BIOPHYSICS
Unit – I
Section - B
1. Explain the Classification of enzymes.
Oxidoreductases. Oxidation-reduction reactions are very common in biochemical
pathways and are catalyzed by a broad class of enzymes called oxidoreductases.
Enzymes participating in reactions with O2 are called hydroxylases and oxidases when one
oxygen atom is incorporated into a substrate and the other oxygen atom into water, or both
atoms are incorporated into water. They are called oxygenases when both atoms of oxygen are
incorporated into the acceptor.
Transferases. Transferases catalyze group transfer reactions—the transfer of a
functional group from one molecule to another. Enzymes catalyzing this last type of reaction are
called transaminases or aminotransferases. When the physiologically important aspect of the
reaction is the compound synthesized,
the transferase may be called a synthase.
Hydrolases. In hydrolysis reactions, C-O, C-N, or C-S bonds are cleaved by the addition of
H2O in the form of OH_ and H_ to the atoms forming the bond
Lyases. The lyase class of enzymes consists of a diverse group of enzymes cleaving C-C,
C-O, and C-N bonds by means other than hydrolysis or oxidation. Some of the enzymes
catalyzing C-C bond cleavage are called aldolases, decarboxylases (when carbon dioxide is
released from a substrate), and thiolases (when the sulfur-containing nucleophile of cysteine or
CoASH is used to break a carbon-carbon bond) This broad class of enzymes also includes
dehydratases and many synthases. Dehydratases remove the elements of water from two
adjacent carbon–carbon bonds to form a double bond.
Isomerases. Many biochemical reactions simply rearrange the existing atoms of a
molecule, that is, create isomers of the starting material enzymes catalyzing movement of a
phosphate from one atom to another are called mutases.
Ligases. Ligases synthesize C-C, C-S, C-O, and C-N bonds in reactions coupled to the
cleavage of a high-energy phosphate bond in ATP or another nucleotide. Carboxylases, for
example, add CO2 to another compound in a reaction requiring ATP cleavage to provide energy
(see Fig. 8.12B). Most carboxylases require the coenzyme biotin. Other ligases are named
synthetases (e.g., fatty acyl CoA synthetase). Synthetases differ from the synthases mentioned
under “lyases” and “group transferases”
2. Define Active Site.
To catalyze a chemical reaction, the enzyme forms an enzyme–substrate
complex in its active catalytic site (Fig. 8.4). The active site is usually a cleft or crevice in the
enzyme formed by one or more regions of the polypeptide chain. Within the active
site, cofactors and functional groups from the polypeptide chain participate in transforming the
bound substrate molecules into products
3. Write a note on Lock and Key Mechanism
4. Write about Induced fit theory.
5. Explain the Mechanism of enzyme catalysis
Enzymes, in general, provide speed, specificity, and regulatory control to reactions
in the body. Enzymes are usually proteins that act as catalysts, compounds that increase the rate
of chemical reactions. Enzyme-catalyzed reactions have three basic steps:
(1) binding of substrate
(2) conversion of bound substrate to bound product
(3) release of product
An enzyme binds the substrates of the reaction it catalyzes and brings them together at the right
orientation to react. The enzyme then participates in the making and breaking of bonds required
for product formation, releases the products, and returns to its original state once the reaction
is completed.
Enzymes do not invent new reactions; they simply make reactions occur faster. The catalytic
power of an enzyme (the rate of the catalyzed reaction divided by the rate of the uncatalyzed
reaction) is usually in the range of 106 to 1014. Without the catalytic power of enzymes,
reactions such as those involved in nerve conduction, heart contraction, and digestion of food
would occur too slowly for life to exist. Each enzyme usually catalyzes a specific biochemical
reaction. The ability of an enzyme to select just one substrate and distinguish this substrate
