amino acid

The first few amino acids were discovered in the early 1800s.{{cite journal | vauthors = Vickery HB, Schmidt CL | year = 1931 | title = The history of the discovery of the amino acids | journal = Chem. Rev. | volume = 9 | issue = 2| pages = 169–318 | doi=10.1021/cr60033a001}}{{cite web | vauthors = Hansen S |title=Die Entdeckung der proteinogenen Aminosäuren von 1805 in Paris bis 1935 in Illinois |location=Berlin |date=May 2015 |url=https://www.arginium.de/wp-content/uploads/2015/12/Entdeckung-der-Aminos%C3%A4uren.pdf |archive-url=https://web.archive.org/web/20171201232937/https://www.arginium.de/wp-content/uploads/2015/12/Entdeckung-der-Aminos%C3%A4uren.pdf |archive-date=1 December 2017 |language=de}} 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.{{Cite journal|title=The discovery of a new plant principle in Asparagus sativus |vauthors=Vauquelin LN, Robiquet PJ |journal=Annales de Chimie |year=1806 |volume=57 |pages=88–93}}{{Cite book |title=Advances in Protein Chemistry |vauthors=Anfinsen CB, Edsall JT, Richards FM |year=1972 |pages=[https://archive.org/details/advancesinprotei26anfi/page/99 99, 103] |publisher=Academic Press |location=New York |isbn=978-0-12-034226-6 |url=https://archive.org/details/advancesinprotei26anfi/page/99 }} Cystine was discovered in 1810,{{Cite journal|title=On cystic oxide, a new species of urinary calculus | vauthors = Wollaston WH |s2cid=110151163 |journal=Philosophical Transactions of the Royal Society |year=1810 |volume=100|pages=223–230 |doi=10.1098/rstl.1810.0015}} although its monomer, cysteine, remained undiscovered until 1884.{{Cite journal |title=Über cystin und cystein | vauthors = Baumann E |journal=Z Physiol Chem |year=1884 |volume=8 |issue=4 |pages=299–305 |url=http://vlp.mpiwg-berlin.mpg.de/library/data/lit16533 |access-date=28 March 2011 |archive-url=https://web.archive.org/web/20110314075450/http://vlp.mpiwg-berlin.mpg.de/library/data/lit16533 |archive-date=14 March 2011 |url-status=dead }}{{efn|The late discovery is explained by the fact that cysteine becomes oxidized to cystine in air.}} Glycine and leucine were discovered in 1820.{{Cite journal|title=Sur la conversion des matières animales en nouvelles substances par le moyen de l'acide sulfurique | vauthors = Braconnot HM |journal=Annales de Chimie et de Physique |series=2nd Series |year=1820 |volume=13 |pages=113–125}} 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 acids and established the minimum daily requirements of all amino acids for optimal growth.{{cite journal | vauthors = Simoni RD, Hill RL, Vaughan M | title = The discovery of the amino acid threonine: the work of William C. Rose [classical article] | journal = The Journal of Biological Chemistry | volume = 277 | issue = 37 | pages = E25 | date = September 2002 | pmid = 12218068 | doi = 10.1016/S0021-9258(20)74369-3 | doi-access = free }}{{cite journal|title=Feeding Experiments with Mixtures of Highly Purified Amino Acids. VIII. Isolation and Identification of a New Essential Amino Acid|vauthors = McCoy RH, Meyer CE, Rose WC|year = 1935|journal = Journal of Biological Chemistry|volume = 112|pages = 283–302|doi = 10.1016/S0021-9258(18)74986-7|doi-access = free}}

The unity of the chemical category was recognized by Wurtz in 1865, but he gave no particular name to it.Menten, P. Dictionnaire de chimie: Une approche étymologique et historique. De Boeck, Bruxelles. [https://books.google.com/books?id=NKTKDgAAQBAJ link] {{Webarchive|url=https://web.archive.org/web/20191228193229/https://books.google.com/books?id=NKTKDgAAQBAJ |date=28 December 2019 }}. The first use of the term "amino acid" in the English language dates from 1898,{{cite web |url=https://www.etymonline.com/word/amino- | vauthors = Harper D |work=Online Etymology Dictionary |title=amino- |access-date=19 July 2010 |archive-date=2 December 2017 |archive-url=https://web.archive.org/web/20171202102757/https://www.etymonline.com/word/amino- |url-status=live }} while the German term, {{lang|de|Aminosäure}}, was used earlier.{{cite journal | vauthors = Paal C | year = 1894 | title = Ueber die Einwirkung von Phenyl-i-cyanat auf organische Aminosäuren | journal = Berichte der Deutschen Chemischen Gesellschaft | volume = 27 | pages = 974–979 | doi = 10.1002/cber.189402701205 | url = https://zenodo.org/record/1425732 | archive-url = https://web.archive.org/web/20200725075835/https://zenodo.org/record/1425732 | url-status = dead | archive-date = 2020-07-25 }} Proteins were found to yield amino acids after enzymatic digestion or acid hydrolysis. In 1902, 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".{{cite book | vauthors = Fruton JS | title = Contrasts in Scientific Style: Research Groups in the Chemical and Biochemical Sciences |volume=191 |year=1990 |chapter=Chapter 5- Emil Fischer and Franz Hofmeister |chapter-url=https://books.google.com/books?id=tRlC9NyNNN8C&pg=PA163 |pages=163–165 |publisher=American Philosophical Society |isbn=978-0-87169-191-0 }}

File:ProteinogenicAminoAcids.svg found in eukaryotes, grouped according to their side chains' pK_a values and charges carried at physiological pH (7.4)]]

2-, alpha-, or α-amino acids{{cite web |url=http://www.merriam-webster.com/medical/alpha-amino%20acid |title=Alpha amino acid |work=Merriam-Webster Medical |access-date=3 January 2015|archive-date=3 January 2015|archive-url=https://web.archive.org/web/20150103191856/http://www.merriam-webster.com/medical/alpha-amino%20acid|url-status=live}}. have the generic formula {{chem2|H2NCHRCOOH}} in most cases,{{efn|Proline and 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 as imino acids.}} where R is an organic substituent known as a "side chain".{{Cite web | vauthors = Clark J |date=August 2007 |title=An introduction to amino acids |url=http://www.chemguide.co.uk/organicprops/aminoacids/background.html |website=chemguide |access-date=4 July 2015 |url-status=live |archive-date=30 April 2015|archive-url=https://web.archive.org/web/20150430051143/http://www.chemguide.co.uk/organicprops/aminoacids/background.html}}

Of the many hundreds of described amino acids, 22 are proteinogenic ("protein-building").{{cite encyclopedia |year=2008|title=Amino acids |encyclopedia=Peptides from A to Z: A Concise Encyclopedia |url=https://books.google.com/books?id=doe9NwgJTAsC&pg=PA20 |publisher=Wiley-VCH|location=Germany|isbn=9783527621170 |via=Google Books|page=20| vauthors = Jakubke HD, Sewald N |access-date=5 January 2016|archive-date=17 May 2016|archive-url = https://web.archive.org/web/20160517144350/https://books.google.com/books?id=doe9NwgJTAsC&pg=PA20|url-status = live}}{{cite book | veditors = Pollegioni L, Servi S | title = Unnatural Amino Acids: Methods and Protocols|year = 2012|publisher = Humana Press|isbn = 978-1-61779-331-8|page = v|oclc = 756512314|series = Methods in Molecular Biology |volume=794|doi = 10.1007/978-1-61779-331-8|s2cid = 3705304 }}{{cite journal | vauthors = Hertweck C | title = Biosynthesis and charging of pyrrolysine, the 22nd genetically encoded amino acid | journal = Angewandte Chemie | volume = 50 | issue = 41 | pages = 9540–9541 | date = October 2011 | pmid = 21796749 | doi = 10.1002/anie.201103769 | s2cid = 5359077 }}{{Closed access}}

It is these 22 compounds that combine to give a vast array of peptides and proteins assembled by ribosomes.{{cite web |title=Chapter 1: Proteins are the Body's Worker Molecules |date=27 October 2011 |website=The Structures of Life |publisher=National Institute of General Medical Sciences |url=https://publications.nigms.nih.gov/structlife/chapter1.html |access-date=20 May 2008 |archive-date=7 June 2014 |archive-url=https://web.archive.org/web/20140607084902/https://publications.nigms.nih.gov/structlife/chapter1.html}} 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 α–carbon. In proteinogenic amino acids, it bears the amine and the R group or side chain specific to each amino acid, as well as a hydrogen atom. With the exception of glycine, for which the side chain is also a hydrogen atom, the α–carbon is stereogenic. All chiral proteogenic amino acids have the L configuration. They are "left-handed" enantiomers, which refers to the stereoisomers of the alpha carbon.

