Download Topic guide 1.2: Enzymes

1: Biochemistry of macromolecules and metabolic pathways
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Enzymes
Enzymes are referred to as biological catalysts – they create new pathways
that allow reactions to occur many times faster than uncatalysed reactions.
Enzymes act on specific molecules called substrates. These substrate
molecules bind to a region of the enzyme known as the active site. The
specificity of the enzyme is due to the fact that the substrate and active site
have structures that are complementary. Hence only specific substrates can fit
and bind to the active site.
On successful completion of this topic you will:
•• understand the chemical principles that apply to the structures of
biological building block molecules (LO1)
•• understand the structures of biological macromolecules and the
relationships to biological functions (LO2).
To achieve a Pass in this unit you need to show that you can:
•• explain the structure, catalytic function and characteristic properties of
enzymes (2.2).
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1 Models to explain the actions of enzymes
Before you start
If you find some parts of this unit challenging, remember you are working at a higher level than
you may be used to. In this unit it is important that you fully understand the following themes and
topics before you begin:
•• structure and function of biological molecules
•• enzyme structure and function
•• aerobic respiration.
If you need to check your understanding of proteins, carbohydrates, lipids and nucleic acids,
Unit 2 Module 1 of OCR AS Biology (P. Kennedy and F. Sochacki, 2008), offers a good introduction
to the topic.
If you need to check your understanding of aerobic respiration and the stages of glycolysis, link
reaction, the Krebs cycle and the electron transport chain, you may find Unit 1 Module 4 of OCR A2
Biology (S. Hocking, 2008) useful.
Several scientists have produced models to help explain the actions of enzymes.
The lock and key hypothesis
Key terms
Enzyme: A protein used as a catalyst
to speed up chemical reactions.
Active site: The functional part of the
enzyme.
Substrate: A substance that binds
to an enzyme’s active site; it is the
reactant molecule.
This model explains that enzyme activity depends on the active site of the
enzyme. The active site is the area or ‘pocket’ on the enzyme where a substrate
molecule fits. The shapes of the substrate molecule and the active site are
complementary, so they are said to fit together like a key fits into a lock. When the
substrate binds to the active site an enzyme-substrate complex is formed and the
substrate then forms a product.
The induced-fit hypothesis
This model, in contrast to the lock and key hypothesis, suggests that the active site
is not exactly the same shape as the substrate – it is said to be in a ‘relaxed’ state.
When the substrate binds to the active site, the active site moulds itself to the
substrate forming an enzyme-substrate complex. Only then is the active site the
correct shape to catalyse the reaction.
Figure 1.2.1: Enzyme structure.
Substrate = H2O2
Active site
Substrate
Active site
Molecular model
of catalase
Schematic model
of an enzyme
The schematic diagram in Figure 1.2.1 shows the complimentary active site of an
enzyme and the substrate. The molecular diagram shows the enzyme catalase and
its complementary substrate hydrogen peroxide.
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2 Lowering activation energy
For chemical reactions to take place bonds need to be broken before new ones
can be formed. The energy needed for these bonds to be broken is known as the
activation energy and this is usually very high. An enzyme carries out its function
by providing an alternative route for the reaction with a lower activation energy by
temporarily combining with the chemicals involved in the reaction. Figure 1.2.2 is
an energy profile showing the effect of a catalyst on activation energy.
Energy
Figure 1.2.2: The activation energy
needed for a chemical reaction to take
place is lower when a catalyst is present.
Activation energy
without catalyst
Activation energy
with catalyst
Reactants
Products
Progress of reaction
3 Factors affecting enzyme activity
There are various factors that affect enzyme activity and all enzymes have their
own optimum conditions. Enzyme rates depend on the surrounding conditions
and substrate concentration. Conditions that affect enzyme activity therefore are
temperature, pH, substrate and enzyme concentration and the presence of any
inhibitors.
Temperature
Key terms
Activation energy: Energy required
to activate a chemical reaction.
Denature: To change an enzyme’s
structure in a way that changes
the shape of the active site so the
enzyme is unable to function.
Applying heat energy to molecules increases their kinetic energy so there will
be an increased number of collisions between enzyme and substrate molecules.
