Amino acids ionization enzyme reactions

Peptides and proteins are composed of a-amino acids linked by amide bonds (see Section 13.1). Their properties, for example the ability of enzymes to catalyse biochemical reactions, are dependent upon the degree of ionization of various acidic and basic side-chains at the relevant pH. This aspect will be discussed in more detail in Section 13.4, but, here, let us consider a simple amino acid dissolved in water at pH 7.0. An a-amino acid has an acidic carboxylic acid group and a basic amine group. Both of these entities need to be treated separately. 

Another good example of the use of affinity labels involves pepsin, and is illustrated in Chapter 16, equations 16.28 and 16.29. The enzyme has two catalyt-ically important aspartic acid residues, one ionized and the other un-ionized. The ionized carboxylate is trapped with an epoxide, which, of course, requires the reaction of a nucleophilic group. The un-ionized carboxyl is trapped with a diazoacetyl derivative of an amino acid ester ... 

Each enzyme has an optimum pH at which the rate of the reaction that it catalyzes is at its maximum. Slight deviations in the pH from the optimum lead to a decrease in the reaction rate. Larger deviations in pH lead to denaturation of the enzyme due to changes in the ionization of amino acid residues and the disruption of noncovalent interactions. 

The two classes of amino acids that exist are based on whether the R-group is hydrophobic or hydrophilic. Hydrophobic or nonpolar amino acids tend to repel the aqueous environment and are located mostly in the interior of proteins. They do not ionize or participate in the formation of hydrogen bonds. On the other hand, the hydrophilic or polar amino acids tend to interact with the aqueous environment, are usually involved in the formation of hydrogen bonds, and are usually found on the exterior surfaces of proteins or in their reactive centers. It is for this reason that certain amino acid R-groups allow enzyme reactions to occur. 

The rate of enzyme-catalyzed reactions typically shows a marked dependence on pH (Figure 8-7). Many of the enzymes in blood plasma show maximum activity in vitro in the pH range from 7 to 8. However, activity has been observed at pH values as low as 1.5 (pepsin) and as high as 10.5 (ALP). The optimal pH for a given forward reaction may be different from the optimal pH found for the corresponding reverse reaction. The form of tlie pH-dependence curve is a result of a number of separate effects including the ionization of the substrate and the extent of dissociation of certain key amino acid side chains in the protein molecule, both at the active center and elsewhere in the molecule. Both pH and ionic environment will also have an effect on the three-dimensional conformation of the protein and... 

The first step in each of these reactions is formation of a -imino group or a jS-iminium ion between the aldehyde of the coenzyme and the amino group of the a-amino acid substrates, thereby providing the j3-electron sink required for decarboxylation or ionization of the a-CH. In the resting state of the enzyme the pyridoxal is covalently sequestered to a lysine s-amino group (ENHj) and the amino acid substrate presumably gives initial transimination, prior to decarboxylation. After decarboxylation, there is yet a second transimination, that enables release of the decarboxylated product and regeneration of the pyridoxal for the next turnover. 

---