A few D-amino acids ("right-handed") have been found in nature, e.g., in bacterial envelopes, as a neuromodulator (D-serine), and in some antibiotics.{{cite book | title = Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology | publisher = Wiley-Blackwell | year = 2012 | isbn = 978-0-470-14684-2 | location = Oxford | veditors = Michal G, Schomburg D | page = 5 | edition = 2nd }}{{Cite book | vauthors = Creighton TH |title=Proteins: structures and molecular properties |publisher=W. H. Freeman |location=San Francisco |year=1993 |chapter=Chapter 1 |isbn=978-0-7167-7030-5 |chapter-url-access=registration |chapter-url=https://archive.org/details/proteinsstructur0000crei }} Rarely, D-amino acid residues are found in proteins, and are converted from the L-amino acid as a post-translational modification.{{cite journal | vauthors = Genchi G | title = An overview on D-amino acids | journal = Amino Acids | volume = 49 | issue = 9 | pages = 1521–1533 | date = September 2017 | pmid = 28681245 | doi = 10.1007/s00726-017-2459-5 | s2cid = 254088816 }}{{efn|The L and D convention for amino acid configuration refers not to the optical activity of the amino acid itself but rather to the optical activity of the isomer of glyceraldehyde from 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) designators to specify the absolute configuration.{{Cite journal | vauthors = Cahn RS, Ingold C, Prelog V | author-link = Robert Sidney Cahn | author2-link = Christopher Kelk Ingold | author3-link = Vladimir Prelog | title = Specification of Molecular Chirality | journal = Angewandte Chemie International Edition | volume = 5 | issue = 4 | pages = 385–415 | year = 1966 | doi = 10.1002/anie.196603851}} Almost all of the amino acids in proteins are (S) at the α carbon, with cysteine being (R) and glycine non-chiral.{{cite web | vauthors = Hatem SM | year = 2006 | url = http://geb.uni-giessen.de/geb/volltexte/2006/3038/index.html | title = Gas chromatographic determination of Amino Acid Enantiomers in tobacco and bottled wines | publisher = University of Giessen | access-date = 17 November 2008 | archive-url = https://web.archive.org/web/20090122104055/http://geb.uni-giessen.de/geb/volltexte/2006/3038/index.html | archive-date = 22 January 2009 | url-status = dead }} Cysteine has its side chain in the same geometric location as the other amino acids, but the R/S terminology is reversed because sulfur has higher atomic number compared to the carboxyl oxygen which gives the side chain a higher priority by the Cahn-Ingold-Prelog sequence rules.}}

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 bridges that maintain structures within a single protein or between interfacing proteins.{{Cite book | vauthors = Garrett RH, Grisham CM |title=Biochemistry |date=2010 |publisher=Brooks/Cole, Cengage Learning |isbn=978-0-495-10935-8 |edition=4th |location=Belmont, CA |pages=74,134–176,430–442 |oclc=297392560}} 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.{{Cite journal | vauthors = Novikov AP, Safonov AV, German KE, Grigoriev MS |date=2023-12-01 |title=What kind of interactions we may get moving from zwitter to "dritter" ions: C–O⋯Re(O₄) and Re–O⋯Re(O₄) anion⋯anion interactions make structural difference between L-histidinium perrhenate and pertechnetate |journal=CrystEngComm |volume=26 |pages=61–69 |language=en |doi=10.1039/D3CE01164J |s2cid=265572280 |issn=1466-8033}}

The two negatively charged amino acids at neutral pH are aspartate (Asp, D) and glutamate (Glu, E). The anionic carboxylate groups behave as 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

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 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 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 L (2S) chiral center at the α-carbon shared by all amino acids apart from achiral glycine, but also (3R) at the β-carbon. The full stereochemical specification is (2S,3R)-L-threonine.

Nonpolar amino acid interactions are the primary driving force behind the processes that 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 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.{{cite journal | vauthors = Papp LV, Lu J, Holmgren A, Khanna KK | title = From selenium to selenoproteins: synthesis, identity, and their role in human health | journal = Antioxidants & Redox Signaling | volume = 9 | issue = 7 | pages = 775–806 | date = July 2007 | pmid = 17508906 | doi = 10.1089/ars.2007.1528 }} Pyrrolysine (Pyl, O) is another amino acid not encoded in DNA, but synthesized into protein by ribosomes.{{cite journal | vauthors = Hao B, Gong W, Ferguson TK, James CM, Krzycki JA, Chan MK | title = A new UAG-encoded residue in the structure of a methanogen methyltransferase | journal = Science | volume = 296 | issue = 5572 | pages = 1462–1466 | date = May 2002 | pmid = 12029132 | doi = 10.1126/science.1069556 | s2cid = 35519996 | bibcode = 2002Sci...296.1462H }} 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

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 zwitterions, 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 physiological pH the so-called "neutral forms" {{chem2|\sNH2\sCHR\sCO2H}} are not present to any measurable degree.{{cite book | vauthors = Steinhardt J, Reynolds JA |title=Multiple equilibria in proteins |publisher=Academic Press |place=New York |isbn=978-0126654509| pages=176–21 |date=1969}} 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 that of Brønsted:{{cite journal | vauthors = Brønsted JN | journal = Recueil des Travaux Chimiques des Pays-Bas | volume = 42 | pages = 718–728 |year= 1923| title = Einige Bemerkungen über den Begriff der Säuren und Basen| issue= 8 | doi= 10.1002/recl.19230420815 |trans-title = Remarks on the concept of acids and bases}} 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.pngs 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 pK_a values, but coexists in equilibrium with small amounts of net negative and net positive ions. At the midpoint between the two pK_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.{{cite book | vauthors = Fennema OR |title=Food Chemistry 3rd Ed |publisher=CRC Press |pages=327–328 |isbn=978-0-8247-9691-4 |date=1996-06-19 }} This pH is known as the isoelectric point pI, so pI = {{sfrac|1|2}}(pK_a1 + pK_a2).

