Principles of

Biochemistry/Enzym
es
< Principles of Biochemistry

Enzymes are organic catalysts that are

important to all living things due to the
continuous-controlled chemical activities
in cells. Enzymes regulate metabolism by
altering the rate of chemical reactions.
Activation energy is decreased in order to
alter chemical reaction rates. In addition,
enzymes are able to transform one form of
energy to another. Due to the fact that
enzymes are highly selective, they may
only catalyze one or a specific class of
reactions. The place where an enzyme
binds onto the substrate is called an active
site. A substrate is the molecule that
enzyme acts upon.

There are two theories that describe the

binding of enzymes: 1) Lock and Key
Theory and 2) Induced Fit Theory.

1) Lock and Key Theory: The shape of the

enzyme's active site is complementary to
that of its substrate

2) Induced Fit Theory: The active site has

a flexibility of shape, thus when an
appropriate substrate comes in contact
with the enzyme's active site, the shape of
the active site would change to fit with the
substrate.

Figure 1 demonstrates the

induced fit theory.
 Reference: en.Wikipedia,
author: TimVickers

Temperature

Because most enzyme reactions are

reversible, an enzyme can synthesize and
decompose molecules. Enzymes reaction
rate is dependable on several factors: pH,
temperature, and concentration of both the
enzyme and substrate. Generally, the rate
of enzyme reaction would increase as
temperature increase; however, if the
optimal temperature—usually around 40°C-
- is reached the enzyme would denatured
and loss its ability to react with the
substrate.

pH

Despite the fact that every enzymes has

their own optimal pH value, most enzyme
reactions have higher reaction rates
between pH value 6 - 9. The maximal
activity rate of enzyme reaction in human
body is around pH 7.2, with the exception
of pepsin, which has a high reaction rate
under acidic condition ( usually around pH
2), and pancreatic enzyme, which has a
high reaction rate under alkaline condition
( usually around pH 9)
Concentrations

Furthermore, concentrations of substrates

and enzymes affect the reaction rates as
well. The lower the concentration of
enzymes and substrates are the slower
the reactions, because less active sites on
enzymes are occupied. On the other hand,
higher concentration of enzymes and
substrate lead to the increase of reaction
rate as more active sites are occupied.
However, the reaction rate will no longer
increase once the reaction velocity of the
enzyme reaction reached a certain level.

Figure 2 shows the relationship between

concentration and reaction rate.
Reference: en.Wikipedia, author:
fullofstars
Enzyme Inhibitors There are two
categories of enzyme inhibitors: 1)
Reversible inhibitors and 2) irreversible
inhibitors. Reversible inhibitors are
kinetically distinguishable, and is
characterized by rapid dissociation of
enzyme-inhibitor complex.

There are three sub-categories in

reversible inhibitors: 1) Competitive 2)
Uncompetitive and 3) Non-competitive
Competitive inhibition

Although the active site of an enzyme is

highly specific, it is possible that
molecules with similar shape to the
substate to bind to the active site. Active
sites bounded to a molecule will interfere
with enzyme reaction. Therefore, the
possibility of substrates bind to active
sites are lower, thus, known as competitive
inhibition. However, competitive inhibition
happens only when similar about of
molecule and substrate are present. In
competitive inhibitors, enzymes can only
bind to either the substrate or inhibitor but
not both. In addition, during competitive
inhibition, concentration of substrate
increases as the maximum velocity
remains constant.

Figure 3 demonstrates how competitive

inhibition of enzymes work. Reference:
en.Wikipedia, Authored by Jerry Crimson
Mann, modified by TimVickers, vectorized
by Fvasconcellos
Uncompetitive inhibition In an
uncompetitive inhibition, inhibitor only
binds to enzyme-substrate complex. In
addition, in an uncompetitive inhibition,
both concentration of substrate and
maximum velocity decrease.

Noncompetitive inhibition

A noncompetitive inhibition reaction is

nonreversible due to the act that strong
covalent bonding, that cannot be
displaced by the addition of excess
substrate, between a molecule and a
enzyme. That molecule is also called a
noncompetitive inhibitor. In non-
competitive inhibition, inhibitor and
substrate can bind to enzyme
simultaneously at different binding sites.
Furthermore, it can bind free enzyme or
enzyme substrate complex. Also, during a
noncompetitive inhibition, concentration of
substrate will increase while maximum
velocity will decrease.

There are three sub-categories of

irreversible inhibitors: 1) group specific, 2)
reactive substrate analogs, 3) mechanism-
based inhibitors. Group Specific inhibitors
only react with specific side chains of
amino acid or with certain chemical
groups.
Reactive substrate analogs, also known as
affinity label. In reactive substrate analogs,
molecules that are structurally similar to
the substrate for an enzyme and that
covalently bind to active-site residue.

Mechanism-based inhibitors is also known

as suicide inhibitors. There are three steps
in the mechanism, the first one is
oxidation which is then followed by
alkylation and lastly by protonation.

Cofactors

Cofactors are needed for some catalytic

reactions. Cofactors can either be
inorganic elements (metals) or complex
organic molecules, in which many of them
are derived from vitamins. A holoenzyme
is a catalytically activated enzyme; while
an apoenzyme is an enzyme without
cofactor.

Gibbs Free Energy (ΔG)

Enzymes decrease activation energy.

Enzymes accelerates reactions by
lowering Gibbs free energy at transition
state, which is also known as the free
energy of activation. Gibbs free energy
also provides information about
spontaneity of a reaction.

Reaction is spontaneous if : ΔG<0

Reaction is not spontaneous if : ΔG > 0

Reaction is at equilibrium if : ΔG=0

This figure

shows the catalytic reaction of enzyme.

Reference: Wikipedia, author:
Fvasconcellos (talk · contribs).

To determine the total Gibbs free energy of

a reaction, take the summation of Gibbs
free energy of formation of products and
subtract the sum of Gibbs free energy of
formation of reactants from it. Another
important point regarding ΔG is that ΔG
does not explain the reaction rate of a
reaction.

Active Site

An active site of an enzyme is where

substrate bind to and is also where
chemical reaction take place. An active
site is a small part on a protein and is cleft,
or crevice. It also has a unique
microenvironment and substrates are bind
by several weak interactions. furthermore,
specificity of the enzyme depends on the
precise arrangement of atoms.

Biochemical Reactions

There are two main enzymatic reactions:

1) Sequential Reactions and 2) Double
Displacement Reaction

1) Sequential Reaction: In sequential

reactions, all substrates are bind to the
enzyme before any product is released. In
an ordered sequential reaction, substrates
bind to enzyme in a defined sequence;
while in a random sequential reaction,
substrates bind to enzyme in an undefined
sequence.

2) Double Displacement Reaction: In

double displacement reactions, one or
more products are released before all
substrates bind to the enzyme.

[1]

References
1. Kaplan PCAT 2010-2011 Edition

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