Amino acid

Overview

Alpha-amino acids are the building blocks of primary structure of the protein. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins.

Twenty essential amino acids.

Functions in proteins

See also: Posttranslational modification

  Amino acids are the basic structural building units of phospholipid membrane.

Non-protein functions

The twenty standard amino acids are either used to synthesize proteins and other biomolecules, or oxidized to gluconeogenesis.^[4]

Hundreds of types of non-protein amino acids have been found in nature and they have multiple functions in living organisms. hormone ethylene.^[6]

In humans, non-protein amino acids also have biologically-important roles. neurotransmitters and many amino acids are used to synthesize other molecules, for example:

• serotonin
• heme
• nitric oxide
• lipid transport within a cell,
• polyamines,
• S-adenosylmethionine recycling

Also present are thyroid hormones are also alpha-amino acids.

Some amino acids have even been detected in meteorites, especially in a type known as carbonaceous chondrites.^[7] This observation has prompted the suggestion that life may have arrived on earth from an extraterrestrial source.

General structure

Further information: List of standard amino acids

 

In the structure shown to the right, the R represents a side chain specific to each amino acid. The central carbon atom called C_α is a list of standard amino acids.

The phrase "branched-chain amino acids" or BCAA is sometimes used to refer to the amino acids having aliphatic side-chains that are non-linear, these are leucine, proteinogenic amino acid whose side group links to the α-amino group, and thus is also the only proteinogenic amino acid containing a secondary amine at this position. Proline has sometimes been termed an imino acid, but this is not correct in the current nomenclature.^[8]

 

Isomerism

Most amino acids can exist in either of two 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.^[9] They are also abundant components of the peptidoglycan cell walls of bacteria.^[10]

The L and D conventions for amino acid configuration do not refer to the optical activity of the amino acid itself, but rather to the optical activity of the isomer of glyceraldehyde having the same stereochemistry as the amino acid. 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.

There are two exceptions to these general rules of amino acid isomerism. Firstly, Cahn-Ingold-Prelog priority rule.

Reactions

As amino acids have both a primary decarboxylation for the carboxylic acid group. The multiple side chains of amino acids can also undergo chemical reactions. The types of these reactions are determined by the groups on these side chains and are discussed in the articles dealing with each specific type of amino acid.

Peptide bond formation

 

For more details on this topic, see Peptide bond.

As both the amine and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can react with another and become joined through an amide linkage. This ribosome, which catalyzes the attack of the amino group of the elongating protein chain on the ester bond.^[12] As a result of this mechanism, all proteins are synthesized starting at their N-terminus and moving towards their C-terminus.

However, not all peptide bonds are formed in this way. In a few cases peptides are synthesized by specific enzymes. For example, the tripeptide glycine by glutathione synthetase to form glutathione.^[14]

In chemistry, peptides are synthesized by a variety of reactions. One of the most used in solid-phase peptide synthesis, which uses the aromatic oxime derivatives of amino acids as activated units. These are added in sequence onto the growing peptide chain, which is attached to a solid resin support.^[15]

Zwitterions

 

As amino acids have both the active groups of an amine and a carboxylic acid they can be considered both acid and base (though their natural pH is usually influenced by the R group). At a certain pH known as the zwitterion, which comes from the German word Zwitter meaning "hybrid". A zwitterion can be extracted from the solution as a white crystalline structure with a very high melting point, due to its dipolar nature. Near-neutral physiological pH allows most free amino acids to exist as zwitterions.

Hydrophilic and hydrophobic amino acids

Depending on 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 amino acids like glutamate and aspartate, while proteins binding to negatively-charged molecules have surfaces rich with positively charged chains like lysine and arginine. Recently a new scale of hydrophobicity based on the free energy of hydrophobic association has been proposed.^[16]

Hydrophilic and hydrophobic interactions of the proteins do not have to rely only on the sidechains of amino acids themselves. By various glycoproteins.

