NOTES ON ENZYMES
By
Syeda Tahira Fatima
Mukabbir university of science and technology
References:
Biochemistry by Satyanaryana Chakrapani 6th edition
Textbook of MEDICAL BIOCHEMISTRY by Chaterjee
ENZYMES
Definition:
Enzymes are biocatalysts – the catalysts of life.
A catalyst is defined as a substance that increases the velocity or rate of a chemical
reaction without itself undergoing any change in the overall process.
“Enzymes may be defined as biocatalysts synthesized by living cells. They are
protein in nature (exception – RNA acting as ribozyme), colloidal and
thermolabile in character, and specific in their action.”
Some RNAs can act like enzymes, usually catalyzing the cleavage and synthesis of
phosphodiester bonds. RNAs with catalytic activity are called ribozymes.
In the laboratory, hydrolysis of proteins by a strong acid at 100°C takes at least a
couple of days. The same protein is fully digested by the enzymes in gastrointestinal
tract at body temperature (37°C) within a couple of hours.
Enzymes are sometimes considered under two broad categories:
(a) Intracellular enzymes – They are functional within cells where they are
synthesized.
(b) Extracellular enzymes – These enzymes are active outside the cell; all the
digestive enzymes belong to this group.
Nomenclature and classification:
Each enzyme is assigned two names. The first is its short, recommended name,
convenient for everyday use. The second is the more complete systematic name,
which is used when an enzyme must be identified without ambiguity.
Recommended name:
Most commonly used enzyme names have the suffix “-ase” attached to the substrate
of the reaction (for example, glucosidase and urease) or to a description of the action
performed (for example, lactate dehydrogenase and adenylyl cyclase).
Note: Some enzymes retain their original trivial names, which give no hint of the
associated enzymic reaction, for example, trypsin and pepsin.
Systematic name :
In the systematic naming system, enzymes are divided into six major classes each
with numerous subgroups.
For a given enzyme, the suffix -ase is attached to a fairly complete description of the
chemical reaction catalyzed, including the names of all the substrates, for example,
lactate:NAD+ oxidoreductase.
1. Oxidoreductases : Enzymes involved in oxidation-reduction reactions. For
example; Alcohol dehydrogenase
2. Transferases : Enzymes that catalyse the transfer of functional groups. For
example; Hexokinase
3. Hydrolases: Enzymes that bring about hydrolysis of various compounds by
addition of water for example; lipase.
4. Lyases : Enzymes specialised in the addition or removal of water, ammonia,
CO2 etc. For example; Aldolase
5. Isomerases : Enzymes involved in all the isomerization reactions. For
example ;retinol isomerase
6. Ligases: Enzymes catalysing the synthetic reactions (Greek : ligate—to bind)
where two molecules are joined together and ATP is used. For example;
succinate thiokinase.
TRANSLOCASES: The group of enzymes catalyzing the transport of ions or
molecules across biological membranes does not fit into any one of the 6 classes of
enzymes, described above. For example: Ornithine translocase.
Structure of enzymes:
• Enzyme molecules contain a special pocket or cleft called as the active site.
ACTIVE SITE:
The active site (or active centre) of an enzyme represents as the small region at
which the substrate(s) binds and participates in the catalysis.
• Active sites generally occupy less than 5% of the total surface area of enzyme.
• Active site has a specific shape due to tertiary structure of protein.
• A change in the shape of protein affects the shape of active site and function
of the enzyme.
o Active site can be further divided into:
o Binding Site: It chooses the substrate and binds it to active site.
o Catalytic Site: It performs the catalytic action.
GENERAL CHARACTERISTICS OF ENZYMES:
Enzymes are well suited to their essential roles in living organisms in three
major ways:
1. They have enormous catalytic power,
2. They are highly specific in the reactions they catalyze, and
3. Their activity as catalysts can be regulated.
Catalytic Efficiency:
Enzymes are true catalysts that speed chemical reactions by lowering
activation energies and allowing reactions to achieve equilibrium more
rapidly.
They increase reaction rates by anywhere from 109 to 1020 times.
ACTIVATION ENERGY:
Minimum amount of energy required to start a reaction.
