Enzyme

AYESHA SHAFI
Pharm-D, (P.U.), M. Phil.
Pharmaceutical chemistry (P.U.)
 Contents
• Introduction
• Chemistry
• Structure of enzyme
• Sites of enzyme synthesis
• Nomenclature
• Classification
 Introduction
• Enzymes are biological catalysts that speed up
the rate of the biochemical reaction.
• A catalyst is an agent which in minute amount
increases the velocity of the chemical reactions
without itself being destroyed or altered upon
completion of a reaction.
• The word enzyme came from Greek(en=in,
zyme =leaven meaning ferment).
• Some special RNA species also act as enzymes
and are called Ribozymes e.g. hammerhead
ribozyme.

Hammerhead enzyme
 Introduction
• Most enzymes are three dimensional globular
proteins (tertiary and quaternary structure).
• It should be cleared that enzymes only accelerate
the rate of chemical reactions, but do not initiate
them.
• Reactions can even be take place without the
enzyme but the rate of reaction will be
extremely low.
CHEMISTRY
 Structure of Enzymes
• Enzyme molecule contain a special pocket or cleft called as the active site .
• The active site of an enzyme is the region that binds substrates, co-factors
and prosthetic groups and contains residue that helps to hold the
substrate.

• 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.
 Active site
o Active site can be further divided into:
Active Site

Binding Site Catalytic Site

It chooses the substrate It performs the

and binds it to active site . Catalytic action

 Co-factors
o Co-factor is the non protein molecule which carries out chemical
reactions that can not be performed by standard 20 amino acids.

o Co-factors are of two types:

 Organic co-factors
 Inorganic cofactors
 Inorganic co-factors
o These are the inorganic molecules required for the proper activity
of enzymes.
Examples:
 ++ activity.
Enzyme carbonic anhydrase requires Zn for it’s
 Hexokinase has co-factor Mg
++

ORGANIC CO-FACTORS
o These are the organic molecules required for the proper activity of
enzymes.
Example:
 Glycogen phosphorylase requires the small organic molecule
pyridoxal phosphate.
 Types of Organic co-factors

Prosthetic Group Coenzyme

o A prosthetic group is a tightly o A coenzyme is loosely bound
bound organic co-factor e.g. organic co-factor. E.g. NAD+
Flavins, heme groups and biotin. +
 Types of co-factors Continued…

• An enzyme with it’s co-factor removed is designated as

apoenzyme.

• The complete complex of a protein with all necessary small organic

molecules, metal ions and other components is termed as
holoenzyme of holoprotein.
 substrate

• The reactant in biochemical reaction is termed as substrate.

• When a substrate binds to an enzyme it forms an enzyme-substrate

complex.

Substrate Joins Enzyme

 Sites of enzyme synthesis
o Enzymes are synthesized by ribosomes which are attached to the rough
endoplasmic reticulum.

o Information for the synthesis of enzyme is carried by DNA.

o Amino acids are bonded together to form specific enzyme according to

the DNA’s codes.
 Intracellular and extracellular
enzymes
o Intracellular enzymes are synthesized and retained in the cell for the use
of cell itself.
o They are found in the cytoplasm, nucleus, mitochondria and chloroplast.
Example :
 Oxydoreductase catalyses biological oxidation.
 Enzymes involved in reduction in the mitochondria.

o Extracellular enzymes are synthesized in the cell but secreted from the cell
to work externally.
Example :
 Digestive enzyme produced by the pancreas, are not used by the cells in
the pancreas but are transported to the duodenum.
 Nomenclature of enzymes
o An enzyme is named according to the name of the substrate it catalyses.
o Some enzymes were named before a systematic way of naming enzyme
was formed.
Example: pepsin, trypsin and rennin
o By adding suffix -ase at the end of the name of the substrate, enzymes
are named.
o Enzyme for catalyzing the hydrolysis is termed as hydrolase.
Example :

