amino acid: Definition and Much More from Answers.com

This article is about the class of chemicals. For the structures and properties of the standardproteinogenic amino acids, seeList of standard amino acids.

Phenylalanine is one of the standard amino acids.
Inchemistry, an amino acid is amolecule thatcontains bothamine andcarboxylfunctional groups. Inbiochemistry, this term refers toalpha-amino acids with the general formula NH2CHRCOOH.[1] These are molecules where the amino and carboxylate groups are attached to the samecarbon, which is called theα–carbon. The various alpha amino acids differin whichside chain (R group) is attached to their alpha carbon. This can vary in size fromjust a hydrogen atom inglycine, through amethyl group inalanine, to a largeheterocyclic group intryptophan.
Alpha-amino acids are the building blocks ofproteins. A protein forms via the condensationof amino acids to form a chain of amino acid "residues" linked bypeptide bonds. Eachdifferent protein has a unique sequence of amino acid residues; this sequence is theprimarystructure 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.
There are twentystandard amino acids used bycells inprotein biosynthesis, and these are specified bythe generalgenetic code. These twenty amino acids arebiosynthesized from other molecules, but organisms differ in which ones they can synthesize and which onesmust be provided in their diet. The ones that cannot be synthesized by an organism are calledessential amino acids.
Overview
Functions in proteins
See also:Primary structure andPosttranslational modification

Apolypeptide is a chain of amino acids.
Amino acids are the basic structural building units ofproteins. They form shortpolymer chains calledpeptides or longer chains either calledpolypeptides orproteins. The process of such formation from anmRNA template is known astranslation whichis part ofprotein biosynthesis. Twenty amino acids are encoded by the standardgenetic code and are calledproteinogenicorstandard amino acids. Other amino acids contained in proteins areusually formed bypost-translational modification, which is modificationafter translation in protein synthesis. These modifications are often essential for the function or regulation of a protein; forexample, thecarboxylation ofglutamate allows forbetter binding ofcalciumcations, and thehydroxylation ofproline is critical for maintainingconnective tissues and responding tooxygen starvation. Such modifications canalso determine the localization of the protein, e.g., the addition of long hydrophobic groups can cause a protein to bind to aphospholipid membrane.
Non-protein functions
The twenty standard amino acids are either used to synthesize proteins and other biomolecules, or oxidized tourea and carbon dioxide as a source of energy.[2] The oxidation pathway starts with the removal of the amino group by atransaminase, the amino group is then fed into theurea cycle. Theother product of transamidation is aketo acid that enters the citric acid cycle.[3]Glucogenic aminoacids can also be converted into glucose, throughgluconeogenesis.[4]
Hundreds of types of non-protein amino acids have been found in nature and they have multiple functions in living organisms.Microorganisms and plants can produce uncommon amino acids. In microbes, examples include2-aminoisobutyric acid andlanthionine,which is a sulfide-bridged alanine dimer. Both these amino acids are both found in peptidiclantibiotics such asalamethicin.[5] While in plants,1-Aminocyclopropane-1-carboxylic acid is a small disubstituted cyclic amino acidthat is a key intermediate in the production of the planthormoneethylene.[6]
In humans, non-protein amino acids also have biologically-important roles.Glycine,gamma-aminobutyric acid andglutamate areneurotransmitters and many amino acids are used to synthesize other molecules, forexample:
Tryptophan is a precursor of the neurotransmitterserotonin
Glycine is a precursor ofporphyrins such asheme
Arginine is a precursor of the hormonenitric oxide
Carnitine is used inlipid transport within acell,
Ornithine andS-adenosylmethionine are precursors ofpolyamines,
Homocysteine is an intermediate inS-adenosylmethionine recycling
Also present arehydroxyproline,hydroxylysine,andsarcosine. Thethyroid hormones are alsoalpha-amino acids.
Some amino acids have even been detected inmeteorites, especially in a type known ascarbonaceous chondrites.[7] This observation has prompted the suggestion that life may have arrived on earth from anextraterrestrial source.
General structure
Further information:List of standard amino acids

