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The Fundamentals of Biochemistry: Interactive Tutorials

10th Edition

The equilibrium constant for the dissociation of a proton from an weak acid is called the acid dissociation constant, designated Ka. To simplify calculations and make easy comparisons, bases are considered in their protonated form. For example, the Ka of the α-amino group of alanine is the measure of the acid strength of its conjugate acid, –NH3+.

Seven of the amino acids (D, E, H, C, Y, K, R) have side chains containing an ionizable group. Aspartate (D) and glutamate (E) are dicarboxylic amino acids. In addition to their α-carboxyl groups, aspartate possesses a β-carboxyl group, and glutamate has a γ-carboxyl. Because the side chains of Asp and Glu are completely ionized at pH 7, they confer negative charges on proteins and are usually found on the surface where they can hydrogen bond to water molecules. [Note: Remember that an acid is 91% deprotonated at pH = pK + 1 and 99% deprotonated at pH = pK + 2.]

The ε-amino group of lysine (Lys, K) has an intrinsic pK value of 11.1 and thus exists as the –NH3+ ion at pH 7.

Why is the pK of the carboxyl group of an amino acid so much lower than that of acetic acid (pK = 4.8)? Consider the table below.

Table I: pKa of Alanine Oligomers

Compound pK1 pK2
Ala 2.34 9.69
(Ala)2 3.12 8.30
(Ala)3 3.39 8.03
(Ala)4 3.42 7.94
This is a simple example of how the microenvironment influences the pKa of an ionizable group. The α-carboxyl group of alanine is a stronger acid than acetic acid because the α-ammonium ion stabilizes the carboxylate anion. Increasing the distance between the α-NH3+ group and the carboxyl group weakens the interaction between the two groups. For example, the γ-carboxyl group of free glutamate (pK = 4.1) is similar in strength to acetic acid (pK = 4.8). In the peptides listed in Table I, the α-amino and α-carboxyl groups of the Ala residues between the two terminal residues lose their charges once they are linked by peptide bonds. At neutral pH the free amino group and free carboxyl group at the opposite ends of the peptide chain are ionized, but their influence on each other diminishes as the length of the peptide increases. However, the C-terminal carboxyl group (pK = 3.4) in the tetrapeptide is a stronger acid than the γ-carboxyl of free glutamate (pK = 4.1). This difference in pKs stems from the effect of inductive electron withdrawal by the peptide bond on the stability of the C-terminal carboxylate ion.

In proteins, the pK values of the ionizable side chains can vary from those of the free amino acids. Two factors are at work. First, as you learned above, the α-amino and α-carboxyl groups no longer carry ionic charges. Second, the microenvironment of an ionizable side chain within the three-dimensional structure of the protein can lead to large perturbations in its pK.