CO2 assimilation provides the carbon skeletons required for the synthesis of the various amino acids (Figure 27.3). 3-Phosphoglycerate is the most important carbon precursor for the synthesis of amino acids and from its converted form, phosphoenolpyruvate (PEP), two pathways branch off leading to pyruvate and oxalacetate. Moreover, PEP in combination with erythrose 4-phosphate is the precursor for the synthesis of aromatic amino acids via the shikimate pathway. The pathways proposed for amino acid biosynthesis in plants are inferred in large part from those defined in Escherichia coli and yeast, where the steps and regulatory mechanisms have been identified using a combination of genetics, biochemistry and molecular biology.
Every protein molecule can be viewed as a polymer of the 20 common amino acids. The centre is comprised of a tetrahedral carbon atom forming a chiral centre called the alpha (αα) carbon (Figure 27.4). It is covalently bonded on one side to an amino group and on the other side to a carboxyl group. The third bond is always hydrogen, and the fourth bond is to a variable side chain (R), eventually resulting in the l-configuration typical of most amino acids. d-amino acids also occur in nature but only as specialised forms, e.g. in peptide antibiotics such as actinomycin C1, fungisporin, gramicidin S, polymixin B1 and valinomycin. d-amino acids are formed by racemases as free intermediates and are subsequently incorporated into peptide bonds but these are ordinarily poor substrates for incorporation. Whether the l-amino acid is incorporated first and then the inversion occurs or vice versa has still to be determined in most cases. In neutral solution, the carboxyl group loses a proton and the amino group gains one. Thus, an amino acid in solution, while neutral overall, is a double charged species called a zwitterion (Figure 27.4). Depending on the structure of the side chain the 20 amino acids commonly found in proteins are grouped into the apolar group (alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan and methionine), the uncharged polar group (glycine, serine, threonine, cysteine, tyrosine, asparagine and glutamine) and the charged group (aspartic acid, glutamic acid, lysine, arginine and histidine). All these amino acids except proline have an ammonium ion attached to the carbon atom. In proline an N-C linkage forming part of a cyclic structure replaces one of the N-H linkages, leading to the formation of an imino acid.
In addition to the 20 commonly occurring αα-amino acids, a variety of other amino acids are found in minor amounts in protein and in non-protein compounds. The unusual amino acids found in proteins result from modification of the common amino acids. In a few cases these amino acids are incorporated directly into the polypeptide chains during synthesis (e.g. selenocysteine). Most frequently the amino acid is modified after incorporation (e.g. modification of proline to hydroxyproline). The types of unusual amino acids found in non-protein compounds are extremely variable and formed by a number of different metabolic pathways.
Amino acids can also be grouped together into ‘families’, each of which is derived from a single ‘head’ amino acid (Figure 27.3). Instead of being grouped according to the functionality of the side group these families are rather based on common precursors of metabolic trees. For example, the ‘aspartate family’ is comprised of asparagine, lysine, threonine, isoleucine and methionine, all synthesised from aspartic acid. Because more than one amino acid may be involved in the synthesis of another, a single amino acid may be assigned to more than one family, and it is not unusual for different authors to differ in their assignment.