Emzymology

Enzymology
•Enzymes are nature’s sustainable catalysts. They are biocompatible,

biodegradable and are derived from renewable resources.
•Enzymes constitute a large biological globular protein molecule responsible for

thousands of metabolic processes that sustain life, and function as catalysts to
facilitate specific chemical reactions within the cell. These reactions are essential
for the life of the organism. The living cell is the site of tremendous biochemical
activity called metabolism.
•This is the process of chemical and physical changes which go on continually in

the living organism; enzyme facilitate life processes in essentially all life-forms
from viruses to man.
Enzymology
•Enzymes have been naturally tailored to perform under different physiological
conditions.
1. Build-up of new tissues

2. Replacement of old tissues
3. Conversion of food into energy
4. Disposal of toxic materials
5. Reproduction
6. Almost all the activities that can be characterized as “life.”
History of evolution of enzymes
•The existence of enzymes has been known for well over a century. Biological
catalysis was first recognized and described in the early 1800s, in studies of the
digestion of meat by secretions of the stomach and the conversion of starch into
sugar by saliva and various plant extracts
•In 1835, Swedish chemist Jon Jakob Berzelius termed their chemical action as
catalytic in nature
•In 1860 Louis Pasteur recognized that enzymes were essential to fermentation
but assumed that their catalytic action was inextricably linked with the structure
and life of the yeast cell
•Not until 1897 was it shown by German chemist Edward Buchner that cell-free
extracts of yeast could ferment sugars to alcohol and carbon dioxide, Buchner
denoted his preparation as zymase
•The term enzyme comes from zymosis, the Greek word for fermentation, a
process accomplished by yeast cells and long known to the brewing industry
•In 1876, William Kuhne proposed that the name 'enzyme' be used as the new
term to denote phenomena previously known as 'unorganised ferments', that
is, ferments isolated from the viable organisms in which they were formed.
Jon Jakob Berzelius Louis Pasteur
Edward Buchner William Kuhne

Nomenclature and classification of enzymes
The nomenclature committee of the “International Union of Biochemistry and

Molecular Biology “(IUBMB) adopted rules in 1992 for the systematic classification and
designation of enzymes based on reaction specificity.
In general many enzymes have been named by adding the suffix “-ase” to the name of
their substrate or to a word or phrase describing their activity. In 1961, according to
the report of the first Enzyme Commission (EC) of International Union of Pure and
Applied Chemistry (IUPAC), Enzymes are classified in to six types on the basis of
reaction they catalyze . They were assigned code numbers, prefixed by E.C., which
contain four elements separated by points and have the following meaning as shown
in the below figure.
Naming of enzyme according to ‘International Union of Biochemistry’

Classification of enzymes
All enzymes are classified into six major classes according to the
nature of the chemical reaction catalyzed:
1. Oxidoreductases
2. Transferases
3. Hydrolases
4. Lyases
5. Isomerases
6. Ligases
Types Reaction type Biochemical Property
These catalyze oxidation and reduction

Oxidoreductases reactions, e.g. pyruvate dehydrogenase,
catalysing the oxidation of pyruvate to
acetyl coenzyme A.
These catalyze transferring of the chemical

Transferase group from one to another compound. An
s example is a transaminase, which transfers an
amino group from one molecule to another.
They catalyze the hydrolysis of a bond. For
Hydrolases example, the enzyme pepsin hydrolyzes
peptide bonds in proteins.
These catalyze the breakage of bonds without

catalysis, e.g. aldolase (an enzyme in glycolysis)
Lyases catalyzes the splitting of fructose-1, 6-
bisphosphate to glyceraldehyde-3-phosphate
and dihydroxyacetone phosphate.
They catalyze the formation of an isomer of a
compound. Example: phosphoglucomutase
catalyzes the conversion of glucose-1-
Isomerases phosphate to glucose-6-phosphate (phosphate
group is transferred from one to another
position in the same compound) in
glycogenolysis (glycogen is converted to
glucose for energy to be released quickly).
Ligases catalyze the association of two
Ligases molecules. For example, DNA ligase catalyzes
the joining of two fragments of DNA by
forming a phosphodiester bond.
Specificity of enzymes
Enzymes are the most remarkable and highly specialized proteins, they have a high degree of
specificity for their substrates, and they accelerate chemical reactions tremendously. In general,
four types of behavior can be described:
1. Absolute specificity - Catalyze only one reaction.

Example: lactase is an enzyme specific for the degradation of lactose into two sugar
monosaccharide's, glucose and galactose.
2. Group specificity – catalyses a particular type of functional group, which can occur in a
variety of substrate.
Example: Pepsin, an enzyme that is crucial in digestion of foods ingested in our diet, that
hydrolyzes peptide bonds in between hydrophobic amino acids, with recognition for
aromatic side chains such as phenylalanine, tryptophan, and tyrosine.
3. Linkage specificity - Catalyses a particular type of chemical bond regardless of the rest of the
molecular structure.
Example: α-amylase enzyme can hydrolyze α-1-4 glycosidic linkage in starch and glycogen,
i.e., the enzyme is specific only to α-1-4 glycosidic bond and not to the substrate.
4. Stereo chemical specificity - the enzyme will act on a particular steric or optical isomer.
Example: D-Lactate Dehydogenase complexed with D-lactic acid.
The important terminologies related to enzymes are:
• Cofactor: A non-protein chemical component required for proteins biological
activity are called co-factor.
• Apoenzyme: The protein part of an enzyme without the cofactor necessary for
catalysis. The cofactor can be a metal ion, an organic molecule (coenzyme), or a
combination of both.
• Holoenzyme: the active enzyme composed of Apoenzyme and a co-factor is

termed as holoenzyme.
• Coenzyme: coenzyme is a non –protein compound or substance that is

necessary for an enzyme to initiate the function of the enzyme.
• Prosthetic group: A coenzyme or metal ion that is very tightly or even

covalently bound to the protein component of the enzyme is called a prosthetic
group.
Active Site
•It is the site where substrate molecule bind for the chemical reaction.
•It is generally found on the surface of the enzyme and in some enzymes it is a
pit like structure.
•The active site is the 3 dimensional cleft
formed by the groups that come from different
parts of the amino acid sequences.
•Substrates are bound to enzymes by multiple
weak interactions.
Binding site: Active site

Form the 4 types of bond with the substrate:
1. Electostatic bond
2. Hydrogen bond
3. Van der waals forces
4. Non-covalent bond
Models for active site of the enzyme
Lock and key model Induced fit model

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Enzymology

•Enzymes are nature’s sustainable catalysts. They are biocompatible,

•Enzymes constitute a large biological globular protein molecule responsible for

•This is the process of chemical and physical changes which go on continually in

1. Build-up of new tissues

Edward Buchner William Kuhne

The nomenclature committee of the “International Union of Biochemistry and

Naming of enzyme according to ‘International Union of Biochemistry’

These catalyze oxidation and reduction

These catalyze transferring of the chemical

These catalyze the breakage of bonds without

1. Absolute specificity - Catalyze only one reaction.

• Holoenzyme: the active enzyme composed of Apoenzyme and a co-factor is

• Coenzyme: coenzyme is a non –protein compound or substance that is

• Prosthetic group: A coenzyme or metal ion that is very tightly or even

Binding site: Active site

Lock and key model Induced fit model

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