The Nature of Enzymatic Catalysis

LECTURE 5
The nature of
enzymatic catalysis
Biology, Campbell & Reece: Ch8, 148-157
By
Dr Mohamed Abumaree
Molecular Reproductive Biology & Immunology
College of Medicine
King Saud bin Abdulaziz University for Health Science
Riyadh
2009
1
Chemical Reactions
Exergonic Endergonic
Reaction Reaction
Exergonic Reaction Endergonic Reaction
Spontaneous Chemical Reaction Non–Spontaneous Chemical
Reaction
Release of free energy Free energy absorbed & stored
G decreases G increases
ΔG is negative ΔG is positive
Magnitude of ΔG: maximum Magnitude of ΔG: quantity of

amount of work a reaction can energy required to drive a
perform reaction
The greater the decrease in free

energy, the greater the amount of
work that can be done
Cell Works
1.Mechanical Work (such as, muscle cell
contraction)
2.Transport Work (such as substance across
membranes against the direction of
spontaneous movement)
3.Chemical Work (such as polymer synthesis)
4
Cell Work
 Cells use ATP to mediate energy coupling
(the use of exergonic process to drive an
endergonic process)
 ATP hydrolysis releases energy greater than

the energy released by other molecules
5
ATP Structure
ATP contains ribose, adenine & three

phosphate groups
ATP Hydrolysis
The break of
bonds
between
phosphate
groups yields
Pi & ADP
The reaction is exergonic releases 7.3

kcal of energy/ mole of ATP hydrolyzed
Why ATP hydrolysis releases
so much energy?
1.Three negatively charged phosphate
groups in ATP molecule
2. So, charges are crowded together!!
3. Their repulsion instable ATP molecule

ATP Performs Work
 ATP hydrolysis generates insufficient
energy to perform cellular works
 So, enzymes couple energy generated
from ATP hydrolysis to endergonic
reactions by phosphorylating a reactant,
which is more reactive (less stable) than
the unphosphorylated reactant
9
ATP Regeneration
ATP cycle couples the exergonic

processes to the endergonic processes
The Activation Energy Barrier
 Energy required to
twist & change the
bonds of reactant
molecules in order
to push them over an
energy barrier (hill)
to begin the downhill
part of the reaction
 EA provides a barrier to determine the rate of the
reaction
 Reactants must absorb enough energy to reach the

top of EA barrier before the reaction occurs
 Some reactions, EA is modest at room temperature

so there is sufficient energy for the reactants to reach
the transition state in a short time…But, in most
cases, EA is high so the transition state cannot be
reached so the reaction doesn’t occur… So, the reaction
will occur only if the reactants are heated
13
How Does Enzymes Lower
EA Barrier?
 Macromolecules (rich in free energy), decompose
spontaneously at temperatures typical for cells, but,
the activation barriers must be overcome for cells to
carry out the metabolic reactions necessary for life
 Heat speeds a reaction by allowing reactants to
achieve the transition state, but this is inappropriate
for the biological systems, for the following reasons:
14
1. High temperature denatures proteins so kills cells
2. Heat will speed up all reactions, not only the
necessary ones!!
 Therefore, cells use enzymes to catalyze a reaction
 Enzymes lower EA barrier to enable the reactant
molecules to absorb enough energy
 Thus reaching the transition state at moderate
temperatures
 Enzymes speed up reactions that occur eventually
anyway
15
1. Enzymes determine (Selective) which chemical
processes will go on in the cell at a specific time
2. Enzyme can not change ΔG for a reaction; it can not
make an endergonic reaction exergonic
Enzyme Specificity
 Enzyme binds specifically to its substrate

(substrates) forming an enzyme substrate
complex
 The enzyme catalytic action converts the

substrate to the product ( products) of the reaction
Molecular Recognition
Enzymes (proteins)
has an active site (a
pocket) on the surface
of the protein, where
the substrate binds
Active site is formed by a few amino acids,

acids while the
rest of the protein molecule provides a framework
determining the active site configuration
The specificity of an
enzyme due to the
compatible fit
between the shape of
its active site and the
shape of the
substrate
The active site is not a rigid receptacle

(container) for the substrate
Catalysis in Enzyme Active Site
The entire cycle happens so fast

 Very small amounts of an enzyme can have a huge
metabolic impact by functioning over & over again in
catalytic cycles
 Enzyme can catalyze the forward & the reverse

reactions
 Which reaction succeeds depends on the

concentrations of reactants & products
 Enzyme always catalyzes a reaction in the direction

of equilibrium
21
 The active site provides a template for the
substrates to come together in the proper
orientation so a reaction can occur between them
 The active site distorts the substrate to approach

the transition state
 Thus reduces the amount of free energy that must

be absorbed to achieve a transition state
 The active site may also provide a

microenvironment,
microenvironment such as pH
22
 The rate at which a specific amount of enzyme
converts substrate to product is partly a function
of the initial concentration of the substrate:
substrate
• The more substrate molecules are available,

available
the more frequently they access the active sites
of the enzyme molecules
 However, there is a limit to how fast the reaction

