Wikipedia

Amino acid

This article is about the class of chemicals. For the structures and properties of the standard proteinogenic amino acids, seeProteinogenic amino acid.

Amino acidsareorganic compoundsthat contain bothaminoandcarboxylic acidfunctional groups.[1]Although over 500 amino acids exist in nature, by far the most important are the22 α-amino acidsincorporated intoproteins.[2]Only these 22 appear in thegenetic codeof life.[3][4]

Structure of a typicalL-alpha-amino acid in the "neutral" form

Amino acids can be classified according to the locations of the core structural functional groups (alpha-(α-),beta-(β-),gamma-(γ-)amino acids, etc.), other categories relate topolarity,ionization,and side chain group type (aliphatic,acyclic,aromatic,polar,etc.). In the form of proteins, amino acidresiduesform the second-largest component (waterbeing the largest) of humanmusclesand othertissues.[5]Beyond their role as residues in proteins, amino acids participate in a number of processes such asneurotransmittertransport andbiosynthesis.It is thought that they played a key role inenabling life on Earth and its emergence.

Amino acids are formally named by theIUPAC-IUBMBJoint Commissionon Biochemical Nomenclature in terms of the fictitious "neutral" structure shown in the illustration. For example, the systematic name of alanine is 2-aminopropanoic acid, based on the formulaCH3−CH(NH2)−COOH.The Commission justified this approach as follows:[6]

The systematic names and formulas given refer to hypothetical forms in which amino groups are unprotonated and carboxyl groups are undissociated. This convention is useful to avoid various nomenclatural problems but should not be taken to imply that these structures represent an appreciable fraction of the amino-acid molecules.

History

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The first few amino acids were discovered in the early 1800s.[7][8]In 1806, French chemistsLouis-Nicolas VauquelinandPierre Jean Robiquetisolated a compound fromasparagusthat was subsequently namedasparagine,the first amino acid to be discovered.[9][10]Cystinewas discovered in 1810,[11]although its monomer,cysteine,remained undiscovered until 1884.[12][10][a]Glycineandleucinewere discovered in 1820.[13]The last of the 20 common amino acids to be discovered wasthreoninein 1935 byWilliam Cumming Rose,who also determined theessential amino acidsand established the minimum daily requirements of all amino acids for optimal growth.[14][15]

The unity of the chemical category was recognized byWurtzin 1865, but he gave no particular name to it.[16]The first use of the term "amino acid" in the English language dates from 1898,[17]while the German term,Aminosäure,was used earlier.[18]Proteinswere found to yield amino acids after enzymatic digestion or acidhydrolysis.In 1902,Emil FischerandFranz Hofmeisterindependently proposed that proteins are formed from many amino acids, whereby bonds are formed between the amino group of one amino acid with the carboxyl group of another, resulting in a linear structure that Fischer termed "peptide".[19]

General structure

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The 21proteinogenic α-amino acidsfound ineukaryotes,grouped according to their side chains'pKavalues and charges carried atphysiological pH (7.4)

2-,alpha-,orα-amino acids[20]have the genericformulaH2NCHRCOOHin most cases,[b]where R is anorganicsubstituentknown as a "side chain".[21]

Of the many hundreds of described amino acids, 22 areproteinogenic( "protein-building" ).[22][23][24]It is these 22 compounds that combine to give a vast array of peptides and proteins assembled byribosomes.[25]Non-proteinogenic or modified amino acids may arise frompost-translational modificationor duringnonribosomal peptidesynthesis.

Chirality

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Thecarbonatom next to thecarboxyl groupis called theα–carbon.In proteinogenic amino acids, it bears the amine and the R group orside chainspecific to each amino acid. With four distinct substituents, the α–carbon isstereogenicin all α-amino acids except glycine. All chiral proteogenic amino acids have theLconfiguration. They are "left-handed"enantiomers,which refers to thestereoisomersof the alpha carbon.

A fewD-amino acids ( "right-handed" ) have been found in nature, e.g., inbacterial envelopes,as aneuromodulator(D-serine), and in someantibiotics.[26][27]Rarely,D-amino acid residuesare found in proteins, and are converted from theL-amino acid as apost-translational modification.[28][c]

Side chains

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Polar charged side chains

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Five amino acids possess a charge at neutral pH. Often these side chains appear at the surfaces on proteins to enable their solubility in water, and side chains with opposite charges form important electrostatic contacts calledsalt bridgesthat maintain structures within a single protein or between interfacing proteins.[31]Many proteins bind metal into their structures specifically, and these interactions are commonly mediated by charged side chains such asaspartate,glutamateandhistidine.Under certain conditions, each ion-forming group can be charged, forming double salts.[32]

The two negatively charged amino acids at neutral pH areaspartate(Asp, D) andglutamate(Glu, E). The anionic carboxylate groups behave asBrønsted basesin most circumstances.[31]Enzymes in very low pH environments, like the aspartic proteasepepsinin mammalian stomachs, may have catalytic aspartate or glutamate residues that act as Brønsted acids.

