Amino acid: Difference between revisions

{{short description|Organic compounds containing amine and carboxylic groups}}

{{About|the class of chemicals|the structures and properties of the standard proteinogenic amino acids|Proteinogenic amino acid}}

[[File:L-amino acid structure.svg|thumb|Structure of a typical <small>L</small>-alpha-amino acid in the "neutral" form.]]

'''Amino acids''' are [[organic compound]]s that contain both [[amino]] and [[carboxylic acid]] [[functional group]]s. Although over 500 amino acids exist in nature, by far the most important are the [[Proteinogenic amino acid|22 α-amino acids]] incorporated into [[protein]]s. Only these 22 appear in the [[genetic code]] of life.

Amino acids can be classified according to the locations of the core structural functional groups ([[Alpha and beta carbon|alpha- <span style="white-space: nowrap">(α-)</span>, beta- <span style="white-space: nowrap">(β-)</span>, gamma- <span style="white-space: nowrap">(γ-)</span>]] amino acids, etc.), other categories relate to [[Chemical polarity|polarity]], [[ionization]], and side chain group type ([[aliphatic]], [[Open-chain compound|acyclic]], [[aromatic]], [[Chemical polarity|polar]], etc.). In the form of proteins, amino acid ''[[Residue (chemistry)#Biochemistry|residues]]'' form the second-largest component ([[water]] being the largest) of human [[muscle]]s and other [[tissue (biology)|tissues]]. Beyond their role as residues in proteins, amino acids participate in a number of processes such as [[neurotransmitter]] transport and [[biosynthesis]]. It is thought that they played a key role in [[abiogenesis|enabling life on Earth and its emergence]].

Amino acids are formally named by the [[International Union of Pure and Applied Chemistry|IUPAC]]-[[International Union of Biochemistry and Molecular Biology|IUBMB]] Joint Commission on 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 formula {{chem2|CH3\sCH(NH2)\sCOOH}}. The Commission justified this approach as follows:

<blockquote>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.</blockquote>

The first few amino acids were discovered in the early 1800s. In 1806, French chemists [[Louis-Nicolas Vauquelin]] and [[Pierre Jean Robiquet]] isolated a compound from [[asparagus]] that was subsequently named [[asparagine]], the first amino acid to be discovered. [[Cystine]] was discovered in 1810, although its monomer, [[cysteine]], remained undiscovered until 1884. [[Glycine]] and [[leucine]] were discovered in 1820. The last of the 20 common amino acids to be discovered was [[threonine]] in 1935 by [[William Cumming Rose]], who also determined the [[essential amino acid]]s and established the minimum daily requirements of all amino acids for optimal growth.

The unity of the chemical category was recognized by [[Charles Adolphe Wurtz|Wurtz]] in 1865, but he gave no particular name to it. The first use of the term "amino acid" in the English language dates from 1898, while the German term, {{lang|de|Aminosäure}}, was used earlier. [[Protein]]s were found to yield amino acids after enzymatic digestion or acid [[hydrolysis]]. In 1902, [[Hermann Emil Fischer|Emil Fischer]] and [[Franz Hofmeister]] independently 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]]".

[[File:ProteinogenicAminoAcids.svg|thumb|600x600px|The 21 [[Proteinogenic amino acid|proteinogenic α-amino acids]] found in [[Eukaryote|eukaryotes]], grouped according to their side chains' [[PKa|p''K''_a]] values and charges carried at [[PH#Living systems|physiological pH (7.4)]].]]

'''2-''', '''alpha-''', or '''α-amino acids''' have the generic [[Chemical formula|formula]] {{chem2|H2NCHRCOOH}} in most cases, where R is an [[organic chemistry|organic]] [[substituent]] known as a "[[Substituent|side chain]]".

Of the many hundreds of described amino acids, 22 are [[Proteinogenic amino acid|proteinogenic]] ("protein-building"). It is these 22 compounds that combine to give a vast array of peptides and proteins assembled by [[Ribosome|ribosomes]]. Non-proteinogenic or modified amino acids may arise from [[post-translational modification]] or during [[nonribosomal peptide]] synthesis.

The [[carbon]] atom next to the [[carboxyl group]] is called the [[alpha carbon|α–carbon]]. In proteinogenic amino acids, it bears the amine and the R group or [[Substituent|side chain]] specific to each amino acid. With four distinct substituents, the α–carbon is [[stereogenic]] in all α-amino acids except glycine. All chiral proteogenic amino acids have the <small>L</small> configuration. They are "left-handed" [[enantiomer]]s, which refers to the [[stereoisomers]] of the alpha carbon.

