Properties of -Amino Acids

The amino acids have in common a dipolar ionic structure and a chiral center. They are differentiated, one from another, by the structures of their side chain groups, designated R in the foregoing formulas. These groups are of varying size and chemical structure. The side chain groups fill much of the space in the interior of a protein molecule and also protrude from the external surfaces of the protein where they determine many of the chemical and physical properties of the molecule.
Show the structures of the side chains of the amino acids commonly found in proteins. The
complete structure is given for proline. Both the threeletter abbreviations and one-letter abbreviations used in describing sequences of amino acids in proteins are also given in this table. Amino acids of groups a–c plus phenylalanine and methionine are sometimes grouped together as nonpolar. They tend to be found in a hydrophobic environment on the inside of a protein molecule. Groups f and i contain polar, charged side chains which usually protrude into the water surrounding the protein. The rest are classified as polar but noncharged.
To get acquainted with amino acid structures, learn first those of glycine, alanine, serine, aspartic acid, and glutamic acid. The structures of many other amino acids can be related to that of alanine (R=CH3) by replacement of a β hydrogen by another group. Metabolic interrelationships will make it easier to learn structures of the rest of the amino acids later.

Since the –COOH groups of glutamic and aspartic acids are completely dissociated to –COO– at neutral pH, it is customary in the biochemical literature to refer to these amino acids as glutamate and aspartate without reference to the nature of the cation or cations present as counter ions. Such “-ate” endings are also used for most other acids (e.g., malate, oxaloacetate, phosphate, and adenylate) and in names of enzymes (e.g., lactate
dehydrogenase).
During the formation of polypeptides, the α-amino and carboxyl groups of the amino acids are converted into the relatively unreactive and uncharged amide (peptide)
groups except at the two chain termini. In many cases the terminal amino and carboxyl groups are also converted within cells into uncharged groups (Chapter 10). Immediately
after the protein is synthesized its terminal carboxyl group is often converted into an amide. The N terminus may be acetylated or cyclized to a pyroglutamyl group. Sometimes a cyclic peptide is formed.
The properties of polypeptides and proteins are determined to a large extent by the chemistry of the side chain groups, which may be summarized briefly as follows. Glycine in a peptide permits a maximum of conformational mobility. The nine relatively nonpolar amino acids–alanine, valine, leucine, isoleucine, proline, methionine, phenylalanine, tyrosine, and tryptophan– serve as building blocks of characteristic shape. Tyrosine and tryptophan also participate in hydrogen bonding and in aromatic: aromatic interactions within proteins.
Much of the chemistry of proteins involves the side chain functional groups –OH, –SH, –COO–, –NH3 +, and imidazole and the guanidinium group of arginine. The side chains of asparagine and glutamine both contain the amide group CONH2, which is relatively inert chemically but which can undergo hydrogen-bonding interactions. The amide linkages of the polypeptide backbone must also be regarded as important functional groups. Most polar groups are found on the outside surfaces of proteins where they can react chemically in various ways. When inside proteins they form H-bonds to the peptide backbone and to other polar groups.