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I couldn't find anywhere the answer to this: the DNA consists of 2 strands, which are complementary. Which strand is selected during gene expression? The choice cannot be random, since it would generate different proteins. For example, suppose one strand contains CTC, then the opposite strand will contain GAG. The first one will translate into mRNA GAG and encode for glutamic acid, the other one into CUC and generate Leucine. — Preceding unsigned comment added by 165.222.184.132 ( talk) 10:27, 22 September 2011 (UTC)
It seems rather redundant to have both - I undestand the reasons for setting up the table both ways but I don't think it adds much to the article to include the 2nd table. If there are no objection, I'll remove it. Hichris 18:49, 28 November 2006 (UTC)
It's not really redundant. For me (and hopefully for others) this table is a valuable resource that may be used for designing mutagenesis primers when exchanging amino acids by PCR. May I ask you to put it back, please? This message is encrypted! You'll need a brain to decode it. 14:53, 12 January 2007 (UTC)
Here's an alternative presentation, using the IUPAC abbreviations from DNA_sequence:
Ala | GCN | Leu | YUR, CUN |
---|---|---|---|
Arg | CGN, AGR (MGR) | Lys | AAR |
Asn | AAY | Met | AUG |
Asp | GAY | Phe | UUY |
Cys | UGY | Pro | CCN |
Gln | CAR | Ser | UCN, AGY |
Glu | GAR | Thr | ACN |
Gly | GGN | Trp | UGG |
His | CAY | Tyr | UAY |
Ile | AUY, AUA (AUH) | Val | GUN |
START | AUG | STOP | UAR, URA |
Currently, in section "RNA codon table", the header on the "Inverse table for the standard genetic code" table refers to "DNA codons", which should be "RNA codons". It looks like the same template is being used for both DNA and RNA codons, and the substitution T->U is made. However, the column name should be specific. Probably having separate tables would simplify things :) DeepCurl ( talk) 16:42, 24 March 2019 (UTC)
I just started reading the article so I am hitting points as I go. The age of the genetic code is estimated to be about as old as the earth itself.Eigen M, Lindemann BF, Tietze M, Winkler-Oswatitsch R, Dress A, von Haeseler A.How old is the genetic code? Statistical geometry of tRNA provides an answer. Science. 1989 May 12;244(4905):673-9. PMID: 2497522 [PubMed - indexed for MEDLINE]
The standard genetic code is universal but there are some modification in mitochondria, chloroplast, some organisms like yeast, etc. Oops! its already there. GetAgrippa 22:18, 17 January 2007 (UTC)
Now that I've read the article, kudos to the authors. Excellent article! GetAgrippa 05:46, 21 January 2007 (UTC)
...is being repeatedly added as an "alternative explanation" of how the genetic code came to be, and the explanation of why it should be added is based on editor bias or supression of alternative viewpoints. So let's figure it out:
Conclusion: does not belong. DMacks 19:57, 30 January 2007 (UTC)
Codon redirects here, but this is not very useful if you more or less know what the genetic code is and are wondering what the heck a codon is. I mean, is it a real physical structure, or is it just a scientific convention? in the first paragraph you get the idea that its a physical structure, later on you learn it can be read from any of three ways. If you chop a strand and have no start/stop sequence do its codons cease to exist? It could use its own article, even if its a short one. Brallan 17:59, 27 March 2007 (UTC)
This article should contain a reference to what ACGTU stand for. There's no obvious way to find the definitions of the symbols if you don't already know the basics. — Preceding unsigned comment added by 71.182.155.221 ( talk) 18:18, 9 February 2021 (UTC)
I thought it was strange that there was a hyperlink from the Introduction to a section later in the same article (the words "variant codes" linking to the section, "5 Variations to the standard genetic code"). Does anybody else agree? richard.decal ( talk) 07:05, 22 June 2010 (UTC)
I have written up my issues with Universal genetic code on its talk page. - Madeleine 21:02, 15 April 2007 (UTC)