The general structure of an α-amino acid, with theamino group on the left and thecarboxyl group on the right.
In the structure shown to the right, the R represents aside chain specific to eachamino acid. The central carbon atom called Cα is achiral centralcarbon atom (with the exception of glycine) to which the two termini and the R-group areattached. Amino acids are usually classified by theproperties of the side chain intofour groups. The side chain can make them behave like aweak acid, aweakbase, ahydrophile if they arepolar, andhydrophobe if they arenonpolar. The chemical structures of the 20 standard amino acids, along with their chemicalproperties, are cataloged in thelist of standard amino acids.
The phrase "branched-chain amino acids" or BCAA is sometimes used to referto the amino acids havingaliphatic side-chains that are non-linear, these areleucine,isoleucine andvaline.Proline is the onlyproteinogenic amino acid whose side group links to the α-amino group, and thus is also the onlyproteinogenic amino acid containing a secondary amine at this position. Proline has sometimes been termed animino acid, but this is not correct in the current nomenclature.[8]
[[Image:D+L-Alanine.gif|thumb|left|200px|The two optical isomers of alanine.]]
Isomerism
Most amino acids can exist in either of twooptical isomers, calledD and L. The L-amino acids represent the vast majority of amino acids found inproteins. D-amino acids are found in some proteins produced by exoticsea-dwelling organisms, such ascone snails.[9] They are also abundant components of thepeptidoglycancell walls ofbacteria.[10]
The L and D conventions for amino acid configuration do not refer to the optical activity, butrather to the optical activity of the isomer ofglyceraldehyde having the samestereochemistry as the amino acid. S-Glyceraldehyde is levorotary, and R-glyceraldehyde is dexterorotary, and soS-amino acids are called L- even if they are not levorotary, and R-amino acids are likewise calledD- even if they are not dexterorotary.
There are two exceptions to these general rules of amino acid isomerism. Firstly,glycine,where R = H, no isomerism is possible because the alpha-carbon bears two identical groups (hydrogen). Secondly, incysteine, the L = S and D = Rassignment is reversed to L = R and D = S. Cysteine is structuredsimilarly (with respect to glyceraldehyde) to the other amino acids but thesulfur atom altersthe interpretation of theCahn-Ingold-Prelog priority rule.
Reactions
As amino acids have both a primaryamine group and a primarycarboxyl group, these chemicals can undergo most of the reactions associated with these functionalgroups. These includenucleophilic addition,amidebond formation andimine formation for the amine group andesterification,amide bond formation anddecarboxylation for the carboxylic acid group. The multiple side chains of amino acids can also undergochemical reactions. The types of these reactions are determined by the groups on these side chains and are discussed in thearticles dealing with each specific type of amino acid.
Peptide bond formation

The condensation of two amino acids to form apeptide bond.
For more details on this topic, seePeptidebond.
As both the amine and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can reactwith another and become joined through an amide linkage. Thispolymerization of aminoacids is what creates proteins. Thiscondensation reaction yields the newly formedpeptide bond and a molecule of water. In cells, this reaction does not occur directly,instead the amino acid is activated by attachment to atransfer RNA molecule through anester bond. This aminoacyl-tRNA is produced in anATP-dependent reaction carried out by anaminoacyltRNA synthetase.[11] This aminoacyl-tRNA is then asubstrate for theribosome, which catalyzes the attack of the amino group of the elongatingprotein chain on the ester bond.[12] As a result of thismechanism, 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. Forexample, the tripeptideglutathione is an essential part of the defenses of cells againstoxidative stress. This peptide is synthesized in two steps from free amino acids.[13] In the first stepgamma-glutamylcysteinesynthetase condensescysteine andglutamic acidthrough a peptide bond formed between the side-chain carboxyl of the glutamate (the gamma carbon of this side chain) and theamino group of the cysteine. This dipeptide is then condensed withglycine byglutathione synthetase to form glutathione.[14]
In chemistry, peptides are synthesized by a variety of reactions. One of the most used insolid-phase peptide synthesis, which uses the aromatic oxime derivatives of amino acids as activatedunits. These are added in sequence onto the growing peptide chain, which is attached to a solid resin support.[15]
Zwitterions

