Enzymes use several catalytic mechanisms to lower the free energy of transition states and greatly increase reaction rates, including acid-base catalysis, covalent catalysis, metal ion catalysis, and bringing substrates into close proximity and proper orientation. Acid-base catalysis involves proton transfer from catalytic amino acid side chains. Covalent catalysis transiently forms covalent bonds between enzyme and substrate. Metal ion catalysis uses transition metals to orient substrates, mediate redox reactions, or stabilize charges. Proximity and orientation align substrates for reaction, while catalysis by approximation brings two substrates together for reaction.

1. ENZYME CATALYSIS,
TYPES OF
MECHANISMS
INVOLVED.
DAVID
ENOMA
17PCP0163
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2. ENZYME CATALYSIS
Enzymes achieve their enormous rate
accelerations via the same catalytic
mechanisms used by chemical catalysts.
Enzymes have simply been better
designed through evolution.
Enzymes, like other catalysts, reduce
the free energy of the transition state
(ΔG); that is, they stabilize the transition
state of the catalysed reaction.
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3. FREE ENERGY
Free energy (G) is the most valuable
thermodynamic function for determining
whether a reaction can take place and
for understanding the energetics of
catalysis
A reaction can occur spontaneously
only if the change in free energy (∆ G) is
negative.
Enzymes do not alter reaction
equilibria; rather, they increase reaction
rates.
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4. ENZYME CATALYSIS-
LOWERING FREE ENERGY
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5. BIOCHEMICAL MECHANISMS
The types of catalytic mechanisms that
enzymes employ have been classified as:
1. Acid–base catalysis
2. Covalent catalysis
3. Metal ion catalysis
4. Proximity and orientation effects
5. Catalysis by approximation.
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6. ACID–BASE CATALYSIS
General acid catalysis is a process in which
proton transfer from an acid lowers the free
energy of a reaction’s transition state.
 The ionisable functional groups of amino
acyl side chains and (where present) of
prosthetic groups contribute to catalysis by
acting as acids or bases.
The ability of enzymes to arrange several
catalytic groups around their substrates
makes concerted acid–base catalysis a
common enzymatic mechanism. 6

7. ACID–BASE CATALYSIS
CONTD.
The catalytic activity of these enzymes is
sensitive to pH, since the pH influences the
state of protonation of side chains at the
active site.
RNase A Is an Acid–Base Catalyst. Bovine
pancreatic RNase A provides an example of
enzymatically mediated acid–base catalysis.
This digestive enzyme is secreted by the
pancreas into the small intestine, where it
hydrolyzes RNA to its component
nucleotides.
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8. RNase A has two essential His residues,
His 12 and His 119, that act in a
concerted manner as general acid and
base catalysts. Evidently, RNase A
catalyzes a two-step reaction .
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BOVINE PANCREATIC RNASE

9. COVALENT CATALYSIS
The process of covalent catalysis involves
the formation of a covalent bond between the
enzyme and one or more substrates.
Covalent catalysis accelerates reaction rates
through the transient formation of a catalyst–
substrate covalent bond.
Usually, this covalent bond is formed by the
reaction of a nucleophilic group on the
catalyst with an electrophilic group on the
substrate, and hence this form of catalysis is
often also called nucleophilic catalysis.
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10. COVALENT CATALYSIS
CONTD.
Covalent catalysis can be conceptually
decomposed into three stages:
1. The nucleophilic reaction between the
catalyst and the substrate to form a
covalent bond.
2. The withdrawal of electrons from the
reaction center by the now
electrophilic catalyst.
3. The elimination of the catalyst, a
reaction that is essentially the reverse 10

11. COVALENT CATALYSIS
CONTD.
Functional groups in proteins that act in
this way include:
the unprotonated amino group of
Lysine,
the imidazole group of Histidine,
the thiol group of Cysteine,
 the carboxyl group of Aspartic acid ,
 and the hydroxyl group of Serine.
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12. Examples of enzymes that participate in
covalent catalysis include the proteolytic
enzyme chymotrypsin and trypsin in which the
nucleophlie is the hydroxyl group on the
serine.
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13. METAL ION CATALYSIS
Nearly one-third of all known enzymes
require metal ions for catalytic activity.
This group of enzymes includes the
metalloenzymes.
Most common transition metal
ions include Fe2+, Fe3+, Cu2+, Mn2+
or, Co2+
Ionic interactions between an
enzyme-bound metal and a
substrate can help orient the
substrate for reaction or stabilize 13

14. METAL ION CATALYSIS
Metal ions participate in the catalytic
process in three major ways:
1. By binding to substrates to orient them
properly for reaction.
2. By mediating oxidation–reduction
reactions through reversible changes in
the metal ion’s oxidation state.
3. By electrostatically stabilizing or
shielding negative charges.
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15. An excellent example of this phenomenon
occurs in the catalytic mechanism of carbonic
anhydrase a widely occurring enzyme that
catalyzes the reaction:
CO2 + H2O ⇌ HCO− 3 + H+
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16. PROXIMITY AND ORIENTATION
Enzyme-substrate interactions align
the reactive chemical groups and hold
them close together in an optimal
geometry, which increases the rate of
the reaction.
This reduces the entropy of the
reactants and thus makes addition or
transfer reactions less unfavorable, since
a reduction in the overall entropy when
two reactants become a single product.
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17. CATALYSIS BY
APPROXIMATION
Many reactions include two distinct
substrates. In such cases, the reaction rate
may be considerably enhanced by bringing
the two substrates together along a single
binding surface on an enzyme.
NMP kinases bring two nucleotides
together to facilitate the transfer of a
phosphoryl group from one nucleotide to
the other.
This strategy takes advantage of binding
energy and positions the substrates in the
correct orientation for the reaction to
proceed. 17

18. An example of catalysis by approximation is when NMP
kinases bring two nucleotides together to facilitate the
transfer of a phosphoryl group from one nucleotide to
the other.
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