Functional groups found in histidine (left), lysine (middle) and arginine (right)

There are three amino acids with side chains that are cations at neutral pH:arginine(Arg, R),lysine(Lys, K) andhistidine(His, H). Arginine has a chargedguanidinogroup and lysine a charged alkyl amino group, and are fully protonated at pH 7. Histidine's imidazole group has a pKaof 6.0, and is only around 10 % protonated at neutral pH. Because histidine is easily found in its basic and conjugate acid forms it often participates in catalytic proton transfers in enzyme reactions.[31]

Polar uncharged side chains

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The polar, uncharged amino acidsserine(Ser, S),threonine(Thr, T),asparagine(Asn, N) andglutamine(Gln, Q) readily form hydrogen bonds with water and other amino acids.[31]They do not ionize in normal conditions, a prominent exception being the catalytic serine inserine proteases.This is an example of severe perturbation, and is not characteristic of serine residues in general. Threonine has two chiral centers, not only theL(2S) chiral center at the α-carbon shared by all amino acids apart from achiral glycine, but also (3R) at the β-carbon. The fullstereochemicalspecification is (2S,3R)-L-threonine.

Hydrophobic side chains

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Nonpolar amino acid interactions are the primary driving force behind the processes thatfold proteinsinto their functional three dimensional structures.[31]None of these amino acids' side chains ionize easily, and therefore do not have pKas, with the exception oftyrosine(Tyr, Y). The hydroxyl of tyrosine can deprotonate at high pH forming the negatively charged phenolate. Because of this one could place tyrosine into the polar, uncharged amino acid category, but its very low solubility in water matches the characteristics of hydrophobic amino acids well.

Special case side chains

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Several side chains are not described well by the charged, polar and hydrophobic categories.Glycine(Gly, G) could be considered a polar amino acid since its small size means that its solubility is largely determined by the amino and carboxylate groups. However, the lack of any side chain provides glycine with a unique flexibility among amino acids with large ramifications to protein folding.[31]Cysteine(Cys, C) can also form hydrogen bonds readily, which would place it in the polar amino acid category, though it can often be found in protein structures forming covalent bonds, calleddisulphide bonds,with other cysteines. These bonds influence the folding and stability of proteins, and are essential in the formation ofantibodies.Proline(Pro, P) has an alkyl side chain and could be considered hydrophobic, but because the side chain joins back onto the alpha amino group it becomes particularly inflexible when incorporated into proteins. Similar to glycine this influences protein structure in a way unique among amino acids.Selenocysteine(Sec, U) is a rare amino acid not directly encoded by DNA, but is incorporated into proteins via the ribosome. Selenocysteine has a lower redox potential compared to the similar cysteine, and participates in several unique enzymatic reactions.[33]Pyrrolysine(Pyl, O) is another amino acid not encoded in DNA, but synthesized into protein by ribosomes.[34]It is found in archaeal species where it participates in the catalytic activity of several methyltransferases.

β- and γ-amino acids

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Amino acids with the structureNH+3−CXY−CXY−CO−2,such asβ-alanine,a component ofcarnosineand a few other peptides, are β-amino acids. Ones with the structureNH+3−CXY−CXY−CXY−CO−2are γ-amino acids, and so on, where X and Y are two substituents (one of which is normally H).[6]

Zwitterions

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Main article:Zwitterion
Ionization and Brønsted character of N-terminal amino, C-terminal carboxylate, and side chains of amino acid residues

The common natural forms of amino acids have azwitterionicstructure, with−NH+3(−NH+2−in the case of proline) and−CO−2functional groups attached to the same C atom, and are thus α-amino acids, and are the only ones found in proteins during translation in the ribosome. In aqueous solution at pH close to neutrality, amino acids exist aszwitterions,i.e. as dipolar ions with bothNH+3andCO−2in charged states, so the overall structure isNH+3−CHR−CO−2.Atphysiological pHthe so-called "neutral forms"−NH2−CHR−CO2Hare not present to any measurable degree.[35]Although the two charges in the zwitterion structure add up to zero it is misleading to call a species with a net charge of zero "uncharged".

