CHAPTER OUTLINE

Amino Acids: Building Blocks for Protein

    Chemical Nature of the Amino Acids

    Classification of Amino Acids

    Acid–Base Properties of the Amino Acids

    Functional Significance of Amino Acid R Groups

    Optical Properties of the Amino Acids

    The Peptide Bond

Amino Acids: Building Blocks for Protein

Chemical Nature of the Amino Acids

All peptides and polypeptides are polymers of α-amino acids. There are 20 α-amino acids relevant to the makeup of mammalian proteins (see later). Several other amino acids found in the body are in free or combined states (ie, not associated with peptides or proteins). These non–protein-associated amino acids perform specialized functions. Several of the amino acids found in proteins also serve functions distinct from the formation of peptides and proteins, for example, tyrosine in the formation of thyroid hormones or glutamate acting as a neurotransmitter.

The α-amino acids in peptides and proteins (excluding proline) consist of a carboxylic acid (–COOH) and an amino (–NH₂) functional group attached to the same tetrahedral carbon atom. This carbon is the α-carbon. Distinct R groups, that distinguish one amino acid from another, are also attached to the α-carbon (except in the case of glycine where the R group is hydrogen). The fourth substitution on the tetrahedral α-carbon of amino acids is hydrogen.

Classification of Amino Acids

Each of the 20 α-amino acids found in proteins can be distinguished by the R group substitution on the α-carbon atom. There are 2 broad classes of amino acids based upon whether the R group is hydrophobic or hydrophilic (Table 1-1).

The hydrophobic amino acids tend to repel the aqueous environment and, therefore, reside predominantly in the interior of proteins. This class of amino acids does not ionize nor participate in the formation of H-bonds. The hydrophilic amino acids tend to interact with the aqueous environment, are often involved in the formation of H-bonds, and are predominantly found on the exterior surfaces of proteins or in the reactive centers of enzymes.

Acid–Base Properties of the Amino Acids

The α-COOH and α-NH₂ groups in amino acids are capable of donating or accepting protons (as are the acidic and basic R groups of the amino acids). As a result of their ionizing, the following ionic equilibrium reactions may be written in the basic form:

The equilibrium constant, K_a, for a reaction of this type is defined as:

For the α-COOH and α-NH₂ groups of the amino acids, these equilibrium reactions would be:

The equilibrium reactions, as written, demonstrate that amino acids contain at least 2 weakly acidic groups. However, the carboxyl group is a far stronger acid than the amino group. At physiological pH (~7.4) the carboxyl group will be unprotonated and the amino group will be protonated.

Like typical organic acids, the acidic strength of the carboxyl, amino, and ionizable R groups in amino acids can be defined by the association or equilibrium constant, K_a, or more commonly the negative logarithm of K_a (−logK_a), the pK_a. This value is determined for any given acid or base from the Hendersen-Hasselbalch equation:

The net charge (the algebraic sum of all the charged groups present) of any amino acid, peptide, or protein will depend upon the pH of the surrounding aqueous environment. As the pH of a solution of an amino acid or protein changes so too does the net charge. This phenomenon can be observed during the titration of any amino acid or protein (Figure 1-1). When the net charge of an amino acid or protein is zero, the pH will be equivalent to the isoelectric point (pI).

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