Principles of Biochemistry
6 | Enzymes
Principles of Biochemistry by Albert Leningher, 6th edition.
Enzymes are a very complicated structures that catalyzes the reaction, which means it speeds up
the reaction rate without being consumed in the process, think of it this way, if you placed a bag
of sugar on the shelf for years, it won’t undergo the respiration process at all even though the
process is thermodynamically favorable, but in our body it will happen in less than a second to
yield huge amount of energy, all because of the catalyzes process.
Properties of biological catalysts:
• highly specialized proteins or RNA
• Extraordinary catalytic power
• High degree of specificity
• Accelerate chemical reactions tremendously
• Function in aqueous solutions under very mild conditions of temperature and pH
Most enzymes are proteins or RNA which decreases the rate of reaction only, it won’t affect the
equilibrium at all. Classification of enzymes can be categorized as followed:
EC 1 (Oxidoreductases): enzymes catalyze oxidation/reduction reactions; transfer of H
and O atoms or electrons from one substance to another like dehydrogenase, or oxidase.
AH + B → A + BH (reduced)
A + O → AO (oxidized)
EC 2 (Transferases): enzymes transfer of a functional group from one substance to
another. The group may be methyl-, acyl-, amino- or phosphate group, like kinase
AB + C → A + BC
EC 3 (Hydrolases): enzymes forms two products from a substrate by hydrolysis like
amylase or protease.
AB + H2O → AOH + BH
EC 4 (Lyases): Non-hydrolytic addition or removal of groups from substrates. Bonds
may be cleaved, like decarboxylase.
RCOCOOH → RCOH + CO
[X-A-B-Y] → [A=B + X-Y]
EC 5 (Isomerases): Intramolecular rearrangement, i.e. isomerization changes within a
single molecule, like isomerase, mutase.
AB → BA
, EC 6 (Ligases): Join two molecules by synthesis of new C-O, C-S, and C-N or C-C
bonds with breakdown of ATP, like Synthetase.
X + Y+ ATP → XY + ADP + Pi
Enzymes can’t mostly work without the help of other chemical groups, like Cofactors which
is either one or more inorganic ions, Coenzymes which is complex organic or metal-organic
molecules, in some enzymes, it requires both, Prosthetic group which is a coenzyme or cofactor
that is covalently bound to enzyme, Holoenzyme which is a complete active enzyme with its
cofactor or coenzyme, and the last, Apoprotein – the protein part of a holoenzyme.
The benefits of enzymes over their reaction are: Greater reaction specificity, milder reaction
conditions, higher reaction rates, and capacity for regulation.
Most of the enzyme reactions ae spotted on this simple form described the reaction coordinate
below:
E + S ES EP E + P
Reaction can be as shown above in which ΔG S> ΔG P, or the opposite, in which ΔG‡ is the
activation energy, or (Ea) or the energy to reach the transition state (TS). While ΔG’o is the free
,energy change that have to be negative for such a reaction to be favorable. It depends on variable
concepts shown as;
K’eq = [P] / [S] (equilibrium constant for the general reaction S P)
and ΔG’o = –RT ln K’eq
The rate of any reaction depends on the concentration of reactant and it is called k (rate
constant)
V = k[S] (1st order reaction) units of k (s–1)
V = k[S1][S2] (2nd order reaction) units of k (M–1s–1)
How does the enzyme decrease the rate in is such a complex reaction? By binding and
proximity. Enzymes binds to the Transition State more strongly than substrate form by the “look
and key” model that had put by Linus Pauling in 1946, it provides proximity as well in the
process by getting the reactants more close to each other, to minimize the entropy and the
possibility of having other favorable reactions yield unrequired products.
, Catalytic mechanisms:
1. Acid-base catalysis: the transfer of protons from one compound to another, by the help of
H2O or proton donor (HA) and proton acceptor (B:), categorized as specific acid-base
catalysis in which H2O act as a proton transfer and stabilizes the transition state of the
reaction, and that’s only when proton transfer is faster than the breakdown of the
transition state, and adding any other different proton acceptor/donor won’t the rate.