Table of standard amino acid abbreviations and side chain properties

Main article: List of standard amino acids

Amino Acid	3-Letter	1-Letter	Side chain polarity	Side chain acidity or basicity	Hydropathy index[17]
Alanine	Ala	A	nonpolar	neutral	1.8
Arginine	Arg	R	polar	basic (strongly)	-4.5
Asparagine	Asn	N	polar	neutral	-3.5
Aspartic acid	Asp	D	polar	acidic	-3.5
Cysteine	Cys	C	polar	neutral	2.5
Glutamic acid	Glu	E	polar	acidic	-3.5
Glutamine	Gln	Q	polar	neutral	-3.5
Glycine	Gly	G	nonpolar	neutral	-0.4
Histidine	His	H	polar	basic (weakly)	-3.2
Isoleucine	Ile	I	nonpolar	neutral	4.5
Leucine	Leu	L	nonpolar	neutral	3.8
Lysine	Lys	K	polar	basic	-3.9
Methionine	Met	M	nonpolar	neutral	1.9
Phenylalanine	Phe	F	nonpolar	neutral	2.8
Proline	Pro	P	nonpolar	neutral	-1.6
Serine	Ser	S	polar	neutral	-0.8
Threonine	Thr	T	polar	neutral	-0.7
Tryptophan	Trp	W	nonpolar	neutral	-0.9
Tyrosine	Tyr	Y	nonpolar	neutral	-1.3
Valine	Val	V	nonpolar	neutral	4.2

In addition to the normal amino acid codes, placeholders were used historically in cases where crystallographic analysis of a peptide or protein could not completely establish the identity of a certain residue in a structure. The ones they could not resolve between are these pairs of amino-acids:

Ambiguous Amino Acids	3-Letter	1-Letter
Asparagine or aspartic acid	Asx	B
Glutamine or glutamic acid	Glx	Z
Leucine or Isoleucine	Xle	J
Unspecified or unknown amino acid	Xaa	X

Unk is sometimes used instead of Xaa, but is less standard.

Nonstandard 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. enzymes that they use to produce methane. It is coded for with the codon UAG.^[19]

Examples of nonstandard amino acids that are not found in proteins include catabolism.^[20]

Nonstandard amino acids are usually formed through modifications to standard amino acids. For example, proline.^[22]

Uses in technology

Amino acid derivative	Use in industry
Aspartame (aspartyl-phenylalanine-1-methyl ester)	Low-calorie artificial sweetener
5-HTP (5-hydroxytryptophan)	Treatment for depression and the neurological problems of phenylketonuria.
L-DOPA (L-dihydroxyphenylalanine)	Treatment for Parkinsonism.
Monosodium glutamate	Food additive that enhances flavor. Confers the taste umami.

Nutritional importance

Further information: Protein in nutrition

Of the 20 standard proteinogenic amino acids, 8 are called arginine are semiessential amino acids in children, because the metabolic pathways that synthesize these amino acids are not fully developed.^[24] 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	Nonessential
Isoleucine	Alanine
Leucine	Asparagine
Lysine	Aspartate
Methionine	Cysteine*
Phenylalanine	Glutamate
Threonine	Glutamine*
Tryptophan	Glycine*
Valine	Proline*
Arginine*	Serine*
Histidine*	Tyrosine*

(*) Essential only in certain cases.^[25][26]

Several common mnemonics have evolved for remembering the ten amino acids often described as essential. PVT TIM HALL ("Private Tim Hall") uses the first letter of each of these amino acids.^[27] Another mnemonic that frequently occurs in student practice materials beneath "TV TILL Past Midnight", which just includes the 8 essential amino acids, is "These ten valuable amino acids have long preserved life in man".^[28]

See also

• Biochemistry
• Beta amino acid
• Strecker amino acid synthesis
• Glucogenic amino acid
• Murchison meteorite, an extraterrestrial source of amino acids.
• Table of codons, 3-nucleotide sequences that encode each amino acid
• List of standard amino acids (including chemical structures)
• Amino acid dating

References and notes

Further reading

• Doolittle, R.F. (1989) Redundancies in protein sequences. In Predictions of Protein Structure and the Principles of Protein Conformation (Fasman, G.D. ed) Plenum Press, New York, pp. 599-623
• David L. Nelson and Michael M. Cox, Lehninger Principles of Biochemistry, 3rd edition, 2000, Worth Publishers, ISBN 1-57259-153-6

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