Amino acids with ionizable side-chains

The ionic states at pH 7.0 of these amino acids with ionizable side-chains are shown below. 

Amino acids with ionizable side-chains... 

There are several ways to think about the amino acid residues in proteins their length and size, their hydrophobicity or hydrophilicity, their charge and ionization state, their hydrogen-bonding potential and their possible metalbinding potentials [73-75]. It is possible to gain or lose charge, hydrophobicity or hydrophilicity in a controlled way, as is required in the active site of an enzyme. This is done by appropriate choices of amino acids with specific side-chain properties. Therefore amino acids must be chosen with care when a... 

Certain amino acids also possess side chains with ionizable groups. For example, the side chain of lysine possesses an ionizable amino group. Because of their structures, alanine, lysine, and the other amino acids can act as effective... 

Because amino acids have both a basic (the amine) and an acidic (the carboxylic acid) functional group, the state of protonation of the molecule varies with pH as shown in Equation 24.1. The presence of a functional group in the side chain may have considerable influence upon the position of this equilibrium at different pHs. The pH at which the vast majority of the molecules are in the zwitterionic form, and therefore have a net charge of zero, is referred to as the isoelectric point, pi. An amino acid is least soluble in water at its isoelectric point, which is different for each amino acid. If the side chain bears an ionizable group such as a carboxylic acid or an amine, the state of protonation of that functional group will also vary as a function of pH. However, the amino acids used in the exjjeriments in this chapter are nonpolar, so we will not concern ourselves with the complexities associated with ionizable side chains. 

Each amino acid has a different R group, or side chain. The side chains of the amino acids in a protein determine the protein s properties. In Table 25.2 the side chains of the amino acids are shown within a color screen. Nine of the amino acids have nonpolar, or hydrocarbon, side chains (left side of table). The remaining 11 amino acids have polar side chains (right side of table), capable of ionizing or forming hydrogen bonds with other amino acids or with water. 

Table 10.11. Distribution of amino acid residues with ionizing side chains (net charge) and with nonpolar side chains (hydrophobicity) in agi-casein and p-casein...

Typical values for pAlg are in the range of 9.0 to 9.8. At physiological pH, the a-carboxyl group of a simple amino acid (with no ionizable side chains) is completely dissociated, whereas the a-amino group has not really begun its dissociation. The titration curve for such an amino acid is shown in Figure 4.7. 

Comparison of solution pH with the pKa of a side chain informs about the protonation state. A unique pKa, termed the standard or model pKa, can be experimentally determined for each ionizable side chain in solution when it is incorporated in a model compound, often a blocked amino acid residue [73] (Table 10-1). In a protein environment, however, the pKa value of an ionizable side chain can substantially deviate from the standard value, due to desolvation effects, hydrogen bonding, charge-charge, charge-dipole, and other electrostatic interactions with the... 

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