule are hydrophilic groups, making the
protein water soluble. Remember, this structure contrasts with that of the
fibrous proteins, such as collagen.
Enzymes as biological catalysts
A catalyst is a molecule that speeds up a chemical reaction but remains
unchanged at the end of the reaction. Most chemical reactions do not occur
spontaneously. In a laboratory or in an industrial process, chemical reactions
may be made to occur by applying high temperatures, high pressures, extremes
of pH and by keeping a high concentration of the reacting molecules. If
these drastic conditions were not applied, very little of the chemical product
would be formed. In contrast, in cells and organisms, many of the chemical
reactions of metabolism occur at exactly the same moment, at extremely
low concentrations, at normal temperatures and under the very mild, almost
neutral, aqueous conditions we find in cells.
How is this brought about?
For a reaction between two molecules to occur, there must be a successful
collision between them. The molecules must collide with each other in the right
way and at the right speed (Figure 3.2). If the angle of collision is not correct,
the molecules bounce apart. Alternatively, if the speed of the collision is wrong
or the impact is too gentle, for example, then there will be insufficient energy
for the rearrangement of electrons. Only if the molecules are lined up and
collide with the correct energies does a reaction occur.
The ‘right’ conditions happen so rarely that the reaction does not happen to a
significant extent normally. If we introduce extreme conditions, such as those
listed above, we can cause the reaction to happen. On the other hand, if we
introduce an enzyme for this particular reaction, then the reaction occurs at
great speed. Enzymes are amazing molecules in this respect.
Where do enzymes operate?
Some enzymes are exported from cells, such as the digestive enzymes. Enzymes
like these, that are parcelled up, secreted and work externally are called
extracellular enzymes. However, many enzymes remain within the cells and
work there. These are intracellular enzymes. They are found inside organelles,
in the membranes of organelles, in the fluid medium around the organelles (the
cytosol) and in the cell surface membrane.
Enzymes control metabolism
There is a huge array of enzymes that facilitate the chemical reactions of
the metabolism. Since these reactions can only take place in the presence of
specific enzymes, we know that if an enzyme is not present then the reaction it
catalyses cannot occur.
Many enzymes are always present in cells and organisms but some enzymes are
produced only under particular conditions or at certain stages. By making some
enzymes and not others, cells can control what chemical reactions happen
in the cytoplasm. Sometimes it is the presence of the substrate molecule
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that triggers the synthesis of the enzyme. In Chapter 4 we see how protein
synthesis (and therefore enzyme production) is directly controlled by the cell
nucleus.
3
How enzymes work
So, enzymes are biological catalysts made of protein. They speed up the rate of
a chemical reaction. The general properties of catalysts are:
3.1 Mode of action of enzymes
» they are effective in small amounts
» they remain unchanged at the end of the reaction.
The presence of enzymes enables reactions to occur at incredible speeds, in an
orderly manner, yielding products that the organism requires, when they are
needed. Sometimes reactions happen even though the reacting molecules are
present in very low concentrations.
CH2OH
1 The reaction: hydrolysis of sucrose
to form glucose and fructose
1
OH
O
HO
HO
from water
oxygen bridge
O
O
CH2OH
CH2OH
2
OH
+
OH
HOH 2C
HO
H O
water H
sucrose
OH
OH
sucrose
HO
O
O
CH2OH
OH
HOH 2C
HO
OH
glucose
fructose
sucrose
sucrose
2 Random collision possibilities:
when sucrose and water collide at
the wrong angle
water
water
water
sucrose
sucrose
sucrose
when sucrose and water collide at
the wrong speed
These events are what happens at
most random collisions
For the reaction to occur, sucrose
and water must collide in
just the right way – glucose and
fructose are formed
Under normal conditions this
happens so infrequently that
it is an insignificant event
water
water
water
sucrose
glucose
water
fructose
3 In the presence of one molecule of the enzyme sucrase (invertase),
approximately 3.0 × 104 molecules of sucrose are hydrolysed each minute!
▲ Figure 3.2 Can a reaction occur without an enzyme?