An amino acid, in its (1) unionized and (2)zwitterionic forms.
As amino acids have both the active groups of an amine and a carboxylic acid they can be considered both acid and base (thoughtheir natural pH is usually influenced by the R group). At a certain pH known as theisoelectric point, the amine group gains a positive charge (isprotonated) and the acid group a negative charge (isdeprotonated).The exact value is specific to each different amino acid. This ion is known as azwitterion, which comes from the German word Zwitter meaning "hybrid". A zwitterion can beextracted 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 thepolarity of the side chain, amino acids vary in theirhydrophilic orhydrophobic character. These propertiesare important inprotein structure andprotein-protein interactions. The importance of the physical properties of the side chainscomes from the influence this has on the amino acid residues‘ interactions with other structures, both within a single proteinand between proteins. The distribution of hydrophilic and hydrophobic amino acids determines thetertiary structure of the protein, and their physical location on the outside structure of theproteins influences theirquaternary structure. For example, soluble proteins havesurfaces rich with polar amino acids likeserine andthreonine, whileintegral membrane proteins tend to haveouter ring ofhydrophobic amino acids that anchors them into thelipid bilayer,and proteins anchored to the membrane have a hydrophobic end that locksinto the membrane.Similarly, proteins that have to bind to positively-charged moleculeshave surfaces rich with negatively charged amino acids likeglutamate and aspartate, while proteins binding to negatively-chargedmolecules have surfaces rich with positively charged chainslike lysine and arginine. Recently a new scale of hydrophobicity basedon the free energy of hydrophobic association has beenproposed[16]
Hydrophilic and hydrophobic interactions of the proteins do not have to rely only on the sidechains of amino acids themselves.By variousposttranslational modifications other chains can be attachedto the proteins, forming hydrophobiclipoproteins or hydrophilicglycoproteins.
Table of standard amino acid abbreviations and side chain properties
Main article:List of standard aminoacids
Amino Acid 3-Letter 1-Letter Side chain polarity Side chain acidity or basicityHydropathy index[17]
Alanine Ala A nonpolar neutral 1.8
Arginine Arg R polar strongly basic -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 weakly basic -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
Serine Ser S polar neutral -0.8
Threonine Thr T polar neutral -0.7
Tryptophan Trp W nonpolar neutral -0.9
Tyrosine Tyr Y polar neutral -1.3
Valine Val V nonpolar neutral 4.2
In addition to the normal amino acid codes, placeholders were used historically in cases wherechemical orcrystallographic analysis of a peptide orprotein could not completely establish the identity of a certain residue in a structure. The ones they could not resolve betweenare 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

The amino acidselenocysteine.
Aside from the twenty standard amino acids, there are a vast number of "nonstandard amino acids". Two of these can be encodedin the genetic code, but are rather rare in proteins.Selenocysteine is incorporated intosome proteins at a UGAcodon, which is normally a stop codon.[18]Pyrrolysine is used by somemethanogenic bacteria inenzymes that they use to producemethane. It is coded for with the codon UAG.[19]
Examples of nonstandard amino acids that are not found in proteins includelanthionine,2-aminoisobutyric acid,dehydroalanineand the neurotransmittergamma-aminobutyric acid. Nonstandard amino acids oftenoccur as intermediates in themetabolic pathways for standard amino acids - forexampleornithine andcitrulline occur in theurea cycle, part of amino acidcatabolism.[20]
Nonstandard amino acids are usually formed through modifications to standard amino acids. For example,homocysteine is formed by the transsulfuration pathway from cysteine or asan intermediate inS-adenosyl methionine metabolism,[21] while dopamine is synthesized from tyrosine, andhydroxyproline is made by aposttranslationalmodification ofproline.[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 ofphenylketonuria.
L-DOPA (L-dihydroxyphenylalanine) Treatment forParkinsonism.
Monosodium glutamateFood additive that enhances flavor. Confers the tasteumami.
Nutritional importance
Further information:Protein in nutrition
Of the 20 standard proteinogenic amino acids, 10 are calledessential aminoacids because thehuman body cannotsynthesize themfrom othercompounds throughchemicalreactions, and they therefore must be obtained from food.Cysteine,tyrosine,histidine andarginine areconsidered as semiessential amino acids in children, because the metabolic pathways that synthesize these amino acids are notfully developed.[23]
Essential Nonessential
IsoleucineAlanine
LeucineAsparagine
LysineAspartate
MethionineCysteine
PhenylalanineGlutamate
ThreonineGlutamine
TryptophanGlycine
ValineProline
Arginine*Serine
Histidine*Tyrosine
(*) Essential only in certain cases
Several commonmnemonics have evolved for remembering the essential amino acids. PVT TIMHALL ("Private Tim Hall") uses the first letter of each essential amino acid, includingarginine.[24] Another mnemonic thatfrequently occurs in student practice materials is "These ten valuable amino acids havelong preserved life in man".[25]