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Theory module: 07
INTRODUCTION TO ENZYME AND BASICS OF ENZYME ASSAY
OBJECTIVE: This section summarizes in simple terms the basic information on enzyme
and enzyme assay.
INTRODUCTION
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Cells function mainly because of the act of enzymes. Life is a dynamic process
that involves invariable changes in chemical composition. These changes are
regulated by catalytic reactions, which are regulated by enzymes.
Ideally, study of enzyme should be carried out within an intact cell, but this is
difficult to manage. Therefore, enzymes are studied in vitro after extraction from
cells.
WHAT IS AN ENZYME?
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Enzymes are the biocatalyst which alters the rate of reaction without undergoing
any permanent change in themselves.
Enzymes are simple or complex proteins, composed of chains of amino acids
linked together by peptide bonds, which are produced by all living cells.
All enzymes are protein but all proteins are not enzymes i.e. all enzymes are
made up of protein. Almost all enzymes are proteins, although some
catalytically active RNAs have been identified.
Enzymes are highly specific in their action and their activity can be regulated.
History of enzyme
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During Nineteen century, when investigating the fermentation of sugar to
alcohol by yeast, Louis Pasteur came to the conclusion that this fermentation was
catalyzed by a fundamental power contained within the yeast cells called
"ferments". He wrote that "alcoholic fermentation is an act correlated with the life
and organization of the yeast cells, not with the death or putrefaction of the
cells."
In 1878 German physiologist Wilhelm Kühne (1837–1900) coin the term enzyme
to describe this process. The word enzyme was used afterwards to refer to
nonliving substances such as pepsin, and the word ferment used to refer to
biochemical reaction produced by living organisms.
In 1897 Eduard Buchner found that the fermentation of sugar was observed even
in presence of non living yeast cells. He named the enzyme that bring the
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fermentation of sucrose as "zymase." In 1907 he was awarded with Nobel Prize in
Chemistry "for his biochemical research and his discovery of cell-free
fermentation".
James Sumner in 1926 demonstrate that the enzyme are protein in nature by
isolating urease in a pure form and crystallized it likewise Sumner did for the
enzyme catalase in 1937. The conclusion that pure proteins can be enzymes was
surely proved by Northrop and Stanley, by undertaking research on the enzymes
pepsin, trypsin and chymotrypsin. These three scientists were awarded the 1946
Nobel Prize in Chemistry.
This finding that enzymes can be crystallized in due course allowed their
structures to be solved by x-ray crystallography. This was first done for
lysozyme which digests the peptidoglycan layer of cell wall of bacteria. The
structure of lysozyme was revealed by a group led by David Chilton Phillips
and published in 1965. This marked the beginning of the field of structural
biology and the effort to understand how enzymes work at an atomic level of
detail.
WHAT IS ACTIVE SITE OF THE ENZYME?
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The active site of an enzyme is the area that binds to the substrate and transfer it
into product. It is generally a very small part of the enzyme molecule.
Active site is a 3D structure formed by amino acids which are being positioned
far apart in the polypeptide chain.
The active site is often a cleft or crevice on the surface of the enzyme that forms
mainly non polar surroundings which enhances the binding of the substrate.
The substrate is bound in the active site by multiple weak interactions like
electrostatic interactions, hydrogen bonds, van der Waals bonds, hydrophobic
interactions and in some cases by reversible covalent bonds.
ENZYME COMPONENTS
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Based on the composition, enzymes are classified in two groups.
1. Simple enzymes :This enzymes are made up of only proteins.On
hydrolysis they give only amino acids. Eg. Pepsin, chymotrypsin, trypsin
2. Holoenzyme or conjugated enzymes
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These enzymes consist of non-proteinic component along with the protienic
component. Such conjugated enzymes are known as Holoenzymes.
Holenzyme is dissociated in to protein component (Apoenzyme) and nonprotein component (cofactor).
