ENZYMES
CHEMISTRY
Introduction
Enzymes are biological catalysts that
speed up the rate of the biochemical
reaction.
Most enzymes are three dimensional
globular proteins (tertiary and
quaternary structure).
Some special RNA species also act as
enzymes and are called Ribozymes e.g.
hammerhead ribozyme.
Hammerhead
enzyme
STRUCTURE OF
ENZYMES
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
Catalytic
Binding Site
Site
It chooses the substrate It performs the
catalytic
and binds it to active site. action of
enzyme.
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:
+
Enzyme carbonic anhydrase requires
+
Zn for it’s
activity.
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 o A coenzyme is loosely
+
tightly bound organic bound organic co-factor.
co-factor e.g. Flavins, E.g. NAD+
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.
CHARACTERISTICS
Enzymes speed up the reaction by lowering the
activation energy of the reaction.
Their presence does not effect the nature and
properties of end product.
They are highly specific in their action that is each
enzyme can catalyze one kind of substrate.
Small amount of enzymes can accelerate chemical
reactions.
Enzymes are sensitive to change in pH, temperature
and substrate concentration.
Turnover number is defined as the number of
substrate molecules transformed per minute by one
enzyme molecule.
Catalase turnover number = 6 x106/min
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 :
maltose + maltase glucose +
water glucose
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
CLASSIFICA
TION
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
(redox) dehydrogenase
Transferases Move chemical Hexokinase
group
Hydrolases Hydrolysis; bond Lysozyme
cleavage with
transfer of
functional group of
water
Lysases Non-hydrolytic Fumarase
bond cleavage
Isomerases Intramolecular Triose phosphate
group transfer isomerase
(isomerization)
Ligases Synthesis of new RNA polymerase
covalent bond
between
substrates, using
MECHANISM OF
ENZYME
ACTION
MECHANISM OF ENZYME
ACTION
The catalytic efficiency of enzymes is explained by
two perspectives:
Thermodynamic Processes at the
changes active site
THERMODYNAMIC CHANGES
All chemical reactions have energy barriers between
reactants and products.
The difference in transitional state and substrate is
called activational barrier.
THERMODYNAMIC CHANGES
Only a few substances cross the activation barrier and
change into products.
That is why rate of uncatalyzed reactions is much
slow.
Enzymes provide an alternate pathway for conversion
of substrate into products.
Enzymes accelerate reaction rates by forming
transitional state having low activational energy.
Hence, the reaction rate is increased many folds in the
presence of enzymes.
The total energy of the system remains the same and
equilibrium state is not disturbed.
THERMO-DYNAMIC
CHANGES OVERVIEW
PROCESSES AT THE
ACTIVE SITE
Covalent
catalysis
Acid
base
Catalysis catalysis
by strain
Catalysis
by
proximit
y
COVALENT CATALYSIS
o Enzymes form covalent linkages with substrate
forming transient enzyme-substrate complex with
very low activation energy.
o Enzyme is released unaltered after completion of
reaction.
ACID-BASE CATALYSIS
Mostly undertaken by oxido- reductases enzyme.
Mostly at the active site, histdine is present which act
as both proton donor and proton acceptor.
CATALYSIS BY PROXIMITY
In this catalysis molecules must come in bond forming
distance.
When enzyme binds:
A region of high substrate concentration is produced
at active site.
This will orient substrate molecules especially in a
position ideal for them.
CATALYSIS BY BOND STRAIN
Mostly undertaken by lyases.
The enzyme-substrate binding causes reorientation of
the structure of site due to in a strain condition.
Thus transitional state is required and here bond is
unstable and eventually broken.
In this way bond between substrate is broken and
converted into products.
LOCK AND KEY MODEL
Proposed by EMIL FISCHER in 1894.
Lock and key hypothesis assumes the active site of an
enzymes are rigid in its shape.
There is no change in the active site before and after a
chemical reaction.
INDUCED FIT MODEL
More recent studies have revealed that the process is
much more likely to involve an induced fit
model(proposed by DANIAL KOSH LAND in 1958).
According to this exposure of an enzyme to substrate
cause a change in enzyme, which causes the active
site to change it’s shape to allow enzyme and
substrate to bind.
ENZYMES
KINETICS
INTRODUCTION
“It is a branch of biochemistry in which we study the
rate of enzyme catalyzed reactions.”
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.
