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Overview
General structure The general structure of proteinogenic alpha amino acids at a physiologically relevant pH: R | +H3N-Cα-COO- | H Where R represents a side chain specific to each amino acid, and Cα the chiral central carbon atom to which the two termini and the R-group are attached. Amino acids are usually classified by the properties of the side chain into four groups. The side chain can make them behave like a weak acid, a weak base, a hydrophile, if they are polar, and hydrophobe if they are nonpolar. The chemical structures of the 20 standard amino acids, along with their chemical properties, are cataloged in the list of standard amino acids. The phrase "branched-chain amino acids" is sometimes used to refer to the amino acids having aliphatic side-chains that are non-linear: leucine, isoleucine and valine. Isomerism Most amino acids occur in two possible optical isomers, called D and L. The L-amino acids represent the vast majority of amino acids found in proteins. D-amino acids are found in some proteins produced by exotic sea-dwelling organisms, such as cone snails. They are also abundant components of the proteoglycan cell walls of bacteria. The D-isomer of aspartic acid is found in some proteins as the result of a spontaneous post-translational modification associated with protein aging or as the by-product of enzymatic modification catalyzed by protein L-isoaspartyl methyltransferase. The L and D conventions for amino acid do not refer to their own optical activity, but rather to the optical activity of glyceraldehyde as an analogue of the amino acids. S-Glyceraldehyde is levorotary, and R-glyceraldehyde is dexterorotary, and so S-amino acids are called L- even if they are not levorotary, and R-amino acids are likewise called D- even if they are not dexterorotary. Exceptions Two exceptions exist: Reactions
Hydrophilic and hydrophobic amino acids Depending on the polarity of the side chain, aminoacids can be hydrophilic or hydrophobic to various degrees. This influences their interaction with other structures, both within the protein itself and within other proteins. The distribution of hydrophilic and hydrophobic aminoacids determines the tertiary structure of the protein, and their physical location on the outside structure of the proteins influences their quaternary structure. For example, soluble proteins have surfaces rich with polar aminoacids like serine and threonine, while integral membrane proteins tend to have outer ring of hydrophobic aminoacids that anchors them to the lipid bilayer, and proteins anchored to the membrane have a hydrophobic end that locks into the membrane. Similarly, proteins that have to bind to positively-charged molecules have surfaces rich with negatively charged aminoacids like glutamate and aspartate, while proteins binding to negatively-charged molecules have surfaces rich with positively charged chains like lysine and arginine. Hydrophilic and hydrophobic interactions of the proteins do not have to rely only on the sidechains of aminoacids themselves. By various posttranslational modifications other chains can be attached to the proteins, forming hydrophobic lipoproteins or hydrophilic glycoproteins. Table of standard amino acid abbreviations A star ( Nonstandard amino acids Aside from the twenty standard amino acids and the two special amino acids, selenocysteine and pyrrolysine, already mentioned above, there are a vast number of "nonstandard amino acids" which are not incorporated into protein. Examples of nonstandard amino acids include the sulfur-containing taurine and the neurotransmitters GABA and dopamine. Other examples are lanthionine, 2-Aminoisobutyric acid, and dehydroalanine. Nonstandard amino acids often occur in the metabolic pathways for standard amino acids - for example ornithine and citrulline occur in the urea cycle, part of amino acid breakdown. Nonstandard amino acids are usually formed through modifications to standard amino acids. For example, taurine can be formed by the decarboxylation of cysteine, while dopamine is synthesized from tyrosine and hydroxyproline is made by a posttranslational modification of proline (common in collagen). Over 79 amino acids were found in the primitive Murchison meteorite. Uses of substances derived from amino acids Nutritional importance Some of the 20 standard proteinogenic amino acids are called essential amino acids because the human body cannot synthesize them from other compounds through chemical reactions, and they therefore must be obtained from food. Histidine and arginine are generally only considered essential in children, because the metabolic pathways that synthesize these amino acids are not fully developed in children. ( A helpful mnemonic for remembering essential amino acids is "Private Tim Hall" (PVT TIM HALL). Arginine, although not required in normal adults is required for infants. Another, that lists them in alphabetical order, is "ILL MPs Take To Valium." Kreb's trick to remember the essential amino acids: Archibald Vivian HILL Member of Parliament Tee Totalist. See also | |||||||||||||
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