List of standard rules to translate DNA encoded information into proteins
The standard RNA codon table organized in a wheel
A codon table can be used to translate a genetic code into a sequence of amino acids.[1][2] The standard genetic code is traditionally represented as an RNAcodon table, because when proteins are made in a cell by ribosomes, it is messenger RNA (mRNA) that directs protein synthesis.[2][3] The mRNA sequence is determined by the sequence of genomic DNA.[4] In this context, the standard genetic code is referred to as 'translation table 1' among other tables.[3] 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.[5]
There are 64 different codons in the genetic code and the below tables; most specify an amino acid.[6] Three sequences, UAG, UGA, and UAA, known as stop codons,[note 1] do not code for an amino acid but instead signal the release of the nascent polypeptide from the ribosome.[7] 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.[3][9][10] 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.[3][10]
The second codon position best determines amino acid hydrophobicity. Color-coding: hydrophobicity from microenvironment in folded proteins [11]
The classical table/wheel of the standard genetic code is arbitrarily organized based on codon position 1. Saier,[12] following observations from,[13] 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.
The genetic code was once believed to be universal:[21] 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,[22] resulting in discrepancies in how a codon is translated depending on the genetic source.[21][22] 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.[21] Stop codons can also be affected: in ciliated protozoa, the universal stop codons UAA and UAG code for glutamine.[22][note 4] 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.[23] The following table displays these alternative codons.
^Each stop codon has a specific name: UAG is amber, UGA is opal and UAA is ochre,[7] (sometimes for UGA, umber is used instead of opal).[8] In DNA, these stop codons are TAG, TGA, and TAA, respectively.
^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).[19] This is the only difference between the standard RNA codon table and the standard DNA codon table.
^ abcdefElzanowski 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.
^"RNA Functions". Scitable. Nature Education. Archived from the original on 18 October 2008. Retrieved 5 January 2021.
^"The Genetic Codes". National Center for Biotechnology Information. Archived from the original on 13 May 2011. Retrieved 2 December 2020.
^"Codon". National Human Genome Research Institute. Archived from the original on 22 October 2020. Retrieved 10 October 2020.
^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. PMID18247345.
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. PMID19056476.
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. ISBN978-1-58829-910-9. PMC2953947. PMID19378146.