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 called [[Salt bridge (protein and supramolecular)|salt bridges]] that maintain structures within a single protein or between interfacing proteins. Many proteins bind metal into their structures specifically, and these interactions are commonly mediated by charged side chains such as [[aspartate]], [[glutamate]] and [[histidine]]. Under certain conditions, each ion-forming group can be charged, forming double salts.

The two negatively charged amino acids at neutral pH are [[Aspartic acid|aspartate]] (Asp, D) and [[Glutamic acid|glutamate]] (Glu, E). The anionic carboxylate groups behave as [[Brønsted–Lowry acid–base theory|Brønsted bases]] in most circumstances. Enzymes in very low pH environments, like the aspartic protease [[pepsin]] in mammalian stomachs, may have catalytic aspartate or glutamate residues that act as Brønsted acids.

[[File:Histidine lysine arginine sidechains.png|thumb|450x450px|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) and [[histidine]] (His, H). Arginine has a charged [[Guanidine|guanidino]] group and lysine a charged alkyl amino group, and are fully protonated at pH 7. Histidine's imidazole group has a pK_a of 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.

The polar, uncharged amino acids [[serine]] (Ser, S), [[threonine]] (Thr, T), [[asparagine]] (Asn, N) and [[glutamine]] (Gln, Q) readily form hydrogen bonds with water and other amino acids. They do not ionize in normal conditions, a prominent exception being the catalytic serine in [[Serine protease#Catalytic mechanism|serine proteases]]. This is an example of severe perturbation, and is not characteristic of serine residues in general. Threonine has two chiral centers, not only the <small>L</small> (2''S'') chiral center at the α-carbon shared by all amino acids apart from achiral glycine, but also (3''R'') at the β-carbon. The full stereochemical specification is (2''S'',3''R'')-<small>L</small>-threonine.

Nonpolar amino acid interactions are the primary driving force behind the processes that [[Protein folding|fold proteins]] into their functional three dimensional structures. None of these amino acids' side chains ionize easily, and therefore do not have pK_as, with the exception of [[tyrosine]] (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.

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. [[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, called [[disulphide bonds]], with other cysteines. These bonds influence the folding and stability of proteins, and are essential in the formation of [[Antibody#Structure|antibodies]]. [[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. [[Pyrrolysine]] (Pyl, O) is another amino acid not encoded in DNA, but synthesized into protein by ribosomes. It is found in archaeal species where it participates in the catalytic activity of several methyltransferases.

Amino acids with the structure {{chem2|NH3+\sCXY\sCXY\sCO2-}}, such as [[β-alanine]], a component of [[carnosine]] and a few other peptides, are β-amino acids. Ones with the structure {{chem2|NH3+\sCXY\sCXY\sCXY\sCO2-}} are γ-amino acids, and so on, where X and Y are two substituents (one of which is normally H).

{{main|Zwitterion}}

[[File:Bronsted_character_of_ionizing_groups_in_proteins.png|thumb|upright=1.8|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 a [[zwitterionic]] structure, with {{chem2|\sNH3+}} ({{chem2|\sNH2+\s}} in the case of proline) and {{chem2|\sCO2-}} functional 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 as [[zwitterion]]s, i.e. as dipolar ions with both {{chem2|NH3+}} and {{chem2|CO2-}} in charged states, so the overall structure is {{chem2|NH3+\sCHR\sCO2-}}. At [[Acid–base homeostasis|physiological pH]] the so-called "neutral forms" {{chem2|\sNH2\sCHR\sCO2H}} are not present to any measurable degree. 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, {{chem2|NH3+\sCHR\sCO2H}}. This is relevant for enzymes like pepsin that are active in acidic environments such as the mammalian stomach and [[lysosomes]], 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 give {{chem2|NH2\sCHR\sCO2-}}.

Although various definitions of acids and bases are used in chemistry, the only one that is useful for chemistry in aqueous solution is [[Brønsted–Lowry acid–base theory|that of Brønsted]]: 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.

[[File:Titration Curves of 20 Amino Acids Organized by Side Chain.png|thumb|right|360px|Composite of [[titration curve]]s of 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 p''K''_a values, but coexists in [[Chemical equilibrium|equilibrium]] with small amounts of net negative and net positive ions. At the midpoint between the two p''K''_a values, the trace amount of net negative and trace of net positive ions balance, so that average net charge of all forms present is zero. This pH is known as the [[isoelectric point]] p''I'', so p''I'' = {{sfrac|1|2}}(p''K''_a1 + p''K''_a2).

