BC10M: Introductory Biochemistry, 2006 Semester 2.

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BC10M Introductory Biochemistry, 2006 Semester 2.

• Tuesday 14 Mar.
• lecture 21
• Enzymic reactions catalysis.
• Andrew Pearson

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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).
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Remember also cobalt, and the coenzyme of which
it provided the core, and the vitamin from which
it is derived?
From Lehninger
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From Lehninger
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Can you conceive how large these numbers are?
Could life have evolved this far without such
power?
From Lehninger
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Two models for enzyme-substrate interaction
(Emil Fischer, 1894)
From Matthews van Holde
(Daniel Koshland Jr., 1958)
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Conformational change during hexokinase mechanism
From Matthews van Holde
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Ionic interaction
Hydrophobic Interaction
H-bond
Adapted From Voet Voet
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The specific attachment of a prochiral centre
to an enzyme binding site permits the enzyme
to differentiate between prochiral groups.
Thus only the correct, naturally occurring
stereoisomer fits into the enzymes binding site
Adapted From Voet Voet
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Some enzymic reactions not all follow this
type of mechanism.
From Matthews van Holde
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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
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Some reaction mechanisms have an intermediate
energy well.
From Matthews van Holde
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Far UV 1200 kJ.mol-1
H-bonds Electrostatic Interactions Van der

Waals
UV 480 to 343 kJ.mol-1
visible
Near IR 120 kJ.mol-1
Recall what forces we are dealing with?
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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.
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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. e.g. lysozyme (see lab
manual) uses acid-base catalysis on a substrate
that has been distorted and bound in the
transition state.
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Some enzyme mechanisms
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Some enzyme mechanisms
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Some enzyme mechanisms
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• 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.

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From Matthews van Holde
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1. Acid base catalysis
From Matthews van Holde
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1. Acid base catalysis
From Matthews van Holde
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(No Transcript)
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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. Sørensen (inventor of the pH
scale), but the definitive paper was published by
Michaelis Menten in 1913.
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Michaelis Menten in 1913.
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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 à 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

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A à 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 amountof A (amount number of molecules in
a volume concentration).
Rate is a quantity of something divided by
time how fast/slowly does it happen?
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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
amountof A (amount number of molecules in a
volume concentration).

• rate dependent on A
• rate constant x A

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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 a small
decrease in x over time is
dx dt
-dx dt
hence the consumption of A, or the production
of B per unit time can be written as
-dA dB constant x A dt dt
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-dA dB 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 à B
-dA dB kA dt dt
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-dA dB kA dt dt
From Matthews van Holde
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Michaelis-Menten Plot
Vmax.S Km S
Vo