Protein – Classification
The structures and abbreviations for the 20 amino acids commonly found in proteins are shown in Figure 4.5. All the amino acids except proline have both free amino and free carboxyl groups. The classifications of amino acids is based on the polarity of the side chains. Thus, the structures shown in Figure 4.5 are grouped into the following categories: (1) nonpolar or hydrophobic amino acids, (2) neutral (uncharged) but polar amino acids, (3) acidic amino acids (which have a net negative charge at pH 7.0), and (4) basic amino acids (which have a net positive charge at neutral pH).
Nonpolar Amino Acids
The nonpolar amino acids include all those with alkyl chain R groups (alanine, valine, leucine, and isoleucine), as well as proline (with its unusual cyclic structure), methionine (one of the two sulfur-containing amino acids), and two aromatic amino acids, phenylalanine and tryptophan. Tryptophan is sometimes considered a borderline member of this group because it can interact favorably with water via the N–H moiety of the indole ring. Proline, strictly speaking, is not an amino acid but rather an a-imino acid.