from a group of very similar compounds is referred to as specificity
6. Explain Lysozyme mechanism:
7. Write a note on Negative and Positive Co-operativity:
SECTION - C
8. Explain MM Kinetics.
The equations of enzyme kinetics provide a quantitative way of describing the
dependence
of enzyme rate on substrate concentration. The simplest of these equations, the
Michaelis-Menten equation, relates the initial velocity (vi) to the concentration of substrate
[S] and the two parameters Km and Vmax (Equation 9.1) The Vmax of the enzyme
is the maximal velocity that can be achieved at an infinite concentration of substrate,
and the Km of the enzyme for a substrate is the concentration of substrate required to
reach 1⁄2 Vmax. The Michaelis-Menten model of enzyme kinetics applies to a simple
reaction in which the enzyme and substrate form an enzyme–substrate complex (ES)
that can dissociate back to the free enzyme and substrate. The initial velocity of product
formation, vi, is proportionate to the concentration of enzyme–substrate complexes
[ES]. As substrate concentration is increased, the concentration of enzyme–substrate
complexes increases, and the reaction rate increases proportionately.
The graph of the Michaelis-Menten equation (vi as a function of substrate concentration)
is a rectangular hyperbola that approaches a finite limit, Vmax, as the
fraction of total enzyme present as enzyme–substrate complex increases
9. Explain Enzyme inhibition.
1. Reversible-Competitive:
A competitive inhibitor “competes” with a substrate for binding at the enzyme’s
substrate recognition site and therefore is usually a close structural analog of
the substrate (Fig. 9.4). An increase of substrate concentration can overcome
competitive inhibition; when the substrate concentration is increased to a sufficiently
high level, the substrate binding sites are occupied by substrate, and inhibitor
molecules cannot bind. Competitive inhibitors, therefore, increase the apparent Km
2. Irreversible inhibition
10. Explain Drug Discovery
Enzymes and receptors as drug targets – HMG CoA reductase inhibitor as a drug for hyper
cholesteraemia.
11. Explain the Regulation of enzyme activity.
Isoenzymes:
Zymogen cleavage. Some enzymes are synthesized as inactive precursors,
called zymogens, that are activated by proteolysis (e.g., the digestive enzyme chymotrypsin).
Changes in enzyme concentration. The concentration of an enzyme can be
regulated by changes in the rate of enzyme synthesis (e.g., induction of gene transcription)
or the rate of degradation.
Regulation of metabolic pathways. The regulatory mechanisms for the ratelimiting
enzyme of a pathway always reflects the function of the pathway in a
particular tissue. In feedback regulation, the end product of a pathway directly
or indirectly controls its own rate of synthesis; in feedforword regulation,
substrate controls the rate of the pathway. Biosynthetic and degradative pathways
are controlled through different but complementary regulation.
Allosteric enzymes:
SECTION - A
1. N-acetylmuramide glycanhydrolase
N-acetylmuramide glycanhydrolase, are glycoside hydrolases, enzymes (EC
3.2.1.17) that damage bacterial cell walls by catalyzing hydrolysis of 1,4-betalinkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in
a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins.
Lysozyme is abundant in a number of secretions, such as tears, saliva, human
milk, and mucus. It is also present in cytoplasmic granules of the
polymorphonuclear neutrophils (PMN). Large amounts of lysozyme can be found
in egg white. C-type lysozymes are closely related to alpha-lactalbumin in
sequence and structure, making them part of the same family.
In humans, the lysozyme enzyme is encoded by the LYZ gene.[1][2]
2 . Active site
molecular biology the active site is part of an enzyme where substrates bind and undergo
a chemical reaction. The majority of enzymes are proteins but RNA enzymes called
ribozymes also exist. The active site of an enzyme is usually found in a cleft or pocket
that is lined by amino acid residues (or nucleotides in ribozymes) that participate in
recognition of the substrate. Residues that directly participate in the catalytic reaction
mechanism are called active site residues.
3. Competitive inhibition
Competitive inhibition is a form of enzyme inhibition where binding of the inhibitor
to the active site on the enzyme prevents binding of the substrate and vice versa.
4. Uncompetitive inhibition
Uncompetitive inhibition, also known as Anti-competitive inhibition, takes place when an
enzyme inhibitor binds only to the complex formed between the enzyme and the substrate (the
E-S complex).