This in turn will increase the rate of reaction and so the products will be formed
more quickly. However, applying too much heat can cause enzymes to denature.
The increased vibrations and collisions put strains on the bonds of the tertiary
structure and can break the hydrogen and ionic bonds. The breaking of these
bonds affects the important three-dimensional shape; more importantly it
changes the shape of the active site. Denaturation causes the enzyme to lose its
ability to function and its function cannot be restored.
Increasing the temperature initially increases the rate of reaction. The temperature
that gives the maximum rate of reaction is the enzyme’s optimum temperature.
However, the rate will decrease if the temperature rises higher than the optimum,
due to denaturation of the enzyme. Figure 1.2.3 shows the effect of temperature
on the rate of an enzyme-controlled reaction.
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Rate of reaction
Figure 1.2.3: Effect of temperature on the
rate of an enzyme-controlled reaction.
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Increasing temperature
increases the rate of
reaction due to increased
kinetic energy
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Optimum temperature gives
maximum rate of reaction
Enzymes inside the body work at an optimum temperature of 37 °C, whereas
genetic engineering techniques require high temperatures, and the enzyme DNA
polymerase has an optimum temperature of 72 °C. Under optimum conditions and
at this temperature DNA polymerase is able to efficiently polymerise a thousand
bases per minute. The amount of the target DNA sequence is doubled, leading to
exponential amplification of the specific DNA fragment.
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Increasing temperature
beyond the optimum
temperature reduces
the rate of reaction due
to the breaking of bonds
holding the enzyme’s
tertiary structure in place
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60
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Temperature/°C
pH
The optimum pH varies for all enzymes – for many enzymes the optimum pH is
pH 7. However, outside their optimum pH range, enzymes are denatured because
free hydrogen and hydroxide ions affect the charge of the amino acid. The threedimensional shape is altered, changing the tertiary structure of the protein and, in
turn, the specific active site.
Pepsin is an enzyme that works in the human body to digest proteins; it works
in the stomach at pH 2. Trypsin, an enzyme in the small intestine, also digests
proteins – however, in contrast, this enzyme works at pH 7.
Key terms
Turnover rate: The number of
substrate molecules converted into
product molecules per unit time,
known as Vmax.
Michaelis-Menten constant:
The substrate concentration needed
for an enzyme to reach one half of
its maximum rate known as Km. The
catalysed reaction rate is equal to
Vmax /2.
1.2: Enzymes
Substrate concentration
When you look at Figure 1.2.4 you can see that as the substrate concentration
increases, the rate of the enzyme-controlled reaction increases until all the
enzymes’ active sites are occupied by substrate. We use the term ‘Vmax’, which is
the maximum rate at which an enzyme catalyses a reaction and is often known
as the turnover rate. When all the enzymes’ active sites are saturated with a
complementary substrate Vmax is reached. The only way to speed up the reaction
further is to add more enzyme. The amount of substrate needed to achieve Vmax
is important and is often expressed as Michaelis-Menten constant, Km, which is
the substrate concentration needed for an enzyme to reach one half its maximum
rate. All enzymes have their own specific Km for a substrate.
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Vmax
Reaction velocity (V0)
Figure 1.2.4: A graph to
show Vmax and Km.
Link
You will find out more about enzymes
in Topic guide 1.4: Investigating
enzymes. Also check out Unit 5:
Chemistry for applied biologists, for
enzyme kinetics.
Vmax/2
Km
Substrate concentration (S)
Enzyme concentration
Enzymes can convert millions of substrate molecules into products every minute,
so the number of enzymes required in a reaction is less than the substrate.
However, if there is a plentiful supply of substrate, the reaction can be limited
by the number of enzymes present; therefore, by increasing the enzyme
concentration, the rate will also increase.
Remember that if there is not an abundant supply of substrate, increasing the
concentration of enzyme will have no effect on the rate of reaction.
Activity
Answer the following questions:
1 How does temperature affect enzyme activity?
2 How does pH affect enzyme activity?
3 If all the enzymes’ active sites are occupied, what effect would adding more substrate have on
the rate of reaction and why?