For amino acids with charged side chains, the pK_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 pK_a values: pI = {{sfrac|1|2}}(pK_a1 + pK_a(R)), where pK_a(R) is the side chain pK_a.{{Cite book | vauthors = Vollhardt KP |title=Organic chemistry : structure and function |date=2007 |publisher=W.H. Freeman |others=Neil Eric Schore |isbn=978-0-7167-9949-8 |edition=5th |location=New York |pages=58–66 |oclc=61448218}}

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 interactions. The water-soluble proteins tend to have their hydrophobic residues (Leu, Ile, Val, Phe, and 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 polymeric chain of a polysaccharide, protein or nucleic acid.) The integral membrane proteins tend to have outer rings of exposed hydrophobic amino acids that anchor them in the lipid bilayer. Some peripheral membrane proteins 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 of nucleic-acid binding proteins.{{cite journal | vauthors = Ntountoumi C, Vlastaridis P, Mossialos D, Stathopoulos C, Iliopoulos I, Promponas V, Oliver SG, Amoutzias GD | title = Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved | journal = Nucleic Acids Research | volume = 47 | issue = 19 | pages = 9998–10009 | date = November 2019 | pmid = 31504783 | pmc = 6821194 | doi = 10.1093/nar/gkz730 }} There are various hydrophobicity scales of amino acid residues.{{cite journal| vauthors = Urry DW | title = The change in Gibbs free energy for hydrophobic association: Derivation and evaluation by means of inverse temperature transitions | journal = Chemical Physics Letters | volume = 399 | issue = 1–3 | pages = 177–183 | year = 2004 | doi = 10.1016/S0009-2614(04)01565-9 | bibcode = 2004CPL...399..177U }}

Some amino acids have special properties. Cysteine can form covalent disulfide bonds to other cysteine residues. Proline forms 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.{{cite journal | vauthors = Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D | title = A census of protein repeats | journal = Journal of Molecular Biology | volume = 293 | issue = 1 | pages = 151–160 | date = October 1999 | pmid = 10512723 | doi = 10.1006/jmbi.1999.3136 }}{{cite journal | vauthors = Haerty W, Golding GB | title = Low-complexity sequences and single amino acid repeats: not just "junk" peptide sequences | journal = Genome | volume = 53 | issue = 10 | pages = 753–762 | date = October 2010 | pmid = 20962881 | doi = 10.1139/G10-063 | veditors = Bonen L }}

Many proteins undergo a range of posttranslational modifications, whereby additional chemical groups are attached to the amino acid residue side chains sometimes producing lipoproteins (that are hydrophobic),{{cite journal | vauthors = Magee T, Seabra MC | title = Fatty acylation and prenylation of proteins: what's hot in fat | journal = Current Opinion in Cell Biology | volume = 17 | issue = 2 | pages = 190–196 | date = April 2005 | pmid = 15780596 | doi = 10.1016/j.ceb.2005.02.003 }} or glycoproteins (that are hydrophilic){{cite journal | vauthors = Pilobello KT, Mahal LK | title = Deciphering the glycocode: the complexity and analytical challenge of glycomics | journal = Current Opinion in Chemical Biology | volume = 11 | issue = 3 | pages = 300–305 | date = June 2007 | pmid = 17500024 | doi = 10.1016/j.cbpa.2007.05.002 }} 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.{{cite journal | vauthors = Smotrys JE, Linder ME | title = Palmitoylation of intracellular signaling proteins: regulation and function | journal = Annual Review of Biochemistry | volume = 73 | issue = 1 | pages = 559–587 | year = 2004 | pmid = 15189153 | doi = 10.1146/annurev.biochem.73.011303.073954 }}

{{Redirect|Amino acid code|base-pair encoding of amino acids|Genetic code#Codons}}

{{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:{{Cite journal |date=10 July 1968 |title=IUPAC-IUB Commission on Biochemical Nomenclature A One-Letter Notation for Amino Acid Sequences |journal=Journal of Biological Chemistry |language=en |volume=243 |issue=13 |pages=3557–3559 |doi=10.1016/S0021-9258(19)34176-6|doi-access=free }}

• Initial letters are used where there is no ambiguity: 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,
• F PHenylalanine and R aRginine are assigned by being phonetically suggestive,
• W tryptophan is assigned based on the double ring being visually suggestive to the bulky letter W,
• 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,{{Cite journal | vauthors = Saffran M |date=April 1998 |title=Amino acid names and parlor games: from trivial names to a one-letter code, amino acid names have strained students' memories. Is a more rational nomenclature possible? |journal=Biochemical Education |language=en |volume=26 |issue=2 |pages=116–118 |doi=10.1016/S0307-4412(97)00167-2}}
• D aspartate was assigned arbitrarily, with the proposed mnemonic asparDic acid;{{Cite journal | vauthors = Adoga GI, Nicholson BH |date=January 1988 |title=Letters to the editor |journal=Biochemical Education |language=en |volume=16 |issue=1 |pages=49 |doi=10.1016/0307-4412(88)90026-X}} E glutamate was assigned in alphabetical sequence being larger by merely one methylene –CH₂– group,
• N asparagine was assigned arbitrarily, with the proposed mnemonic asparagiNe; 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 Qlutamine.

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

! rowspan=2 | Amino acid

! colspan=2 | 3- and 1-letter symbols

! colspan=3 | Side chain

! rowspan=2 | Hydropathy
index{{cite journal | vauthors = Kyte J, Doolittle RF | title = A simple method for displaying the hydropathic character of a protein | journal = Journal of Molecular Biology | volume = 157 | issue = 1 | pages = 105–132 | date = May 1982 | pmid = 7108955 | doi = 10.1016/0022-2836(82)90515-0 | citeseerx = 10.1.1.458.454 }}

! colspan=2 | Molar absorptivity{{Cite book| title=Physical Biochemistry| vauthors=Freifelder D| publisher=W. H. Freeman and Company| isbn=978-0-7167-1315-9| edition=2nd| year=1983}}{{Page needed|date=September 2010}}

! rowspan=2 | Molecular mass

! rowspan=2 | Abundance in proteins (%){{cite journal | vauthors = Kozlowski LP | title = Proteome-pI: proteome isoelectric point database | journal = Nucleic Acids Research | volume = 45 | issue = D1 | pages = D1112–D1116 | date = January 2017 | pmid = 27789699 | pmc = 5210655 | doi = 10.1093/nar/gkw978 }}

! rowspan=2 | Standard genetic coding,
IUPAC notation

|-

! 3

! 1

! Class

! Chemical polarity{{cite book | vauthors = Hausman RE, Cooper GM |title=The cell: a molecular approach |publisher=ASM Press |location=Washington, D.C. |year=2004 |page=51 |isbn=978-0-87893-214-6}}

! Net charge
at pH 7.4

! Wavelength,
λ_max (nm)

! Coefficient ε
(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{{efn|Codons can also be expressed by: CGN, AGR.}}

|-

| 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{{efn|Codons can also be expressed by: CUN, UUR.}}

|-

| 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 by codons that are usually interpreted as stop codons:

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

|-

! 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 where chemical or crystallographic analysis of a peptide or protein cannot conclusively determine the identity of a residue. They are also used to summarize conserved protein sequence motifs. The use of single letters to indicate sets of similar residues is similar to the use of abbreviation codes for degenerate bases.{{cite journal | vauthors = Aasland R, Abrams C, Ampe C, Ball LJ, Bedford MT, Cesareni G, Gimona M, Hurley JH, Jarchau T, Lehto VP, Lemmon MA, Linding R, Mayer BJ, Nagai M, Sudol M, Walter U, Winder SJ | title = Normalization of nomenclature for peptide motifs as ligands of modular protein domains | journal = FEBS Letters | volume = 513 | issue = 1 | pages = 141–144 | date = February 2002 | pmid = 11911894 | doi = 10.1111/j.1432-1033.1968.tb00350.x }}{{cite journal | vauthors = ((IUPAC–IUB Commission on Biochemical Nomenclature)) | title = A one-letter notation for amino acid sequences | journal = Pure and Applied Chemistry | volume = 31 | issue = 4 | pages = 641–645 | year = 1972 | pmid = 5080161 | doi = 10.1351/pac197231040639 | doi-access = free }}