ENZYMES LOWER THE ACTIVATION
ENERGY OF A REACTION
Energy levels of molecules
Activation
energy
Initial energy state Activation energy of uncatalysed
of substrates of enzyme catalysed reactions
reaction
Final energy state
of products
Progress of reaction (time)
KINETICS OF ENZYMES
CATALYSIS
Enzymes catalysis:
“ It is an increase in the rate of reaction with the
help of enzyme(as catalyst).”
Catalysis by enzymes that proceed via unique reaction
mechanism, typically occurs when the transition state
intermediate forms a covalent bond with the
enzyme(covalent catalysis).
During the process of catalysis enzymes always
emerge unchanged at the completion of the reaction.
FACTORS AFFECTING RATE OF
ENZYME CATALYZED REACTIONS
Temperature
Hydrogen ion concentration(pH)
Substrate concentration
EFFECT OF TEMPERATURE
Raising the temperature increases the rate of enzyme
catalyzed reaction by increasing kinetic energy of
reacting molecules.
Enzymes work maximum over a particular
temperature known as optimum temperature.
Enzymes for humans generally exhibit stability
temperature up to 35-45 ᵒC.
The temperature coefficient is a factor Q₁₀ by which
the rate of biological processes increases for a 10 ᵒC
increase in temperature.
For most biological processes Q₁₀ = 2.
However some times heat energy can also increase
kinetic energy to a point that exceed the energy
barrier which results in denaturing of enzymes.
5- 40oC Temperature
Increase in Activity
40oC - denatures
Rate of Reaction
0 10 20 30 40 50 60
<5oC - inactive
EFFECT OF PH
Rate of almost all enzymes catalyzed reactions
depends on pH
Most enzymes exhibit optimal activity at pH value
between 5 and 9
High or low pH value than optimum value will cause
ionization of enzyme which result in denaturation of
enzyme
MICHAELIS-MENTEN MODEL &
EFFECTS OF SUBSTRATE
CONCENTRATION
Michaelis-Menten Model:
“According to this model the enzyme reversibly combines
with substrate to form an ES complex that subsequently
yields product, regenerating the free enzyme.”
E + S k₁ ES k₂ E
+ P k₋₁
where:
S is the substrate
E is the enzyme
ES-is the enzyme substrate complex
P is the product
K1,K-1 and K2 are rate constants
MICHAELIS-MENTEN
EQUATION
Michaelis-Menten Equation:
“It is an equation which describes how reaction velocity
varies with substrate concentration.”
Vmax [S]
Vo=
Km+[S]
Where
Vo is the initial reaction velocity.
Vmax is the maximum velocity.
Km is the Michaelis constant = (k₋₁+k₂)/k₁.
[S] is the substrate concentration.
ASSUMPTIONS FOR MICHAELIS-
MENTEN EQUATION
Following assumptions are made in deriving the
Michaelis-Menten equation:
Relative concentrations of E and S.
Steady-State assumptions
Initial Velocity
SUBSTRATE
CONCENTRATION
SUBSTRATE CONCENTRATION
PHARMACEUTICAL
IMPORTANCE
Enzymes are virtually involved in all physiological
processes which makes them the targets of choice for
drugs that cure or ameliorate human disease.
Applied enzyme kinetics represents the principal tool
by which scientist identify and characterize
therapeutic agents that selectively inhibit the rates of
specific enzymes catalyzed processes.
Enzymes kinetics thus play a critical role in drug
discovery as well as elaborating the mode of action of
drugs.
INHIBITION
INHIBITION
o The prevention of an enzyme process as a result of
interaction of inhibitors with the enzyme.
INHIBITORS:
Any substance that can diminish the velocity
of an enzyme catalyzed reaction is called an inhibitor.
TYPES OF INHIBITION
Inhibition
Reversible Irreversible
Uncompetitiv Non-
Competitive Mixed
e competitive
REVERSIBLE INHIBITION
o It is an inhibition of enzyme activity in which the
inhibiting molecular entity can associate and
dissociate from the protein‘s binding site.
TYPES OF REVERSIBLE INHIBITION
o There are four types:
Competitive inhibition.
Uncompetitive inhibition.
Mixed inhibition.
Non-competitive inhibition.
COMPETITIVE INHIBITION
In this type of inhibition, the inhibitors compete with
the substrate for the active site. Formation of E.S
complex is reduced while a new E.I complex is formed.
EXAMPLES OF COMPETITIVE
INHIBITION
Statin Drug As Example Of Competitive
Inhibition:
Statin drugs such as lipitor compete with HMG-
CoA(substrate) and inhibit the active site of HMG CoA-
REDUCTASE (that bring about the catalysis of cholesterol
synthesis).
