Enzymes

Learning Objectives

Identify the 6 classes of enzymes and the types of chemical

reactions they catalyze.

Define the following terms: cofactor, coenzyme, prosthetic group,

holoenzyme, apoenzyme, active site, substrate.

Describe a reaction coordinate diagram, including definitions of

the terms reaction coordinate, ground state, transition state,
and activation energy. Label a diagram with the above
mentioned terms.

Describe what enzymes do to chemical reactions, and what

they do not do.

Define reaction intermediates and describe what is meant by

rate-limiting step in a multi-step reaction sequence.
 Enzymes have extraordinary catalytic power, often far
greater than synthetic or inorganic catalysts.

They have a high degree of specificity for their substrates.

Enzymes accelerate chemical reactions tremendously.
They function in an aqueous environment under very mild
conditions of temperature and pH.

Few (if any) nonbiological catalysts have all these properties.

 Most enzymes are proteins

With the exception of a small group of catalytic RNA molecules,

all enzymes are proteins.
The catalytic activity of an enzyme depends upon the integrity of
its native protein conformation. If an enzyme is denatured or
dissociated into subunits, catalytic activity is usually lost.
The primary, secondary, tertiary, and quaternary structure of
enzymes are essential to their catalytic activity.
Some enzymes require no additional functional groups other
than those of their amino acid sequence. Others require an
additional chemical component called a cofactor.

cofactor: an inorganic ion or a coenzyme required for

enzymatic activity.
coenzyme: an organic cofactor required for the action of
certain enzymes; often containing a vitamin or vitamin
derivative as a component.
prosthetic group: a metal ion or an organic compound (other
than an amino acid) that is covalently bound to a protein and is
essential for its activity.

holoenzyme: a catalytically active enzyme, including all necessary

subunits, prosthetic groups, and cofactors.

apoenzyme (apoprotein): the protein portion of an enzyme,

exclusive of any organic or inorganic cofactor or prosthetic groups
that might be required for activity.

Some enzymes are modified covalently (post-translational

modification) by phosphorylation, glycosylation, and other
processes.
 How enzymes work

Reactions required to digest food, send nerve signals, or

contract a muscle simply do not occur at a useful rate without
catalysis.
An enzyme provides a specific environment within which an
enzyme-catalyzed reaction is energetically more favorable, and
thus occurs at a faster rate.

The distinguishing feature of an enzyme-catalyzed reaction is

that it occurs within the confines of a pocket on (or in) the
enzyme called the active site.
The molecule that is bound at the active site is called the
substrate. (There may be more than one substrate for a
reaction.)
The active site of an enzyme is lined with amino acid residues
whose functional groups bind the substrate and catalyze its
chemical transformation. (active site residues)

The enzyme-substrate complex (ES) is the starting point for

kinetic treatments of enzyme reactions and for descriptions of
enzyme mechanisms.
Binding of a substrate to an enzyme at the active site

The enzyme
chymotrypsin is
shown with the bound
substrate in red.
 Enzymes affect reaction rates, not equilibria.

A simple, one substrate, one product enzyme-catalyzed reaction:

E + S ES EP E + P

The function of an enzyme is to increase the rate of a reaction.

Enzymes do not affect the reaction equilibria.
Any reaction: S P can be described by a reaction
coordinate diagram. This is a diagram that graphically represents
the energy changes during a reaction.

The starting point for either the forward or reverse reaction is

called the ground state: the ground state for S, the ground state
for P. This is the contribution to the free energy of the system by
an average molecule of either S or P under a given set of
standard conditions.

The change in this free energy (going from S to P) is ∆ G’o, the

biochemical standard free energy change.
Reaction coordinate: reflects the progressive changes
(alignments, bond breakage or formation, charge development)
as S is converted to P.
The equilibrium between S and P: S P
reflects the difference in the free energy of their ground states.

∆ G’o = -RT ln K’eq

∆ G’o is an alternative way of expressing the equilibrium

constant for a reaction under standard conditions.

The free energy of the product (P) is less than the free energy
of the reactant (S), so ∆ G’o is negative and the equilibrium
favors the formation of P.
A favorable equilibrium does not mean that the S P
conversion will occur at a detectable rate. The rate of a
reaction is dependent on an entirely different parameter.
 Energy barrier
between S and P

The energy barrier is the energy required for alignment of reacting

groups, formation of transient unstable charges, bond
rearrangements, and other transformations required for the
reaction to proceed in either direction.
Molecules of S must be raised to this higher energy level before
conversion to P can take place.
At the top of the energy barrier is a point called the transition state.
This is a fleeting molecular moment in which events such as bond
breakage or formation, and charge development have proceeded to
the precise point at which decomposition to either S or P is equally
probable

The difference between the energy levels of the ground state of S

and the transition state is called the activation energy, ∆ G

The rate of a reaction is directly related to the magnitude of the

activation energy: the higher the activation energy, the slower
the reaction rate.
Enzymes enhance reaction rates by lowering activation energies.
An enzyme that catalyzes S P, also catalyzes P S.
The role of enzymes is to speed up these conversions; the
enzyme is not used up in the process, and the equilibrium
point is unaffected. The reaction reaches equilibrium much
faster when the reaction is enzyme catalyzed.

sucrose + O2 CO2 + H2O

∆ G’o is very large and negative

Yet…sucrose is very stable in the presence of oxygen:

the activation energy barrier is high.
A reaction may have several steps involved in the formation and
decay of transient chemical species called reaction intermediates.

E + S ES EP E + P
ES and EP are reaction intermediates, and occupy valleys in
the reaction coordinate diagram.

The overall rate of a reaction is primarily determined by the step

(or steps) with the highest activation energy: this is called the
rate-limiting step (i.e. the slowest step in a multi-step process).

In a series of enzyme catalyzed reactions (i.e. the glycolytic

pathway), there is usually one reaction that is rate-limiting.