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

|-

! Ambiguous amino acids

! 3-letter

! 1-letter

! Amino acids included

! Codons included

|-

| Any / unknown

| Xaa

| X

| All

| NNN

|-

| Asparagine or aspartate

| Asx

| B

| D, N

| RAY

|-

| Glutamine or glutamate

| Glx

| Z

| E, Q

| SAR

|-

| Leucine or isoleucine

| Xle

| J

| I, L

| YTR, ATH, CTY{{efn|Codons can also be expressed by: CTN, ATH, TTR; MTY, YTR, ATA; MTY, HTA, YTG.}}

|-

| Hydrophobic

|

| Φ

| V, I, L, F, W, Y, M

| NTN, TAY, TGG

|-

| Aromatic

|

| Ω

| F, W, Y, H

| YWY, TTY, TGG{{efn|Codons can also be expressed by: TWY, CAY, TGG.}}

|-

| Aliphatic (non-aromatic)

|

| Ψ

| V, I, L, M

| VTN, TTR{{efn|Codons can also be expressed by: NTR, VTY.}}

|-

| Small

|

| π

| P, G, A, S

| BCN, RGY, GGR

|-

| Hydrophilic

|

| ζ

| S, T, H, N, Q, E, D, K, R

| VAN, WCN, CGN, AGY{{efn|Codons can also be expressed by: VAN, WCN, MGY, CGP.}}

|-

| Positively-charged

|

| +

| K, R, H

| ARR, CRY, CGR

|-

| Negatively-charged

|

| −

| D, E

| GAN

|}

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.{{Cite web |url=http://varnomen.hgvs.org/recommendations/protein/variant/substitution/ |title=HGVS: Sequence Variant Nomenclature, Protein Recommendations |access-date=23 September 2021 |url-status=live |archive-date=24 September 2021 |archive-url=https://web.archive.org/web/20210924091505/http://varnomen.hgvs.org/recommendations/protein/variant/substitution/}}

In addition, many nonstandard amino acids have a specific code. For example, several peptide drugs, such as Bortezomib and MG132, are artificially synthesized and retain their protecting groups, which have specific codes. Bortezomib is Pyz–Phe–boroLeu, and MG132 is Z–Leu–Leu–Leu–al. To aid in the analysis of protein structure, photo-reactive amino acid analogs are available. These include photoleucine (pLeu) and photomethionine (pMet).{{cite journal | vauthors = Suchanek M, Radzikowska A, Thiele C | title = Photo-leucine and photo-methionine allow identification of protein-protein interactions in living cells | journal = Nature Methods | volume = 2 | issue = 4 | pages = 261–267 | date = April 2005 | pmid = 15782218 | doi = 10.1038/nmeth752 | doi-access = free }}

{{multiple image

| align = right

| direction = vertical

| total_width = 300

| header_align =

| header =

| image5 = Protein primary structure.svg

| alt5 = A protein depicted as a long unbranched string of linked circles each representing amino acids

| width5 =

| height5 =

| caption5 = A polypeptide is an unbranched chain of amino acids.

| image6 = Beta alanine comparison.svg

| alt6 = Diagrammatic comparison of the structures of β-alanine and α-alanine

| width6 =

| height6 =

| caption6 = β-Alanine and its α-alanine isomer

| image7 = Selenocysteine skeletal 3D.svg

| alt7 = A diagram showing the structure of selenocysteine

| width7 =

| height7 =

| caption7 = The amino acid selenocysteine

}}

{{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 RNA genetic material is called translation and involves the step-by-step addition of amino acids to a growing protein chain by a ribozyme that is called a ribosome.{{cite journal | vauthors = Rodnina MV, Beringer M, Wintermeyer W | title = How ribosomes make peptide bonds | journal = Trends in Biochemical Sciences | volume = 32 | issue = 1 | pages = 20–26 | date = January 2007 | pmid = 17157507 | doi = 10.1016/j.tibs.2006.11.007 }} The order in which the amino acids are added is read through the genetic code from an mRNA template, which is an RNA derived from one of the organism's genes.

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.{{cite journal | vauthors = Driscoll DM, Copeland PR | title = Mechanism and regulation of selenoprotein synthesis | journal = Annual Review of Nutrition | volume = 23 | issue = 1 | pages = 17–40 | year = 2003 | pmid = 12524431 | doi = 10.1146/annurev.nutr.23.011702.073318 }} Pyrrolysine is used by some methanogenic 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.{{cite journal | vauthors = Krzycki JA | title = The direct genetic encoding of pyrrolysine | journal = Current Opinion in Microbiology | volume = 8 | issue = 6 | pages = 706–712 | date = December 2005 | pmid = 16256420 | doi = 10.1016/j.mib.2005.10.009 }}

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.{{cite journal | vauthors = Wong JT | title = A co-evolution theory of the genetic code | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 72 | issue = 5 | pages = 1909–1912 | date = May 1975 | pmid = 1057181 | pmc = 432657 | doi = 10.1073/pnas.72.5.1909 | doi-access = free | bibcode = 1975PNAS...72.1909T }}{{cite journal | vauthors = Trifonov EN | title = Consensus temporal order of amino acids and evolution of the triplet code | journal = Gene | volume = 261 | issue = 1 | pages = 139–151 | date = December 2000 | pmid = 11164045 | doi = 10.1016/S0378-1119(00)00476-5 }}{{cite journal | vauthors = Higgs PG, Pudritz RE | title = A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code | journal = Astrobiology | volume = 9 | issue = 5 | pages = 483–490 | date = June 2009 | pmid = 19566427 | doi = 10.1089/ast.2008.0280 | arxiv = 0904.0402 | s2cid = 9039622 | bibcode = 2009AsBio...9..483H }}

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) is often incorporated in place of methionine as the initial amino acid of proteins in bacteria, mitochondria and plastids (including 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,{{cite journal | vauthors = Kryukov GV, Castellano S, Novoselov SV, Lobanov AV, Zehtab O, Guigó R, Gladyshev VN | title = Characterization of mammalian selenoproteomes | journal = Science | volume = 300 | issue = 5624 | pages = 1439–1443 | date = May 2003 | pmid = 12775843 | doi = 10.1126/science.1083516 | s2cid = 10363908 | bibcode = 2003Sci...300.1439K }} and the structurally characterized enzymes (selenoenzymes) employ selenocysteine as the catalytic moiety in their active sites.{{cite journal | vauthors = Gromer S, Urig S, Becker K | title = The thioredoxin system--from science to clinic | journal = Medicinal Research Reviews | volume = 24 | issue = 1 | pages = 40–89 | date = January 2004 | pmid = 14595672 | doi = 10.1002/med.10051 | s2cid = 1944741 }} Pyrrolysine and selenocysteine are encoded via variant codons. For example, selenocysteine is encoded by stop codon and SECIS element.{{cite thesis |url= https://diginole.lib.fsu.edu/islandora/object/fsu%3A175939 | vauthors = Tjong H |title=Modeling Electrostatic Contributions to Protein Folding and Binding|date=2008|publisher=Florida State University|type=PhD thesis|page=1 footnote|access-date=28 January 2020|archive-date=28 January 2020|archive-url=https://web.archive.org/web/20200128234717/https://diginole.lib.fsu.edu/islandora/object/fsu:175939|url-status=live}}{{cite journal| vauthors = Stewart L, Burgin AB |journal=Frontiers in Drug Design & Discovery |date=2005|title=Whole Gene Synthesis: A Gene-O-Matic Future|url=https://books.google.com/books?id=VoJw6fIISSkC&pg=PA299|publisher=Bentham Science Publishers|volume=1|page=299|doi=10.2174/1574088054583318|isbn=978-1-60805-199-1|issn=1574-0889|access-date=5 January 2016|archive-date=14 April 2021|archive-url=https://web.archive.org/web/20210414224011/https://books.google.com/books?id=VoJw6fIISSkC&pg=PA299|url-status=live}}{{cite web|date=7 April 2008|title=The Genetic Codes|url=https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c|access-date=10 March 2010|publisher=National Center for Biotechnology Information (NCBI)|vauthors=Elzanowski A, Ostell J|archive-date=20 August 2016|archive-url=https://web.archive.org/web/20160820125755/http://130.14.29.110/Taxonomy/Utils/wprintgc.cgi?mode=c|url-status=live}}

