C1.

1 Enzymes & Metabolism

Theme: C Interaction and interdependence
How do molecules interact together to support cellular metabolism? How can connected chains of
reactions be controlled?
Level of organisation: Molecules

Guiding Questions:
1. In what ways do enzymes interact with other molecules?
2. What are the interdependent components of metabolism?

C1.1.1 Enzymes as Catalyst: Recall

 Enzymes are _____________ ___________
 biological _________ – speed up chemical reactions
 Without enzymes, chemical reactions will either not
occur or be ____ ________ to be able to sustain life
 Convert ____________ to ___________
 By ____________ ____________ ___________
 _____________ - enzyme substrate specificity
 Bind to ____________ ___________
 ____________ of __________ _______ on enzyme -
_________________ to shape of substrate
 Enzymes can be ______________ after releasing products

C1.1.2 Role of Enzymes in Metabolism

• Cells = over 5000 different types of enzymes
• _____________ is a very complex network of chemical
reactions that are ___________ and ______________
with each other (link together)
• Due to the _____________ of enzymes
• There are a large amount of ______________ enzymes
• That can exert a control over ________________
• This can happen via _______________ of
____________, production of enzymes via ________
_____________________, etc

C1.1.3 Anabolic & Catabolic Reactions

_____________________
• ________________ (make) of
___________________ from _______________
• _______________ REACTION  form water
• Require ______________ (ATP)
• Example:
• ______________ ____________
 • _____________  ___________ formation
• ____________________
___________________
• ________________ of macromolecules into monomers
• _________________ REACTION  ___________________ (use) water
• Release _____________ (ATP)
• Example:
• _____________ of food in digestion
• _____________ of substrates in
______________

C1.1.4 Enzymes as globular proteins with an active

site for catalyst
•Enzymes are globular proteins that have an ________
___________ that _________ to the ______________
• The active site is composed of only a few ___________ ________
• But the _______________ between the _______ _________
within the overall _____ _____________ of enzyme ensure that
the active site has the necessary properties for ____________ &
____________ of _____________ molecules
• Each enzymes exhibit _________________ for a particular
substrate
Linking question: What are other examples of structure-function
relationship in biological macromolecules?

C1.1.5 Interactions between substrate and active site to allow induced-fit binding
• ___________ & ________ model (traditional) 
the enzyme’s active site ______________ the
substrate _____________
• explains how enzymes exhibit specificity for a
particular substrate
• _________________ ____ model  active site will
undergo a _________________
____________ when exposed to a substrate to
______________ ______________
• ____________ will ______ ___________
_________ when binding occurs
• _______________ _________ change
______________ __________ in the
________________, (easier to break), increasing reactivity)
• This model supports the fact that some enzymes exhibit _______________ _________ (e.g. lipase can
bind to a variety of lipids)
C1.1.6 Role of molecular motion and substrate-active site collisions in enzyme
catalysts
• For catalysis to happen, substrate molecules must
____________ and ________ with the active site in the
______________ ___________ (and with
_________________ __________)
• substrate molecules and / or enzymes must be able to
________________ ___________
• Most enzyme-catalysed activity occurs in _________ as
in______ state, substrate molecules are able to _____________ ___________ in different directions
• In some cases, substrate molecules may be _______________ (eg: enzymes to breakdown cell wall)
• While sometimes enzymes might be immobilised by being _____________ in membranes (eg: maltase
in intestinal wall, ______________ bound to ______________ beads)

C1.1.7 Relationships between the structure of the active site, enzyme-substrate

specificity and denaturation

 An enzyme has a cleft, called the

active site that has a
_________________ shape to
the substrate. This allows
enzyme-substrate ________________. Some
enzymes are very specific and only binds to
_________ substrate while some enzymes are _____
specific (eg: hexokinase can bind to any hexose
sugar)
 Random movement of molecules and successful
collisions allows substrate to bind to the active site,
forming an ________________ __________.
 The _____________ of the ________ _____ in the active
site interact with the substrate, causing a
________________ ___________ of _________ of the
___________, change thus ______________ the
___________ _____________.
 The substrate is then break apart and the ________
leaves the enzyme, leaving the enzyme unchanged and
ready to bind to another substrate.
 Since enzymes are proteins with a ____________ ______ ___________ and structure, factors such as
temperature and pH may affect the __________ __________ such as the ______________
______________ and _______________ bonds (hydrogen bonds) between the amino acids.
 Even small changes can _____________ the ___________ of substrate or the ______________
____________ of the enzyme.
 If the changes are too great to be _____________, the enzyme is said to be ________________.
C1.1.8 Effects of temperature on the rate of enzyme activity
• low temperatures result in _____________ thermal
energy for the ______________ of an
__________________ reaction
• Increasing the temperature will ___________ ____ &
___________ of _________________ for both enzyme
and substrate
• higher KE will result in ________ ______________
_______________ ______________
• At an optimal temperature (may differ for different
enzymes), the rate of enzyme activity will be at its peak
• Higher temperature than the optimal temperature will
cause enzyme ____________ to __________  thermal
energy ______________ the ____________ bonds of
enzymes  change ____________ of active site

