Abstract
Within this chapter, the fundamental properties of amino acids are presented. The basic chemical features of amino acids are the ubiquitous amino and acid groups; the residue of the molecule is usually referred to as side chain. Of an infinite number of conceivable amino acids, twenty (plus a few more or less frequent) members are found in proteins of living beings and thus play a crucial role in the chemistry of life. From a chemical point of view, the chirality of most amino acids is an important feature, which is discussed in regard with the nomenclature systems conventionally employed. Chirality is related with symmetry, both of the molecule and the crystal structure of amino acids (or their salts). Moreover, the chemical flexibility of amino acids, both in terms of symmetry and in terms of their amphoteric nature, is reviewed, thus forming the frame of reference for the following chapters which deal with the actual amino acid salts.
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Notes
- 1.
The etymological background of the trivial names is explained in the respective parts of Chap. 2.
- 2.
The numbering of atoms within an amino acid molecule should be done following the rules set by the IUPAC (1983). In acyclic amino acids, the carbon atoms are numbered as follows:
The C atom of the carboxyl group next to the C atom which carries the amino group is C-1, the rest follows consequently. As an alternative, Greek letters can be used, where the C-2 atom is designated α. Although the IUPAC recommend the numbers, not the Greek letters, the terms “α-amino acids” or “α-carbon atom” are frequently used in the literature.
Heteroatoms are given the same number as the carbon atom to which they are attached. The nitrogen atom of the “α-amino group” would thus be N-2. When identical side chains occur, such as in valine or leucine, they are given the same number, one with an apostrophe. In said examples, these methyl atoms are thus labeled C-4 and C-4’ (valine) and C-5 and C-5’ (leucine). In arginine, where the terminal amino groups are formally different (see scheme in Fig. 1.4) but in fact identical due to resonance, this system is also employed.
Amino acids with rings are numbered along the rules of the systematic nomenclature of rings; for rings with heteroatoms, the numbering scheme of the mother compound is used (see scheme for Pro, Phe, Trp, His in Fig. 1.4).
- 3.
One might wonder why a small excess of one form resulted in chiral biochemistry, as the other enantiomer would still be present, only in lower quantities. In other words, how come the chemical machinery of proteins is chiral at all? What prevented the development of achiral proteins, i.e., proteins made of amino acids of both chiralities? It was found that homochirality is necessary for the origin of life. Peptides of both l- and d- amino acids cannot fold into bioactive configurations, as, for instance, the α-helix (Bada 1996). Proteins from d- or l-amino acids work equally well, but proteins from racemates do not form effective enzymes.
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Fleck, M., Petrosyan, A.M. (2014). Introduction. In: Salts of Amino Acids. Springer, Cham. https://doi.org/10.1007/978-3-319-06299-0_1
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