Enzymes

Biological Catalysts

Definition
Enzymes are the biological catalysts ; which
accelerate the rate of biochemical reactions. Like
catalysts,the enzymes regulate the speed and
specificity of reactions without being used up
but unlike catalysts they are produced by the
living cells only.

Nomenclature
Enzymes are classified according the report of
a Nomenclature Committee appointed by the
International Union of Biochemistry (1984).
6 main groups.

NAMING
NAMING IS EASY COMPARED TO
OTHER COMPOUNDS.
NAME IS BASED ON:
WHAT IT REACTS WITH
HOW IT REACTS
ADD ase IN THE END

OXIDOREDUCTASES
CATALYZE REDOX REACTIONS
SOME COMMON TYPES:

REDUCTASES
DEHYDROGENASES
OXIDASES
OXYGENASES

LOOK FOR INVOLVEMENT OF COENZYMES

NAD+ , NADP+, FAD, FMN

TRANSFERASES
TRANSFER OF FUNCTIONAL GROUPS
SOME EXAMPLES:
TRANSFERASES
PHOSPHORYLASES
KINASES
A PHOSPHATE TRANSFER
UTILIZE OR GENERATE ATP

HYDROLASES
HYDROLYSIS REACTIONS
WATER MOLECULES USED TO BREAK
BONDS
EXAMPLES:

PHOSPHATASES
PEPTIDASES
ATPase, GTPase
Example: Peptidase hydrolyzes a peptide bond

LYASES
CATALYZES REACTIONS THAT
GENERATE A DOUBLE BOND
ADDS A SUBSTRATE MOLECULE TO
DOUBLE BOND OF A SECOND SUBSTRATE

EXAMPLES:
DECARBOXYLASES
DEHYDRATASES
ALDOLASE

ISOMERASES
CONVERSION OF ONE ISOMERIC FORM INTO
ANOTHER
EXAMPLES:

ISOMERASES
EPIMERASES
RACEMASES
MUTASES

LIGASES
TWO MOLECULES ARE JOINED
ANABOLIC REACTIONS
REQUIRE NUCLEOTIDES (ATP, GTP) TO DRIVE
THEM
A PYROPHOSPHATE BOND MUST BE BROKEN

EXAMPLES:
CARBOXYLASE
SYNTHETASES

The mechanism of enzyme

catalysis
In order for a reaction to occur, reactant
molecules must contain sufficient energy to
cross a potential energy barrier, the
activation energy. The lower the potential
energy barrier to reaction, the more reactants
have sufficient energy and, hence, the faster
the reaction will occur.

How enzymes work

Binding of a substrate to an enzyme

at the active site

Enzyme catalyzed reaction

Catalyst: substance that increases rate of chemical
reaction without itself being consumed
Lowers activation energy necessary to induce reaction

Enzymes: Protein catalysts

Control almost all important biological reactions

The Active Site of an Enzyme

1. The active site is the region that binds the substrates (&
cofactors if any)
2. It contains the residues that directly participate in the making &
breaking of bonds (these residues are called catalytic groups)

3. The interaction of the enzyme and substrate at the active site

promotes the formation of the transition state
4. The active site is the region that most directly lowers G of the
reaction - resulting in rate enhancement of the reaction

The Nature of Enzyme Catalysis

Enzyme provides a catalytic surface

This surface stabilizes transition state
Transformed transition state to product
B
A
A

Catalytic surface
Juang RH (2004) BCbasics

Active Site Is a Deep Buried Pocket

Why energy required to reach transition state

is lower in the active site?

It is a magic pocket

+
CoE (1)
(4)

(3)

(2)

(1) Stabilizes transition

(2) Expels water
(3) Reactive groups
(4) Coenzyme helps
Juang RH (2004) BCbasics

Active site
of
chymotrypsin

Active sites - distant residues

Enzyme Inhibition (Mechanism)

Equation and Description

Cartoon Guide

Competitive

Non-competitive

Substrate

E
I

Compete for
Inhibitor active site

Uncompetitive

E
I

Different site

E + S
ES E + P
+
I

EI

E + S
ES E + P
+
+
I
I

EI + S EIS

[I] binds to free [E] only,

and competes with [S];
increasing [S] overcomes
Inhibition by [I].