C1.1.8 Effects of pH on the rate of enzyme

activity
• Changing the __________  changes the amount of
______________ and _________ ions
• will ____________ the _____________ of the
enzyme/active site
• which also ______________ _________ __________/
_________________ ___________  change in shape
of active site  protein ____________/ become
insoluble
• _________________ _________to ____________ to
substrate
• Different enzymes have different optimal pH and
moving outside the range of their optimum pH reduces
enzyme activity

C1.1.8 Effects of substrate concentration on

the rate of enzyme activity
• As _______________ ______________ increases
• frequency of successful collisions___________
• more reaction & more products form  ____________
of ___________ ______________
• As substrate conc. increases to a certain point
• ______ ____________ ___________ ______________
• rate of reaction reaches a _____________
C1.1.10 Effect of Enzyme on Activation Energy
• Substrates  ___________ ____  products
• __________ is required to reach transition
state  ____________________
• Bond _____________________ of substrate
– ______________ energy,
• ________________ when forming products
______________ _________
• When substrate bind to active site of enzyme,
it _________________ and
_______________ the ________ in substrate
• Binding ___________ the ____________
____________ to reach
___________________
• Activation energy is therefore lowered

Exothermic – Endothermic

_______________ reaction: Usually

______________ (breaking down) 
_____________ energy
Products have less bonds, less energy?

________________ reaction: Usually ______________ (building up)  ____________ energy

Products have more bonds, more energy?

Application of skills & NOS

• Rate of reaction = amount of substrate used / product form ÷ time taken
• You should be able to describe the relationship between variables as shown in graphs.
• You should recognize that generalized sketches of relationships are examples of models in biology.
• Models in the form of sketch graphs can be evaluated using results from enzyme experiments.
AHL: C1.1.11 Intracellular & extracellular enzyme-catalysed reactions
• Some enzyme-catalysed reactions happen in the cell
• _____________ enzymes are usually produced by _______ __________
• Eg: ____________ and _________ __________ are catalysed by
enzymes in the ____________ and ________ of ______________
(mitochondria have their own 70S ribosomes)
• While some happens outside the cells
• _____________ enzymes are usually produced by __________ on the
___________ and transported out of the cells by ___________
• Example: _____________ _____________ in the gut  enzymes are
produced and secreted by ____________ _________ in the __________

AHL: C1.1.12 Generation of heat energy by the reactions of metabolism

• Metabolic reactions such as respiration are _____ ______ ______________ in energy transfer
• Some of the energy are used to ______
________
• But some are released as _______ __________
• For endotherms such as mammals, birds, etc, the
heat energy can be used to maintain __________
_________ _________________
• Higher physical activity will ___________
______________ rate and ________ __________
• ______________ _____________ tend to have
______________ _____________ __________ as
the ____________ the animal, the ________
___________________ it uses energy*

AHL: C.1.13 Cyclical and linear pathways in metabolism

 • Most chemical changes happen in ___________ of _______ __________  _________ __________
• Involving __________ of _________
that maybe ___________ pathway
• Eg: ______________ in
___________________ (C1.2)
• Some metabolic pathway form a
_____________  ________
____________ of reaction becomes
_______________ that _________
the rest of the pathway
• Eg: ___________ _______ during
______________ in mitochondria
• ___________ __________ during
______________ in chloroplast

AHL: C.1.14 Allosteric sites and non-competitive inhibition

• _________________  substance that bind to enzymes
and ____________ its ________________
• ______________________ ____________  bind at
location other than active site (___________ _______)
 causes ________________ within an enzyme that
leads to a ________________ _____________ of the
_____________ of ____________ ________ so that
substrate can no longer bind to enzyme
• Binding are ____________ _______________
• Only ______________ substance can bind to an
allosteric site
• __________________ ____________  __________
shape to _______________ & ____________ with
substrate for the binding with active site
• so __________ of inhibitors can be _____________ by ___________ _________ _______________