In strongly acidic conditions (pH below 3), the carboxylate group becomes protonated and the structure becomes an ammonio carboxylic acid,NH+3−CHR−CO2H.This is relevant for enzymes like pepsin that are active in acidic environments such as the mammalian stomach andlysosomes,but does not significantly apply to intracellular enzymes. In highly basic conditions (pH greater than 10, not normally seen in physiological conditions), the ammonio group is deprotonated to giveNH2−CHR−CO−2.

Although various definitions of acids and bases are used in chemistry, the only one that is useful for chemistry in aqueous solution isthat of Brønsted:[36][37]an acid is a species that can donate a proton to another species, and a base is one that can accept a proton. This criterion is used to label the groups in the above illustration. The carboxylate side chains of aspartate and glutamate residues are the principal Brønsted bases in proteins. Likewise, lysine, tyrosine and cysteine will typically act as a Brønsted acid. Histidine under these conditions can act both as a Brønsted acid and a base.

Isoelectric point

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Composite oftitration curvesof twenty proteinogenic amino acids grouped by side chain category

For amino acids with uncharged side-chains the zwitterion predominates at pH values between the two pKavalues, but coexists inequilibriumwith small amounts of net negative and net positive ions. At the midpoint between the two pKavalues, the trace amount of net negative and trace of net positive ions balance, so that average net charge of all forms present is zero.[38]This pH is known as theisoelectric pointpI,so pI=⁠1/2⁠(pKa1+ pKa2).

For amino acids with charged side chains, the pKaof the side chain is involved. Thus for aspartate or glutamate with negative side chains, the terminal amino group is essentially entirely in the charged form−NH+3,but this positive charge needs to be balanced by the state with just one C-terminal carboxylate group is negatively charged. This occurs halfway between the two carboxylate pKavalues: pI=⁠1/2⁠(pKa1+ pKa(R)), where pKa(R)is the side chain pKa.[37]

Similar considerations apply to other amino acids with ionizable side-chains, including not only glutamate (similar to aspartate), but also cysteine, histidine, lysine, tyrosine and arginine with positive side chains.

Amino acids have zero mobility inelectrophoresisat their isoelectric point, although this behaviour is more usually exploited for peptides and proteins than single amino acids. Zwitterions have minimum solubility at their isoelectric point, and some amino acids (in particular, with nonpolar side chains) can be isolated by precipitation from water by adjusting the pH to the required isoelectric point.

Physicochemical properties

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The 20 canonical amino acids can be classified according to their properties. Important factors are charge,hydrophilicityorhydrophobicity,size, and functional groups.[27]These properties influenceprotein structureandprotein–protein interactions.The water-soluble proteins tend to have their hydrophobic residues (Leu,Ile,Val,Phe,andTrp) buried in the middle of the protein, whereas hydrophilic side chains are exposed to the aqueous solvent. (Inbiochemistry,a residue refers to a specificmonomerwithinthepolymericchain of apolysaccharide,protein ornucleic acid.) Theintegral membrane proteinstend to have outer rings of exposedhydrophobicamino acids that anchor them in thelipid bilayer.Someperipheral membrane proteinshave a patch of hydrophobic amino acids on their surface that sticks to the membrane. In a similar fashion, proteins that have to bind to positively charged molecules have surfaces rich in negatively charged amino acids such asglutamateandaspartate,while proteins binding to negatively charged molecules have surfaces rich in positively charged amino acids likelysineandarginine.For example, lysine and arginine are present in large amounts in thelow-complexity regionsof nucleic-acid binding proteins.[39]There are varioushydrophobicity scalesof amino acid residues.[40]

Some amino acids have special properties. Cysteine can form covalentdisulfide bondsto other cysteine residues.Prolineformsa cycleto the polypeptide backbone, and glycine is more flexible than other amino acids.

Glycine and proline are strongly present within low complexity regions of both eukaryotic and prokaryotic proteins, whereas the opposite is the case with cysteine, phenylalanine, tryptophan, methionine, valine, leucine, isoleucine, which are highly reactive, or complex, or hydrophobic.[39][41][42]

Many proteins undergo a range ofposttranslational modifications,whereby additional chemical groups are attached to the amino acid residue side chains sometimes producinglipoproteins(that are hydrophobic),[43]orglycoproteins(that are hydrophilic)[44]allowing the protein to attach temporarily to a membrane. For example, a signaling protein can attach and then detach from a cell membrane, because it contains cysteine residues that can have the fatty acidpalmitic acidadded to them and subsequently removed.[45]

Table of standard amino acid abbreviations and properties

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"Amino acid code" redirects here. For base-pair encoding of amino acids, seeGenetic code § Codons.
Main article:Proteinogenic amino acid

Although one-letter symbols are included in the table, IUPAC–IUBMB recommend[6]that "Use of the one-letter symbols should be restricted to the comparison of long sequences".