maltase
maltose + water glucose + glucose
 Nomenclature (continue)
• Few enzymes exist in their inactive forms and
are called as proenzymes or zymogens, e.g.
pepsin has pepsinogen as its zymogen.
• Autocatalysis: The zymogens become active
after undergoing some prior modification in its
structure by certain agents. Many times the
active form of enzyme acts on zymogen and
catalyses its conversion into active form and
this process is called as autocatalysis.
 Examples
substrate enzymes products
lactose lactase glucose + galactose
maltose maltase Glucose
cellulose cellulase Glucose
lipid lipase Glycerol + fatty acid
starch amylase Maltose
protein protease Peptides + polypeptide
CLASSIFICATIO
N
 Classification of enzymes
• A systematic classification of enzymes has been developed by
International Enzyme Commission.

• This classification is based on the type of reactions catalyzed by enzymes.

• There are six major classes.

• Each class is further divided into sub classes, sub sub-classes and so on, to
describe the huge number of different enzyme-catalyzed reactions.
 Classification of enzymes Continued……..

ENZYME CLASS REACTION TYPE EXAMPLES

Oxidoreductases Reduction-oxidation Lactate dehydrogenase
(redox)
Transferases Move chemical group Hexokinase
Hydrolases Hydrolysis; bond Lysozyme
cleavage with transfer of
functional group of
water
Lyases Non-hydrolytic bond Fumarase
cleavage
Isomerases Intramolecular group Triose phosphate
transfer (isomerization) isomerase
Ligases Synthesis of new RNA polymerase
covalent bond between
substrates, using ATP
hydrolysis
 Classification of enzymes
1. Oxido reductase: Enzymes involved in oxidations and
reductions of their substrates, e.g. alcohol
dehydrogenase, lactate dehydrogenase, xanthine
oxidase, glutathione reductase, glucose-6-phosphate
dehydrogenase etc.
2. Transferases: Enzymes that catalyze transfer of a
particular group from one substrate to another, e.g.
aspartate and alanine transaminase (AST/ALT),
hexokinase, phosphoglucomutase, hexose-1-phosphate
uridyltransferase, ornithine carbamoyl transferase, etc.
 Classification of enzymes
• Hydrolases: Enzymes that bring about hydrolysis,
e.g. glucose-6-phosphatase, pepsin, trypsin,
esterases, glycoside hydrolases, etc.
• 4. Lyases: Enzymes that facilitate removal of small
molecule from a large substrate, e.g. fumarase,
arginosuccinase, histidine decarboxylase.
• 5. Isomerases: Enzymes involved in isomerisation of
substrate, e.g. UDP-glucose, epimerase, retinal
isomerase, racemases, triosephosphate isomerase.
 Classification of enzymes
• Ligases: Enzymes involved in joining together
two substrates, e.g. alanyl-t. RNA synthetase,
glutamine synthetase, DNA ligases.
• Many times the word ‘OTHLIL’ is used to
remember the six classes.
 Properties of enzymes
a. Specificity: enzymes are highly specific in their action. The specificity is of three
different types namely:
• 1. Stereo-chemical specificity There can be many optical isomers of a substrate.
For example, for the oxidation of D- and L-amino acids, there are two types of
enzyme which will act on D- and L-isomers of amino acid.
• 2. Reaction specificity A substrate can undergo many reactions but in a reaction
specificity one enzyme can catalyse only one of the various reactions. For
example, oxaloacetic acid can undergo several reactions but each reaction is
catalyzed by its own separate enzyme which catalyses only that reaction and none
of the others.
• 3. Substrate specificity. There are two types of substrate specificity absolute
specificity (enzyme will act on one type of substrate)and relative specificity
(enzyme act on more than one type of substrate). e.g. hexokinase catalyze the
conversion of hexoses like glucose, fructose and mannose to their 6-phosphate
derivatives but glucokinase is specific for the glucose only.
 Properties (continue)
b. Protein nature: all enzymes are the proteins, therefore
they are colloids , heat labile and have isoelectric PH values.
On denaturation they lose their catalytic activity. They are
produced by living cell but may act in-vivo and in-vitro.
c. Catalytic efficiency: Most enzyme catalyzed reactions are
highly efficient,proceeding from 103-108 times faster than
unanalyzed reactions. Typically each enzyme molecule is
capable of transforming 100-1000 substrate molecules into
