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BC1020: Cellular Biochemistry,

2014-15 Semester 2.
Enzymic
reactions &
catalysis.
Andrew Pearson

Enzymes are proteins that catalyse the


formation and breaking of covalent bonds.
(and yet enzyme structure depends upon weak
H-bonds!)
Some enzymes contain non-protein components
called cofactors.
Cofactors can be: metal atoms/ions
organic groups
Coenzymes are usually just special substrates
often derived from vitamins
(containing nucleotides).

From Lehninger

From Lehninger

Can you conceive how large these numbers are?

Could life have evolved this far without such power?


From Lehninger

Two models for enzyme-substrate interaction

(Emil Fischer, 1894)

(Daniel Koshland Jr., 1958)

From Matthews
& van Holde

Conformational change during hexokinase


mechanism

From Matthews
& van Holde

Hydrophobic
Interaction

Ionic
interaction

H-bond
Adapted From
Voet & Voet

The specific attachment of a prochiral centre to


an enzyme binding
Thus only
site permits the
the correct,
enzyme to
naturally
differentiate
occurring
between
stereoisomer
prochiral
fits into the
groups.
enzymes
binding site
Adapted From
Voet & Voet

Some enzymic
reactions not all
follow this type of
mechanism.

From Matthews
& van Holde

Many of you may well be familiar with this


diagram showing the activation energy
hump of chemical reactions, and how
enzymes reduce the height of the hump.

From Matthews
& van Holde

Some reaction
mechanisms have an
intermediate energy
well.
From Matthews
& van Holde

Far UV
= 1200 kJ.mol-1
H-bonds
UV = 480 to
343 kJ.mol-1

Electrostatic
Interactions

visible
Near IR =
120 kJ.mol-1
Recall what
forces we are
dealing with?

Van der

Some enzyme
mechanisms

1. Acid base catalysis

From Matthews
& van Holde

1. Acid base catalysis

From Matthews
& van Holde

Some enzyme
mechanisms

Enzymes achieve catalysis mainly by:


bringing reactants together in the optimum
orientation, to make new covalent bonds;
or breaking covalent bonds by:
causing the susceptible bond to weaken, by
distorting its angle, or lengthening it;
causing the susceptible bond to weaken by
attacking one of the bonding nuclei
(nucleophilic attack);
causing the susceptible bond to weaken by
withdrawing electrons from it.

From Matthews
& van Holde

Catalytic mechanisms have been classified as:


1. Acid base catalysis
2. Covalent catalysis
3. Metal ion catalysis
4. Electrostatic catalysis
5. Proximity & orientation effects
6. Preferential binding of the transition
state.
But any particular enzymic mechanism may
have one or several of these characteristics.

A simple model which explains one aspect of the


behaviour of almost all enzymes, was pioneered
by Victor Henri in 1902, who has been largely
forgotten.
His work was partly confirmed in 1909 by
S.P.L. Srensen (inventor of the pH scale), but
the definitive paper was published by:

Michaelis & Menten in 1913.

Michaelis & Menten in 1913.

The derivation of the Michaelis-Menten Rate


Equation (appended to enzymology lab) is based
upon simple chemical reaction kinetics.
Consider a reaction in which reactant A is
converted to product B:
A B
The rate at which this reaction occurs can
depend upon:
the amount of A
the temperature
the amount of B, only if the reaction is reversible

A B
Let us say that the reaction is irreversible, and
performed at a constant temperature.
This means that the rate* of the reaction,
that is:
the amount of A consumed,
or the amount of B produced

per unit time


must be dependent only on the amount of A

(amount = number of molecules in a volume = concentration).

* Rate is a quantity of something divided


by time: how fast/slowly does it happen?

Let us say that the reaction is irreversible, and


performed at a constant temperature.
This means that the rate of the reaction,
that is:

the consumption of A, or the production of B

per unit time


must be dependent only on the amount of A

(amount = number of molecules in a volume = concentration).

rate = dependent on [A]


rate = constant x [A]

the consumption of A, or the production of B per unit time

rate = dependent on [A]


rate = constant x [A]

A shorthand way to express


a small change in x in a small amount of time
is:
dx a small decrease -dx
in x over time is
dt
dt
hence: the consumption of A, or the production of B per unit time
can be written as:
-d[A] = d[B] = constant x [A]
dt
dt

-d[A] = d[B] = constant x [A]


dt
dt
The proportionality constant in this equation will
be the same for this reaction, provided that all
other conditions (temperature, pressure, pH etc.)
remain the same, every time the reaction is
observed.
The whole lot can be written in shorthand thus:
A B
-d[A] = d[B] = k[A]
dt
dt

-d[A] = d[B] = k[A]


dt
dt

From Matthews
& van Holde

Michaelis-Menten Plot

Vmax.[S]
Vo =
Km + [S]