4 If there was a plentiful supply of substrate how could the rate of reaction be increased?
5 What does denature mean and how does it occur?
Presence of inhibitors
Enzymes: competitive inhibitors
As the name suggests, competitive inhibitors compete with the substrate for the
active site of the enzyme. Therefore the inhibitors are the same size and shape
as the substrate to enable the complementary fit inside the enzyme’s active
site. However, the inhibitor cannot form a product. If competitive inhibitors are
present, the rate of reaction is decreased as they stop the substrate from binding
to the enzyme and producing a product. Many competitive inhibitors do not bind
permanently and so their action is reversible. They bind to the enzyme’s active site
for a short period and then detach, leaving the enzyme active again.
Enzymes: non-competitive inhibitors
These inhibitors do not compete for the active site but they bind to an alternative
part of the enzyme called an allosteric region. This changes the shape of the active
site and means that the substrate will no longer be a complementary shape to
fit into the active site. If there are enough inhibitors present they may fill all the
enzymes’ allosteric regions and, if this happens, the reaction will stop.
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Figure 1.2.5 shows competitive inhibition and non-competitive inhibition taking
place.
Figure 1.2.5: Competitive inhibition
and non-competitive inhibition.
Substrate
Competitive inhibitor
interferes with active
site of enzyme so
substrate cannot bind
Substrate
Enzyme
Enzyme
(a) Competitive inhibition
Non-competitive inhibitor changes
shape of enzyme so it cannot bind
to substrate
(b) Non-competitive inhibition
Permanent inhibitors
The effect of many non-competitive inhibitors is not reversible because they bind
permanently to the enzymes; the enzyme is therefore described as denatured
because the shape of the active site is no longer complementary or the correct
shape for its specific substrate to bind to.
Checklist
In this topic you should now be familiar with the following ideas about enzymes:
 enzymes are biological catalysts
 enzymes are proteins
 enzymes have an active site that enables them to bind to substrate molecules
 two models can be used to explain enzyme action – the lock and key hypothesis and the
induced-fit model
 enzymes can be affected by temperature and pH
 an enzyme’s shape can be altered, which stops the enzyme working; this is known as
denaturation
 the rate of reaction can be affected by the concentration of the substrate and the enzyme
 Vmax is the maximum rate reached in an enzyme-controlled reaction
 competitive inhibitors affect the rate of reaction by competing with the substrate molecules
 non-competitive inhibitors affect the rate of reaction by binding to an alternative region and
changing the active site shape.
The following Case study is a real life example of enzymes in action.
Case study
In biochemistry, fermentation is used to produce alcohol, yoghurt, vinegar and many other
everyday products. Alcoholic and glycolysis fermentation both begin with glucose and are
both anaerobic fermentation processes (do not require oxygen). Glycolysis uses many enzymes
to transform glucose to lactic acid. Alcoholic fermentation follows the same enzymatic
pathway; however, lactate dehydrogenase is replaced by pyruvate decarboxylase and alcoholic
dehydrogenase. During alcoholic fermentation these two enzymes convert pyruvic acid into
carbon dioxide and ethanol.
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Further reading
Boyle, M. & Senior, K. (2008) Biology, 3rd Edition, HarperCollins
Kennedy, P., Sochacki, F. & Hocking, S. (2008) OCR Biology AS, Heinemann (Pearson Education
Limited)
Kennedy, P., Sochacki, F., Winterbottom, M. & Hocking, S. (2008) OCR Biology A2, Heinemann
(Pearson Education Limited)
Loomis, H.F. (2005) Enzymes: The Key to Health, 21st Century Nutrition Publishing
Moran, L., Horton, R., Scrimgeour, G., Perry, M. & Rawn, D. (2011) Principles of Biochemistry
(International Edition), 5th Edition, Pearson
Acknowledgements
The publisher would like to thank the following for their kind permission to reproduce their
photographs:
Getty Images: Martin McCarthy / E+
All other images © Pearson Education
We are grateful to the following for permission to reproduce copyright material:
Figure 1.2.3: Table showing the effect of temperature on the rate of an enzyme-controlled reaction
from Figure 4 on page 129 of Pearson’s AS Biology for OCR. Used with permission.
In some instances we have been unable to trace the owners of copyright material, and we would
appreciate any information that would enable us to do so.
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