Proteins: Amino Acids and the Peptide Bond

Proteins are the polymers built up from $\alpha$-amino acid monomer units, joined together in long chains by a characteristic amide linkage called the peptide bond.

The general structure of a naturally occurring $\alpha$-amino acid is $\text{R}{-}\text{CH}(\text{NH}_2){-}\text{COOH}$: a central carbon (called the alpha carbon, because it sits directly next to the carboxyl group) that carries a basic amino group ($-\text{NH}_2$), an acidic carboxyl group ($-\text{COOH}$), a hydrogen atom, and a fourth, variable side chain denoted R, whose identity distinguishes one amino acid from another (in glycine, the simplest amino acid, R is simply another hydrogen atom).

Because an $\alpha$-amino acid carries both an acidic $-\text{COOH}$ group and a basic $-\text{NH}_2$ group on the very same carbon, an internal acid-base (proton-transfer) reaction takes place within the molecule itself: the $-\text{COOH}$ group donates its proton to the neighbouring $-\text{NH}_2$ group, converting the molecule into a dipolar ion with a negatively charged carboxylate, $-\text{COO}^-$, and a positively charged ammonium group, $-\text{NH}_3^+$, existing side by side on the same molecule, even though the molecule as a whole carries no net charge. This dipolar form is called a zwitterion, and it is the form in which amino acids predominantly exist, both in the solid crystalline state and in aqueous solution near neutral pH. The zwitterionic structure directly explains two otherwise puzzling physical properties of amino acids: their unusually high melting points compared with ordinary carboxylic acids or amines of similar size (because the solid is held together by strong ionic, salt-like attractions between zwitterions, rather than weaker molecular forces), and their good solubility in water (because the charged $-\text{COO}^-$ and $-\text{NH}_3^+$ groups are both strongly attracted to polar water molecules). …