For amino acids with charged side chains, the p''K''_a of 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 {{chem2|\sNH3+}}, 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 p''K''_a values: p''I'' = {{sfrac|1|2}}(p''K''_a1 + p''K''_a(R)), where p''K''_a(R) is the side chain p''K''_a.

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 in [[electrophoresis]] at 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.

The 20 canonical amino acids can be classified according to their properties. Important factors are charge, [[hydrophilicity]] or [[hydrophobicity]], size, and functional groups. These properties influence [[protein structure]] and [[protein–protein interaction]]s. The water-soluble proteins tend to have their hydrophobic residues ([[leucine|Leu]], [[isoleucine|Ile]], [[valine|Val]], [[phenylalanine|Phe]], and [[tryptophan|Trp]]) buried in the middle of the protein, whereas hydrophilic side chains are exposed to the aqueous solvent. (In [[biochemistry]], a residue refers to a specific [[monomer]] ''within'' the [[polymer]]ic chain of a [[polysaccharide]], protein or [[nucleic acid]].) The [[integral membrane protein]]s tend to have outer rings of exposed [[hydrophobic]] amino acids that anchor them in the [[lipid bilayer]]. Some [[peripheral membrane protein]]s have 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 as [[glutamate]] and [[aspartate]], while proteins binding to negatively charged molecules have surfaces rich in positively charged amino acids like [[lysine]] and [[arginine]]. For example, lysine and arginine are present in large amounts in the [[Low complexity regions in proteins|low-complexity regions]] of nucleic-acid binding proteins. There are various [[hydrophobicity scale]]s of amino acid residues.

Some amino acids have special properties. Cysteine can form covalent [[disulfide bond]]s to other cysteine residues. [[Proline]] forms [[cyclic compound|a cycle]] to 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.

Many proteins undergo a range of [[posttranslational modification]]s, whereby additional chemical groups are attached to the amino acid residue side chains sometimes producing [[lipoprotein]]s (that are hydrophobic), or [[glycoprotein]]s (that are hydrophilic) 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 acid [[palmitic acid]] added to them and subsequently removed.

{{Main|Proteinogenic amino acid}}

Although one-letter symbols are included in the table, IUPAC–IUBMB recommend 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:

* Initial letters are used where there is no ambuiguity: C cysteine, H histidine, I isoleucine, M methionine, S serine, V valine,

* Where arbitrary assignment is needed, the structurally simpler amino acids are given precedence: A Alanine, G glycine, L leucine, P proline, T threonine,

* N asparagine was assigned arbitrarily, with the proposed mnemonic asparagi''N''e; 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 mnemonic ''Q''lutamine.

{| class="wikitable sortable" style="text-align:center;"

! rowspan=2 | Amino acid

|}

Two additional amino acids are in some species coded for by [[codons]] that are usually interpreted as [[stop codon]]s:

{| class="wikitable" style="text-align:center;"

|-

|}

In addition to the specific amino acid codes, placeholders are used in cases where [[Protein sequencing|chemical]] or [[X-ray crystallography|crystallographic]] analysis of a peptide or protein cannot conclusively determine the identity of a residue. They are also used to summarize [[Conserved sequence|conserved protein sequence]] motifs. The use of single letters to indicate sets of similar residues is similar to the use of [[Nucleic acid notation|abbreviation codes for degenerate bases]].

{| class="wikitable" style="text-align:center;"

|-

|}

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

'''Ter''' or '''*''' (from termination) is used in notation for mutations in proteins when a stop codon occurs. It corresponds to no amino acid at all.

In addition, many [[Non-proteinogenic amino acids|nonstandard amino acids]] have a specific code. For example, several peptide drugs, such as [[Bortezomib]] and [[MG132]], are [[peptide synthesis|artificially synthesized]] and retain their [[protecting group]]s, which have specific codes. Bortezomib is [[pyrazinoic acid|Pyz]]–Phe–boroLeu, and MG132 is [[Carboxybenzyl|Z]]–Leu–Leu–Leu–al. To aid in the analysis of protein structure, [[photo-reactive amino acid analog]]s are available. These include [[photoleucine]] ('''pLeu''') and [[photomethionine]] ('''pMet''').