I do not agree with the word "scientific". As this is a science related article, any theory provided here should be scientific in the first place. CharonZ 22:22, 25 April 2007 (UTC)
One of the "arguments" creationists often use is that the code is too complicated to have evolved on its own. I recently tried to see if the code could be condensed in order to simplify it. I simply placed the second base of the triplets in the middle of the code-sun, followed by the first, followed by the third. If you do that you manage to get all the codons for leucine, serine, arginine and stop together! Futhermore you can twist the codons in such a way that amino acids seem to cluster into structural/ functional groups (unpolar, polar, charged, intermediary, and special properties). If you are interested, please have a look at http://www.rna-game.org and leave comments. The Journal of Theoretical Biology seemed interested but they are known to take forever to process manuscripts. So, in the spirit of the opensource movement I went ahead and published a very rough first sketch on the net. Agabirhei 12:55, 18 July 2007 (UTC)
Is there the possibility to delete this particular talk section (Alternate representations of the genetic code)? The Journal of Theoretical Biology accepted my article and I have calmed down considerably after my initial shock at the results of playing sudoku with the genetic code. Apologies again for not following proper procedures. I don't know if I'm entitled to delete the section but I give my full consent to anyone who wishes and is entitled to do so. Agabirhei ( talk) 19:36, 4 July 2008 (UTC)
Popular accounts often misuse the phrase "genetic code" to mean "genome". See, for example, this Scientific American article: Genetic Code of Deadly Mosquito Cracked. Should the entry for "genetic code" or "genome" address this? — Tyrrell McAllister 09:57, 18 May 2007 (UTC)
Coming at this from a background of linguistics, I have a problem with using "code" to describe the subject matter of the article, as well as describing the codon as "transmitting information." The problem is that the codon describes the relatively circumscribed behavior of a limited series of chemical compounds, and the only "information" conveyed is the actual configuration of those chemical compounds. I recognize that a linguistic metaphor is useful, and possibly deemed essential by biologists in order to understand the workings of the codon and communicate it to others, but there should be a clear and unambiguous statement somewhere in the article that this is a heuristic device, and that the codon is not identical to a linguistic code. Digthepast ( talk) 15:19, 26 September 2011 (UTC)
What is the source of the codon usage statistics given in the picture? The values for Arginine in E. coli seem to contradict information given at http://www.biology.ualberta.ca/pilgrim.hp/links/codontable.html (which is apparently from Escherichia coli and Salmonella, Vol. 2, Ch. 114:2047-2066, 1996, Neidhardt FC ed., ASM press, Washington, D.C). It says in the image that the agg and aga codons are not used at all in E. coli, which seems to be wrong. Also, there is a very large difference according to the source I cited between usage of cgg and cgt, which the picture doesn't reflect. I haven't checked anything besides those, though. —Preceding unsigned comment added by 129.206.92.200 ( talk) 12:50, 24 January 2008 (UTC)
Doug Youvan ( talk) 02:04, 25 April 2008 (UTC)
Is this more understandable? OR-ish does not apply, because this is data already on WP, and I have published in the field.
Doug youvan ( talk) 16:43, 30 May 2008 (UTC)
Sorry - This out of sequence, but I now see Holley goes to Salk with Crick in 1968. Historical. Doug youvan ( talk) 02:39, 3 June 2008 (UTC)
Note: Exactly the same text as the current article with one sentence (bold) inserted with one or two references, and one small figure already on Commons:
U1 = UNN
A2 = NAN
C2 = NCN
U2 = NUN
Solubility -> Hydropathy
Size -> Molar Volume Doug youvan ( talk) 13:42, 3 June 2008 (UTC)
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].
