Editing Amino acid (section)

===Standard vs nonstandard amino acids===

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 [[plastid]]s (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,<ref>{{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 }}</ref> and the structurally characterized enzymes (selenoenzymes) employ selenocysteine as the catalytic [[moiety (chemistry)|moiety]] in their active sites.<ref>{{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 }}</ref> Pyrrolysine and selenocysteine are encoded via variant codons. For example, selenocysteine is encoded by stop codon and [[SECIS element]].<ref name="Tjong">{{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}}</ref><ref name="VoJw6fIISSkC p.299">{{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}}</ref><ref name="url_The_Genetic_Codes_NCBI">{{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}}</ref>

[[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.<ref name="pmid16260173">{{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 }}</ref><ref name="pmid19318213">{{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 }}</ref><ref name="isbn0-387-22046-1">{{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 }}</ref>