AHL: C.1.15 Competitive inhibition as a

consequence of an inhibitor binding
reversibly to an active site
• Competitive inhibition  substrate will still
reach ___________ rate of reaction as substrate
concentration increases, just ____________
• As number of enzymes have not changed
• The __________ _______________, the
___________ the __________of reaction
• ____________________ inhibition 
_____________ _________ of reaction will be
_____________as ___________ _____________ _______________
Examples (need to know):
• __________________ is a medicinal drug used to control the ______ ________ of ______________
• Statin is a ______________ ____________ of the __________ HMG-CoA reductase which is
involved in the _______________ of __________________
• ______________  ___________________ _________
• Poison that __________ _______ ________________ in
aerobic respiration
• It binds to one of the ________________ ______________
____________ _____________
• Called cytochrome oxidase – a _____________
____________ in electron transport chain

AHL: C.1.16 Regulation of metabolic pathways by

feedback inhibition
1. Many enzymes that catalyse the ______
____________ in a ____________ _________
2. Is ______________ at the ______________
site by the end product (_____
_______________ inhibition)
3. economical way to ________ metabolic
pathway
4. As the metabolic pathway will be switched _____________ – ____________rapidly if there is a
______________ of ___________
5. And turn ‘off’ if there is an _______________ of ________ _________________
6. _________________ of _________ ___________ ________ of _____________ 
_______________ ______________ ___________
7. Helps to ____________ _______________ of ________________products
8. Usually reaction will never completely end and will reach an equilibrium ratio of substrate &
product
Example: ___________________ to ________________ Inhibition
• Isoleucine cannot be made by our body, so they need to be ingested
• Eg: eggs, seaweed, cheese, fish, chicken, lamb
• In plants & bacteria, i_______________ are made from _________________ in a ___
____________ process by _________________ ______________ ________________
AHL: C.1.17 Mechanism-based inhibition as a consequence of chemical changes
to the active site caused by the irreversible binding of an inhibitor
• A _______________ ___________ ________________ is__________________ as the binding of the
inhibitor causes __________________ _____________ to the _____________ _________
• It will _____________ or _________ the enzyme, rendering it _______________ to ___________ to
the substrate anymore
• Example: ______________ is a mechanism-based inhibitor that binds to _______________ subunit
• Transpeptidase is an ____________ used to _____________ ________________ __________ in
the ________ ______________ of ______________
• In some _____________ ___________ bacteria, eg: methicillin-insensitive Staphylococcus aureus
(________) express _____________ PBP2a (transpeptidase) that have a _____________
___________ for ____________ and at the same time, retain _______________ ____________ .

This shows how penicillin – common antibiotic works by interfering with transpeptidase

This shows the low affinity of penicilin binding to transpeptidase (PBP2a) in penicillin – antibiotic resistant
bacteria due to mutation/evolution as an effect of wide-spread use of antibiotic
C1.1 Enzymes & Metabolism
Theme: C Interaction and interdependence
How do molecules interact together to support cellular metabolism? How can connected chains of
reactions be controlled?
Level of organisation: Molecules

Guiding Questions:
3. In what ways do enzymes interact with other molecules?
4. What are the interdependent components of metabolism?

C1.1.1 Enzymes as Catalyst: Recall

 Enzymes are globular proteins
 biological catalysts – speed up chemical reactions
 Without enzymes, chemical reactions will either not
occur or be too slow to be able to sustain life
 Convert substrate to products
 By lowering activation energy
 Specific  enzyme substrate specificity
 Bind to active site
 Shape of active sit on enzyme  complementary to
shape of substrate
 Enzymes can be reused after releasing products

C1.1.2 Role of Enzymes in Metabolism

• Cells = over 5000 different types of enzymes
• Metabolism is a very complex network of
chemical reactions that are interdependent and
interact with each other (link together)
• Due to the specificity of enzymes
• There are a large amount of different enzymes
• That can exert a control over metabolism
• This can happen via inhibition of enzymes,
production of enzymes via gene expression, etc

C1.1.3 Anabolic & Catabolic Reactions

Anabolism
• Synthesis (make) of macromolecules from monomers
• CONDENSATION REACTION  form water
• Require ENERGY (ATP)
• Example:
• protein synthesis
• glucose  glycogen formation
 • Photosynthesis
Catabolism
• Breakdown of macromolecules into monomers
• HYDROLYSIS REACTION  breakdown (use) water
• Release ENERGY (ATP)
• Example:
• Hydrolysis of food in digestion
• Oxidation of substrates in respiration

C1.1.4 Enzymes as globular proteins with an active

site for catalyst
• Enzymes are globular proteins that have an active site that
binds to the substrate
• The active site is composed of only a few amino acids
• But the interactions between the amino acid within the the
overall 3D structure of enzyme ensure that the active site has
the necessary properties for catalysis & binding of substrate
molecules
• Each enzymes exhibit specificity for a particular substrate

Linking question: What are other examples of structure-function

relationship in biological macromolecules?