[I] binds to free [E] or [ES]

complex; Increasing [S] can
not overcome [I] inhibition.

E + S
ES E + P
+
I

EIS
[I] binds to [ES] complex
only, increasing [S] favors
the inhibition by [I].
Juang RH (2004) BCbasics

Enzyme inhibition

Specificity
Enzymes are usually specific as to the
reactions they catalyze and the substrates that
are involved in these reactions. Shape and
charge complementarity of enzyme and
substrate are responsible for this specificity.

Enzyme catalyzed reaction

Lock and key hypothesis: Enzyme specificity is
associated with unique active site
Proposed by Emil Fisher
Tight fit between enzyme and substrate

E+S

ES

+P

Substrate

Products

Active site

Enzyme

Enzyme-substrate
complex
Recycle

Enzyme

 LOCK AND KEY HYPOTHESIS

1. Lock and key hypothesis

Enzymes are very specific and it was
suggested by Emil Fischer in 1890 that this
was because the enzyme had a particular
shape into which the substrate(s) fit exactly.
This is often referred to as "the lock and
key" hypothesis. An enzyme combines with
its substrate(s) to form a short lived
enzyme-substrate complex.

Lock-and-key model

2. Induced fit hypothesis

In 1958 Daniel Koshland suggested a modification
to the "lock and key" hypothesis. Enzymes are
rather flexible structures. The active site of an
enzyme could be modified as the substrate
interacts with the enzyme.

Induced-fit model

A Few Definitions
Cofactor additional chemical component needed for catalysis.
- often an inorganic metal ion (mineral).

Coenzyme complex organic molecule needed for catalysis.

- often a vitamin.
Prosthetic group non amino acid portion of the enzyme
needed for catalysis. Often a coenzyme or metal ion.
Holoenzyme complete catalytically active enzyme, with all
necessary prosthetic groups.
Apoenzyme The protein part of the holoenzyme.
Prosthetic groups are absent.

Some enzymes utilize cofactors for catalysis

Turnover numbers vary widely

Temperature
Temperature has two effects on enzymes.
Changes the rate of molecular motion
Increasing temperature increases molecular motion.
Increases the rate of catalysis

Optimum temperature-the temperature at which the enzyme has the

highest rate of catalysis.
Decreasing temperature decreases molecular movement.
Decreases the rate of catalysis

Causes changes in the shape of an enzyme

Temperature changes above optimum will denature the enzyme.
This changes its shape, and it can no longer bind substrate and
catalyze the reaction.
This is why a high fever is potentially dangerous.
5-35

Temperature
Factors affecting enzymes activity

pH
pH

Gene Regulation
Enzymes are proteins.
Protein production is controlled by genes.

Certain chemicals in the cell turn particular

enzyme-producing genes on or off
depending on the situation.
Called gene-regulator proteins

5-38

Those that decrease the amount of an enzyme made

are called gene-repressor proteins.
Those that increase the amount of an enzyme made
are called gene-activator protein.

Biochemical Pathways
A series of enzyme-catalyzed reactions
Also called metabolic pathways
Catabolism-the breakdown of compounds
Anabolism-the synthesis of new, larger compounds

Examples: photosynthesis, respiration, protein synthesis, etc.

5-39

Negative-Feedback Inhibition
As the end-product of the sequence accumulates,

Those molecules feedback and bind to an

enzyme early in the sequence.
They inhibit that enzyme, and stop the
sequence.
This decreases the amount of end-product
made.
This functions to keep levels of the end-product within a
certain range.
5-40

Products of a reaction pathway

often are feedback inhibitors
of an enzyme within the pathway.
Example:
Threonine is converted to isoleucine.
The product, isoleucine, feedback
inhibits the enzyme threonine dehydratase.