6.2.1 Redistribution of electrons in the substrate
Consider the hydrolysis of an amide bond (e.g. a peptide bond) (Figure 38). This reaction requires that the N–C bond is broken and that new bonds are formed between an OH group and the C atom and between an H atom and the N atom, with the OH and H groups deriving from a water molecule (H2O).
Many enzymes have charged groups at critical positions in their active sites, such that they can affect bonds in the bound substrate. An acidic atom or group, such as the N atom on histidine, has a partial positive charge at neutral pH and has a tendency to donate its proton (H+) to other atoms. If the substrate binds so that the O atom of its carbonyl group is in close proximity to the acidic group, then the latter, with its net positive charge, tends to draw the electrons of the carbonyl double bond towards itself, giving the C of the carbonyl group a partial positive charge (Figure 39a). This C atom is now much more attractive to the electronegative O atom of the water molecule and the hydrolysis reaction illustrated in Figure 38 is accelerated. This kind of catalysis is called general acid catalysis.
A basic group, such as the carboxylate group of aspartate and glutamate side-chains, positioned close to the water molecule, can similarly affect electron distribution. In this case, the negatively charged carboxylate group tends to push electrons in the water molecule towards the O atom, making this molecule more polar and more ready to donate electrons to the C atom of the amide bond (Figure 39b). This type of catalysis is general base catalysis. Enzymes can, in fact, use both general acid and general base catalysis simultaneously; thereby further accelerating the reaction (Figure 39c).
Enzymes are extremely efficient catalysts because they simultaneously use several catalytic mechanisms. We will now look more closely at two enzymes, lysozyme and carboxypeptidase A, to demonstrate how enzymes apply these mechanisms to great effect. These enzymes have been chosen because they have been studied extensively and their mechanisms are particularly well characterised. They also have very different modes of action.