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Enzymes lower the activation energy
As molecules react, they become unstable, high-energy intermediates, but
they are in this state only momentarily. We say they are in a transition state
because the products are formed immediately. The products have a lower
energy level than the substrate molecules. Energy is needed to raise molecules
to a transition state and the minimum amount of energy needed to do this is
called the activation energy (Figure 3.3). It is an energy barrier that has to
be overcome before the reaction can happen. Enzymes work by lowering the
amount of energy required to activate the reacting molecules.
3 Enzymes
3
A model of what is going on is the boulder (the substrate) perched on a slope,
prevented from rolling down by a small hump (the activation energy) in front
of it. The boulder can be pushed over the hump. Alternatively, the hump can be
dug away (the activation energy can be lowered), allowing the boulder to roll
and shatter at a lower level (into the products).
‘boulder on hillside’ model of activation energy
without a catalyst, this
amount of energy needs
to be put in to start the
reaction
triggering the fall,
either by pushing
effect of catalyst
or by removing
the hump (the
enzyme way)
energy
activation energy
free energy change
products
(at lower
energy level)
reactant
products
▲ Figure 3.3 Activation energy
The enzyme has an active site
In a reaction catalysed by an enzyme, the starting substance is called the
substrate. It is converted to the product. The way an enzyme works is for the
substrate molecule to become attached to (we say ‘bind to’) the enzyme at
a specially formed pocket in the enzyme – very briefly. This binding point is
called the active site. The active site takes up a relatively small part of the
total volume of the enzyme.
So, an enzyme (E) works by binding to its substrate (S) molecule at a specially
formed pocket in the enzyme. This concept is referred to the ‘lock and key’
hypothesis of enzyme action. As the enzyme and substrate form a complex
(E–S), the substrate is raised in energy to a transition state and then breaks
down into products (Pr) plus unchanged enzyme (Figure 3.4).
E + S → E – S → Pr + E
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The sequence of steps to an enzyme-catalysed reaction:
enzyme + substrate
E–S complex
product + enzyme available for reuse
(substrate raised to
transition state)
E + S
E–S
Pr + E
enzyme
(large protein
molecule)
3
3.1 Mode of action of enzymes
active site (here
the substrate
molecule is held
and reaction occurs) –
the lock
substrate molecule –
the key
enzyme–substrate
complex
product
molecules
substrate
molecule now at
transition state
▲ Figure 3.4 The lock and key hypothesis of enzyme action
Enzymes are typically large globular protein molecules. Most substrate
molecules are quite small molecules by comparison. Even when the
substrate molecules are very large, such as certain macromolecules like the
polysaccharides, only one bond in the substrate is in contact with the active
site of the enzyme.
Enzymes are highly specific
Enzymes are highly specific in their action. They catalyse only one type of
reaction or only a very small group of very similar reactions.
This means that an enzyme ‘recognises’ a very small group of substrate
molecules or even only a single type of molecule. This is because the active
site where the substrate molecule binds has a precise shape and distinctive
chemical properties (meaning the presence of particular chemical groups and
bonds). Only particular substrate molecules can fit to a particular active site.
All other substrate molecules are unable to fit and so cannot bind.
Question
1 Explain why the shape of globular proteins that are enzymes is important in
enzyme action.
Catalysis by ‘induced fit’
We have seen that enzymes are highly specific in their action. This makes them
different from most inorganic catalysts. Enzymes are specific because of the
way they bind with their substrate at a pocket or crevice in the protein. The
‘lock and key’ hypothesis, however, does not fully account for the combined
events of ‘binding’ and simultaneous chemical change observed in most
enzyme-catalysed reactions.
At the active site, the arrangement of certain amino acid molecules in the
enzyme exactly matches certain groupings on the substrate molecule, enabling
the enzyme–substrate complex to form. As the complex is formed, an essential,
critical change of shape is caused in the enzyme molecule. It is this change of
shape that is important in momentarily raising the substrate molecule to the
transitional state. It is then able to react (Figures 3.5 and 3.6).
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With a transitional state achieved, other amino acid molecules of the active site
bring about the breaking of particular bonds in the substrate molecule, at the
point where it is temporarily held by the enzyme. It is because different enzymes
have different arrangements of amino acids in their active sites that each enzyme
catalyses either a single chemical reaction or a group of closely related reactions.
3
polypeptide of 49 amino acid residues,
making up a simple enzyme
3 Enzymes
substrate
active site (pocket/crevice
in the protein molecule)
The amino acids in a
protein have different
roles.
