Proteins are polymers of the bifunctional monomer, amino acids. The twenty common naturally-occurring amino acids each contain an α-carbon, an α-amino group, an α-carboxylic acid group, and an α-side chain or side group. These side chains (or R groups) may be either nonpolar, polar and uncharged, or charged, depending on the pH and pKa of the ionizable group. Two other amino acids occasionally appear in proteins. One is selenocysteine, which is found in Archaea, eubacteria, and animals and just recently found is pyrrolysine, found in Archaea. We will concentrate on only the 20 abundant, naturally-occurring amino acids.