Each amino acid has a unique side chain. The simplest side chain is just one carbon atom with three hydrogen atoms and this side chain belongs to alanine. Some side chains contain sulfur, some contain nitrogen, some are branched and some are ring-shaped. About.com's Chemistry guide has more information about the chemical structure of amino acids.
The side chains also determine whether the amino acids are acidic, neutral, or basic (has to do with pH) and whether they are polar or non-polar (size of the difference of the electronegativity between the chemical bonds). So there are four classes of amino acids based on the different side chains:
- Non-polar and neutral: alanine, glycine, isoleucine, leucine, methionine, phenylalanine, proline, and valine.
- Polar and neutral: asparagine, cysteine, glutamine, serine, threonine, tryptophan, and tyrosine.
- Acidic and polar: aspartic acid, and glutamic acid.
- Basic and polar: arginine, histidine, and lysine.
Amino acids are the building blocks of protein. When you eat protein, your body breaks the protein down into individual amino acids and uses those amino acids to build all the proteins your body needs. If you eat animal sources of food or eat a variety of nuts, grains, seeds and legumes, you will get all of the eight essential amino acids that your body can't make for itself. Unless you are a vegan, you really don't have to worry about getting enough of the individual amino acids.
Sometimes individual amino acids are used therapeutically and sold as dietary supplements. For example, tryptophan is sometimes used to help treat depression and mood disorders and arginine has been used for lowering high blood pressure. Always speak to your health care provider before taking any dietary supplements, including amino acid supplements.
Sources:
Yetik-Anacak G, Catravas JD. "Nitric oxide and the endothelium: History and impact on cardiovascular disease." Vascul Pharmacol. 2006 Aug 17.
aan het Rot M, Moskowitz DS, Pinard G, Young SN. "Social behaviour and mood in everyday life: the effects of tryptophan in quarrelsome individuals." J Psychiatry Neurosci. 2006 Jul;31(4):253-62.