The one-letter notation was chosen by IUPAC-IUB based on the following rules:[46]

  • Initial letters are used where there is no ambuiguity: C cysteine, H histidine, I isoleucine, M methionine, S serine, V valine,[46]
  • Where arbitrary assignment is needed, the structurally simpler amino acids are given precedence: A Alanine, G glycine, L leucine, P proline, T threonine,[46]
  • FPHenylalanine and R aRginine are assigned by being phonetically suggestive,[46]
  • W tryptophane is assigned based on the double ring being visually suggestive to the bulky letter W,[46]
  • K lysine and Y tyrosine are assigned as alphabetically nearest to their initials L and T (note that U was avoided for its similarity with V, while X was reserved for undetermined or atypical amino acids); for tyrosine the mnemonic tYrosine was also proposed,[47]
  • D aspartate was assigned arbitrarily, with the proposed mnemonic asparDic acid;[48]E glutamate was assigned in alphabetical sequence being larger by merely onemethylene–CH2– group,[47]
  • N asparagine was assigned arbitrarily, with the proposed mnemonic asparagiNe;[48]Q glutamine was assigned in alphabetical sequence of those still available (note again that O was avoided due to similarity with D), with the proposed mnemonicQlutamine.[48]
Amino acid 3- and 1-letter symbols Side chain Hydropathy
index[49] 		Molar absorptivity[50] Molecular mass Abundance in
proteins (%)[51] 		Standard genetic coding,
IUPAC notation
3 1 Class Chemical polarity[52] Net charge
at pH 7.4[52] 		Wavelength,
λmax(nm) 		Coefficientε
(mM−1·cm−1)
Alanine Ala A Aliphatic Nonpolar Neutral 1.8 89.094 8.76 GCN
Arginine Arg R Fixed cation Basic polar Positive −4.5 174.203 5.78 MGR, CGY[53]
Asparagine Asn N Amide Polar Neutral −3.5 132.119 3.93 AAY
Aspartate Asp D Anion Brønsted base Negative −3.5 133.104 5.49 GAY
Cysteine Cys C Thiol Brønsted acid Neutral 2.5 250 0.3 121.154 1.38 UGY
Glutamine Gln Q Amide Polar Neutral −3.5 146.146 3.9 CAR
Glutamate Glu E Anion Brønsted base Negative −3.5 147.131 6.32 GAR
Glycine Gly G Aliphatic Nonpolar Neutral −0.4 75.067 7.03 GGN
Histidine His H Cationic Brønsted acid and base Positive, 10%
Neutral, 90% 		−3.2 211 5.9 155.156 2.26 CAY
Isoleucine Ile I Aliphatic Nonpolar Neutral 4.5 131.175 5.49 AUH
Leucine Leu L Aliphatic Nonpolar Neutral 3.8 131.175 9.68 YUR, CUY[54]
Lysine Lys K Cation Brønsted acid Positive −3.9 146.189 5.19 AAR
Methionine Met M Thioether Nonpolar Neutral 1.9 149.208 2.32 AUG
Phenylalanine Phe F Aromatic Nonpolar Neutral 2.8 257, 206, 188 0.2, 9.3, 60.0 165.192 3.87 UUY
Proline Pro P Cyclic Nonpolar Neutral −1.6 115.132 5.02 CCN
Serine Ser S Hydroxylic Polar Neutral −0.8 105.093 7.14 UCN, AGY
Threonine Thr T Hydroxylic Polar Neutral −0.7 119.119 5.53 ACN
Tryptophan Trp W Aromatic Nonpolar Neutral −0.9 280, 219 5.6, 47.0 204.228 1.25 UGG
Tyrosine Tyr Y Aromatic Brønsted acid Neutral −1.3 274, 222, 193 1.4, 8.0, 48.0 181.191 2.91 UAY
Valine Val V Aliphatic Nonpolar Neutral 4.2 117.148 6.73 GUN

Two additional amino acids are in some species coded for bycodonsthat are usually interpreted asstop codons:

21st and 22nd amino acids 3-letter 1-letter Molecular mass
Selenocysteine Sec U 168.064
Pyrrolysine Pyl O 255.313

In addition to the specific amino acid codes, placeholders are used in cases wherechemicalorcrystallographicanalysis of a peptide or protein cannot conclusively determine the identity of a residue. They are also used to summarizeconserved protein sequencemotifs. The use of single letters to indicate sets of similar residues is similar to the use ofabbreviation codes for degenerate bases.[55][56]

Ambiguous amino acids 3-letter 1-letter Amino acids included Codons included
Any / unknown Xaa X All NNN
Asparagineoraspartate Asx B D, N RAY
Glutamineorglutamate Glx Z E, Q SAR
Leucineor isoleucine Xle J I, L YTR, ATH, CTY[57]
Hydrophobic Φ V, I, L, F, W, Y, M NTN, TAY, TGG
Aromatic Ω F, W, Y, H YWY, TTY, TGG[58]
Aliphatic(non-aromatic) Ψ V, I, L, M VTN, TTR[59]
Small π P, G, A, S BCN, RGY, GGR
Hydrophilic ζ S, T, H, N, Q, E, D, K, R VAN, WCN, CGN, AGY[60]
Positively-charged + K, R, H ARR, CRY, CGR
Negatively-charged − D, E GAN

Unkis sometimes used instead ofXaa,but is less standard.

Teror*(from termination) is used in notation for mutations in proteins when a stop codon occurs. It corresponds to no amino acid at all.[61]

In addition, manynonstandard amino acidshave a specific code. For example, several peptide drugs, such asBortezomibandMG132,areartificially synthesizedand retain theirprotecting groups,which have specific codes. Bortezomib isPyz–Phe–boroLeu, and MG132 isZ–Leu–Leu–Leu–al. To aid in the analysis of protein structure,photo-reactive amino acid analogsare available. These includephotoleucine(pLeu) andphotomethionine(pMet).[62]

Occurrence and functions in biochemistry

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Apolypeptideis an unbranched chain of amino acids.
β-Alanine and its α-alanine isomer
The amino acidselenocysteine

Proteinogenic amino acids

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Main article:Proteinogenic amino acid
See also:Protein primary structureandPosttranslational modification

Amino acids are the precursors to proteins.[25]They join by condensation reactions to form short polymer chains called peptides or longer chains called either polypeptides or proteins. These chains are linear and unbranched, with each amino acid residue within the chain attached to two neighboring amino acids. In nature, the process of making proteins encoded by RNA genetic material is calledtranslationand involves the step-by-step addition of amino acids to a growing protein chain by aribozymethat is called aribosome.[63]The order in which the amino acids are added is read through thegenetic codefrom anmRNAtemplate, which is anRNAderived from one of the organism'sgenes.

Twenty-two amino acids are naturally incorporated into polypeptides and are calledproteinogenicor natural amino acids.[27]Of these, 20 are encoded by the universal genetic code. The remaining 2,selenocysteineandpyrrolysine,are incorporated into proteins by unique synthetic mechanisms. Selenocysteine is incorporated when the mRNA being translated includes aSECIS element,which causes the UGA codon to encode selenocysteine instead of a stop codon.[64]Pyrrolysineis used by somemethanogenicarchaeain enzymes that they use to producemethane.It is coded for with the codon UAG, which is normally a stop codon in other organisms.[65]

Several independent evolutionary studies have suggested that Gly, Ala, Asp, Val, Ser, Pro, Glu, Leu, Thr may belong to a group of amino acids that constituted the early genetic code, whereas Cys, Met, Tyr, Trp, His, Phe may belong to a group of amino acids that constituted later additions of the genetic code.[66][67][68]

Standard vs nonstandard amino acids

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The 20 amino acids that are encoded directly by the codons of the universal genetic code are calledstandardorcanonicalamino acids. A modified form of methionine (N-formylmethionine) is often incorporated in place of methionine as the initial amino acid of proteins in bacteria, mitochondria andplastids(including chloroplasts). Other amino acids are callednonstandardornon-canonical.Most of the nonstandard amino acids are also non-proteinogenic (i.e. they cannot be incorporated into proteins during translation), but two of them are proteinogenic, as they can be incorporated translationally into proteins by exploiting information not encoded in the universal genetic code.

