DNA and RNA codon tables: Difference between revisions

Revision as of 12:42, 6 June 2024

Latest revision as of 20:29, 17 July 2025

(23 intermediate revisions by 12 users not shown)

Line 8:

| alt1 = A circular diagram is separated into three rings, broken down into sections labeled with the letters: G, U, A, and C. Each represents a nucleotide found in RNA.

}}

A '''codon table''' can be used to translate a [[genetic code]] into a sequence of [[amino acid]]s.<ref name="RNA codon table">{{cite web|url=http://sites.science.oregonstate.edu/genbio/otherresources/aminoacidtranslation.htm|title=Amino Acid Translation Table|publisher=Oregon State University|access-date=2 December 2020|archive-date=29 May 2020|archive-url=https://web.archive.org/web/20200529000711/http://sites.science.oregonstate.edu/genbio/otherresources/aminoacidtranslation.htm|url-status=dead}}</ref><ref name="oregon"/> The standard genetic code is traditionally represented as an [[RNA]] [[codon]] table, because when [[protein]]s are made in a [[Cell (biology)|cell]] by [[ribosome]]s, it is [[messenger RNA]] (mRNA) that directs [[protein synthesis]].<ref name="oregon">{{cite book|last1=Bartee|first1=Lisa|last2=Brook|first2=Jack|title=MHCC Biology 112: Biology for Health Professions|url=https://mhccbiology112.pressbooks.com|publisher=Open Oregon|page=42|access-date=6 December 2020|archive-date=6 December 2020|archive-url=https://web.archive.org/web/20201206173711/https://mhccbiology112.pressbooks.com/|url-status=live}}</ref><ref name="geneticcodes">{{Cite web|title=The Genetic Codes|publisher=National Center for Biotechnology Information|vauthors=Elzanowski A, Ostell J|date=7 January 2019|access-date=21 February 2019| url=https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi|archive-url=https://web.archive.org/web/20201005105339/https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi|archive-date=5 October 2020}}</ref> The mRNA sequence is determined by the sequence of genomic [[DNA]].<ref>{{cite web|url=https://www.nature.com/scitable/topicpage/rna-functions-352/|title=RNA Functions|website=Scitable|publisher=Nature Education|access-date=5 January 2021|archive-url=https://web.archive.org/web/20081018170459/https://www.nature.com/scitable/topicpage/rna-functions-352/|archive-date=18 October 2008|url-status=live}}</ref> In this context, the standard genetic code is referred to as 'translation table 1' among [[List of genetic codes|other tables]].<ref name="geneticcodes"/> It can also be represented in a DNA codon table. The DNA codons in such tables occur on the [[Sense (molecular biology)|sense]] DNA strand and are arranged in a [[Directionality (molecular biology)|5{{prime}}-to-3{{prime}} direction]]. Different tables with alternate codons are used depending on the source of the genetic code, such as from a [[cell nucleus]], [[mitochondrion]], [[plastid]], or [[hydrogenosome]].<ref>{{cite web|url=https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi|title=The Genetic Codes|publisher=National Center for Biotechnology Information|access-date=2 December 2020|archive-date=13 May 2011|archive-url=https://web.archive.org/web/20110513014234/http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi|url-status=live}}</ref>

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> (sometimes for UGA, ''umber'' is used instead of ''opal'').<ref>Stanley Maloy: ''[https://www.sciencedirect.com/science/article/abs/pii/B9780123749840016004 Umber codon]''</ref> 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"/> 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|doi-access=free |pmid=3467347 |pmc=304163 |bibcode=1987PNAS...84..166M }}</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.

Line 16 ⟶ 20:

==Translation table 1==

===Standard RNA codon table===

{| class="wikitable" style="border:none; background:none; text-align:center;"

| [[Amino acids|Amino-acid]] biochemical properties

| style="background-color:#ffe75f; width: 50px;" | Nonpolar (np)

Line 22 ⟶ 26:

| style="background-color:#bbbfe0; width: 50px;" | Basic (b)

| style="background-color:#f8b7d3; width: 50px;" | Acidic (a)

| style="border:none; background:none; width: 100px;" |

| style="background-color:#B0B0B0;" | Termination: stop codon *

| style="border:none; background:none; width: 10px;" |

| style="background-color:#97D8F7;" | Initiation: possible start codon ⇒

|}

Line 263 ⟶ 267:

===Standard DNA codon table===

{| class="wikitable" style="border:none; background:none; text-align:center;"

| [[Amino acids|Amino-acid]] biochemical properties

| style="background-color:#ffe75f; width: 50px;" | Nonpolar (np)

Line 269 ⟶ 273:

| style="background-color:#bbbfe0; width: 50px;" | Basic (b)

| style="background-color:#f8b7d3; width: 50px;" | Acidic (a)

| style="border:none; background:none; width: 100px;" |

| style="background-color:#B0B0B0;" | Termination: stop codon *

| style="border:none; background:none; width: 10px;" |

| style="background-color:#97D8F7;" | Initiation: possible start codon ⇒

|}

Line 499 ⟶ 503:

|-

! style="text-align:center;"| START

| ATG, TTG, GTG, CTG<ref>{{Cite web |title=Choose a start codon |url=https://depts.washington.edu/agro/genomes/students/stanstart.htm |access-date=2024-08-14 |website=depts.washington.edu}}</ref>|| NTG

| ATG, CTG, UTG || HTG

! style="text-align:center;"| STOP

| {{{T|T}}}AA, {{{T|T}}}GA, {{{T|T}}}AG

Line 506 ⟶ 510:

==Alternative codons in other translation tables==

{{missing information|section|start codon in these tables, aka the "sncbieaa" row in NCBI data|date=December 2023}}

{{Further|List of genetic codes}}

The genetic code was once believed to be universal:<ref name="evolve1"/> a codon would code for the same amino acid regardless of the organism or source. However, it is now agreed that the genetic code evolves,<ref name="evolve2"/> resulting in discrepancies in how a codon is translated depending on the genetic source.<ref name="evolve1">{{cite journal|last1=Osawa|first1=A|date=November 1993|title=Evolutionary changes in the genetic code|url=https://pubmed.ncbi.nlm.nih.gov/8281749/|journal=Comparative Biochemistry and Physiology|volume=106|issue=2|pages=489–94|doi=10.1016/0305-0491(93)90122-l|pmid=8281749|access-date=2020-12-05|archive-date=2020-12-06|archive-url=https://web.archive.org/web/20201206173716/https://pubmed.ncbi.nlm.nih.gov/8281749/|url-status=live}}</ref><ref name="evolve2">{{cite journal |vauthors=Osawa S, Jukes TH, Watanabe K, Muto A|date=March 1992|title=Recent evidence for evolution of the genetic code|journal= Microbiological Reviews|volume=56|issue=1|pages=229–64|doi=10.1128/MR.56.1.229-264.1992|pmc=372862|pmid=1579111}}</ref> For example, in 1981, it was discovered that the use of codons AUA, UGA, AGA and AGG by the coding system in mammalian mitochondria differed from the universal code.<ref name="evolve1"/> Stop codons can also be affected: in [[Ciliate|ciliated protozoa]], the universal stop codons UAA and UAG code for glutamine.<ref name="evolve2"/>{{efn|group=note|''[[Euplotes octacarinatus]]'' is an exception.<ref name="evolve2"/>}} Four novel alternative genetic codes (numbered here 34–37) were discovered in bacterial genomes by Shulgina and Eddy, revealing the first sense codon changes in bacteria.<ref name="Shulgina">{{cite journal |last1=Shulgina |first1=Yekaterina |last2=Eddy |first2=Sean R. |date=9 November 2021 |title=A computational screen for alternative genetic codes in over 250,000 genomes. |journal=eLife |volume=10 |doi=10.7554/eLife.71402|doi-access=free |pmid=34751130 |pmc=8629427 }}</ref> The following table displays these alternative codons.

{| class="wikitable" style="border:none; background:none; text-align:center;"

| [[Amino acids|Amino-acid]] biochemical properties

| style="background-color:#ffe75f; width: 50px;" | Nonpolar (np)

Line 517 ⟶ 520:

| style="background-color:#bbbfe0; width: 50px;" | Basic (b)

| style="background-color:#f8b7d3; width: 50px;" | Acidic (a)

| style="border:none; background:none; width: 100px;" |

| style="background-color:#B0B0B0;" | Termination: stop codon *

|}

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

|+ Comparison between codon translations with alternative and standard genetic codes<ref name="geneticcodes"/><ref name="Shulgina" />

! scope="col" style="width: 200px;" | Code

! scope="col" style="width: 25px;" | Translation <br/> table

Line 859 ⟶ 862:

|style="background-color:#B0B0B0;" | [[Stop codon|Stop]] *

|-

| TGTGA

| UGA

|style="width: 50px; background-color:#B0B0B0;" | [[Stop codon|Stop]] * || style="width: 10px;" | or || style="width: 50px; background-color:#ffe75f;" | Trp (W) (np)

Line 948 ⟶ 951:

|colspan="3" style="background-color:#ffe75f;" | Trp (W) (np)

|style="background-color:#B0B0B0;" | [[Stop codon|Stop]] *

|-

!scope=row rowspan="1" | [[Enterosoma code|Enterosoma]]

|rowspan="1" | 34

| AGG

| AGG

|colspan="3" style="background-color:#ffe75f;" | Met (M) (np)

|style="background-color:#bbbfe0;" | Arg (R) (b)

|

|-

!scope=row rowspan="1" | [[Peptacetobacter code|''Peptacetobacter'']]

|rowspan="1" | 35

| CGG

| CGG

|colspan="3" style="background-color:#b3dec0;" | Gln (Q) (p)

|style="background-color:#bbbfe0;" | Arg (R) (b)

|

|-

!scope=row rowspan="1" | [[Anaerococcus and Onthovivens code|''Anaerococcus and Onthovivens'']]

|rowspan="1" | 36

| CGG

| CGG

|colspan="3" style="background-color:#ffe75f;" | Trp (W) (np)

|style="background-color:#bbbfe0;" | Arg (R) (b)

|

|-

!scope=row rowspan="3" | [[Absconditabacteraceae code|''Absconditabacteraceae'']]

|rowspan="3" | 37

| CGA

| CGA

|colspan="3" style="background-color:#ffe75f;" | Trp (W) (np)

|style="background-color:#bbbfe0;" | Arg (R) (b)

|

|-

| CGG

| CGG

|colspan="3" style="background-color:#ffe75f;" | Trp (W) (np)

|style="background-color:#bbbfe0;" | Arg (R) (b)

|

|-

| TGA

| UGA

|colspan="3" style="background-color:#ffe75f;" | Gly (G) (np)

|style="background-color:#B0B0B0;" | [[Stop codon|Stop]] *

|

|}