N-formylmethionine (which is often the initial amino acid of proteins in bacteria, mitochondria, and chloroplasts) is generally considered as a form of methionine rather than as a separate proteinogenic amino acid. Codon–tRNA combinations not found in nature can also be used to "expand" the genetic code and form novel proteins known as alloproteins incorporating non-proteinogenic amino acids.{{cite journal | vauthors = Xie J, Schultz PG | title = Adding amino acids to the genetic repertoire | journal = Current Opinion in Chemical Biology | volume = 9 | issue = 6 | pages = 548–554 | date = December 2005 | pmid = 16260173 | doi = 10.1016/j.cbpa.2005.10.011 }}{{cite journal | vauthors = Wang Q, Parrish AR, Wang L | title = Expanding the genetic code for biological studies | journal = Chemistry & Biology | volume = 16 | issue = 3 | pages = 323–336 | date = March 2009 | pmid = 19318213 | pmc = 2696486 | doi = 10.1016/j.chembiol.2009.03.001 }}{{cite book | vauthors = Simon M | title = Emergent computation: emphasizing bioinformatics | url = https://archive.org/details/emergentcomputat00simo_754 | url-access = limited | publisher = AIP Press/Springer Science+Business Media | location = New York | year = 2005 | pages = [https://archive.org/details/emergentcomputat00simo_754/page/n116 105–106] | isbn = 978-0-387-22046-8 }}

{{main|Non-proteinogenic amino acids}}

Aside from the 22 proteinogenic amino acids, many non-proteinogenic amino acids are known. Those either are not found in proteins (for example carnitine, 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.{{cite journal | vauthors = Blenis J, Resh MD | title = Subcellular localization specified by protein acylation and phosphorylation | journal = Current Opinion in Cell Biology | volume = 5 | issue = 6 | pages = 984–989 | date = December 1993 | pmid = 8129952 | doi = 10.1016/0955-0674(93)90081-Z }} Examples:

• the carboxylation of glutamate allows for better binding of calcium cations,{{cite journal | vauthors = Vermeer C | title = Gamma-carboxyglutamate-containing proteins and the vitamin K-dependent carboxylase | journal = The Biochemical Journal | volume = 266 | issue = 3 | pages = 625–636 | date = March 1990 | pmid = 2183788 | pmc = 1131186 | doi = 10.1042/bj2660625 }}
• Hydroxyproline, generated by hydroxylation of proline, is a major component of the connective tissue collagen.{{cite journal | vauthors = Bhattacharjee A, Bansal M | title = Collagen structure: the Madras triple helix and the current scenario | journal = IUBMB Life | volume = 57 | issue = 3 | pages = 161–172 | date = March 2005 | pmid = 16036578 | doi = 10.1080/15216540500090710 | s2cid = 7211864 }}
• Hypusine in the translation initiation factor EIF5A, contains a modification of lysine.{{cite journal | vauthors = Park MH | title = The post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5A (eIF5A) | journal = Journal of Biochemistry | volume = 139 | issue = 2 | pages = 161–169 | date = February 2006 | pmid = 16452303 | pmc = 2494880 | doi = 10.1093/jb/mvj034 }}

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 pathways for standard amino acids – for example, ornithine and citrulline occur in the urea cycle, part of amino acid catabolism (see below).{{cite journal | vauthors = Curis E, Nicolis I, Moinard C, Osowska S, Zerrouk N, Bénazeth S, Cynober L | title = Almost all about citrulline in mammals | journal = Amino Acids | volume = 29 | issue = 3 | pages = 177–205 | date = November 2005 | pmid = 16082501 | doi = 10.1007/s00726-005-0235-4 | s2cid = 23877884 }} 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.{{cite journal | vauthors = Coxon KM, Chakauya E, Ottenhof HH, Whitney HM, Blundell TL, Abell C, Smith AG | title = Pantothenate biosynthesis in higher plants | journal = Biochemical Society Transactions | volume = 33 | issue = Pt 4 | pages = 743–746 | date = August 2005 | pmid = 16042590 | doi = 10.1042/BST0330743 }}

File:Amino acids in food and blood.png

{{Main|Essential amino acid}}

{{further|Protein (nutrient)|Amino acid synthesis}}

Animals ingest amino acids in the form of protein. The protein is broken down into its constituent amino acids in the process of digestion. The amino acids are then used to synthesize new proteins and other nitrogenous biomolecules, or they are further catabolized through oxidation to provide a source of energy.{{cite journal | vauthors = Sakami W, Harrington H | title = Amino Acid Metabolism | journal = Annual Review of Biochemistry | volume = 32 | issue = 1 | pages = 355–398 | year = 1963 | pmid = 14144484 | doi = 10.1146/annurev.bi.32.070163.002035 }} 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.{{cite journal | vauthors = Brosnan JT | title = Glutamate, at the interface between amino acid and carbohydrate metabolism | journal = The Journal of Nutrition | volume = 130 | issue = 4S Suppl | pages = 988S–990S | date = April 2000 | pmid = 10736367 | doi = 10.1093/jn/130.4.988S | doi-access = free }} Glucogenic amino acids can also be converted into glucose, through gluconeogenesis.{{cite journal | vauthors = Young VR, Ajami AM | title = Glutamine: the emperor or his clothes? | journal = The Journal of Nutrition | volume = 131 | issue = 9 Suppl | pages = 2449S–2459S, 2486S–2487S | date = September 2001 | pmid = 11533293 | doi = 10.1093/jn/131.9.2449S | doi-access = free }}

Of the 20 standard amino acids, nine (His, Ile, Leu, Lys, Met, Phe, Thr, Trp and Val) are called essential amino acids because the human body cannot synthesize them from other compounds at the level needed for normal growth, so they must be obtained from food.{{cite journal | vauthors = Young VR | title = Adult amino acid requirements: the case for a major revision in current recommendations | journal = The Journal of Nutrition | volume = 124 | issue = 8 Suppl | pages = 1517S–1523S | date = August 1994 | pmid = 8064412 | doi = 10.1093/jn/124.suppl_8.1517S | doi-access = free }}{{cite journal | vauthors = Fürst P, Stehle P | title = What are the essential elements needed for the determination of amino acid requirements in humans? | journal = The Journal of Nutrition | volume = 134 | issue = 6 Suppl | pages = 1558S–1565S | date = June 2004 | pmid = 15173430 | doi = 10.1093/jn/134.6.1558S | doi-access = free }}{{cite journal | vauthors = Reeds PJ | title = Dispensable and indispensable amino acids for humans | journal = The Journal of Nutrition | volume = 130 | issue = 7 | pages = 1835S–1840S | date = July 2000 | pmid = 10867060 | doi = 10.1093/jn/130.7.1835S | doi-access = free }}

In addition, cysteine, tyrosine, and arginine are considered semiessential amino acids, and taurine a semi-essential aminosulfonic acid in children. Some amino acids are conditionally essential for certain ages or medical conditions. Essential amino acids may also vary from species to species.{{efn|For example, ruminants such as cows obtain a number of amino acids via microbes in the first two stomach chambers.}} The metabolic pathways that synthesize these monomers are not fully developed.{{cite journal | vauthors = Imura K, Okada A | title = Amino acid metabolism in pediatric patients | journal = Nutrition | volume = 14 | issue = 1 | pages = 143–148 | date = January 1998 | pmid = 9437700 | doi = 10.1016/S0899-9007(97)00230-X }}{{cite journal | vauthors = Lourenço R, Camilo ME | title = Taurine: a conditionally essential amino acid in humans? An overview in health and disease | journal = Nutricion Hospitalaria | volume = 17 | issue = 6 | pages = 262–270 | year = 2002 | pmid = 12514918 }}