References
The Freeland et al. reference in this article links to an abstract at PubMed. As usual, further reading of the actual paper is blocked by copyright. However, there appears to be an on-line copy: http://www.evolvingcode.net/PDF/thecasefor.pdf . In fact, this verbose pdf paper supports the opposite view as what it is referenced to support in this genetic code article. The Freeland reference has excellent historical literature citations in mutational analyses, but nothing is cited in terms of an a priori mathematical analyses of the structure of the genetic code. Should we agree on how to fix this reference and the re-statement of its conclusion in this article? Doug youvan ( talk) 16:09, 1 June 2008 (UTC)
Image:GeneticCode21-version-2.svg needs replaced at higher resolution with a more common file format. Any ideas that aren't a copyvio? Doug youvan ( talk) 01:14, 3 June 2008 (UTC)
The following codon and the corresponding amino acid combinations do not occur in nature.
These combinations are found only in certain genetically modified clones and hypothetical proteins. To verify this (this won't take not more than a miniute):
I removed the following parenthetical statement from the "Transfer of information via the genetic code" section:
(Practically speaking, one would need at least 2 bits to represent a nucleotide, and 6 for a codon, in a typical computer.)
It's correct, but I think it's more information than the section needs, and it interrupts the flow of the article. No need to nitpick. James A. Stewart ( talk) 10:34, 7 October 2009 (UTC)
Codons appear to code for different amino acids in prokaryotic and eukaryotic cells—can someone add a table or at least a comprehensive list of differences? Bongo matic 06:21, 8 October 2009 (UTC)
Starting GA reassessment as part of the GA Sweeps process. Jezhotwells ( talk) 21:15, 26 February 2010 (UTC)
Could you provide some specific examples of where you consider the artcle's tone to be unencyclopedic? At first glance I don't notice any clear infringements of WP:NOTTEXTBOOK, like leading questions or systemic problem solutions as examples. Emw ( talk) 04:46, 1 March 2010 (UTC)
Here we can coordinate the collaboration of the month of this article. We need to find open points and unsolved issues and areas where be believe we can improve the article.
Open points / questions:
Greetings -- hroest 11:23, 4 March 2010 (UTC)
Just to add to the work list to remember (also for myself):
2. Section Genetic code#Sequence reading frame: Add the term Open reading frame = ORF. I will check some references since this article in WP is not well referenced as well. -- Firefly's luciferase ( talk) 03:14, 9 March 2010 (UTC) 3. Two details to be added: wobble base (for the base that is not necessary to determinate a particular amino acid. And, more details on Selenocysteine and Pyrrolysine, I think. -- Firefly's luciferase ( talk) 03:19, 9 March 2010 (UTC)
It's been proposed that Codon Dictionary be merged here; discussion is at Talk:Codon Dictionary. I note it here because there's only been one comment since the merge was proposed nearly a month ago. Adrian J. Hunter( talk• contribs) 16:25, 1 June 2010 (UTC)
Not sure when you guys changed the codon table, but it's be more useful to leave the table as a DNA codon table rather than a mRNA codon table. Reason is that there is a lot more people working at a DNA rather than at a mRNA level. I am going to change the uracils back to thymine. —Preceding unsigned comment added by 142.150.215.185 ( talk) 22:59, 9 September 2010 (UTC)
Hmm... It appears you are right. For some reason, I was under the impression that DNA codons have always been used but I could've confused this page with some other sites. You are right again in that a lot of biochem and genetics textbooks use an RNA codon table instead of a DNA codon table because that reflects the biochemistry of the process.
I made the change from the standpoint that RNA codons should be of less interest than DNA codons in practice. Unless a genome biologist is working exclusively with mRNA, he'd likely be much more interested in DNA codons than RNA codons. That stems partly from the fact that much of genes that are annotated are now stored as DNA sequences rather than RNA sequences.