The substrate molecule
combines (temporarily)
with the enzyme by
inducing a change in
shape of the enzyme
molecule.
the ‘induced fit’ process plays a
part in bringing about the chemical
changes, which are the enzymecatalysed reaction
some amino acid residues
match certain groupings on the
substrate molecule, enabling the
enzyme–substrate complex to form,
e.g. residues 3–4–5 and 24–25–26
3
4
5
substrate
41
20
Specificity:
• Some amino acid residues allow a
particular substrate molecule to ‘fit’.
• Some amino acid residues bring about
particular chemical changes.
24
25
26
other amino acid
residues are ‘reactive’,
i.e. catalytic residues
that induce the
breaking of bonds,
and the formation
of product(s),
e.g. 20 and 41
other amino acid residues interact to form the
three-dimensional structure of the enzyme
▲ Figure 3.5 The induced fit hypothesis of enzyme action
glucose
+ ATP
slight change in
shape of active
site as substrate
molecule fits,
and reaction
takes place
two polypeptide
chains make up
the enzyme
hexokinase
(computer-generated
molecular model)
▲ Figure 3.6 Computer-generated image of the induced fit hypothesis in action
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Naming enzymes
Many enzymes have a name based on the name of their substrate, with the
ending -ase added. For example, lactase hydrolyses lactose and amylase
hydrolyses amylose.
3
Other enzymes have been given names that tell us little or nothing about
what they do, such as many of the enzymes of digestion, for example, pepsin,
trypsin and rennin.
Question
2 a Define the term ‘catalyst’.
b List two differences between inorganic catalysts and enzymes.
3.1 Mode of action of enzymes
Today, systematic naming of enzymes is based on an agreed classification of
enzymes and on the name of the substrate catalysed. These types of name are
long and detailed and are outside the scope of this book. They are used in the
communications of enzymologists but not in everyday usage. However, you are
already familiar with certain enzymes. For example, the enzymes that catalyse
the formation of two products from a larger substrate molecule by a hydrolysis
reaction are classified as ‘hydrolases’. Can you name a hydrolase?
SUMMARY
n
n
n
Metabolism, all the chemical reactions of life, consists
of anabolic reactions, the build up of complex
molecules from smaller ones, e.g. protein synthesis,
and catabolic reactions, the breakdown of complex
molecules, e.g. oxidation of sugar in respiration.
All reactions of metabolism are made possible by
enzymes. Enzymes are biological catalysts and
most are made of globular protein. An enzyme
is highly specific to the type(s) of substrate
molecule and type of reaction that it catalyses.
Enzymes work by forming a temporary complex
with a substrate molecule at a special part of the
enzyme surface, called the active site (the lock
n
n
and key hypothesis). Enzymes work by lowering the
activation energy needed for a reaction to occur.
A slight change in shape of the substrate molecule
when it binds to the active site helps raise the
molecule to a transition state (the induced fit
hypothesis), from which the products may form.
The enzyme is released for reuse.
The rate of an enzyme-catalysed reaction is found
by measuring the disappearance of the substrate or
the accumulation of the product in a given period
of time. The initial rate of reaction is taken since
the reaction rate falls with time under experimental
conditions.
Examination practice questions
1 The enzyme sucrase catalyses the breakdown of the glycosidic bond in sucrose.
A student investigated the effect of increasing the concentration of sucrose
on the rate of activity of sucrase.
Ten test tubes were set up with each containing 5 cm3 of different concentrations
of a sucrose solution. The test tubes were placed in a water bath at 40°C for
10 minutes. A flask containing a sucrase solution was also put into the water bath.
After 10 minutes, 1 cm3 of the sucrase solution was added to each test tube.
The reaction mixtures were kept at 40°C for a further 10 minutes.
After 10 minutes, the temperature of the water bath was raised to boiling
point. Benedict’s solution was added to each test tube. The time taken for a
colour change was recorded and used to calculate rates of enzyme activity.
The results are shown in the graph on the next page.
a i Name the type of reaction catalysed by sucrase.
[1]
ii Explain why the temperature of the water was raised to boiling point. [2]
b Describe and explain the results shown in the graph.