The two nonstandard proteinogenic amino acids are selenocysteine (present in many non-eukaryotes as well as most eukaryotes, but not coded directly by DNA) andpyrrolysine(found only in somearchaeaand at least onebacterium). The incorporation of these nonstandard amino acids is rare. For example, 25 human proteins include selenocysteine in their primary structure,[69]and the structurally characterized enzymes (selenoenzymes) employ selenocysteine as the catalyticmoietyin their active sites.[70]Pyrrolysine and selenocysteine are encoded via variant codons. For example, selenocysteine is encoded by stop codon andSECIS element.[71][72][73]

N-formylmethionine(which is often the initial amino acid of proteins in bacteria,mitochondria,andchloroplasts) is generally considered as a form ofmethioninerather than as a separate proteinogenic amino acid. Codon–tRNAcombinations not found in nature can also be used to"expand" the genetic codeand form novel proteins known asalloproteinsincorporatingnon-proteinogenic amino acids.[74][75][76]

Non-proteinogenic amino acids

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Main article:Non-proteinogenic amino acids

Aside from the 22proteinogenic amino acids,manynon-proteinogenicamino acids are known. Those either are not found in proteins (for examplecarnitine,GABA,levothyroxine) or are not produced directly and in isolation by standard cellular machinery. For example,hydroxyproline,is synthesised fromproline.Another example isselenomethionine).

Non-proteinogenic amino acids that are found in proteins are formed bypost-translational modification.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 aphospholipidmembrane.[77]Examples:

Some non-proteinogenic amino acids are not found in proteins. Examples include2-aminoisobutyric acidand the neurotransmittergamma-aminobutyric acid.Non-proteinogenic amino acids often occur as intermediates in themetabolic pathwaysfor standard amino acids – for example,ornithineandcitrullineoccur in theurea cycle,part of amino acidcatabolism(see below).[81]A rare exception to the dominance of α-amino acids in biology is the β-amino acidbeta alanine(3-aminopropanoic acid), which is used in plants and microorganisms in the synthesis ofpantothenic acid(vitamin B5), a component ofcoenzyme A.[82]

In mammalian nutrition

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Share of amino acid in various human diets and the resulting mix of amino acids in human blood serum. Glutamate and glutamine are the most frequent in food at over 10%, while alanine, glutamine, and glycine are the most common in blood.
Main article:Essential amino acid
Further information:Protein (nutrient)andAmino acid synthesis

Amino acids are not typical component of food: animals eat proteins. The protein is broken down into amino acids in the process of digestion. They are then used to synthesize new proteins, other biomolecules, or are oxidized toureaandcarbon dioxideas a source of energy.[83]The oxidation pathway starts with the removal of the amino group by atransaminase;the amino group is then fed into theurea cycle.The other product of transamidation is aketo acidthat enters thecitric acid cycle.[84]Glucogenic amino acidscan also be converted into glucose, throughgluconeogenesis.[85]

Of the 20 standard amino acids, nine (His,Ile,Leu,Lys,Met,Phe,Thr,TrpandVal) are calledessential amino acidsbecause thehuman bodycannotsynthesizethem from other compounds at the level needed for normal growth, so they must be obtained from food.[86][87][88]

Semi-essential and conditionally essential amino acids, and juvenile requirements

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In addition, cysteine,tyrosine,andarginineare considered semiessential amino acids, and taurine a semi-essential aminosulfonic acid in children. Some amino acids areconditionally essentialfor certain ages or medical conditions. Essential amino acids may also vary fromspeciesto species.[d]The metabolic pathways that synthesize these monomers are not fully developed.[89][90]

Non-protein functions

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Biosynthetic pathways forcatecholaminesandtrace aminesin thehuman brain[91][92][93]
Catecholaminesandtrace aminesare synthesized from phenylalanine and tyrosine in humans.
Further information:Amino acid neurotransmitter

Many proteinogenic and non-proteinogenic amino acids have biological functions beyond being precursors to proteins and peptides.In humans, amino acids also have important roles in diverse biosynthetic pathways.Defenses against herbivoresin plants sometimes employ amino acids.[94]Examples:

Standard amino acids

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Roles for nonstandard amino acids

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Uses in industry

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Animal feed

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Amino acids are sometimes added toanimal feedbecause some of the components of these feeds, such assoybeans,have low levels of some of theessential amino acids,especially of lysine, methionine, threonine, and tryptophan.[106]Likewise amino acids are used to chelate metal cations in order to improve the absorption of minerals from feed supplements.[107]

Food

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Thefood industryis a major consumer of amino acids, especiallyglutamic acid,which is used as aflavor enhancer,[108]andaspartame(aspartylphenylalanine 1-methyl ester), which is used as anartificial sweetener.[109]Amino acids are sometimes added to food by manufacturers to alleviate symptoms of mineral deficiencies, such as anemia, by improving mineral absorption and reducing negative side effects from inorganic mineral supplementation.[110]

