DNA and RNA codon tables: Difference between revisions

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There are 64 different codons in the genetic code and the below tables; most specify an amino acid.<ref>{{cite web|url=https://www.genome.gov/genetics-glossary/Codon|title=Codon|website=National Human Genome Research Institute|access-date=10 October 2020|archive-date=22 October 2020|archive-url=https://web.archive.org/web/20201022081214/https://www.genome.gov/genetics-glossary/Codon|url-status=live}}</ref> Three sequences, UAG, UGA, and UAA, known as [[stop codon]]s,{{efn|group=note|Each stop codon has a specific name: UAG is ''amber'', UGA is ''opal'' or ''umber'', and UAA is ''ochre''.<ref name="stop"/> In DNA, these stop codons are TAG, TGA, and TAA, respectively.}} do not code for an amino acid but instead signal the release of the nascent [[polypeptide]] from the ribosome.<ref name="stop">{{cite web| url=http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/rev-sup/amber-name.html|title=How nonsense mutations got their names|author=Maloy S.|date=29 November 2003|work=Microbial Genetics Course|publisher=San Diego State University|access-date=10 October 2020|archive-url=https://web.archive.org/web/20200923075442/http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/rev-sup/amber-name.html|archive-date=23 September 2020}}</ref> In the standard code, the sequence AUG—read as [[methionine]]—can serve as a [[start codon]] and, along with sequences such as an [[initiation factor]], initiates translation.<ref name="geneticcodes"/><ref>{{cite journal|vauthors=Hinnebusch AG|date=2011|title=Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes|journal= Microbiology and Molecular Biology Reviews|volume=75|issue=3|pages=434–467|doi=10.1128/MMBR.00008-11|pmid=21885680|pmc=3165540|doi-access=free}}</ref><ref name="pmid12867081">{{cite journal |vauthors=Touriol C, Bornes S, Bonnal S, Audigier S, Prats H, Prats AC, Vagner S| title = Generation of protein isoform diversity by alternative initiation of translation at non-AUG codons|journal=Biology of the Cell|volume=95|issue=3–4|pages=169–78|date=2003|pmid=12867081|doi=10.1016/S0248-4900(03)00033-9|doi-access=free}}</ref> In rare instances, start codons in the standard code may also include GUG or UUG; these codons normally represent [[valine]] and [[leucine]], respectively, but as start codons they are translated as [[methionine]] or [[formylmethionine]].<ref name="geneticcodes"/><ref name="pmid12867081"/>

[[File:Codon wheels.png|thumb|The second codon position best determines amino acid hydrophobicity. Color-coding: hydrophobicity from microenvironment in folded proteins <ref>{{cite journal |last1=Bandyopadhyay |first1=Debashree |last2=Mehler |first2=Ernest L. |date=August 2008 |title=Quantitative expression of protein heterogeneity: Response of amino acid side chains to their local environment. |journal=Proteins |volume=72 |number=2 |pages=646-59 |doi=10.1002/prot.21958|pmid=18247345 }}</ref>]]

The classical table/wheel of the standard genetic code is arbitrarily organized based on codon position 1. Saier <ref>{{cite journal |last1=Saier |first1=Milton H. Jr. |date=10 July 2019 |title=Understanding the Genetic Code. |journal=J Bacteriol |volume=201 |number=15 |pages=e00091-19 |doi=10.1128/JB.00091-19|pmid=31010904 |pmc=6620406 }}</ref>, following observations from <ref>{{cite journal |last1=Muto |first1=A. |last2=Osawa |first2=S. |date=January 1987 |title=The guanine and cytosine content of genomic DNA and bacterial evolution. |journal=Proc Natl Acad Sci USA |volume=84 |number=1 |pages=166-9 |doi=10.1073/pnas.84.1.166|pmid=3467347 |pmc=304163 }}</ref>, showed that reorganizing the wheel based instead on codon position 2 (and reordering from UCAG to UCGA) better arranges the codons by the hydrophobicity of their encoded amino acids. This suggests that early ribosomes read the second codon position most carefully, to control hydrophobicity patterns in protein sequences.

The first table—the standard table—can be used to translate [[nucleotide]] triplets into the corresponding amino acid or appropriate signal if it is a start or stop codon. The second table, appropriately called the inverse, does the opposite: it can be used to deduce a possible triplet code if the amino acid is known. As multiple codons can code for the same amino acid, the [[International Union of Pure and Applied Chemistry]]'s (IUPAC) [[nucleic acid notation]] is given in some instances.