product each second. The number of molecules of substrate
converted into product per enzyme molecule per second is
called as the turnover number.
 Properties( continue)
d. Regulation: Enzyme activity can be regulated ,
that is, enzymes can be activated or inhibited ,
so that the rate of product formation responds
to the needs of the cell.
e. Location within the cell: Many enzymes are
localized in specific organelles within the cell.
Enzymes are present in random way within the
cell but in many cases occur within a certain
intracellular compartment.
 Mechanism of enzyme action
• Michaelis and Menten have proposed a hypothesis
for enzyme action, which is most acceptable.
According to their hypothesis, the enzyme molecule
(E) first combines with a substrate molecule (S) to
form an enzyme substrate (ES) complex which
further dissociates to form product (P) and enzyme
(E) back. Enzyme once dissociated from the complex
is free to combine with another molecule of
substrate and form product in a similar way.
E + S ES E + P
 Mechanism of action (continue)
• The ES complex is an intermediate or transient complex and the bonds
involved are weak non-covalent bonds, such as H-bonds, Van der Waals
forces, hydrophobic interactions.
• Bi substrate reaction: Sometimes two substrates can bind to an enzyme
molecule and such reactions are called as bi substrate reactions.
• Catalytic site: The site to which a substrate can bind to the enzyme molecule
is extremely specific and is called as active site or catalytic site. The active
site is made up of several amino acid residues that come together as a result
of folding of secondary and tertiary structures of the enzyme. So, the active
site possesses a complex three dimensional form and shape, provides a
predominantly non-polar cleft or crevice to accept and bind the substrate.
Few groups of active site amino acids are bound to substrate while few
groups bring about change in the substrate molecule.
 Models of enzyme substrate complex
• Two models are described to explain the enzyme
substrate complex interaction.
Template or lock and key model:
• This model was originally proposed by Fischer.
• Substrate fits into active site of an enzyme as the key
fits into the lock and hence it is called the lock-and-
key model.
 Models (continue)
• The active site already exists in proper conformation
even in absence of substrate. Thus the active site by
itself provides a rigid, pre-shaped template fitting
with the size and shape of the substrate molecule.
• This model proposes that substrate binds with rigid
pre-existing template of the active site, provides
additional groups for binding other ligands.
 Induce fit model
• Another model was proposed by Koshland in 1963 which is
known as induced-fit model.
• According to this, active site does not possess a rigid,
preformed structure on enzyme to fit the substrate. On the
contrary, the substrate during its binding induces
conformational changes in the active site to attain the final
catalytic shape and form . And after the release of product, the
active site returns to its original shape.
This explains several matters related to enzyme action such as:
• Enzymes become inactive on denaturation,
• Saturation kinetics,
• Competitive inhibition, and • Allosteric modulation.
Induce fit model(continue)
 Reaction kinetics
• Kinetic analysis reveals the number and order of the
individual steps by which enzymes transform
substrate into products.
• Studying an enzyme's kinetics in this way can reveal
the catalytic mechanism of that enzyme, its role
in metabolism, how its activity is controlled, and how
a drug or an agonist might inhibit the enzyme
 Rates of reaction and their dependence on
activation energy
• Activation Energy (Ea):
“The least amount of energy needed for a chemical reaction to take place.”
• Enzyme (as a catalyst) acts on substrate in such a way that they lower the
activation energy by changing the route of the reaction.
• The reduction of activation energy (Ea) increases the amount of reactant
molecules that achieve a sufficient level of energy, so that they reach the
activation energy and form the product.
Example:
• Carbonic anhydrase catalyses the hydration of 10⁶ CO₂ molecules per
second which is 10⁷x faster than spontaneous hydration.