INTRODUCTION TO AMINO ACIDS

Standard amino acids

Amino acids are the basic structural building units of proteins. They form short polymer chains called peptides or longer chains called either polypeptides or proteins. These polymers are linear and unbranched. The process of making proteins is called translation and involves the step-by-step addition of amino acids to a growing protein chain by a ribozyme that is called a ribosome.^[18] The order in which the amino acids are added is read through the genetic code from an mRNA template, which is a RNA copy of one of the organism's genes. Twenty amino acids are encoded by the standard genetic code and are called proteinogenic or standard amino acids.^[8]

The amino acid selenocysteine

[edit] Non-standard amino acids

Aside from the twenty standard amino acids, there are a vast number of "non-standard" amino acids. Two of these can be specified by the genetic code, but are rather rare in proteins. Selenocysteine is incorporated into some proteins at a UGA codon, which is normally a stop codon.^[19] Pyrrolysine is used by some methanogenic archaea in enzymes that they use to produce methane. It is coded for with the codon UAG.^[20] Other non-standard amino acids found in proteins are formed by post-translational modification, which is modification after translation in protein synthesis. These modifications are often essential for the function or regulation of a protein; for example, the carboxylation of glutamate allows for better binding of calcium cations,^[21] and the hydroxylation of proline is critical for maintaining connective tissues.^[22] Another example is the formation of hypusine in the translation initiation factor EIF5A, through modification of a lysine residue.^[23] Such modifications can also determine the localization of the protein, e.g., the addition of long hydrophobic groups can cause a protein to bind to a phospholipid membrane.^[24]

β-alanine and its α-alanine isomer.

Examples of nonstandard amino acids that are not found in proteins include lanthionine, 2-aminoisobutyric acid, dehydroalanine and the neurotransmitter gamma-aminobutyric acid. Nonstandard amino acids often occur as intermediates in the metabolic pathways for standard amino acids — for example ornithine and citrulline occur in the urea cycle, part of amino acid catabolism (see below).^[25] A rare exception to the dominance of α-amino acids in biology is the β-amino acid beta alanine (3-aminopropanoic acid), which is used in plants and microorganisms in the synthesis of pantothenic acid (vitamin B5), a component of coenzyme A.^[26]

[edit] In human nutrition

When taken up into the body in the diet, the 20 standard amino acids are either used to synthesize proteins and other biomolecules or oxidized to urea and carbon dioxide as a source of energy.^[27] The oxidation pathway starts with the removal of the amino group by a transaminase, the amino group is then fed into the urea cycle. The other product of transamidation is a keto acid that enters the citric acid cycle.^[28] Glucogenic amino acids can also be converted into glucose, through gluconeogenesis.^[29]

Of the 20 standard amino acids, 8 are called essential amino acids because the human body cannot synthesize them from other compounds at the level needed for normal growth, so they must be obtained from food.^[30] However, the situation is quite complicated since cysteine, taurine, tyrosine, histidine and arginine are semiessential amino acids in children, because the metabolic pathways that synthesize these amino acids are not fully developed.^[31][32] The amounts required also depend on the age and health of the individual, so it is hard to make general statements about the dietary requirement for some amino acids.

(*) Essential only in certain cases.^[33][34]

Several common mnemonics have evolved for remembering the essential amino acids. PVT TIM HALL ("Private Tim Hall") uses the first letter of each of these amino acids.^[35] Another mnemonic that frequently occurs in student practice materials beneath "AH TV TILL Past Midnight", is "These ten valuable amino acids have long preserved life in man". Note that these are based on the first letter of the common name for the amino acid and not the single letter codes used in molecular biology.^[36]

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