UNCOMPETITIVE INHIBITION
In this type of inhibition, inhibitor does not compete
with the substrate for the active site of enzyme
instead it binds to another site known as allosteric
site.
EXAMPLES OF
UNCOMPETITIVE
INHIBITION
Drugs to treat cases of poisoning by methanol or
ethylene glycol act as uncompetitive inhibitors.
Tetramethylene sulfoxide and 3- butylthiolene 1-oxide
are uncompetitive inhibitors of liver
alcohaldehydrogenase.
MIXED INHIBITION
o In this type of inhibition both E.I and E.S.I complexes
are formed.
o Both complexes are catalytically inactive.
NON COMPETITIVE INHIBITION
o It is a special case of inhibition.
o In this inhibitor has the same affinity for either
enzyme E or the E.S complex.
IRREVERSIBLE INHIBITION
This type of inhibition involves the covalent attachment of
the inhibitor to the enzyme.
The catalytic activity of enzyme is completely lost.
It can only be restored only by synthesizing molecules.
EXAMPLES OF IRREVERSIBLE
INHIBITION
Aspirin which targets and covalently modifies a key
enzyme involved in inflammation is an irreversible
inhibitor.
SUICIDE INHIBITION :
It is an unusual type of irreversible inhibition where
the enzyme converts the inhibitor into a reactive form
in its active site.
ACTIVATI
ON
ACTIVATION
Activation is defined as the conversion of an inactive
form of an enzyme to active form which processes the
metabolic activity.
TYPES OF ACTIVATION
Activation by co-factors.
Conversion of an enzyme precursor.
ACTIVATION BY CO
FACTORS
Many enzymes are activated by co-factors.
Examples:
DNA polymerase is a holoenzyme that catalyzes the
polymerization of de -oxyribonucleotide into a DNA
strand. It uses Mg- ion for catalytic activity.
Horse liver dehydrogenase uses Zn- ion for it’s
activation.
CONVERSION OF AN ENZYME
PRECURSOR
Specific proteolysis is a common method of activating
enzymes and other proteins in biological system.
Example:
The generation of trypsin from trypsinogen leads to
the activation of other zymogens.
ZYMOGEN ACTIVATION BY
PROTEOLYTIC CLEAVAGE
ENZYME
SPECIFICITY
ENZYME SPECIFICITY
Enzymes are highly specific in nature, interacting with
one or few substrates and catalyzing only one type of
chemical reaction.
Substrate specificity is due to complete fitting of
active site and substrate .
Example:
Oxydoreductase do not catalyze hydrolase reactions
and hydrolase do not catalyze reaction involving
oxidation and reduction.
TYPES OF ENZYME
SPECIFICITY
Enzymes show different degrees of specificity:
Bond specificity.
Group specificity.
Absolute specificity.
Optical or stereo-specificity.
Dual specificity.
BOND SPECIFICITY
In
this type, enzyme acts on substrates that are similar in structure
and contain the same type of bond.
Example :
Amylase
which acts on α-1-4 glycosidic ,bond in starch dextrin and
glycogen, shows bond specificity.
B- LIPASE that hydrolyzes ester bonds in different triglycerides
GROUP SPECIFICITY
In this type of specificity, the enzyme is specific not
only to the type of bond but also to the structure
surrounding it.
Example:
Pepsin is an endopeptidase enzyme, that hydrolyzes
central peptide bonds in which the amino group
belongs to aromatic amino acids e. g phenyl alanine,
tyrosine and tryptophan.
SUBSTRATE SPECIFICITY
In this type of specificity ,the enzymes acts only on
one substrate
Example :
Uricase ,which acts only on uric acid, shows substrate
specificity.
Maltase , which acts only on maltose, shows substrate
specificity.
OPTICAL / STEREO-SPECIFICITY
Inthis type of specificity , the enzyme is not specific to substrate but also to its optical configuration
Example:
D amino acid oxidase acts only on D amino acids.
L amino acid oxidase acts only on L amino acids.
in
DUAL SPECIFICITY
There are two types of dual specificity.
The enzyme may act on one substrate by two different
reaction types.
Example:
Isocitrate dehydrogenase enzyme acts on isocitrate
(one substrate) by oxidation followed by
decarboxylation(two different reaction types) .
DUAL SPECIFICITY
The enzyme may act on two substrates by one
reaction type
Example:
• Xanthine oxidase enzyme acts on xanthine and
hypoxanthine(two substrates) by oxidation (one
reaction type)