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{{main|Proteinogenic amino acid}} {{See also|Protein primary structure|Posttranslational modification}}

Amino acids are the precursors to proteins. 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 DNA/RNA genetic material is called ''[[translation (biology)|translation]]'' and involves the step-by-step addition of amino acids to a growing protein chain by a [[ribozyme]] that is called a [[ribosome]] The order in which the amino acids are added is read through the [[genetic code]] from an [[Messenger RNA|mRNA]] template, which is an [[RNA]] copy of one of the organism's [[gene]]s.

Twenty-two amino acids are naturally incorporated into polypeptides and are called [[proteinogenic]] or natural amino acids. Of these, 20 are encoded by the universal genetic code. The remaining 2, [[selenocysteine]] and [[pyrrolysine]], are incorporated into proteins by unique synthetic mechanisms. Selenocysteine is incorporated when the mRNA being translated includes a [[SECIS element]], which causes the UGA codon to encode selenocysteine instead of a stop codon. [[Pyrrolysine]] is used by some [[methanogen]]ic [[archaea]] in enzymes that they use to produce [[methane]]. It is coded for with the codon UAG, which is normally a stop codon in other organisms. This UAG codon is followed by a [[PYLIS downstream sequence]].

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.

The 20 amino acids that are encoded directly by the codons of the universal genetic code are called ''standard'' or ''canonical'' amino acids. A modified form of methionine ([[N-Formylmethionine|''N''-formylmethionine]]) is often incorporated in place of methionine as the initial amino acid of proteins in bacteria, mitochondria and chloroplasts. Other amino acids are called ''nonstandard'' or ''non-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) and [[pyrrolysine]] (found only in some [[archaea]] and at least one [[bacterium]]). The incorporation of these nonstandard amino acids is rare. For example, 25 human proteins include selenocysteine in their primary structure, and the structurally characterized enzymes (selenoenzymes) employ selenocysteine as the catalytic [[moiety (chemistry)|moiety]] in their active sites. Pyrrolysine and selenocysteine are encoded via variant codons. For example, selenocysteine is encoded by stop codon and [[SECIS element]].

[[N-Formylmethionine|''N''-formylmethionine]] (which is often the initial amino acid of proteins in bacteria, [[Mitochondrion|mitochondria]], and [[chloroplast]]s) is generally considered as a form of [[methionine]] rather than as a separate proteinogenic amino acid. Codon–[[transfer RNA|tRNA]] combinations not found in nature can also be used to [[Expanded genetic code|"expand" the genetic code]] and form novel proteins known as [[alloprotein]]s incorporating [[non-proteinogenic amino acid]]s.

{{main|Non-proteinogenic amino acids}}

Aside from the 22 [[proteinogenic amino acid]]s, many ''non-proteinogenic'' amino acids are known. Those either are not found in proteins (for example [[carnitine]], [[Gamma-aminobutyric acid|GABA]], [[levothyroxine]]) or are not produced directly and in isolation by standard cellular machinery. For example, [[hydroxyproline]] , is synthesised from [[proline]]. Another example is [[selenomethionine]]).

Non-proteinogenic amino acids that are found in proteins are formed by [[post-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 a [[phospholipid]] membrane. Examples:

*the [[carboxylation]] of [[glutamate]] allows for better binding of [[calcium in biology|calcium cations]],  

* [[Hypusine]] in the [[Eukaryotic initiation factor|translation initiation factor]] [[EIF5A]], contains a modification of lysine.

Some non-proteinogenic amino acids are not found in proteins. Examples include [[2-aminoisobutyric acid]] and the neurotransmitter [[gamma-aminobutyric acid]]. Non-proteinogenic amino acids often occur as intermediates in the [[metabolic pathway]]s for standard amino acids&nbsp;– for example, [[ornithine]] and [[citrulline]] occur in the [[urea cycle]], part of amino acid [[catabolism]] (see below). 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]].

[[File:Amino acids in food and blood.png|thumb|right|380px|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.|alt=Diagram showing the relative occurrence of amino acids in blood serum as obtained from diverse diets.]]

{{Main|Essential amino acid}}

{{further|Protein (nutrient)|Amino 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 to [[urea]] and [[carbon dioxide]] as a source of energy. 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]]. [[Glucogenic amino acid]]s can also be converted into glucose, through [[gluconeogenesis]].