{{Catecholamine and trace amine biosynthesis|align=right|caption=Catecholamines and trace amines 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. Defenses against herbivores in plants sometimes employ amino acids.{{Cite journal| vauthors = Hylin JW |year=1969 |title=Toxic peptides and amino acids in foods and feeds |journal=Journal of Agricultural and Food Chemistry |volume=17 |issue=3 |pages=492–496 |doi=10.1021/jf60163a003|bibcode=1969JAFC...17..492H }} Examples:

• Tryptophan is a precursor of the neurotransmitter serotonin.{{cite journal | vauthors = Savelieva KV, Zhao S, Pogorelov VM, Rajan I, Yang Q, Cullinan E, Lanthorn TH | title = Genetic disruption of both tryptophan hydroxylase genes dramatically reduces serotonin and affects behavior in models sensitive to antidepressants | journal = PLOS ONE | volume = 3 | issue = 10 | pages = e3301 | year = 2008 | pmid = 18923670 | pmc = 2565062 | doi = 10.1371/journal.pone.0003301 | veditors = Bartolomucci A | doi-access = free | bibcode = 2008PLoSO...3.3301S }}
• Tyrosine (and its precursor phenylalanine) are precursors of the catecholamine neurotransmitters dopamine, epinephrine and norepinephrine and various trace amines.
• Phenylalanine is a precursor of phenethylamine and tyrosine in humans. In plants, it is a precursor of various phenylpropanoids, which are important in plant metabolism.
• Glycine is a precursor of porphyrins such as heme.{{cite journal | vauthors = Shemin D, Rittenberg D | title = The biological utilization of glycine for the synthesis of the protoporphyrin of hemoglobin | journal = The Journal of Biological Chemistry | volume = 166 | issue = 2 | pages = 621–625 | date = December 1946 | pmid = 20276176 | doi = 10.1016/S0021-9258(17)35200-6 | doi-access = free }}
• Arginine is a precursor of nitric oxide.{{cite journal | vauthors = Tejero J, Biswas A, Wang ZQ, Page RC, Haque MM, Hemann C, Zweier JL, Misra S, Stuehr DJ | title = Stabilization and characterization of a heme-oxy reaction intermediate in inducible nitric-oxide synthase | journal = The Journal of Biological Chemistry | volume = 283 | issue = 48 | pages = 33498–33507 | date = November 2008 | pmid = 18815130 | pmc = 2586280 | doi = 10.1074/jbc.M806122200 | doi-access = free }}
• Ornithine and S-adenosylmethionine are precursors of polyamines.{{cite journal | vauthors = Rodríguez-Caso C, Montañez R, Cascante M, Sánchez-Jiménez F, Medina MA | title = Mathematical modeling of polyamine metabolism in mammals | journal = The Journal of Biological Chemistry | volume = 281 | issue = 31 | pages = 21799–21812 | date = August 2006 | pmid = 16709566 | doi = 10.1074/jbc.M602756200 | hdl-access = free | doi-access = free | bibcode = 2006JBiCh.28121799R | hdl = 10630/32289 }}
• Aspartate, glycine, and glutamine are precursors of nucleotides.{{cite book | vauthors = Stryer L, Berg JM, Tymoczko JL |title=Biochemistry |url=https://archive.org/details/biochemistry200100jere |url-access=registration |date=2002 |publisher=W.H. Freeman |location=New York |isbn=978-0-7167-4684-3 |edition=5th |pages=[https://archive.org/details/biochemistry200100jere/page/693 693–698]}}

• Carnitine is used in lipid transport.
• gamma-aminobutyric acid is a neurotransmitter.{{cite journal | vauthors = Petroff OA | title = GABA and glutamate in the human brain | journal = The Neuroscientist | volume = 8 | issue = 6 | pages = 562–573 | date = December 2002 | pmid = 12467378 | doi = 10.1177/1073858402238515 | s2cid = 84891972 }}
• 5-HTP (5-hydroxytryptophan) is used for experimental treatment of depression.{{cite journal | vauthors = Turner EH, Loftis JM, Blackwell AD | title = Serotonin a la carte: supplementation with the serotonin precursor 5-hydroxytryptophan | journal = Pharmacology & Therapeutics | volume = 109 | issue = 3 | pages = 325–338 | date = March 2006 | pmid = 16023217 | doi = 10.1016/j.pharmthera.2005.06.004 | s2cid = 2563606 | url = https://escholarship.org/uc/item/58h866d5 }}
• L-DOPA (L-dihydroxyphenylalanine) for Parkinson's treatment,{{cite journal | vauthors = Kostrzewa RM, Nowak P, Kostrzewa JP, Kostrzewa RA, Brus R | title = Peculiarities of L: -DOPA treatment of Parkinson's disease | journal = Amino Acids | volume = 28 | issue = 2 | pages = 157–164 | date = March 2005 | pmid = 15750845 | doi = 10.1007/s00726-005-0162-4 | s2cid = 33603501 }}
• Eflornithine inhibits ornithine decarboxylase and used in the treatment of sleeping sickness.{{cite journal | vauthors = Heby O, Persson L, Rentala M | title = Targeting the polyamine biosynthetic enzymes: a promising approach to therapy of African sleeping sickness, Chagas' disease, and leishmaniasis | journal = Amino Acids | volume = 33 | issue = 2 | pages = 359–366 | date = August 2007 | pmid = 17610127 | doi = 10.1007/s00726-007-0537-9 | s2cid = 26273053 }}
• Canavanine, an analogue of arginine found in many legumes is an antifeedant, protecting the plant from predators.{{cite journal | vauthors = Rosenthal GA | title = L-Canavanine: a higher plant insecticidal allelochemical | journal = Amino Acids | volume = 21 | issue = 3 | pages = 319–330 | year = 2001 | pmid = 11764412 | doi = 10.1007/s007260170017 | s2cid = 3144019 }}
• Mimosine found in some legumes, is another possible antifeedant.{{cite journal | vauthors = Hammond AC | title = Leucaena toxicosis and its control in ruminants | journal = Journal of Animal Science | volume = 73 | issue = 5 | pages = 1487–1492 | date = May 1995 | pmid = 7665380 | doi = 10.2527/1995.7351487x }} This compound is an analogue of tyrosine and can poison animals that graze on these plants.

However, not all of the functions of other abundant nonstandard amino acids are known.

Amino acids are sometimes added to animal feed because some of the components of these feeds, such as soybeans, have low levels of some of the essential amino acids, especially of lysine, methionine, threonine, and tryptophan.{{cite journal | vauthors = Leuchtenberger W, Huthmacher K, Drauz K | title = Biotechnological production of amino acids and derivatives: current status and prospects | journal = Applied Microbiology and Biotechnology | volume = 69 | issue = 1 | pages = 1–8 | date = November 2005 | pmid = 16195792 | doi = 10.1007/s00253-005-0155-y | s2cid = 24161808 }} Likewise amino acids are used to chelate metal cations in order to improve the absorption of minerals from feed supplements.{{cite book| vauthors = Ashmead HE |title=The Role of Amino Acid Chelates in Animal Nutrition|year=1993|publisher=Noyes Publications|location=Westwood}}

The food industry is a major consumer of amino acids, especially glutamic acid, which is used as a flavor enhancer,{{cite journal | vauthors = Garattini S | title = Glutamic acid, twenty years later | journal = The Journal of Nutrition | volume = 130 | issue = 4S Suppl | pages = 901S–909S | date = April 2000 | pmid = 10736350 | doi = 10.1093/jn/130.4.901S | doi-access = free }} and aspartame (aspartylphenylalanine 1-methyl ester), which is used as an artificial sweetener.{{cite journal | vauthors = Stegink LD | title = The aspartame story: a model for the clinical testing of a food additive | journal = The American Journal of Clinical Nutrition | volume = 46 | issue = 1 Suppl | pages = 204–215 | date = July 1987 | pmid = 3300262 | doi = 10.1093/ajcn/46.1.204 }} 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 feedstocks used in chiral pool synthesis as enantiomerically pure building blocks.{{cite journal | vauthors = Hanessian S | year =1993 | title = Reflections on the total synthesis of natural products: Art, craft, logic, and the chiron approach |journal=Pure and Applied Chemistry | volume = 65 | issue = 6 | pages = 1189–1204 | doi = 10.1351/pac199365061189 | s2cid =43992655 | doi-access = free }}{{cite journal | vauthors = Blaser HU | year = 1992 | title = The chiral pool as a source of enantioselective catalysts and auxiliaries |journal=Chemical Reviews |volume=92 |issue=5 |pages=935–952 |doi=10.1021/cr00013a009}}

Amino acids are used in the synthesis of some cosmetics.

