6-3 CHEMICAL MODES OF ENZYMATIC CATALYSIS
Introduction

The ES complex places reactants close to reactive __________ __________ __________
in the active site.

Ionizable side chains participate in two modes of chemical catalysis: ____________________ catalysis and _______________ catalysis.
Polar Amino Acid Residues in Active Sites

Most amino acid residues in active sites are _______________, but a few __________,
_______________ residues (plus a few __________ molecules) are also present.
o The polar amino acid residues are sometimes called _______________.

These polar amino acid residues undergo _______________ changes, and make up much
of the _______________ center of the enzyme.

The amino acids below have reactive side chains that have catalytic functions. Identify
the reactive group and their functions.
Amino Acid
Aspartate
Glutamate
Histidine
Cysteine
Tyrosine
Lysine
Arginine
Serine
Reactive Group
Functions

The pKa values of the ionizable side chains of the above amino acids may differ within a
_______________ compared to when they are _______________ amino acids.

This can be used to _______________ a certain ionic amino acid by measuring the effect
of _____ on reaction rate.
o If the change in rate correlates with the pKa of a certain ionic amino acid, then a
residue of that amino acid may take part in catalysis.

Only a few amino acid residues participate directly in the _______________ of
catalyzing reactions. The rest have a variety of roles. Some help in…

substrate _______________,

_______________ the transition state, or

Interacting with essential _______________ (to be studied later).
Acid-Base Catalysis

Acceleration of a reaction is achieved by catalytic transfer of a _______________.
o Most common form of catalysis in organic chemistry, and also very common in
enzymatic catalysis.

The amino acids must be able to _______________ or _______________ protons under
the nearly neutral pH conditions of cells.

Bases (B:, or proton acceptors) can cleave O–H bonds, N–H bonds, and C–H bonds:
–X–H

:B
Bases can also cleave other bonds containing carbon by generating the equivalent of OH–
ions:

Protonated atoms can assist in cleavage:

The imidazole/imidazolium of histidine is an ideal group for proton transfer.
Covalent Catalysis

A substrate is bound _______________ to the enzyme to form a reactive
______________.
o Ex:

This is a common mechanism for the _______________ of two different reactions, an
important property of enzymes.
o Ex: This reaction is catalyzed by bacterial sucrose phosphorylase.
Overall rxn:
Sucrose + Pi
Step 1:
Sucrose + Enzyme
Step 2:
Glucosyl-Enzyme + Pi
Glucose 1-phosphate + Fructose
Glucosyl-Enzyme + Fructose
Glucose 1-phosphate + Enzyme
pH Affects Enzymatic Rates

The effect of pH on the reaction rate of an enzyme can suggest which ionizable amino
acid residues are in its _______________ __________.

Titration of a protein can yield experimental evidence of specific ionizable side chains in
the active site.
o If reaction rate is plotted vs. pH, inflection points indicate _______________ of
certain side chains at specific pH values, which correspond to the pKa values,
which are used to _______________ the active amino acid side chains.
Ex: The activity of the enzyme papain depends on two ionizable residues in the active site. The
diagram below shows the three ionic forms, but only the __________ structure is active.