Of the 20 standard amino acids, nine ([[Histidine|His]], [[Isoleucine|Ile]], [[Leucine|Leu]], [[Lysine|Lys]], [[Methionine|Met]], [[Phenylalanine|Phe]], [[Threonine|Thr]], [[Tryptophan|Trp]] and [[Valine|Val]]) are called [[essential amino acid]]s because the [[human body]] cannot [[biosynthesis|synthesize]] them from other compounds at the level needed for normal growth, so they must be obtained from food.

In addition, cysteine, [[tyrosine]], and [[arginine]] are considered semiessential amino acids, and taurine a semi-essential aminosulfonic acid in children. Some amino acids are [[Essential amino acid#Essentiality in humans|conditionally essential]] for certain ages or medical conditions. Essential amino acids may also vary from [[species]] to species. The metabolic pathways that synthesize these monomers are not fully developed.

{{Catecholamine and trace amine biosynthesis|align=right|caption=[[Catecholamine]]s and [[trace amine]]s are synthesized from phenylalanine and tyrosine in humans.}}

{{Further|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. [[Plant defense against herbivory|Defenses against herbivores]] in plants sometimes employ amino acids. Examples:

* [[Tryptophan]] is a precursor of the neurotransmitter [[serotonin]].

* [[Tyrosine]] (and its precursor phenylalanine) are precursors of the [[catecholamine]] [[neurotransmitter]]s [[dopamine]], [[epinephrine]] and [[norepinephrine]] and various [[trace amine]]s.

* [[Aspartate]], [[glycine]], and [[glutamine]] are precursors of [[nucleotide]]s. However, not all of the functions of other abundant nonstandard amino acids are known.

*[[Carnitine]] is used in [[lipid|lipid transport]].  

*[[gamma-aminobutyric acid]] is a neurotransmitter.

*[[Mimosine]] found in some legumes, is another possible [[antifeedant]]. This compound is an analogue of [[tyrosine]] and can poison animals that graze on these plants.

===Animal feed===

Amino acids are sometimes added to [[Compound feed|animal feed]] because some of the components of these feeds, such as [[soybean]]s, have low levels of some of the [[essential amino acid]]s, especially of lysine, methionine, threonine, and tryptophan. Likewise amino acids are used to chelate metal cations in order to improve the absorption of minerals from feed supplements.

The [[food industry]] is a major consumer of amino acids, especially [[glutamic acid]], which is used as a [[flavor enhancer]], and [[aspartame]] (aspartylphenylalanine 1-methyl ester), which is used as an [[artificial sweetener]]. 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.

{{further|Asymmetric synthesis}}

Amino acids are low-cost [[feedstock]]s used in [[chiral pool synthesis]] as [[enantiomer|enantiomerically pure]] building blocks.

Amino acids are used in the synthesis of some [[cosmetics]].

===Fertilizer===

The [[Chelation|chelating]] ability 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.

{{further|Biodegradable plastic|Biopolymer}}

Amino acids have been considered as components of biodegradable polymers, which have applications as [[environmentally friendly]] packaging and in medicine in [[drug delivery]] and the construction of [[prosthetic implant]]s. An interesting example of such materials is [[polyaspartate]], a water-soluble biodegradable polymer that may have applications in disposable [[diaper]]s and agriculture. Due to its solubility and ability to [[chelate]] metal ions, polyaspartate is also being used as a biodegradable anti[[Fouling|scaling]] agent and a [[corrosion inhibitor]].

{{Main|Amino acid synthesis}}

[[File:Strecker amino acid synthesis scheme.svg|thumb|400px|right|The Strecker amino acid synthesis|alt=For the steps in the reaction, see the text.]]

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 acid]] is an intermediate in one industrial synthesis of [[cysteine|<small>L</small>-cysteine]] for example. [[Aspartic acid]] is produced by the addition of ammonia to [[fumarate]] using a lyase.

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

Nonstandard amino acids are usually formed through modifications to standard amino acids. For example, [[homocysteine]] is formed through the [[transsulfuration pathway]] or by the demethylation of methionine via the intermediate metabolite [[S-adenosylmethionine|''S''-adenosylmethionine]], while [[hydroxyproline]] is made by a [[post translational modification]] of [[proline]].

[[Microorganism]]s and plants synthesize many uncommon amino acids. For example, some microbes make [[2-aminoisobutyric acid]] and [[lanthionine]], which is a sulfide-bridged derivative of alanine. Both of these amino acids are found in peptidic [[lantibiotics]] such as [[alamethicin]]. However, in plants, [[1-aminocyclopropane-1-carboxylic acid]] is a small disubstituted cyclic amino acid that is an intermediate in the production of the plant hormone [[ethylene#Ethylene as a plant hormone|ethylene]].