When H2O fails to overcome the rate of breaking down the unstable transition state,
General acid-base catalysis comes handy here in which the addition of B: and HA will
increase the rate itself.
2. Covalent catalysis: it changes the pathway of the reaction, transient covalent bond
between the enzyme and the substrate works in such catalysis.
Un-catalyzed: AB ---H2O--- > A + B (slow/ unfavorable)
Catalyzed: AB+X: ------ > AX + B ----H2O--- > A + B + X:
3. Metal-ion catalysis: uses redox action, and changes the pKa by forming a weak bond
between the metal and the substrate.
4. Electrostatic catalysis: preferential interactions with TS.
Kinetics is the study of the rate at which compounds react, affected by enzyme, substrate,
effectors, temperature, and so on.
Kinetic measurement are done by mixing different concentrations of the substrate [S], with a
constant concentration of enzymes, and the rate in which product/s are made (initial velocity) is
recorded with each [S], and then the records are plotted between the initial velocity vs [S]. The
relationship between them both is similar for all the enzymes mostly, they confirm a rectangular
hyperbola diagram, which describes the following equation (called Michaelis-Menten
equation):
V0 = Vmax[S] ÷ (Km+[S])
The deviations in the equation may be due to: limitation of measurements, substrate inhibition,
substrate prep contains inhibitors, and enzyme prep contains inhibitors.
V0 is the initial velocity in which the first product is made, Vmax is the maximum amount the rate
can reach –mainly constant- with the increase of [S], and Km is the Michalis constant which
equals (k2+k -1) ÷ k1, it is also described as the amount of [S] in which V0 will reach half Vmax
When Km <<<[S], the equation will be (V0 = Vmax) it will be liner and parallel to the X axis, and
when Km>>>[S], the equation is liner but not completely as shown in the figure below.
Note: make sure to know the axis meanings and value (if mm or mM or otherwise)
6 | Enzymes
Principles of Biochemistry by Albert Leningher, 6th edition.
Enzymes are a very complicated structures that catalyzes the reaction, which means it speeds up
the reaction rate without being consumed in the process, think of it this way, if you placed a bag
of sugar on the shelf for years, it won’t undergo the respiration process at all even though the
process is thermodynamically favorable, but in our body it will happen in less than a second to
yield huge amount of energy, all because of the catalyzes process.
Properties of biological catalysts:
• highly specialized proteins or RNA
• Extraordinary catalytic power
• High degree of specificity
• Accelerate chemical reactions tremendously
• Function in aqueous solutions under very mild conditions of temperature and pH
Most enzymes are proteins or RNA which decreases the rate of reaction only, it won’t affect the
equilibrium at all. Classification of enzymes can be categorized as followed:
EC 1 (Oxidoreductases): enzymes catalyze oxidation/reduction reactions; transfer of H
and O atoms or electrons from one substance to another like dehydrogenase, or oxidase.
AH + B → A + BH (reduced)
A + O → AO (oxidized)
EC 2 (Transferases): enzymes transfer of a functional group from one substance to
another. The group may be methyl-, acyl-, amino- or phosphate group, like kinase
AB + C → A + BC
EC 3 (Hydrolases): enzymes forms two products from a substrate by hydrolysis like
amylase or protease.
AB + H2O → AOH + BH
EC 4 (Lyases): Non-hydrolytic addition or removal of groups from substrates. Bonds
may be cleaved, like decarboxylase.
RCOCOOH → RCOH + CO
[X-A-B-Y] → [A=B + X-Y]
EC 5 (Isomerases): Intramolecular rearrangement, i.e. isomerization changes within a
single molecule, like isomerase, mutase.
AB → BA
, EC 6 (Ligases): Join two molecules by synthesis of new C-O, C-S, and C-N or C-C
bonds with breakdown of ATP, like Synthetase.