Co-factor
o A cofactor is a non-protein chemical compound that is attached to a
protein and is necessary for the protein's action. Cofactors can be
considered as a "helper molecules" that assist in biochemical reactions.
o Cofactors are divided in to two groups (organic and inorganic).
o They can also be classified as
o Coenzymes: loosely-bound cofactors
o Prosthetic groups: tightly-bound cofactors
o Metal activators:
o There are few enzymes which require sevaral cofactors like, the
multienzyme complex pyruvate dehydrogenase need five organic
cofactors and one metal ion.
General properties of an enzyme
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Required in small quantity:
Remain unaltered at the end
Biological catalyst
Reversibility of enzyme action
Specificity
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1. Required in little amount :
 Since the enzyme is not consume in the reaction, only a small quantity of enzyme
is needed to bring a large amount of reaction product. In fact, the amount of a
single typical enzyme in a cell would be below the detection limits of even the
most sensitive protein assays.
 This is determined by the turnover reactions. The total number of products
produced by a given enzyme in a given time is called turnover
number. Different enzymes exhibit different turnover rates.
 Example: Substrate molecules transformed into products per enzyme/min/
a. Catalase 56,00,000
b. Amylase 11,00,000
c. Succinic dehydrogenase 1,150
2. Remains unchanged at the end: Enzymes remain unaltered at the end of a
reaction. Once the reaction is complete, enzymes are prepared for another
sequence of reactions.
3. Biological catalyst: They increase or accelerate the rate of reaction towards
equilibrium. Most biochemical reactions are so slow that they would not occur
under the cellular environment. Enzymes accelerate the rate of such reaction by
many-fold.
4. Reversibility of enzyme action: Majority of the enzymes are competent of bring
reversible reactions depend on the concentration of the reactant. If the
concentration of substrates is more than the concentration of products, the
enzyme favours forward reaction. On the contrary, if the concentration of
substrates is less than the concentration of products, the enzymes favour reverse
reactions. However, not all enzymes are capable of bringing about reversible
reactions and they exhibit unidirectional reactions.
5. Specificity: The catalytic activity of enzymes is highly specific in terms of their
substrates and the kind of reactions they bring about. Enzymes exhibits different
kind of specificity which are discussed as follows.
A. General Specificity: Enzymes like RNAase degrade RNA molecules of
every kind irrespective of their type. DNAases digest all kinds of DNA
molecules irrespective of their nucleotide sequences.
B. Absolute group specificity: Trypsin and pepsin are proteolytic enzymes, but
they cleave peptide bonds at specific amino acids, ex. Trypsin is specific to the
carboxyl side of arginine or lysine. Pepsin is specific to amino acids of
tyrosine or phenylalanine residue in the protein.
C. Stereo chemical specificity: There are enzymes which recognize only
specific isomers with either α or β or D or L forms. Such enzymes are called
stereo specific enzymes, which are capable of transforming one isomer to
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another or vice versa. The binding forces responsible for such an association
may be due to metal ions, hydrophobic interactions or ionic interactions.
Classification and Nomenclature of Enzymes
General principles
1. Suffix -ase, should be used only for single enzymes, i.e. single catalytic unit. It
should not be used to systems containing more than one enzyme. When it is
required to name such a system on the basis of the overall reaction catalysed by
it, the word system should be used in the name.
For example succinate dehydrogenase and succinate oxidase system.
2. Enzymes are mainly classified and named according to the reaction they
catalyse.
3. Enzymes are divided into groups on the basis of the type of reaction catalysed,
and this, together with the name(s) of the substrate(s) provides a basis for
naming individual enzymes. It is also the basis for classification and code
numbers.
4.
Common and Systematic Names :The Enzyme Commission recommended that
there should be two names for enzyme, one systematic and other trivial name.
The systematic name should be given in unity with definite rules which gives
idea of the action of an enzyme as accurately as possible. The trivial names are
generally short for common use.
5. Enzyme code number: Enzyme code numbers, prefixed by EC, consist of four
essentials/numbers broken up by points. First number indicates about class of
enzyme (1-6), The second numeral indicates the subclass, the third figure gives
the sub-subclass and the fourth numeral indicates the serial number of the
enzyme in its sub-subclass.
SIX CLASSES OF ENZYME:
Class 1. Oxidoreductases.
