Talk:Genetic code

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Genetic code has been listed as one of the Natural sciences good articles under the good article criteria. If you can improve it further, please do so. If it no longer meets these criteria, you can reassess it. Article milestones Date Process Result September 21, 2006 Good article nominee Listed March 1, 2010 Good article reassessment Kept Current status: Good article This  level-4 vital article is rated GA-class on Wikipedia's content assessment scale. It is of interest to the following WikiProjects: Molecular Biology: Genetics / MCB This article is within the scope of WikiProject Molecular Biology, a collaborative effort to improve the coverage of molecular biology on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.Molecular BiologyWikipedia:WikiProject Molecular BiologyTemplate:WikiProject Molecular BiologyMolecular Biology ??? This article has not yet received a rating on the project's importance scale. This article is supported by the Genetics task force (assessed as Top-importance). This article is supported by the Molecular and Cell Biology task force (assessed as Top-importance). Biology Top‑importance Genetic code is part of the WikiProject Biology, an effort to build a comprehensive and detailed guide to biology on Wikipedia. Leave messages on the WikiProject talk page.BiologyWikipedia:WikiProject BiologyTemplate:WikiProject BiologyBiology Top This article has been rated as Top-importance on the project's importance scale. A summary of this article appears in gene. This article is substantially duplicated in one or more external publications. Since these publication(s) copied Wikipedia, rather than the reverse, please do not flag this article as a copyright violation of the following source: Surhone, L. M., Timpledon, M. T., & Marseken, S. F. (2010), Protein methods: Protein, Site-Directed Mutagenesis, Genetic Code, Green fluorescent Protein, His-Tag, BLAST, Genetic Linkage, Betascript Publishing{{citation}}: CS1 maint: multiple names: authors list (link) Additional comments OCLC 694818613, ISBN 9786130495107.

Despite the variations that exist, the genetic codes used by all known forms of life on Earth are very similar. Since there are many possible genetic codes that are thought to have similar utility to the one used by Earth life, the theory of evolution suggests that the genetic code was established very early in the history of life and meta-analysis of transfer RNA suggest it was established soon after the formation of earth.

One can ask the question: is the genetic code completely random, just one set of codon-amino acid correspondences that happened to establish itself and be "frozen in" early in evolution, although functionally any of the many other possible transcription tables would have done just as well? Already a cursory look at the table shows patterns that suggest that this is not the case. For example, C in 2nd position of the codon yields amino acid residues that are small in size and moderate in hydropathy; U in 2nd position encodes average size hydrophobic residues; A in 2nd position encodes average size hydrophilic residues; U in 1st position encodes residues that are not hydrophilic, see Image:Codon_Bias.jpg, adapted from http://www.complexity.org.au/ci/vol01/fullen01/html] and (Yang et al. 1990. In Reaction Centers of Photosynthetic Bacteria. M.-E. Michel-Beyerle. (Ed.) (Springer-Verlag, Germany) 209-218).

There are three themes running through the many theories that seek to explain the evolution of the genetic code (and hence the origin of these patterns).^[1] One is illustrated by recent aptamer experiments which show that some amino acids have a selective chemical affinity for the base triplets that code for them.^[2] This suggests that the current, complex translation mechanism involving tRNA and associated enzymes may be a later development, and that originally, protein sequences were directly templated on base sequences. Another is that the standard genetic code that we see today grew from a simpler, earlier code through a process of "biosynthetic expansion". Here the idea is that primordial life 'discovered' new amino acids (e.g. as by-products of metabolism) and later back-incorporated some of these into the machinery of genetic coding. Although much circumstantial evidence has been found to suggest that fewer different amino acids were used in the past than today,^[3] precise and detailed hypotheses about exactly which amino acids entered the code in exactly what order has proved far more controversial.^[4][5] A third theory is that natural selection has led to codon assignments of the genetic code that minimize the effects of mutations.^[6].

