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A codon table can be used to translate a genetic code into a sequence of amino acids. The standard genetic code is traditionally represented as an RNA codon table, because when proteins are made in a cell by ribosomes, it is messenger RNA (mRNA) that directs protein synthesis. The mRNA sequence is determined by the sequence of genomic DNA. In this context, the standard genetic code is referred to as translation table 1. It can also be represented in a DNA codon table. The DNA codons in such tables occur on the sense DNA strand and are arranged in a 5′-to-3′ 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.

There are 64 different codons in the genetic code and the below tables; most specify an amino acid. Three sequences, UAG, UGA, and UAA, known as stop codons, do not code for an amino acid but instead signal the release of the nascent polypeptide from the ribosome. 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. 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.

The classical table/wheel of the standard genetic code is arbitrarily organized based on codon position 1. Saier, following observations from, 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.

Translation table 1

Standard RNA codon table

As shown in the above table, NCBI table 1 includes the less-canonical start codons GUG and UUG.

Inverse RNA codon table

Standard DNA codon table

Inverse DNA codon table

Alternative codons in other translation tables

The genetic code was once believed to be universal: 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, resulting in discrepancies in how a codon is translated depending on the genetic source. 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. Stop codons can also be affected: in ciliated protozoa, the universal stop codons UAA and UAG code for glutamine. 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. The following table displays these alternative codons.

See also

• Bioinformatics
• List of genetic codes

Notes

1. Each stop codon has a specific name: UAG is amber, UGA is opal or umber, and UAA is ochre. In DNA, these stop codons are TAG, TGA, and TAA, respectively.
2. ^ The historical basis for designating the stop codons as amber, ochre and opal is described in the autobiography of Sydney Brenner and in a historical article by Bob Edgar.
3. The major difference between DNA and RNA is that thymine (T) is only found in the former. In RNA, it is replaced with uracil (U). This is the only difference between the standard RNA codon table and the standard DNA codon table.
4. Euplotes octacarinatus is an exception.

References

1. ^ "Amino Acid Translation Table". Oregon State University. Archived from the original on 29 May 2020. Retrieved 2 December 2020.
2. ^ Bartee, Lisa; Brook, Jack. MHCC Biology 112: Biology for Health Professions. Open Oregon. p. 42. Archived from the original on 6 December 2020. Retrieved 6 December 2020.
3. ^ Elzanowski A, Ostell J (7 January 2019). "The Genetic Codes". National Center for Biotechnology Information. Archived from the original on 5 October 2020. Retrieved 21 February 2019.
4. "RNA Functions". Scitable. Nature Education. Archived from the original on 18 October 2008. Retrieved 5 January 2021.
5. "The Genetic Codes". National Center for Biotechnology Information. Archived from the original on 13 May 2011. Retrieved 2 December 2020.
6. "Codon". National Human Genome Research Institute. Archived from the original on 22 October 2020. Retrieved 10 October 2020.
7. ^ Maloy S. (29 November 2003). "How nonsense mutations got their names". Microbial Genetics Course. San Diego State University. Archived from the original on 23 September 2020. Retrieved 10 October 2020.
8. Hinnebusch AG (2011). "Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes". Microbiology and Molecular Biology Reviews. 75 (3): 434–467. doi:10.1128/MMBR.00008-11. PMC 3165540. PMID 21885680.
9. ^ Touriol C, Bornes S, Bonnal S, Audigier S, Prats H, Prats AC, Vagner S (2003). "Generation of protein isoform diversity by alternative initiation of translation at non-AUG codons". Biology of the Cell. 95 (3–4): 169–78. doi:10.1016/S0248-4900(03)00033-9. PMID 12867081.
10. Bandyopadhyay, Debashree; Mehler, Ernest L. (August 2008). "Quantitative expression of protein heterogeneity: Response of amino acid side chains to their local environment". Proteins. 72 (2): 646–59. doi:10.1002/prot.21958. PMID 18247345.
11. Saier, Milton H. Jr. (10 July 2019). "Understanding the Genetic Code". J Bacteriol. 201 (15): e00091-19. doi:10.1128/JB.00091-19. PMC 6620406. PMID 31010904.
12. Muto, A.; Osawa, S. (January 1987). "The guanine and cytosine content of genomic DNA and bacterial evolution". Proc Natl Acad Sci USA. 84 (1): 166–9. Bibcode:1987PNAS...84..166M. doi:10.1073/pnas.84.1.166. PMC 304163. PMID 3467347.
13. "The Information in DNA Determines Cellular Function via Translation". Scitable. Nature Education. Archived from the original on 23 September 2017. Retrieved 5 December 2020.
14. Brenner, Sydney; Wolpert, Lewis (2001). A Life in Science. Biomed Central Limited. pp. 101–104. ISBN 9780954027803.
15. Edgar B (2004). "The genome of bacteriophage T4: an archeological dig". Genetics. 168 (2): 575–82. doi:10.1093/genetics/168.2.575. PMC 1448817. PMID 15514035. see pages 580–581
16. ^ IUPAC—IUB Commission on Biochemical Nomenclature. "Abbreviations and Symbols for Nucleic Acids, Polynucleotides and Their Constituents" (PDF). International Union of Pure and Applied Chemistry. Archived (PDF) from the original on 9 July 2021. Retrieved 5 December 2020.
17. "What does DNA do?". Your Genome. Welcome Genome Campus. Archived from the original on 29 November 2020. Retrieved 12 January 2021.
18. "Genes". DNA, Genetics, and Evolution. Boston University. Archived from the original on 28 April 2020. Retrieved 10 December 2020.
19. "Choose a start codon". depts.washington.edu. Retrieved 2024-08-14.
20. ^ Osawa, A (November 1993). "Evolutionary changes in the genetic code". Comparative Biochemistry and Physiology. 106 (2): 489–94. doi:10.1016/0305-0491(93)90122-l. PMID 8281749. Archived from the original on 2020-12-06. Retrieved 2020-12-05.
21. ^ Osawa S, Jukes TH, Watanabe K, Muto A (March 1992). "Recent evidence for evolution of the genetic code". Microbiological Reviews. 56 (1): 229–64. doi:10.1128/MR.56.1.229-264.1992. PMC 372862. PMID 1579111.
22. ^ Shulgina, Yekaterina; Eddy, Sean R. (9 November 2021). "A computational screen for alternative genetic codes in over 250,000 genomes". eLife. 10. doi:10.7554/eLife.71402. PMC 8629427. PMID 34751130.