These enzymes catalysing oxidoreduction reactions. The substrate that is oxidized is
consider as hydrogen donor.( Systematic name: donor:acceptor oxidoreductase while
the trival name will be dehydrogenase or reducatase).
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Class 2. Transferases.
These enzymes will transfer a group, like a methyl group or a glycosyl group, from
one compound (donor) to another compound (acceptor). .( Systematic name:
donor:acceptor grouptransferase while the trival name will be acceptor grouptransferase
or donor grouptransferase).
X-Y + Z = X + Z-Y
Class 3. Hydrolases.
These enzymes carry out the hydrolytic cleavage of C-O, C-N, C-C and some other.
(Systematic name: includes hydrolase, the trival name is, in many cases, formed by
the name of the substrate with the suffix -ase. eg. protease esterase, glycosidases)
Class 4. Lyases.
Lyases are enzymes cleaving C-C, C-O, C-N, and other bonds by elimination,
leaving double bonds or rings, or conversely adding groups to double bonds. The
systematic name is formed according to the pattern substrate group-lyase.
Class 5. Isomerases.
These enzymes carry out structural changes within one molecule. Based on the type
of isomerism, they may be known as racemases, cis-trans-isomerases,
epimerases, isomerases, tautomerase or mutases
Class 6. Ligases.
Ligases will carry out the joining of two molecules coupled with the hydrolysis of a
ATP or a similar triphosphate. ( systematic name: X:Y ligase).
HOW ENZYME WORKS?
E + S---------> ES complex--------> Product + Enzyme
E=Enzyme
S=Substrate
ES=Enzyme substrate complex
P=Product
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ENZYME ASSAY
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Enzyme assays is used to measure the enzymatic activity. They are required to
study the enzyme kinetics. It has many applications in enzyme kinetics. It helps
in understanding the rates of reactions which assist in judging the kind of
reaction that enzyme follows. (single- or multiple-substrate mechanism).
Enzyme activity measures the amount of enzyme in a reaction. There are two
methods to measure enzyme activity: loss of substrate and formation of product.
Measuring the amount of product formed is more accurate because detecting
small changes in [P] (when [P]=0) is simple than detecting small changes in [S].
Through Michaelis-Menten Kinetics, Enzyme Assays are used to calculate Km,
Vmax, and Ki. Enzyme assays can also disclose information on the substrates
and inhibitors that may affect the enzyme.
In order to assay an enzyme, the overall equation of the reaction should
be known. An analytical technique must be on hand for determining either the
loss of substrate or the formation of product. Optimum conditions like
temperature, pH and requirement of cofactor should be known. Enzyme activity
being assayed is a measure of the enzyme activity present and is not limited by
an inadequate supply of substrate. If the substrate or product absorbs light of a
particular wavelength, then changes in the concentration of these molecules can
be measured by following the change of absorbance at this wavelength. This
is carried out using a spectrophotometer. Since absorbance is proportional to
concentration, the rate of change in absorbance is proportional to the rate of
enzyme activity in moles of substrate used (or product formed) per unit time.
Enzyme activity:
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The enzyme unit (U) is a unit for the amount of a particular enzyme. One unit of
enzyme is defined as the amount of the enzyme that catalyzes the conversion of
1 micro mole of substrate per minute. The enzyme unit was approved by the
International Union of Biochemistry. This is unit is depressed because the minute
is not an SI unit. Katal is favoured unit of the enzyme activity. It is recommended
by the General Conference on Weights and Measures in 1978 and officially
adopted in 1999. One katal equals to amount of enzyme which converts 1 mole
of substrate per second, so
1 U = 1/60 micro katal = 16.67 nano katal.
Specific activity:
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It is defined as the amount of substrate the enzyme converts (reactions catalyzed),
per mg protein in the enzyme preparation, per unit of time. It is a measure of
enzyme purity. The value becomes larger as an enzyme preparation becomes more
pure, since the amount of protein (mg) is typically less, but the rate of reaction stays
the same (or may increase due to reduced interference or removal of inhibitors).
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