Editing Amino acid (section)

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

Amino acids are the precursors to proteins.<ref name="NIGMS"/> 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 (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]].<ref>{{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 }}</ref> 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]] derived from one of the organism's [[gene]]s.

Twenty-two amino acids are naturally incorporated into polypeptides and are called [[proteinogenic]] or natural amino acids.<ref name="Creighton" /> 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.<ref>{{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 }}</ref> [[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.<ref>{{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 }}</ref>

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.<ref>{{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 }}</ref><ref>{{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 }}</ref><ref>{{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 }}</ref>