DNA and RNA codon tables: Difference between revisions

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| 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.

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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>]]

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{{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; text-align:center;"

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{|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 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 952:

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

|-

!scope=row rowspan="1" | [[Enterosoma code|Enterosoma]]<ref name="Shulgina" />

|rowspan="1" | 34

| AGG

Line 958:

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

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

|

|-

!scope=row rowspan="1" | [[Peptacetobacter code|''Peptacetobacter'']]<ref name="Shulgina" />

|rowspan="1" | 35

| CGG

Line 965 ⟶ 966:

|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'']]<ref name="Shulgina" />

|rowspan="1" | 36

| CGG

Line 972 ⟶ 974:

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

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

|

|-

!scope=row rowspan="3" | [[Absconditabacteraceae code|''Absconditabacteraceae'']]<ref name="Shulgina" />

|rowspan="3" | 37

| CGA

Line 979 ⟶ 982:

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

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

|

|-

| CGG

Line 984 ⟶ 988:

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

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

|

|-

| TGA

Line 989 ⟶ 994:

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

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

|

|}