Continued from 3AA-3 to 3AA-5
Contents of 3AA-6 to 3AA-10
Part 1, Section B: Nomenclature of Non-Peptide Derivatives of Amino Acids
Continued in 3AA-11 to 3AA-13
If an amino acid is substituted on a saturated carbon, it remains an amino acid. Its naming is therefore described in 3AA-2. This section extends some of the procedures described there, and also covers modification of functional groups.
A number of special procedures are given below to allow names to be based on the trivial names of the α-amino acids, so that they may indicate biochemical relationships. These procedures, which yield names such as N6-lysino (3AA-7), alanin-3-yl (3AA-8), leucinamide (3AA-9.2), phenylalanylchloromethane (3AA-10.2), alaninol (3AA-10.3), etc., should not be extended to other areas.
3AA-6. IONIZATION OF FUNCTIONAL GROUPS AND NAMING OF SALTS
The predominant form at pH 7 of a mono-amino-mono-carboxylic acid is R-CH(NH3+)-COO- rather than R-CH(NH2)-COOH. It is nevertheless often convenient to draw the latter conventional form (e.g. in Table 1) and to name alanine as 2-aminopropanoic acid rather than as 2-ammoniopropanoate. This is particularly so for representing the isoeleetric form of amino acids that contain other ionizing groups. A solution of lysine, for example, would contain appreciable amounts of both NH3+-[CH2]4-CH(NH2)-COO- and NH2-[CH2]4-CH(NH3+)-COO-.
When it is desirable to mention or stress the ionic nature of an amino acid, the three kinds of ions possible for a mono-aminomono-carboxylic compound may be indicated as follows:
NH3+-CH2 -COO– glycine zwitterion (or dipolar ion, or amphion);
NH3+-CH2-COOH glycinium, or glycine cation;
NH2-CH2-COO– glycinate, or glycine anion.
In indicating an anion the ending 'ate' replaces 'ic acid' or the final 'e' of the trivial name, or is added to the name tryptophan.
Further forms are required for amino acids that contain ionizing side chains. The singly charged anions of aspartic and glutamic acids (strictly each has two negative and one positive charge, but this nomenclature refers to net charge) may be distinguished from the doubly charged anions by placing the charge after the name, or by stating the number of neutralizing ions. Thus the form of glutamate (glutamate refers to glutamic acid; glutaminate is the anion from glutamine) with a charge of minus one, –OOC-CH2-CH2-CH(NH3+)-COO–, may be called glutamate(1–), glutamic acid monoanion, or hydrogen glutamate, and its sodium salt may be called sodium glutamate(1–), sodium hydrogen glutamate, or monosodium glutamate. The corresponding terms for the dianion, –OOC-CH2-CH2-CH(NH2)-COO–, include glutamate(2–), glutamic-acid dianion, and disodium glutamate. Unqualified, the word glutamate systematically means the dianion; hence the usage 'sodium hydrogen glutamate'; in normal use, however, it means the ion of net charge –1, since this is the form that predominates in neutral solution, and it is used in this way in, for example, 'a glutamate-dependent reaction' and 'glutamate dehydrogenase'.
Similarly, forms such as lysinium(1+) or lysine monocation may be used for the ion of unit net charge derived from lysine. Its salts may be indicated by adding the name of the anion to the lysinium form, e.g. lysinium(1+) chloride, or by naming it lysine monohydrochloride. The fully protonated form is the lysine dication or lysinium(2+).
3AA-7. AMINO ACIDS SUBSTITUTED ON NITROGEN
Since N-2 is the atom most easily modified in many amino acids, the locant can often be omitted without ambiguity, e.g. acetylglycine for N-acetylglycine.
It is sometimes convenient to use the name of a group derived by loss of hydrogen from a nitrogen atom of an amino acid as a prefix in forming another name. Such prefixes are formed by substituting 'o' for the terminal 'e' in those names that end in 'e' (by analogy with amine -> amino); e.g. alanino, valino. Tryptophan adds the 'o' directly, and the two dicarboxylic acids become asparto and glutamo. Where there is more than one nitrogen atom in the amino acid, a locant of the form Nx must precede the group name. e.g. N6-lysino, Nω-arginino, N5-glutamino, Nπ-histidino.
3AA-8. SIDE-CHAIN MODIFICATIONS (excluding modifications of carboxyl or nitrogen)
Most modified amino acids can be named according to 3AA-2, e.g. S-(carboxymethyl)-L-cysteine. Groups formed by loss of hydrogen atoms from carbon, sulfur or oxygen atoms (excluding the carboxylic oxygen atoms, which are dealt with under 3AA-9) are named by substituting '-x-yl' for the terminal 'e' of the trivial name, where 'x' is the locant of the atom from which the hydrogen atom has been lost, e.g. cystein-S-yl, threonin-O3-yl, alanin-3-yl, or by adding '-x-yl' to aspartic, glutamic and tryptophan, e.g. aspartic-2-yl, tryptophan-2-yl (see 3AA-2.2.3).
Comment. Tryptophan-1-yl should be named l-tryptophano according to 3AA-7.
