In this blog post, I will point out important features of amino acids that you should know and some tips on how to learn them.
First off, all of the twenty amino acids you are expected to know are alpha amino acids. This means that there is only one carbon (the alpha carbon) attached to the carboxylic acid group. These amino acids, in general, consist of an amino group (which, under physiological conditions is always protonated, pKa ~ 9), the alpha carbon (which is connected to one hydrogen and the R group) and the carboxylic acid group (always deprotonated under physiological conditions, pKa ~ 2).
The Fischer projections of the naturally occurring amino acids in the body tell us that all the chiral amino acids (which includes all of them except glycine, with two hydrogens attached to the alpha carbon) are L amino acids. This means that in the Fischer projection, the amino group is on the left side.
18 out of the 19 L amino acids rotate plane polarized light in the counter-clockwise direction, meaning that they are S (remember, the D/L conventions do not necessarily correlate with the R/S conventions). Only cysteine is R due to the higher priority of the sulfur atom over the oxygen. Despite this, cysteine is still an L amino acid because the positioning of all the groups still matches the L form of the Fischer projection (D/L conventions don’t use Cahn-Ingold-Prelog priority assignments).
Finally, of course, know all the chemical properties of the amino acids. All amino acids are polar to some extent (since they exist as zwitterions and contain a number of hydrogen bond donors and acceptors) but, rather, are classified based on the identity of their R group. Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, and Methionine are non-polar and non-aromatic (aliphatic). Methionine is sulfur-containing, making it a good candidate to track via radioactive sulfur labeling. The non-polar amino acids tend to be found in the interior of proteins and the increase in entropy as a result of the formation of their hydrophobic interactions and the subsequent release of water drive polypeptide folding. Phenylalanine, Tyrosine, and Tryptophan are aromatic amino acids. They can form stable structures through pi-stacking. Asparagine, Glutamine, Serine, Threonine and Cysteine are polar and tend be found on the exterior of proteins, forming interactions with water, salts, and other polar compounds. Glutamate and Aspartate are considered to be acidic amino acids, but will generally be found in their deprotonated, negatively charged state due to their carboxyl groups. They can form nice ionic interactions with metal ions. Finally, we have the basic amino acids which include arginine, lysine, and histidine. All of their side chains are nitrogen-containing.