The formation of amino acids and peptides are assumed to precede and perhaps induce the [[abiogenesis|emergence of life on earth]]. Amino acids can form from simple precursors under various conditions. 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. Amino acids and similar building blocks could have been elaborated into proto-[[peptide]]s, with peptides being considered key players in the origin of life.

In the famous [[Urey-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. Several hypotheses invoke the [[Strecker synthesis]] whereby hydrogen cyanide, simple aldehydes, ammonia, and water produce amino acids.

According to a review, amino acids, and even peptides, "turn up fairly regularly in the [[primordial soup|various experimental broths]] that have been allowed to be cooked from simple chemicals. This is because [[nucleotide]]s are 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]]'. [[Codon]]–amino acids mappings may be the [[biology|biological]] information system at the primordial origin of life on Earth. 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.

Amino acids undergo the reactions expected of the constituent functional groups.

{{see also|Peptide synthesis|Peptide bond}}

[[File:Peptidformationball.svg|thumbnail|right|400px|The condensation of two amino acids to form a [[dipeptide]]. The two amino acid ''residues'' are linked through a ''[[peptide bond]]''|alt=Two amino acids are shown next to each other. One loses a hydrogen and oxygen from its carboxyl group (COOH) and the other loses a hydrogen from its amino group (NH2). This reaction produces a molecule of water (H2O) and two amino acids joined by a peptide bond (–CO–NH–). The two joined amino acids are called a dipeptide.]]

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 [[polymerization]] of amino acids is what creates proteins. This [[condensation reaction]] yields 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 a [[transfer RNA]] molecule through an [[ester]] bond. This aminoacyl-tRNA is produced in an [[Adenosine triphosphate|ATP]]-dependent reaction carried out by an [[aminoacyl tRNA synthetase]]. 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. As a result of this mechanism, all proteins made by ribosomes are synthesized starting at their ''N''-terminus and moving toward 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 [[glutathione]] is an essential part of the defenses of cells against oxidative stress. This peptide is synthesized in two steps from free amino acids. In the first step, [[gamma-glutamylcysteine synthetase]] condenses cysteine and [[glutamate]] through 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 by [[glutathione synthetase]] to form glutathione.

In chemistry, peptides are synthesized by a variety of reactions. One of the most-used in [[peptide synthesis|solid-phase peptide synthesis]] 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. Libraries of peptides are used in drug discovery through [[high-throughput screening]].

The combination of functional groups allow amino acids to be effective polydentate ligands for metal–amino acid chelates.

The multiple side chains of amino acids can also undergo chemical reactions.

[[File:Amino acid catabolism revised.png|thumb|300px|Catabolism of proteinogenic amino acids. Amino acids can be classified according to the properties of their main degradation products:

<br/>* ''Glucogenic'', with the products having the ability to form [[glucose]] by [[gluconeogenesis]]

<br/>* Amino acids catabolized into both glucogenic and ketogenic products.]]

Degradation of an amino acid often involves [[deamination]] by moving its amino group to α-ketoglutarate, forming [[glutamate]]. This process involves transaminases, often the same as those used in amination during synthesis. In many vertebrates, the amino group is then removed through the [[urea cycle]] and is excreted in the form of [[urea]]. However, amino acid degradation can produce [[uric acid]] or ammonia instead. For example, [[serine dehydratase]] converts serine to pyruvate and ammonia. 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 entering [[glycolysis]] or the [[citric acid cycle]], as detailed in image at right.

Amino acids are bidentate ligands, forming [[transition metal amino acid complexes]].

[[File:AAcomplexation.png|420 px]]

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, the [[Kjeldahl method]] is applied. More sensitive methods are available.

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* {{cite book | last = Tymoczko | first = John L. | name-list-style = vanc | year = 2012 | title = Biochemistry | url = https://archive.org/details/biochemistryseve00berg | url-access = limited | publisher = W. H. Freeman and company | location = New York | chapter = Protein Composition and Structure | pages = 28–31 | chapter-url = https://archive.org/details/biochemistryseve00berg/page/n61 | isbn = 9781429229364}}

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{{Amino acids}}

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[[Category:Nitrogen cycle]]

[[Category:Zwitterions]]