Chemical building blocks

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Further information:Asymmetric synthesis

Amino acids are low-costfeedstocksused inchiral pool synthesisasenantiomerically purebuilding blocks.[111][112]

Amino acids are used in the synthesis of somecosmetics.[106]

Aspirational uses

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Fertilizer

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Thechelatingability of amino acids is sometimes used in fertilizers to facilitate the delivery of minerals to plants in order to correct mineral deficiencies, such as iron chlorosis. These fertilizers are also used to prevent deficiencies from occurring and to improve the overall health of the plants.[113]

Biodegradable plastics

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Further information:Biodegradable plasticandBiopolymer

Amino acids have been considered as components of biodegradable polymers, which have applications asenvironmentally friendlypackaging and in medicine indrug deliveryand the construction ofprosthetic implants.[114]An interesting example of such materials ispolyaspartate,a water-soluble biodegradable polymer that may have applications in disposablediapersand agriculture.[115]Due to its solubility and ability tochelatemetal ions, polyaspartate is also being used as a biodegradable antiscalingagent and acorrosion inhibitor.[116][117]

Synthesis

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Main article:Amino acid synthesis
The Strecker amino acid synthesis

Chemical synthesis

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The commercial production of amino acids usually relies on mutant bacteria that overproduce individual amino acids using glucose as a carbon source. Some amino acids are produced by enzymatic conversions of synthetic intermediates.2-Aminothiazoline-4-carboxylic acidis an intermediate in one industrial synthesis ofL-cysteinefor example.Aspartic acidis produced by the addition of ammonia tofumarateusing a lyase.[110]

Biosynthesis

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In plants, nitrogen is first assimilated into organic compounds in the form ofglutamate,formed from alpha-ketoglutarate and ammonia in the mitochondrion. For other amino acids, plants usetransaminasesto move the amino group from glutamate to another alpha-keto acid. For example, aspartate aminotransferase converts glutamate and oxaloacetate to alpha-ketoglutarate and aspartate.[118]Other organisms use transaminases for amino acid synthesis, too.

Nonstandard amino acids are usually formed through modifications to standard amino acids. For example,homocysteineis formed through thetranssulfuration pathwayor by the demethylation of methionine via the intermediate metaboliteS-adenosylmethionine,[119]whilehydroxyprolineis made by apost translational modificationofproline.[120]

Microorganismsand plants synthesize many uncommon amino acids. For example, some microbes make2-aminoisobutyric acidandlanthionine,which is a sulfide-bridged derivative of alanine. Both of these amino acids are found in peptidiclantibioticssuch asalamethicin.[121]However, in plants,1-aminocyclopropane-1-carboxylic acidis a small disubstituted cyclic amino acid that is an intermediate in the production of the plant hormoneethylene.[122]

Primordial synthesis

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The formation of amino acids and peptides are assumed to precede and perhaps induce theemergence of life on earth.Amino acids can form from simple precursors under various conditions.[123]Surface-based chemical metabolism of amino acids and very small compounds may have led to the build-up of amino acids, coenzymes and phosphate-based small carbon molecules.[124][additional citation(s) needed]Amino acids and similar building blocks could have been elaborated into proto-peptides,with peptides being considered key players in the origin of life.[125]

In the famousUrey-Miller experiment,the passage of an electric arc through a mixture of methane, hydrogen, and ammonia produces a large number of amino acids. Since then, scientists have discovered a range of ways and components by which the potentially prebiotic formation and chemical evolution of peptides may have occurred, such as condensing agents, the design of self-replicating peptides and a number of non-enzymatic mechanisms by which amino acids could have emerged and elaborated into peptides.[125]Several hypotheses invoke theStrecker synthesiswhereby hydrogen cyanide, simple aldehydes, ammonia, and water produce amino acids.[123]

According to a review, amino acids, and even peptides, "turn up fairly regularly in thevarious experimental brothsthat have been allowed to be cooked from simple chemicals. This is becausenucleotidesare far more difficult to synthesize chemically than amino acids. "For a chronological order, it suggests that there must have been a 'protein world' or at least a 'polypeptide world', possibly later followed by the 'RNA world' and the 'DNA world'.[126]Codon–amino acids mappings may be thebiologicalinformation system at the primordial origin of life on Earth.[127]While amino acids and consequently simple peptides must have formed under different experimentally probed geochemical scenarios, the transition from an abiotic world to the first life forms is to a large extent still unresolved.[128]