Until several weeks ago the codon table in this article looked like this:

An IP changed it to the following:

This was reverted a few times, until the IP (editing from 220.253.25.118) explained the change: "codons are not polar etc but amino acids are." In other words, the color scheme applies to the amino acids, not the codons, so the colored shading should not be applied to the codons themselves. I agree with this reasoning. The problems with this table are that (1) As noted above, it's very bulky, and (2) Consequently, it obscures the non-random nature of the genetic code – the tendency for single-base substitutions to result in codons with similar chemical properties. In the sandbox, 220.253.25.118 created a new table which I think combines the best features of both other tables: it does not apply color shading to the codons, it's compact, and the non-random nature of the code is readily apparent. I've applied minor tweaks to this table, and the result is below:

I'm not sure why 220.253.25.118 didn't incorporate this into the article, but if there's no objection I'd like to replace the current table with this one. Adrian J. Hunter^{(talk•contribs)} 11:21, 11 September 2010 (UTC)Reply

Support. Looks like an improvement in the current (making trends more apparent and table less bulky) while still retaining the valid polarity concern of the IP. An alternative solution is to simply clearly state in the table legend or intro that the coloring refers to the amino acid polarity, not just "polarity". The IP-current and Adrian's improvements still make horizontal (second-base for constant first and third) trends harder to notice (though obviously no 2D table can alow all three base-positions' comparisons by adjacency). DMacks (talk) 15:55, 11 September 2010 (UTC)Reply

I see what you mean about the second base trends, though those are weaker than for the other bases anyway (2nd base changes are never synonymous). For now I've changed the table to the third option as the first option uses horizontal lines inconsistently (eg look at the lines between leucines), but I wouldn't object to coloring of the codons if someone wants to implement it. Maybe one day someone will present the table as a 4x4x4 Borg cube that shows all trends equally :-) Adrian J. Hunter^{(talk•contribs)} 11:59, 19 September 2010 (UTC)Reply

Just so you have something to look forward to, that was added to the article a while ago and looks great! We also have developed time-travel. DMacks (talk) 12:25, 19 September 3010 (UTC)Reply

Would be cool if there were a VR or at least user-rotatable-3D format supported. DMacks (talk) 12:25, 19 September 2010 (UTC)Reply

I think the intended code for Opal was UGA, not UAG. - Surakmath (talk) 00:52, 13 August 2026 (UTC)Reply

^A The codon ATG both codes for methionine and serves as an initiation site: the first ATG in the coding region is where translation into protein begins.^[1]

With all due respect to the OCD who like the data presentation in tabular form, it's just not very useful. The 2nd illustration/diagram with the caption "The genetic code" is great, imho. I see three problems with it. 1. There's a modification for Proline denoted with a "G" which doesn't appear in the key table. (oG and nG do appear, but no G). 2. The title is misleading. It is not "The" genetic code, it is one of the genetic codes. So, which organism(s) does this one refer to?? 3. There's no context/discussion. 3a. It probably would be useful to explain how to read the diagram (from the center out; the 1st position is the closest to the 5' end of the RNA). 3b. It probably would be useful to mention that 3 amino acids occur twice, in each case with different 1st position nucleotides. It might even be useful to list them (Leu, Ser, Arg). ___ Also, while I'm at it: the lead states:"The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries." Well, no. Yes and no. It is "highly similar" - whatever that means, but it can not be expressed in a simple table with 64 entries - unless you add the qualification "for a given organism". I suggest that rather than "highly similar" - weasle-words - you say the 64 possible combinations of the four nucleotides have slight variations in which amino acid they encode for different species. (I don't know if any of the combos have conserved output (as far as known), but perhaps the ones known to produce different amino acids (or stops) could be marked (with a ' or a *, for example) in the diagram. (Or contrarily, if most aren't conserved but some are, then mark the conserved ones).) _ _ I don't know whether or how this relates, but the 4 nucleotides are the canonical nucleotides, there are (last I looked) 18 other nucleotides known (known as non-canonical nucleotides). Whether this DNA factoid applies to RNA, I don't know. But maybe it needs be said? (another problem with a "simple 64-entry table" claim.)~2026-92463-4 (talk) 18:10, 12 April 2026 (UTC)Reply

The table entitled "Human genome codon frequency table" employs certain endnote links. Only problem: the links are dead, and there are no endnotes to the article. How does one read the intended endnotes? - Surakmath (talk) 00:41, 13 August 2026 (UTC)Reply