X + Y+ ATP → XY + ADP + Pi
Enzymes can’t mostly work without the help of other chemical groups, like Cofactors which
is either one or more inorganic ions, Coenzymes which is complex organic or metal-organic
molecules, in some enzymes, it requires both, Prosthetic group which is a coenzyme or cofactor
that is covalently bound to enzyme, Holoenzyme which is a complete active enzyme with its
cofactor or coenzyme, and the last, Apoprotein – the protein part of a holoenzyme.
The benefits of enzymes over their reaction are: Greater reaction specificity, milder reaction
conditions, higher reaction rates, and capacity for regulation.
Most of the enzyme reactions ae spotted on this simple form described the reaction coordinate
below:
E + S ES EP E + P
Reaction can be as shown above in which ΔG S> ΔG P, or the opposite, in which ΔG‡ is the
activation energy, or (Ea) or the energy to reach the transition state (TS). While ΔG’o is the free
,energy change that have to be negative for such a reaction to be favorable. It depends on variable
concepts shown as;
K’eq = [P] / [S] (equilibrium constant for the general reaction S P)
and ΔG’o = –RT ln K’eq
The rate of any reaction depends on the concentration of reactant and it is called k (rate
constant)
V = k[S] (1st order reaction) units of k (s–1)
V = k[S1][S2] (2nd order reaction) units of k (M–1s–1)
How does the enzyme decrease the rate in is such a complex reaction? By binding and
proximity. Enzymes binds to the Transition State more strongly than substrate form by the “look
and key” model that had put by Linus Pauling in 1946, it provides proximity as well in the
process by getting the reactants more close to each other, to minimize the entropy and the
possibility of having other favorable reactions yield unrequired products.
, Catalytic mechanisms:
1. Acid-base catalysis: the transfer of protons from one compound to another, by the help of
H2O or proton donor (HA) and proton acceptor (B:), categorized as specific acid-base
catalysis in which H2O act as a proton transfer and stabilizes the transition state of the
reaction, and that’s only when proton transfer is faster than the breakdown of the
transition state, and adding any other different proton acceptor/donor won’t the rate.
When H2O fails to overcome the rate of breaking down the unstable transition state,
General acid-base catalysis comes handy here in which the addition of B: and HA will
increase the rate itself.
2. Covalent catalysis: it changes the pathway of the reaction, transient covalent bond
between the enzyme and the substrate works in such catalysis.
Un-catalyzed: AB ---H2O--- > A + B (slow/ unfavorable)
Catalyzed: AB+X: ------ > AX + B ----H2O--- > A + B + X:
3. Metal-ion catalysis: uses redox action, and changes the pKa by forming a weak bond
between the metal and the substrate.
4. Electrostatic catalysis: preferential interactions with TS.
Kinetics is the study of the rate at which compounds react, affected by enzyme, substrate,
effectors, temperature, and so on.
Kinetic measurement are done by mixing different concentrations of the substrate [S], with a
constant concentration of enzymes, and the rate in which product/s are made (initial velocity) is
recorded with each [S], and then the records are plotted between the initial velocity vs [S]. The
relationship between them both is similar for all the enzymes mostly, they confirm a rectangular
hyperbola diagram, which describes the following equation (called Michaelis-Menten
equation):
V0 = Vmax[S] ÷ (Km+[S])
The deviations in the equation may be due to: limitation of measurements, substrate inhibition,
substrate prep contains inhibitors, and enzyme prep contains inhibitors.
V0 is the initial velocity in which the first product is made, Vmax is the maximum amount the rate
can reach –mainly constant- with the increase of [S], and Km is the Michalis constant which
equals (k2+k -1) ÷ k1, it is also described as the amount of [S] in which V0 will reach half Vmax
When Km <<<[S], the equation will be (V0 = Vmax) it will be liner and parallel to the X axis, and
when Km>>>[S], the equation is liner but not completely as shown in the figure below.
Note: make sure to know the axis meanings and value (if mm or mM or otherwise)