C1.1.5 Interactions between substrate and active site to allow induced-fit binding
• Lock and key model (traditional)  the
enzyme’s active site complements the substrate
precisely
• explains how enzymes exhibit specificity for a
particular substrate
• Induced fit model  active site will undergo
a conformational change when exposed to a
substrate to improve binding
• Substrate will also change shape when binding
occurs
• conformational change stresses bonds in the
substrate, (easier to break), increasing
reactivity)
• Some enzymes may exhibit broad specificity (e.g. lipase can bind to a variety of lipids)

C1.1.6 Role of molecular motion and substrate-active site collisions in enzyme

catalysts
 • For catalysis to happen, substrate molecules must collide and bind with the active site in the correct
orientation (with sufficient energy)
• substrate molecules and / or enzymes must be able to move randomly
• Most enzyme-catalysed activity occurs in water as in
liquid state, substrate molecules are able to move
randomly in different directions
• In some cases, substrate molecules may be
immobilised (eg: enzymes to breakdown cell wall)
• While sometimes enzymes might be immobilised by
being embedded in membranes (eg: maltase in
intestinal wall, lactase bound to alginate beads)

C1.1.7 Relationships between the structure of the active site, enzyme-substrate

specificity and denaturation

 An enzyme has a cleft, called the active site that has a

complementary shape to the substrate. This allows enzyme-
substrate specificity. Some enzymes are very specific and only
binds to one substrate while some enzymes are less specific (eg:
hexokinase can bind to any hexose sugar, protease)
 Random movement of molecules and successful
collisions allows substrate to bind to the active
site, forming an enzyme-substrate complex.
 The R-group of the amino acids in the active site
interact with the substrate, causing a
conformational change of shape of the substrate,
change thus lowering the activation energy.
 The substrate is then break apart and the product
leaves the enzyme, leaving the enzyme
unchanged and ready to bind to another
substrate.
 Since enzymes are proteins with a precise 3D
shape and structure, factors such as temperature
and pH may affect the weak bonds such as the
hydrophobic interactions and intermolecular
bonds (hydrogen bonds) between the amino
acids.
 Even small changes can affect the binding of substrate or the catalytic activity of the enzyme.
 If the changes are too great to be reversed, the enzyme is said to be denatured.
C1.1.8 Effects of temperature on the rate of enzyme activity
• low temperatures result in insufficient thermal
energy for the activation of an enzyme-catalyzed
reaction
• Increasing the temperature will increase KE & speed
of movement for both enzyme and substrate
• higher KE will result in more frequent successful
collisions
• At an optimal temperature (may differ for different
enzymes), the rate of enzyme activity will be at its
peak
• Higher temperatures will cause enzyme stability to
decrease  thermal energy disrupts the hydrogen
bonds of enzymes  change shape of active site

C1.1.8 Effects of pH on the rate of enzyme

activity
• Changing the pH  changes the amount of H+ and
OH- ions
• will alter the charge of the enzyme/active site
• which also disrupt ionic bonds/ R group
interactions  change in shape of active site 
protein denature / become insoluble
• Reduced ability to bind to substrate
• Different enzymes have different optimal pH and
moving outside the range of their optimum pH
reduces enzyme activity

C1.1.8 Effects of substrate concentration

on the rate of enzyme activity
• As substrate concentration increases
• frequency of successful collisions increases
• more reaction & more products form  rate of
reaction increases
• As substrate conc. increases to a certain point
• all active sites filled
• rate of
reaction
reaches a
plateau
C1.1.10 Effect of Enzyme on Activation Energy
• Substrates  transition state  products
• Energy is required to reach transition state
 activation energy
• Bond weaken/breaking of substrate – absorb
energy,
• bond making when forming products release
energy
• When substrate bind to active site of enzyme,
it stresses and destabilise the bonds in
substrate
• Binding lowers the energy needed to reach
transition stage
• Activation energy is therefore lowered

Exothermic – Endothermic

Exergonic reaction: Usually catabolic (breaking

down)  release energy
Products have less bonds, less energy?