A common side-chain modification is the oxidation of cysteine to yield cystine (formula in Appendix). Hydrogen atoms are removed from the -SH groups of two molecules, which are joined by an S-S bond. The term 'half cystine' refers to each half. It occurs seldom in naming compounds, since half a cystine molecule is a substituted cysteine and is named as such. In stating amount of substance, however, any specified entity may be used, so moles or numbers of residues of half cystine may usefully be compared with these quantities of other amino acids in stating protein composition.
3AA-9. ESTERS AND AMIDES OF THE CARBOXYL GROUP
Esters are named with the anion name (3AA-6), e.g. methyl prolinate, methyl cysteinate, or from the amino acid, e.g. proline methyl ester, cysteine methyl ester.
3AA-9.2. Amides, Anilides and Analogous Derivatives (H2N-CHR-CO-NH-R')
In amides, anilides and analogous derivatives of α-amino acids the hydroxyl group of the carboxyl has been replaced by an amino, anilino, or analogous group. They may be named by replacing the final 'e' of the trivial name of the amino acid by the word 'amide', 'anilide', etc., e.g. glycinamide, leucinamide, argininanilide. Alternatively, these compounds may be described as glycine amide, leucine amide, etc.
Note that the 4-amide of aspartic acid and the 5-amide of glutamic acid have specific trivial names, asparagine and glutamine. Their 1-amides are named aspartic 1-amide and glutamic 1-amide, or isoasparagine and isoglutamine.
The acyl group of an α-amino-mono-carboxylic acid is a structure that lacks the hydroxyl group of the carboxyl (H2N-CHR-CO-). The names of such groups are formed by replacing the ending 'ine' (or 'an' in tryptophan) by 'yl' (C-421 of reference [14]), e.g. alanyl, arginyl, tryptophyl. 'Cysteinyl' is used instead of 'cysteyl', because of potential confusion with the group from cysteic acid. 'Cystyl' is the diacyl group of cystine, and 'half-cystyl' is the acyl group of cysteine lacking also the H of its SH group.
The monoacyl groups derived from aspartic acid, HOOC-CH2 -CH(NH2)-CO- and -CO-CH2-CH(NH2)-COOH, are designated α-aspartyl (or aspart-1-yl) and β-aspartyl (or aspart-4-yl) respectively; the corresponding groups derived from glutamic acid are α-glutamyl (or glutam-l-yl) and γ-glutamyl (or glutam-5-yl) (C-421.3 of reference [14]). The diacyl groups formed from the dicarboxylic amino acids are aspartoyl and glutamoyl. The acyl groups derived from asparagine and glutamine are termed asparaginyl and glutaminyl respectively.
3AA-10. CARBOXYL GROUP MODIFICATIONS OTHER THAN ESTER AND AMIDE FORMATION
3AA-10.1. Removal of the Carboxyl Group
Several decarboxylated amino acids have trivial names terminated with 'amine': tyramine, histamine, cysteamine, tryptamine, methioninamine. Similarly cystine (see Appendix) forms cystamine.
If the hydroxyl group of the 1-carboxyl is replaced by an alkyl group, the name of the ketone formed can use the name of the amino acid by naming the compound as a substituted hydrocarbon, e.g. phenylalanylchloromethane for C6H5-CH2-CH(NH2)CO-CH2Cl, 3-amino-1-chloro-4-phenylbutan-2-one (see also 3AA-18.2). This type of name is based on the trivial names of amino acids (or peptides), so does not place the substituents of methane in alphabetical order (as systematic nomenclature does), but places 'chloromethane' at the end because this indicates C-terminal modification (see 3AA-13.1). The practice of using names such as 'phenylalanine chloromethyl ketone' is discouraged, because they erroneously specify the carbonyl group twice.
3AA-10.3. Aldehydes and Alcohols
Aldehydes and alcohols obtained by successive stages of reduction of the carboxyl group of α-amino acids are named by replacing the final 'e' of a trivial name ending in 'ine' (or the 'ic acid' of aspartic and glutamic acids) with the endings 'al' and 'ol' respectively.
Examples. R-CH(NH2)-CHO: alaninal, leucinal, lysinal, serinal, aspart-l-al, glutaminal. R-CH(NH2)-CH2OH: alaninol, leucinol, lysinol, serinol, aspart-l-ol, glutaminol. The aldehyde and alcohol derivatives of tryptophan take the names tryptophanal and tryptophanol. The name glycinol is little used, because the systematic name 2-aminoethanol is short, and this already has the trivial name ethanolamine [19].
Note. The derivative of lysine in which the -CH2-NH2 group is replaced by -CHO has the trivial name allysine (see Appendix).
7. International Union of Biochemistry (1978) Biochemical Nomenclature and Related Documents, The Biochemical Society, London.
14. International Union of Pure and Applied Chemistry (1979) Nomenclature of Organic Chemistry, Sections A, B, C, D, E, F and H, Pergamon Press, Oxford.
19. IUPAC-IUB Commission on Biochemical Nomenclature (CBN), The Nomenclature of Lipids, Recommendations l976, Biochem. J. 171, 21-35 (1978); Eur. J. Biochem. 79, 11-21 (1977); Hoppe-Seyler's. Z. Physiol. Chem. 358, 617-631 (1977); Lipids, 12, 455-468 (1977); also pp. 122-132 in [7].
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