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The priority for assigning one-letter symbols to amino acids is based on their frequency of occurrence. If multiple amino acids start with the same letter, the most commonly occurring amino acid is given that letter as its symbol. For instance, glycine, being more common than glutamate, is represented by the letter G.

Another criterion for assigning symbols is based on the similarity between the sound of the symbol and the amino acid it represents. For example, phenylalanine is represented by the letter F, and tryptophan by the letter W, as it sounds like "twyptophan" when pronounced in a certain way.

In cases where the first criterion cannot be applied, a one-letter symbol is assigned that is as close as possible in the alphabet to the initial letter of the amino acid. For instance, lysine is represented by the letter K. In addition, the symbols B and Z are assigned to represent aspartic acid or asparagine and glutamic acid or glutamine, respectively. The symbol X is used for an unidentified amino acid.

Amino acids with a chiral α-carbon, except glycine, exist in two isomeric forms, designated as D and L. These forms are enantiomers or mirror images of each other. The designation of the (+) form is given to the isomer that causes the plane of polarized light to rotate clockwise. While L-configuration amino acids are found in mammalian proteins, D-amino acids are present in certain antibiotics and bacterial cell walls.

Amino acids in aqueous solution have weakly acidic α-carboxyl groups and weakly basic α-amino groups. Additionally, acidic and basic amino acids have ionizable groups in their side chains. Therefore, both free amino acids and peptides can act as buffers. Acids donate protons, while bases accept protons. Weak acids or bases ionize to a limited extent. The concentration of protons in an aqueous solution is expressed as pH, where pH = log 1/[H+] or –log [H+]. The relationship between the pH, concentration of a weak acid (HA), and its conjugate base (A-) is described by the Henderson-Hasselbalch equation.

The derivation of the Henderson-Hasselbalch equation involves considering the release of a proton by a weak acid (HA) and the formation of its conjugate base (A-). The dissociation constant of the acid, Ka, determines the strength of the acid. By solving for the [H+], taking the logarithm of both sides of the equation, and substituting pH = −log [H+] and pKa = −log Ka, the Henderson-Hasselbalch equation is obtained.

Buffers are substances that can resist changes in pH. They consist of a weak acid and its conjugate base, which can maintain the pH of a solution within a certain range.

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Most commonly occurring amino acids have priority: If more than one amino acid begins with a particular letter, the most common of these amino acids receives this letter as its symbol. For example, glycine is more common than glutamate, so G = glycine.
3.
Similar sounding names: Some one-letter symbols sound like the amino acid they represent. For example, F = phenylalanine, or W = tryptophan (“twyptophan” as Elmer Fudd would say).
4.
Letter close to initial letter: For the remaining amino acids, a one-letter symbol is assigned that is as close in the alphabet as possible to the initial letter of the amino acid, for example, K = lysine. Furthermore, B is assigned to Asx, signifying either aspartic acid or asparagine; Z is assigned to Glx, signifying either glutamic acid or glutamine; and X is assigned to an unidentified amino acid.
F. Amino acid isomers
Because the α-carbon of an amino acid is attached to four different chemical groups, it is an asymmetric (chiral) atom. Glycine is the exception because its α-carbon has two hydrogen substituents. Amino acids with a chiral αcarbon exist in two different isomeric forms, designated D and L, which are enantiomers, or mirror images (Fig. 1.8). [Note: Enantiomers are optically active. If an isomer, either D or L, causes the plane of polarized light to rotate clockwise, it is designated the (+) form.] All amino acids found in mammalian proteins are of the L configuration. However, D-amino acids are found in some antibiotics and in bacterial cell walls (see p. 252). [Note: Racemases enzymatically interconvert the D-and L-isomers of free amino acids.]
III. ACIDIC AND BASIC PROPERTIES
Amino acids in aqueous solution contain weakly acidic α-carboxyl groups and weakly basic α-amino groups. In addition, each of the acidic and basic amino acids contains an ionizable group in its side chain. Thus, both free amino acids and some amino acids combined in peptide linkages can act as buffers. Acids may be defined as proton donors and bases as proton acceptors. Acids (or bases) described as weak ionize to only a limited extent. The concentration of protons ([H+]) in aqueous solution is expressed as pH, where pH = log 1/[H+] or –log [H+]. The quantitative relationship between the pH of the solution and concentration of a weak acid (HA) and its conjugate base (A−) is described by the Henderson-Hasselbalch equation.
A. Equation derivation
Consider the release of a proton by a weak acid represented by HA: The salt or conjugate base, A−, is the ionized form of a weak acid. By definition, the dissociation constant of the acid, Ka, is: [Note: The larger the Ka, the stronger the acid, because most of the HA has dissociated into H+ and A−. Conversely, the smaller the Ka, the less acid has dissociated and, therefore, the weaker the acid.] By solving for the [H+] in the above equation, taking the logarithm of both sides of the equation, multiplying both sides of the equation by −1, and substituting pH = −log [H+] and pKa = −log Ka, we obtain the Henderson-Hasselbalch equation:
B. Buffers