(Reactants) A+BC (Product)
This reaction needs energy to start. Different reactions have different energy of
activation; for example if some reaction requires minimum 100J of energy to start ,
it will not start with energy below 100J. Outside the body, mostly heat energy is
given to start a reaction.
Enzymes increase speed of reaction by decreasing the activation energy.
Specificity:
Enzymes are highly specific in their action. Specificity is a characteristic property
of the active site. There are three types of enzyme specifity:
1. Stereospecificity/optical specificity
2. Reaction specificity
3. Substrate specifity
STEREOSPECIFICITY:
Stereoisomers are the compounds which have the same molecular formula, but differ
in their structural configuration.
The enzymes act only on one isomer and, therefore, exhibit stereospecificity. e.g. L-
amino acid oxidase and D-amino acid oxidase act on L-and D-amino acids
respectively. Hexokinase acts on D-hexoses; glucokinase on D-glucose; amylase
acts on (α-glycosidic linkages; cellulase cleaves β-glycosidic bonds.)
The class of enzymes belonging to isomerases does not exhibit stereospecificity,
since they are specialized in the interconversion of isomers.
D-Amino acids are converted reversibly into its isomeric form, L-Amino acid in the
presence of Racemase.
REACTION SPECIFITY:
The same substrate can undergo different types of reactions, each catalysed by a
separate enzyme and this is referred to as reaction specificity. An amino acid can
undergo transamination, oxidative deamination, decarboxylation, racemization etc.
The enzymes however, are different for each of these reactions.
Transamination: If reaction is targeting transfer of amino group in the presence of
transaminase.
Decarboxylation : If reaction is targeting COO group in the presence of
decarboxylase.
Racemization: If amino is in D form, it can be brought into L form in the presence
of racemase.
SUBSTRATE SPECIFICITY:
It has three types:
1. Absolute specificity:
Certain enzymes act only on one substrate, for example glucokinase act only
on glucose and convert it into glucose 6 phosphate.
Similary, urease acts on urea and convert it into CO2 and NH2.
2. Relative specificity:
Some enzymes act on structurally related substrate. It is subdivided into group
specificity and bond specificity.
Group specificity:
Some enzymes act on COOH- group, some can act on NH2 group. Trypsin
will act on any group containing arginine or lysine.
Bond specificty:
Enzyme looks for specific bond to act on; for example glycosidase act on
those compounds which contain glycosidic bond.
Lipases act on ester bonds of lipids for example fatty acids form ester bond
with glycerol.
3. Broad specificity:
Enzymes act on closely related substrates.
Examples: Hexokinases can act on glucose, mannose, and fructose.
MECHANISM OF ENZYME ACTION:
About 100 years ago, Arrhenius suggested that catalysts speed up reactions
by combining with the substrate to form some kind of intermediate compound.
In an enzyme-catalyzed reaction, this intermediate is called the enzyme–
substrate (ES) complex.
The ES complex is formed when a substrate molecule binds to the active site
of an enzyme.
This binding occurs through hydrophobic interactions, hydrogen binding,
and/or ionic binding.
Once this complex is formed, the conversion of substrate (S) to product (P)
may take place:
General reaction:
The chemical transformation of the substrate occurs at the active site, usually
aided by enzyme functional groups that participate directly in the making and
breaking of chemical bonds.
After chemical conversion has occurred, the product is released from the
active site, and the enzyme is free for another round of catalysis.
To account for the high substrate specificity of most enzyme-catalyzed
reactions, a number of models have been proposed.
A. Lock-and-Key Model
B. Induced-Fit Model
Lock-and-Key Model:
According to the lock-and-key theory, enzyme surfaces will accommodate
only those substrates having specific shapes and sizes.
Thus, only specific substrates “fit” a given enzyme and can form complexes
with it, just as only the proper key can fit exactly into a lock and turn it open.
A limitation of the lock-and-key theory is the implication that enzyme
conformations are fixed or rigid.
Fig: In the lock-and-key model, the rigid enzyme and substrate have matching shapes
Induced-Fit Model:
Induced-fit model was introduced by an American biochemist, Daniel
Koshland.
Induced-fit model proposes that enzymes have somewhat flexible
conformations to accommodate incoming substrates.
The active site has a shape that becomes complementary to that of the
substrate only after the substrate is bound.
Fig: In the induced-fit model, the flexible enzyme changes shape to match the substrate.
