1. The definition and structure of an amino acid are summarized with the three letters, AAA. Two functional groups that like water are the key characteristic of all amino acids however it can be noted that amino acids have limited solubilities in most solvents. With the exception of Pro, which is soluble in alcohol, free amino acids are relatively insoluble in common neutral solvents. Even in water, amino acids with large hydrophobic groups are very poorly soluble. Altering the charges by salt formation (next paragraph) will have a great affect on the solubilities in water and in polar organic solvents. With all three on one carbon, the carbon–hydrogen bond will be more labile; a property that is used both in chemistry and in metabolism. Ionization: At pH7, the amino group reaches out (→) for a proton to become positively charged; its pK is the number of words (9 words) in this definition. The pKs of the α-amino groups range from 9 to 10. They are comparable to the pK of ammonia (pK=9.2) and a bit lower than the 10–11pK range normally reported for aliphatic amines. As in the computer world one interprets bit as ±1 to recall these pK differences and the pKs of several other R groups (see endnotes 8,9,11,18). The carboxyl group drops (↓) a proton to become negatively charged, its pK is the number of lines (2 lines) in this definition (pK∼2). The arrows indicate the counting direction for each pK. Due to proximity effects, the pK of the amino group is about one order of magnitude less than the 10–11pK range of aliphatic amines, the pK of the acid group is about two orders of magnitude less acidic than that of normal aliphatic carboxyls and the alpha hydrogen is at least three orders of magnitude more reactive (more acidic) than a normal aliphatic hydrogen. One can note that the first A is ONE order of magnitude, the second, TWO, and the third, THREE, orders of magnitude more acidic than the comparable group on its own.
2. Stereochemistry: These two lines are part of a general method for determining absolute configurations (Using one's hands for naming optical isomers and other stereochemical positions (Mezl, V.A., Biochem. Educ. 24, 99–101, 1996)) In brief, when this method is used for amino acids, the forearm is considered as the bond going to the R group and fingers are named in the order A,A,A (thumb, amino group; index, carboxyl; third finger, α-hydrogen). When one points up with the index finger and down with the other two, the left hand models the absolute configuration of an L-amino acid and the right hand that of a D-amino acid. The lines recall that natural amino acids are of the L-configuration.
3. Another hydrogen on AAA (See endnote 1) gives a symmetrical α-carbon. Gly is the only amino acid that does not have a chiral atom.
4. Ala is the typical amino acid; they all have at least this carbon. One should consider that each of the following sections starts with the structure of Ala.
5. Ser is just Ala with an alcohol group. Another methyl on a carbon that already has a hydroxyl group (Ser) means that Thr has another chiral atom. Another always indicates another chiral centre in the AAA mnemonic (see endnote 7). Gives recalls that Thr is an essential amino acids (Section 2). For a quick list of the 10 essential amino acids for humans, one can use “Any Help In Learning These Little Molecules Proves Truly Valuable” to obtain the first letter of each essential amino acid or to obtain the first two letters of the abbreviations, one can learn a little philosophy in French: “Arrogant Historien Traditionel, Il Va Philosopher Le Meme Theme Lyrique”. Both lines start with the two essential amino acids that need some qualifications as to their requirements (see endnotes 11,18); the second line has the advantage that the following amino acids are then ranked essentially according to increasing hydrophilicity of their side chains and to their increasing solubility in boiling water. Boiling water is brought up in this overview to point out that in spite of the stability considerations that will be presented amino acids are very stable in aqueous solution, even at high temperature (with the exception of Gln, (see endnote 16).