Endergonic reaction: Usually anabolic (building up)

 absorb energy
Products have more bonds, more energy?
AHL: C1.1.11 Intracellular & extracellular enzyme-catalysed reactions
• Some enzyme-catalysed reactions happen in the cell
• Intracellular enzymes are usually produced by free ribosomes
• Eg: Glycolysis and Krebs cycle are catalysed by enzymes in the cytosol
and matrix of mitochondria (mitochondria have their own ribosomes)
• While some happens outside the cells
• Extracellular enzymes are usually produced by ribosomes on the RER
and transported out of the cells by vesicles
• Example: chemical digestion in the gut  enzymes are produced and
secreted by exocrine glands in the pancreas

AHL: C1.1.12 Generation of heat energy by the reactions of metabolism

• Metabolic reactions such as respiration are
not 100% efficient in energy transfer
• Some of the energy are used to make ATP
• But some are released as heat energy
• For endotherms such as mammals, birds,
etc, the heat energy can be used to
maintain constant body temperature
• Higher physical activity will increase
metabolic rate and heat production
• Smaller animals tend to have higher
metabolic rate as the bigger the animal,
the more efficient it uses energy*

AHL: C.1.13 Cyclical and linear pathways in metabolism

• Most chemical changes happen in sequence of small changes  metabolic pathway
 • Involving chain of reactions
• Eg: Glycolysis in respiration (C1.2)
• Some metabolic pathway form a
cycle  end product of reaction
becomes reactant that start the rest
of the pathway
• Eg: Krebs cycle during respiration
in mitochondria (C1.2)
• Calvin Cycle during photosynthesis
in chloroplast (C1.2)

AHL: C.1.14 Allosteric sites and

non-competitive inhibition
• Inhibitors  substance that bind to enzymes and reduces its activity
• Non-competitive inhibitors  bind at location other
than active site (allosteric site)  causes interaction
within an enzyme that leads to a conformational
change of the shape of active site so that substrate
can no longer bind to enzyme
• Binding are usually reversible
• Only specific substance can bind to an allosteric site
• Competitive inhibitors  similar shape to substrate
& compete with substrate for the active site
• so effect of inhibitors can be reduced by increasing
substrate concentration

AHL: C.1.15 Competitive inhibition as a

consequence of an inhibitor
binding reversibly to an active site
• Competitive inhibition  substrate will
still reach max rate of reaction as
substrate concentration increases, just
slower
• As number of enzymes have not
changed
• The more inhibitors, the slower the
rate of reaction
• Non-competitive inhibition  max rate
of reaction will be reduced as less
enzymes available
Examples (need to know):
• Statin is a medicinal drug used to control the high levels of cholesterol
• Statin is a competitive inhibitor of the enzyme HMG-CoA
reductase which is involved in the biosynthesis of
cholesterol
• Cyanide  non-competitive inhibitor
• Poison that prevent ATP production in aerobic respiration
• It binds to one of the mitochondria membrane bound
enzyme
• Called cytochrome oxidase – a carrier protein in electron
transport chain (C1.2 Cell respiration)

AHL: C.1.16 Regulation of metabolic pathways by feedback inhibition

9. Many enzymes that catalyse
the first reaction in a
metabolic pathway
10. Is inhibited at the allosteric
site by the end product (non-
competitive inhibition)
11. economical way to control
metabolic pathway
12. As the metabolic pathway will
be switched ‘on’ – work
rapidly if there is a shortage of end product.
13. And turn ‘off’ if there is an excess of end product
14. Concentration of product  control rate of reaction  negative feedback loop
15. Helps to prevent build up of intermediate products
16. Usually reaction will never completely end and will reach an equilibrium ratio of substrate &
product

Example: Threonine to Isoleucine Inhibition

• Isoleucine cannot be made by our body, so they need to be ingested
• Eg: eggs, seaweed, cheese, fish, chicken, lamb
• In plants & bacteria, isoleucine are made from threonine in a 5 step process by enzyme threonine
deaminase
AHL: C.1.17 Mechanism-based
inhibition as a consequence of chemical
changes to the active site caused by the
irreversible binding of an inhibitor
• A mechanism-based inhibitor is irreversible
as the binding of the inhibitor causes
chemical changes to the active site
• It will lock up or destroy the enzyme,
rendering it incapable to bind to the
substrate anymore
• Example:
• Penicillin is a mechanism-based inhibitor that
binds to transpeptidase subunit
• Transpeptidase is an enzyme used to
crosslink peptidoglycan chains in the cell

walls of bacteria
• In some penicillin resistance bacteria, eg:
methicillin-insensitive Staphylococcus aureus
(MRSA) express modified PBP2a (transpeptidase) that have a reduced affinity for penicillin but, at
the same time, retain catalytic functions .