The 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.{{cite book| vauthors = Ashmead HE |title=Foliar Feeding of Plants with Amino Acid Chelates|year=1986|publisher=Noyes Publications|location=Park Ridge}}

{{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 implants.{{cite journal | vauthors = Sanda F, Endo T | year = 1999 | title = Syntheses and functions of polymers based on amino acids | journal = Macromolecular Chemistry and Physics | volume = 200 | issue = 12 | pages = 2651–2661 | doi = 10.1002/(SICI)1521-3935(19991201)200:12<2651::AID-MACP2651>3.0.CO;2-P | doi-access = free }} An interesting example of such materials is polyaspartate, a water-soluble biodegradable polymer that may have applications in disposable diapers and agriculture.{{cite journal | vauthors = Gross RA, Kalra B | title = Biodegradable polymers for the environment | journal = Science | volume = 297 | issue = 5582 | pages = 803–807 | date = August 2002 | pmid = 12161646 | doi = 10.1126/science.297.5582.803 | url = https://zenodo.org/record/1231185 | access-date = 12 June 2019 | url-status = live | bibcode = 2002Sci...297..803G | archive-url = https://web.archive.org/web/20200725075829/https://zenodo.org/record/1231185 | archive-date = 25 July 2020 }} Due to its solubility and ability to chelate metal ions, polyaspartate is also being used as a biodegradable antiscaling agent and a corrosion inhibitor.{{Cite book|title= Commercial poly(aspartic acid) and Its Uses | vauthors = Low KC, Wheeler AP, Koskan LP |series= Advances in Chemistry Series |volume= 248 |publisher= American Chemical Society |location= Washington, D.C. |year= 1996}}{{cite journal| vauthors = Thombre SM, Sarwade BD | year = 2005 | title = Synthesis and Biodegradability of Polyaspartic Acid: A Critical Review | journal = Journal of Macromolecular Science, Part A | volume = 42 | issue = 9 | pages = 1299–1315 | doi = 10.1080/10601320500189604| s2cid = 94818855 }}

{{Main|Amino acid synthesis}}

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 L-cysteine for example. Aspartic acid is produced by the addition of ammonia to fumarate using a lyase.{{Ullmann | vauthors = Drauz K, Grayson I, Kleemann A, Krimmer HP, Leuchtenberger W, Weckbecker C |year=2007| doi=10.1002/14356007.a02_057.pub2|title=Amino Acids}}

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 transaminases 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.{{Cite book | vauthors = Jones RC, Buchanan BB, Gruissem W | title = Biochemistry & molecular biology of plants | publisher = American Society of Plant Physiologists | location = Rockville, Md | year = 2000 | pages = [https://archive.org/details/biochemistrymole00buch/page/371 371–372] | isbn = 978-0-943088-39-6 | url = https://archive.org/details/biochemistrymole00buch/page/371 }} 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,{{cite journal | vauthors = Brosnan JT, Brosnan ME | title = The sulfur-containing amino acids: an overview | journal = The Journal of Nutrition | volume = 136 | issue = 6 Suppl | pages = 1636S–1640S | date = June 2006 | pmid = 16702333 | doi = 10.1093/jn/136.6.1636S | doi-access = free }} while hydroxyproline is made by a post translational modification of proline.{{cite book | vauthors = Kivirikko KI, Pihlajaniemi T | chapter = Collagen Hydroxylases and the Protein Disulfide Isomerase Subunit of Prolyl 4-Hydroxylases | title = Advances in Enzymology and Related Areas of Molecular Biology | volume = 72 | pages = 325–398 | year = 1998 | pmid = 9559057 | doi = 10.1002/9780470123188.ch9 | isbn = 9780470123188 | series = Advances in Enzymology – and Related Areas of Molecular Biology }}

Microorganisms 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.{{cite journal | vauthors = Whitmore L, Wallace BA | title = Analysis of peptaibol sequence composition: implications for in vivo synthesis and channel formation | journal = European Biophysics Journal | volume = 33 | issue = 3 | pages = 233–237 | date = May 2004 | pmid = 14534753 | doi = 10.1007/s00249-003-0348-1 | s2cid = 24638475 }} 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.{{cite journal | vauthors = Alexander L, Grierson D | title = Ethylene biosynthesis and action in tomato: a model for climacteric fruit ripening | journal = Journal of Experimental Botany | volume = 53 | issue = 377 | pages = 2039–2055 | date = October 2002 | pmid = 12324528 | doi = 10.1093/jxb/erf072 | doi-access = free }}

The formation of amino acids and peptides is assumed to have preceded and perhaps induced the 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.{{cite journal | vauthors = Danchin A | title = From chemical metabolism to life: the origin of the genetic coding process | journal = Beilstein Journal of Organic Chemistry | volume = 13 | issue = 1 | pages = 1119–1135 | date = 12 June 2017 | pmid = 28684991 | pmc = 5480338 | doi = 10.3762/bjoc.13.111 }}{{additional citation needed|date=September 2022}} Amino acids and similar building blocks could have been elaborated into proto-peptides, with peptides being considered key players in the origin of life.{{cite journal | vauthors = Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ | title = Prebiotic Peptides: Molecular Hubs in the Origin of Life | journal = Chemical Reviews | volume = 120 | issue = 11 | pages = 4707–4765 | date = June 2020 | pmid = 32101414 | doi = 10.1021/acs.chemrev.9b00664 | s2cid = 211536416 | bibcode = 2020ChRv..120.4707F }}

File:Strecker amino acid synthesis scheme.svg

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.{{cite journal |doi=10.1016/j.gsf.2017.07.007|title=Origins of building blocks of life: A review |year=2018 | vauthors = Kitadai N, Maruyama S |journal=Geoscience Frontiers |volume=9 |issue=4 |pages=1117–1153 |bibcode=2018GeoFr...9.1117K |s2cid=102659869 |doi-access=free }}

According to a review, amino acids, and even peptides, "turn up fairly regularly in the various experimental broths that have been allowed to be cooked from simple chemicals. This is because nucleotides 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'.{{cite journal | vauthors = Milner-White EJ | title = Protein three-dimensional structures at the origin of life | journal = Interface Focus | volume = 9 | issue = 6 | pages = 20190057 | date = December 2019 | pmid = 31641431 | pmc = 6802138 | doi = 10.1098/rsfs.2019.0057 }} Codon–amino acids mappings may be the biological information system at the primordial origin of life on Earth.{{cite journal | vauthors = Chatterjee S, Yadav S | title = The Coevolution of Biomolecules and Prebiotic Information Systems in the Origin of Life: A Visualization Model for Assembling the First Gene | journal = Life | volume = 12 | issue = 6 | pages = 834 | date = June 2022 | pmid = 35743865 | pmc = 9225589 | doi = 10.3390/life12060834 | doi-access = free | bibcode = 2022Life...12..834C }} 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.{{cite journal | vauthors = Kirschning A | title = The coenzyme/protein pair and the molecular evolution of life | journal = Natural Product Reports | volume = 38 | issue = 5 | pages = 993–1010 | date = May 2021 | pmid = 33206101 | doi = 10.1039/D0NP00037J | s2cid = 227037164 | doi-access = free }}

