Introduction to Enzyme and Coenzyme Chemistry - E-Library Home

Enzymes are Wonderful Catalysts 37
binds only the substrate more tightly: this generates a ‘thermodynamic pit’ for
the ES complex and hence increases the activation energy, so the reaction is
slower! However, if, as in Figure 3.8d, the enzyme can bind selectively the
transition state, then it can reduce the activation energy and hence speed up
the reaction.
The conclusion of this thought experiment is that in order to achieve
optimal catalysis, enzymes should selectively bind the transition state, rather
than the substrate. Hence, it is not advantageous for enzymes to bind their
substrates too tightly. This is evident when one looks at substrate binding
constants for enzymes (these will be discussed in more detail in Section 4.3).
Typical K M values for enzymes are in the mm–mm range (10 3 --10 6 m),
whereas dissociation constants for binding proteins and antibodies whose
function is to bind small molecules tightly are in the range nm–pm
(10 9 --10 12 m). We shall meet several examples of speciWc transition statestabilising
interactions later in the chapter.
3.5 Acid/base catalysis in enzymatic reactions
Acid and base catalysis is involved in all enzymatic processes involving proton
transfer, so in practice there are very few enzymes that do not have acidic or
basic catalytic groups at their active sites. However, unlike organic reactions
which can be carried out under a very wide range of pH conditions to suit the
reaction, enzymes have a strict limitation that they must operate at physiological
pH, in the range 5–9. Given this restriction, and the fairly small range of
amino acid side chains available for participation in acid/base chemistry (shown
in Figure 3.9), a remarkably diverse range of acid/base chemistry is achieved.
General acid catalysis takes place when the substrate is protonated by a
catalytic residue which in turn gives up a proton, as shown in Figure 3.10. The
active site acidic group must, therefore, be protonated at physiological pH but
its pK a must be just above (i.e. in the range 7–10). If the pK a of a side chain was
in excess of 10 then it would become thermodynamically unfavourable to
transfer a proton.
General base catalysis takes place either when the substrate is deprotonated,
or when water is deprotonated prior to attack on the substrate, as shown in
Figure 3.11.
Enzyme active site bases must therefore be deprotonated at physiological
pH but have pK a values just below. Typical pK a ranges for amino acid side
chains in enzyme active sites are shown in Figure 3.12. They can be measured by
analysis of enzymatic reaction rate versus pH, as described in Section 4.7.
Although the pK a values given in Figure 3.12 are the typical values found in
proteins, in some cases the pK a values of active site acidic and basic groups can
be strongly inXuenced by their micro-environment. Thus, for example, the