[5]
[Total: 8]
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12
3 Enzymes
rate of enzyme activity/arbitrary units
3
10
8
6
4
2
0
0
20
40
60
concentration of sucrose/g dm–3
80
100
Cambridge International AS and A Level Biology 9700, Paper 21 Q4 June 2011
2 a Describe how enzymes take part in chemical reactions.
[4]
Starch phosphorylase is an enzyme found in plant cells. In potato tuber cells,
the enzyme takes part in the breakdown of starch when the tuber begins to
grow.
starch phosphorylase
glucose-1-phosphate
starch + phosphate ions
A student investigated the effect of pH on this reaction using two buffer
solutions.
The student prepared four test tubes, A to D, as shown in the table and
described below.
The student made an extract of potato tissue that contained the enzyme.
Some of this extract was boiled.
A solution of potassium dihydrogen phosphate was added to some tubes as a
source of phosphate ions.
The test tubes were left for 10 minutes in a water bath at 30 °C and then
samples were tested with iodine solution.
b i State what the student would conclude from a positive result with
iodine solution.
[1]
ii Explain why the student boiled some of the extract in this
investigation.
[2]
c Explain the results shown in the table below.
[4]
[Total: 11]
Test Contents
tube Volume of
starch
solution/cm3
Volume of
glucose-1phosphate
solution/cm3
Volume of
potassium
dihydrogen
phosphate
solution/cm3
pH of
Enzyme
buffer
extract
solution
Results
with iodine
solution
after
10 minutes
A
2
0.5
6.5
unboiled negative
B
2
0.5
2.0
unboiled positive
C
2
0.5
6.5
boiled
positive
6.5
boiled
negative
D
2
Cambridge International AS and A Level Biology 9700, Paper 02 Q2 June 2007
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Enzyme concentration
0.2 g dm−3
Enzyme concentration
0.4 g dm−3
0.2 g dm−3
Substrate concentration/g dm−3
0.4 g dm−3
Product concentration/g dm−3
3
3.1 Mode of action of enzymes
3 The diagram shows
an apparatus used in
an investigation using
substrate solution
immobilised enzymes. It is
not expected that you will
immobilised enzyme in
have done this investigation.
burette
A solution of a substrate
was poured into a burette
containing an enzyme
immobilised onto alginate
liquid collected
beads. The liquid passing
from burette
through the burette was
collected into a beaker
and the concentration of
substrate and the concentration of the product measured. The table shows
the results obtained by five students.
Repeat 1 Repeat 2 Repeat 1 Repeat 2 Repeat 1 Repeat 2 Repeat 1 Repeat 2
Student A
24
26
14
13
32
33
60
64
Student B
25
22
12
12
34
39
60
63
Student C
22
23
10
13
35
32
59
61
Student D
18
24
11
12
34
33
62
68
Student E
25
28
13
18
30
32
65
64
b Identify two variables and explain how each might be controlled.
[2]
c On a copy of the table above, indicate by placing a circle around the value,
two results that are anomalous.
[2]
d A student drew the following conclusion from this investigation:
Doubling the enzyme concentration doubled the rate of reaction of the
enzyme.
i State one way in which the evidence in the table above supports the
conclusion. [1]
ii State two ways in which the reliability of the results might be
improved.
[2]
[Total: 7]
Cambridge International AS and A Level Biology 9700, Paper 05 Q3 June 2007
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throughout the student text, with answers at the
back of the book, so students can check their
understanding as they work their way through the
chapters.
» Build scientific communication skills and
vocabulary in written responses with a variety of
exam-style questions.
» Encourage understanding of historical context
and scientific applications with extension boxes in
the student text.
» Have confidence that lessons cover the full
syllabus content with a free Scheme of Work
available online
» Help prepare students for assessment with
answers to questions available online for free.
» Provide additional practice with the accompanying
write-in Practical Skills Workbook which once
completed, can also be used to recap learning for
revision.
This resource is endorsed by
Cambridge Assessment International Education
W
Confidently navigate the updated Cambridge
International AS & A Level Biology (9700) syllabus
with a structured approach ensuring that the
link between theory and practice is consolidated,
scientific skills are applied, and analytical skills
developed.
Dynamic Learning
This book is fully supported by Dynamic Learning – the online
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481404 CAIE A Level Biology 2E CV SAMPLE.indd 3
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