Reactions

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Amino acids undergo the reactions expected of the constituent functional groups.[129][130]

Peptide bond formation

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See also:Peptide synthesisandPeptide bond
The condensation of two amino acids to form adipeptide.The two amino acidresiduesare linked through apeptide 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. Thispolymerizationof amino acids is what creates proteins. Thiscondensation reactionyields the newly formed peptide bond and a molecule of water. In cells, this reaction does not occur directly; instead, the amino acid is first activated by attachment to atransfer RNAmolecule through anesterbond. This aminoacyl-tRNA is produced in anATP-dependent reaction carried out by anaminoacyl tRNA synthetase.[131]This aminoacyl-tRNA is then a substrate for the ribosome, which catalyzes the attack of the amino group of the elongating protein chain on the ester bond.[132]As a result of this mechanism, all proteins made by ribosomes are synthesized starting at theirN-terminus and moving toward theirC-terminus.

However, not all peptide bonds are formed in this way. In a few cases, peptides are synthesized by specific enzymes. For example, the tripeptideglutathioneis an essential part of the defenses of cells against oxidative stress. This peptide is synthesized in two steps from free amino acids.[133]In the first step,gamma-glutamylcysteine synthetasecondenses cysteine andglutamatethrough a peptide bond formed between the side chain carboxyl of the glutamate (the gamma carbon of this side chain) and the amino group of the cysteine. This dipeptide is then condensed with glycine byglutathione synthetaseto form glutathione.[134]

In chemistry, peptides are synthesized by a variety of reactions. One of the most-used insolid-phase peptide synthesisuses 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.[135]Libraries of peptides are used in drug discovery throughhigh-throughput screening.[136]

The combination of functional groups allow amino acids to be effective polydentate ligands for metal–amino acid chelates.[137] The multiple side chains of amino acids can also undergo chemical reactions.

Catabolism

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Catabolism of proteinogenic amino acids. Amino acids can be classified according to the properties of their main degradation products:[138]
*Glucogenic,with the products having the ability to formglucosebygluconeogenesis
*Ketogenic,with the products not having the ability to form glucose. These products may still be used forketogenesisorlipid synthesis.
* Amino acids catabolized into both glucogenic and ketogenic products.

Degradation of an amino acid often involvesdeaminationby moving its amino group to α-ketoglutarate, formingglutamate.This process involves transaminases, often the same as those used in amination during synthesis. In many vertebrates, the amino group is then removed through theurea cycleand is excreted in the form ofurea.However, amino acid degradation can produceuric acidor ammonia instead. For example,serine dehydrataseconverts serine to pyruvate and ammonia.[99]After removal of one or more amino groups, the remainder of the molecule can sometimes be used to synthesize new amino acids, or it can be used for energy by enteringglycolysisor thecitric acid cycle,as detailed in image at right.

Complexation

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Amino acids are bidentate ligands, formingtransition metal amino acid complexes.[139]

Chemical analysis

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The total nitrogen content of organic matter is mainly formed by the amino groups in proteins. The Total Kjeldahl Nitrogen (TKN) is a measure of nitrogen widely used in the analysis of (waste) water, soil, food, feed and organic matter in general. As the name suggests, theKjeldahl methodis applied. More sensitive methods are available.[140][141]

See also

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Notes

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  1. ^The late discovery is explained by the fact that cysteine becomes oxidized to cystine in air.
  2. ^Prolineand other cyclic amino acids are an exception to this general formula. Cyclization of the α-amino acid creates the corresponding secondary amine. These are occasionally referred to asimino acids.
  3. ^TheLandDconvention for amino acid configuration refers not to the optical activity of the amino acid itself but rather to the optical activity of the isomer ofglyceraldehydefrom which that amino acid can, in theory, be synthesized (D-glyceraldehyde is dextrorotatory;L-glyceraldehyde is levorotatory). An alternative convention is to use the(S) and (R) designatorsto specify theabsolute configuration.[29]Almost all of the amino acids in proteins are (S) at the α carbon, withcysteinebeing (R) and glycine non-chiral.[30]Cysteine has its side chain in the same geometric location as the other amino acids, but theR/Sterminology is reversed becausesulfurhas higher atomic number compared to the carboxyl oxygen which gives the side chain a higher priority by theCahn-Ingold-Prelog sequence rules.
  4. ^For example,ruminantssuch as cows obtain a number of amino acids viamicrobesin thefirst two stomach chambers.

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