can be pushed by adding more substrate to a fixed
concentration of enzyme
23
 When the concentration of the substrate is high
enough, all enzymes’ active sites will be engaged
(Enzyme
(E is saturated )
 When the product exits an active site, another
substrate molecule enters
 The reaction rate is determined by the speed at
which the active site converts substrate to product
 When an enzyme is saturated,
saturated the rate of product
formation is increased by adding more enzymes
24
Effects of Local Conditions
on Enzyme Activity
 The activity of an enzyme (how
efficiently the enzyme functions) is
affected by:
1) Temperature
2) pH
3) Chemicals that specifically influence enzyme
function
25
Effects of Temperature
The rate of an
enzymatic reaction
increases with
increasing
temperature
 Because substrates crash with active sites more
frequently when the molecules move rapidly
 Each enzyme has an optimal temperature at which its
reaction rate is greatest
26
Above the optimal
temperature of the
enzyme, the speed of
the enzymatic
reaction drops
sharply
 The thermal disturbance of the enzyme molecule

disrupts the bonds (hydrogen & ionic bonds & other
weak interactions) that stabilize the active conformation,
then the protein molecule eventually denatures
27
Most human
enzymes have
optimal
temperatures of
about 35–40°C
(close to human body
temperature)
 Without denaturing the enzyme, the optimal
temperature allows the greatest number of molecular
collisions & the fastest conversion of the reactants to
product molecules
28
Effects of pH
 Enzyme has an
optimal pH (pH 6–
8) in which enzyme
is most active
 Exceptions:
 Pepsin (a digestive enzyme in the stomach) works best
at pH 2
 Trypsin (a digestive enzyme in the intestine) works
best at pH 8
29
Cofactors
 A nonprotein molecule or ion (zinc, iron & copper)
that is required for the enzyme function
 Can be permanently bound to the active site or may

bind loosely & reversibly with the substrate during
catalysis
 If the cofactor is an organic molecule, it is called a

coenzyme,
coenzyme such as vitamins
30
Enzyme Inhibitors
 Some chemicals
selectively inhibit enzyme
function
 If the inhibitors bind to
the enzyme by covalent
bonds,
bonds inhibition is usually
irreversible,
irreversible but many
inhibitors bind weakly to
the enzyme so the
inhibition is reversible 31
 Some reversible inhibitors resemble the normal
substrate molecule & compete for admission into the
active site
 This is called competitive inhibitors
 The competitive inhibition can be overcome by

increasing the concentration of substrate
 So the active sites become available, more

substrate molecules than inhibitor molecules are
around to gain entry to the sites
32
Noncompetitive inhibitor binds
to the enzyme away from the
active site, altering the
conformation of the enzyme so
that its active site no longer
functions
 Toxins & poisons are irreversible enzyme inhibitors.

For example, sarin (a nerve gas) causes death
 Not all inhibitors are harmful, natural inhibitors
(selective inhibition) regulate enzyme activity to control
cellular metabolism
33
Allosteric Regulation of Enzymes
Regulatory Molecules
 Naturally regulate enzyme activity
(Reversible; noncompetitive inhibitors)
 They bind to a site elsewhere on the enzyme,

enzyme
via noncovalent bonds; thus change the shape
and the function of its active site
34
Allosteric regulation
The function of a protein at one site
is affected by the binding of a
regulatory molecule to a separate site
resulting in inhibition or stimulation
of the activity of an enzyme
Feedback Inhibition
In feedback
inhibition, a
metabolic pathway is
switched off by the
inhibitory binding of
its end product to an
enzyme that acts early
in the pathway
36
Enzymes Localization Within the Cell
 Enzymes have fixed locations within the cell
 Act as structural components of particular
membranes or in solution within specific membrane–
enclosed eukaryotic organelles,
organelles each with its own
internal chemical environment
 For example, in eukaryotic cells, the enzymes for
cellular respiration reside in specific locations within
mitochondria
37

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LECTURE 5

Magnitude of ΔG: maximum Magnitude of ΔG: quantity of

The greater the decrease in free

 ATP hydrolysis releases energy greater than

ATP contains ribose, adenine & three

The reaction is exergonic releases 7.3

2. So, charges are crowded together!!

3. Their repulsion instable ATP molecule

ATP cycle couples the exergonic

 Reactants must absorb enough energy to reach the

 Some reactions, EA is modest at room temperature

 Enzyme binds specifically to its substrate

 The enzyme catalytic action converts the

Active site is formed by a few amino acids,

The active site is not a rigid receptacle

The entire cycle happens so fast

 Enzyme can catalyze the forward & the reverse

 Which reaction succeeds depends on the

 Enzyme always catalyzes a reaction in the direction

 The active site distorts the substrate to approach

 Thus reduces the amount of free energy that must

 The active site may also provide a

• The more substrate molecules are available,

 However, there is a limit to how fast the reaction

 The thermal disturbance of the enzyme molecule

 Can be permanently bound to the active site or may

 If the cofactor is an organic molecule, it is called a

 This is called competitive inhibitors

 The competitive inhibition can be overcome by

 So the active sites become available, more

 Toxins & poisons are irreversible enzyme inhibitors.

 They bind to a site elsewhere on the enzyme,

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