Amino acids undergo the reactions expected of the constituent functional groups.{{cite book | vauthors = Elmore DT, Barrett GC | title = Amino acids and peptides | url = https://archive.org/details/aminoacidspeptid00barr_040 | url-access = limited |publisher=Cambridge University Press |location=Cambridge, UK |year=1998 |pages=[https://archive.org/details/aminoacidspeptid00barr_040/page/n64 48]–60 |isbn=978-0-521-46827-5}}{{cite journal | vauthors = Gutteridge A, Thornton JM | title = Understanding nature's catalytic toolkit | journal = Trends in Biochemical Sciences | volume = 30 | issue = 11 | pages = 622–629 | date = November 2005 | pmid = 16214343 | doi = 10.1016/j.tibs.2005.09.006 }}

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

File:Peptidformationball.svg. 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 ATP-dependent reaction carried out by an aminoacyl tRNA synthetase.{{cite journal | vauthors = Ibba M, Söll D | title = The renaissance of aminoacyl-tRNA synthesis | journal = EMBO Reports | volume = 2 | issue = 5 | pages = 382–387 | date = May 2001 | pmid = 11375928 | pmc = 1083889 | doi = 10.1093/embo-reports/kve095 }} 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.{{cite journal | vauthors = Lengyel P, Söll D | title = Mechanism of protein biosynthesis | journal = Bacteriological Reviews | volume = 33 | issue = 2 | pages = 264–301 | date = June 1969 | pmid = 4896351 | pmc = 378322 | doi = 10.1128/MMBR.33.2.264-301.1969 }} 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.{{cite journal | vauthors = Wu G, Fang YZ, Yang S, Lupton JR, Turner ND | title = Glutathione metabolism and its implications for health | journal = The Journal of Nutrition | volume = 134 | issue = 3 | pages = 489–492 | date = March 2004 | pmid = 14988435 | doi = 10.1093/jn/134.3.489 | doi-access = free }} 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.{{cite journal | vauthors = Meister A | title = Glutathione metabolism and its selective modification | journal = The Journal of Biological Chemistry | volume = 263 | issue = 33 | pages = 17205–17208 | date = November 1988 | pmid = 3053703 | doi = 10.1016/S0021-9258(19)77815-6 | doi-access = free }}

In chemistry, peptides are synthesized by a variety of reactions. One of the most-used in 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.{{cite journal | vauthors = Carpino LA |year=1992 |title=1-Hydroxy-7-azabenzotriazole. An efficient peptide coupling additive |journal=Journal of the American Chemical Society |volume=115 |issue=10 |pages=4397–4398 |doi=10.1021/ja00063a082}} Libraries of peptides are used in drug discovery through high-throughput screening.{{cite journal | vauthors = Marasco D, Perretta G, Sabatella M, Ruvo M | title = Past and future perspectives of synthetic peptide libraries | journal = Current Protein & Peptide Science | volume = 9 | issue = 5 | pages = 447–467 | date = October 2008 | pmid = 18855697 | doi = 10.2174/138920308785915209 }}

The combination of functional groups allow amino acids to be effective polydentate ligands for metal–amino acid chelates.{{cite journal |vauthors=Konara S, Gagnona K, Clearfield A, Thompson C, Hartle J, Ericson C, Nelson C |title=Structural determination and characterization of copper and zinc bis-glycinates with X-ray crystallography and mass spectrometry |journal=Journal of Coordination Chemistry |year=2010 |volume=63 |issue=19 |doi=10.1080/00958972.2010.514336 |pages=3335–3347 |s2cid=94822047}}

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

[[File:Amino acid catabolism revised.png|class=skin-invert-image|thumb|upright=1.75 |Catabolism of proteinogenic amino acids. Amino acids can be classified according to the properties of their main degradation products:{{cite book |vauthors=Stipanuk MH |date=2006 |title=Biochemical, physiological, & molecular aspects of human nutrition |edition=2nd |publisher=Saunders Elsevier}}

* Glucogenic, with the products having the ability to form glucose by gluconeogenesis

* Ketogenic, with the products not having the ability to form glucose. These products may still be used for ketogenesis or lipid synthesis.

* 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.{{cite journal | vauthors = Dghaym RD, Dhawan R, Arndtsen BA | title = The Use of Carbon Monoxide and Imines as Peptide Derivative Synthons: A Facile Palladium-Catalyzed Synthesis of α-Amino Acid Derived Imidazolines | journal = Angewandte Chemie | volume = 40 | issue = 17 | pages = 3228–3230 | date = September 2001 | pmid = 29712039 | doi = 10.1002/(SICI)1521-3773(19980703)37:12<1634::AID-ANIE1634>3.0.CO;2-C }}

File:AAcomplexation.png

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.{{cite journal | vauthors = Muñoz-Huerta RF, Guevara-Gonzalez RG, Contreras-Medina LM, Torres-Pacheco I, Prado-Olivarez J, Ocampo-Velazquez RV | title = A review of methods for sensing the nitrogen status in plants: advantages, disadvantages and recent advances | journal = Sensors | volume = 13 | issue = 8 | pages = 10823–10843 | date = August 2013 | pmid = 23959242 | pmc = 3812630 | doi = 10.3390/s130810823 | doi-access = free | bibcode = 2013Senso..1310823M }}{{cite journal | vauthors = Martin PD, Malley DF, Manning G, Fuller L |date=2002 |title=Determination of soil organic carbon and nitrogen at thefield level using near-infrared spectroscopy |journal=Canadian Journal of Soil Science |volume=82 |issue=4 |pages=413–422 |doi=10.4141/S01-054 |bibcode=2002CaJSS..82..413M }}

{{Portal|Biology|Chemistry}}

{{div col|colwidth=20em}}

• Amino acid dating
• Beta-peptide
• Degron
• Erepsin
• Homochirality
• Hyperaminoacidemia
• Leucines
• Miller–Urey experiment
• Nucleic acid sequence
• RNA codon table

{{div col end}}

{{notelist}}

{{Reflist}}

{{refbegin}}

• {{cite book | vauthors = Tymoczko JL | 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}}
• {{cite book | vauthors = Doolittle RF | author-link = Russell Doolittle | veditors = Fasman GD | year = 1989 | title = Predictions of Protein Structure and the Principles of Protein Conformation | publisher = Plenum Press | location = New York | chapter = Redundancies in protein sequences | pages = 599–623 | isbn = 978-0-306-43131-9 | lccn = 89008555}}
• {{cite book | vauthors = Nelson DL, Cox MM | year = 2000 | title = Lehninger Principles of Biochemistry | publisher = Worth Publishers | edition = 3rd | isbn = 978-1-57259-153-0 | lccn = 99049137 | url-access = registration | url = https://archive.org/details/lehningerprincip01lehn}}
• {{cite book | vauthors = Meierhenrich U | author-link = Uwe Meierhenrich | year = 2008 | title = Amino acids and the asymmetry of life | publisher = Springer Verlag | location = Berlin | isbn = 978-3-540-76885-2 | lccn = 2008930865 | url = http://rogov.zwz.ru/Macroevolution/amino.pdf | url-status = dead | archive-url = https://web.archive.org/web/20120112005425/http://rogov.zwz.ru/Macroevolution/amino.pdf | archive-date = 12 January 2012}}

{{refend}}

• {{Commons-inline}}

{{Amino acids}}

{{Chemical bonds}}

{{Protein primary structure}}

{{Amino acid metabolism enzymes}}

{{Authority control}}

{{Good article}}

{{DEFAULTSORT:Amino Acid}}

Category:Nitrogen cycle

Category:Zwitterions