classification of amino acids

Twenty amino acids is a lot to hold in your head all at once. So chemists sort them into a few families by the personality of their side chains, the same way you might sort a tool drawer into 'cutting,' 'gripping,' and 'measuring.' Knowing which family an amino acid belongs to tells you, at a glance, how it will behave inside a protein.

The most useful grouping has four families. Nonpolar (hydrophobic) amino acids — such as leucine, valine, phenylalanine — have greasy, water-fearing side chains; in water they shy away and tend to cluster in a protein's interior. Polar (uncharged) amino acids — such as serine, threonine, glutamine — carry side chains that can hydrogen-bond with water and so are comfortable on the surface. Acidic amino acids — aspartate and glutamate — have side chains that lose a proton and end up negatively charged at the body's pH. Basic amino acids — lysine, arginine, histidine — have side chains that pick up a proton and end up positively charged. (Special cases like glycine, proline, and cysteine sit a little outside this scheme.)

This sorting is not bookkeeping for its own sake; it predicts structure. Because water-fearing side chains bury themselves and water-loving ones face out, the pattern of nonpolar versus polar residues along a sequence is the main thing that drives folding. Charged side chains of opposite sign form salt bridges that staple the fold; clusters of basic residues are how many proteins grip the negatively charged backbone of DNA. Read the families and you can begin to read the protein.