Further reading

• Chevance FV, Hughes KT (2 May 2017). "Case for the genetic code as a triplet of triplets". Proceedings of the National Academy of Sciences of the United States of America. 114 (18): 4745–4750. Bibcode:2017PNAS..114.4745C. doi:10.1073/pnas.1614896114. JSTOR 26481868. PMC 5422812. PMID 28416671.
• Dever TE (29 June 2012). "A New Start for Protein Synthesis". Science. 336 (6089). American Association for the Advancement of Science: 1645–1646. Bibcode:2012Sci...336.1645D. doi:10.1126/science.1224439. JSTOR 41585146. PMID 22745408. S2CID 44326947. Archived from the original on 8 June 2022. Retrieved 17 October 2020.
• Gardner RS, Wahba AJ, Basilio C, Miller RS, Lengyel P, Speyer JF (December 1962). "Synthetic polynucleotides and the amino acid code. VII". Proceedings of the National Academy of Sciences of the United States of America. 48 (12): 2087–2094. Bibcode:1962PNAS...48.2087G. doi:10.1073/pnas.48.12.2087. PMC 221128. PMID 13946552.
• Nakamoto T (March 2009). "Evolution and the universality of the mechanism of initiation of protein synthesis". Gene. 432 (1–2): 1–6. doi:10.1016/j.gene.2008.11.001. PMID 19056476.
• Wahba AJ, Gardner RS, Basilio C, Miller RS, Speyer JF, Lengyel P (January 1963). "Synthetic polynucleotides and the amino acid code. VIII". Proceedings of the National Academy of Sciences of the United States of America. 49 (1): 116–122. Bibcode:1963PNAS...49..116W. doi:10.1073/pnas.49.1.116. PMC 300638. PMID 13998282.
• Yanofsky C (9 March 2007). "Establishing the Triplet Nature of the Genetic Code". Cell. 128 (5): 815–818. doi:10.1016/j.cell.2007.02.029. PMID 17350564. S2CID 14249277.
• Zaneveld J, Hamady M, Sueoka N, Knight R (28 February 2009). "CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition". Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology. Vol. 537. pp. 207–232. doi:10.1007/978-1-59745-251-9_10. ISBN 978-1-58829-910-9. PMC 2953947. PMID 19378146.

External links

• DNA codon chart organized in a wheel

• Gene expression
• Molecular genetics
• Protein biosynthesis
• Bioinformatics