If the consensus is that a RNA codon table is more appropriate, then I'd concede. However, I'd prefer to have a DNA codon table in this wiki so that people who are actually working with codons will be able to refer to those tables. Although of course... it's really just a matter of changing an U to a T, but that can be tedious depending on what one's using it for. —Preceding unsigned comment added by Bobthefish2 ( talk • contribs) 17:34, 10 September 2010 (UTC)
Textbooks I checked
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Until several weeks ago the codon table in this article looked like this:
2nd base | |||||
---|---|---|---|---|---|
U | C | A | G | ||
1st base |
U | UUU (Phe/F)
Phenylalanine UUC (Phe/F) Phenylalanine |
UCU (Ser/S)
Serine UCC (Ser/S) Serine |
UAU (Tyr/Y)
Tyrosine UAC (Tyr/Y) Tyrosine |
UGU (Cys/C)
Cysteine UGC (Cys/C) Cysteine |
UUA (Leu/L) Leucine | UCA (Ser/S) Serine | UAA Ochre (Stop) | UGA Opal (Stop) | ||
UUG (Leu/L) Leucine | UCG (Ser/S) Serine | UAG Amber (Stop) | UGG (Trp/W) Tryptophan | ||
C | CUU (Leu/L) Leucine CUC (Leu/L) Leucine |
CCU (Pro/P)
Proline CCC (Pro/P) Proline |
CAU (His/H)
Histidine CAC (His/H) Histidine |
CGU (Arg/R)
Arginine CGC (Arg/R) Arginine | |
CUA (Leu/L) Leucine CUG (Leu/L) Leucine |
CCA (Pro/P) Proline CCG (Pro/P) Proline |
CAA (Gln/Q)
Glutamine
CAG (Gln/Q) Glutamine |
CGA (Arg/R) Arginine CGG (Arg/R) Arginine | ||
A | AUU (Ile/I)
Isoleucine AUC (Ile/I) Isoleucine |
ACU (Thr/T)
Threonine ACC (Thr/T) Threonine |
AAU (Asn/N)
Asparagine AAC (Asn/N) Asparagine |
AGU (Ser/S) Serine AGC (Ser/S) Serine | |
AUA (Ile/I) Isoleucine | ACA (Thr/T) Threonine | AAA (Lys/K) Lysine | AGA (Arg/R) Arginine | ||
AUG
[A] (Met/M)
Methionine |
ACG (Thr/T) Threonine | AAG (Lys/K) Lysine | AGG (Arg/R) Arginine | ||
G | GUU (Val/V)
Valine GUC (Val/V) Valine |
GCU (Ala/A)
Alanine GCC (Ala/A) Alanine |
GAU (Asp/D)
Aspartic acid GAC (Asp/D) Aspartic acid |
GGU (Gly/G)
Glycine GGC (Gly/G) Glycine | |
GUA (Val/V) Valine GUG (Val/V) Valine |
GCA (Ala/A) Alanine GCG (Ala/A) Alanine |
GAA (Glu/E)
Glutamic acid GAG (Glu/E) Glutamic acid |
GGA (Gly/G) Glycine GGG (Gly/G) Glycine |
An IP changed it to the following:
2nd base | |||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
U | C | A | G | ||||||||||||||||||||||||||||||||||
1st base |
U |
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C |
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A |
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G |
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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:
2nd base | |||||||||
---|---|---|---|---|---|---|---|---|---|
U | C | A | G | ||||||
1st base | U | UUU | (Phe/F) Phenylalanine | UCU | (Ser/S) Serine | UAU | (Tyr/Y) Tyrosine | UGU | (Cys/C) Cysteine |
UUC | (Phe/F) Phenylalanine | UCC | (Ser/S) Serine | UAC | (Tyr/Y) Tyrosine | UGC | (Cys/C) Cysteine | ||
UUA | (Leu/L) Leucine | UCA | (Ser/S) Serine | UAA | Ochre ( Stop) | UAG | Opal (Stop) | ||
UUG | (Leu/L) Leucine | UCG | (Ser/S) Serine | UAG | Amber (Stop) | UGG | (Trp/W) Tryptophan | ||
C | CUU | (Leu/L) Leucine | CCU | (Pro/P) Proline | CAU | (His/H) Histidine | CGU | (Arg/R) Arginine | |
CUC | (Leu/L) Leucine | CCC | (Pro/P) Proline | CAC | (His/H) Histidine | CGC | (Arg/R) Arginine | ||
CUA | (Leu/L) Leucine | CCA | (Pro/P) Proline | CAA | (Gln/Q) Glutamine | CGA | (Arg/R) Arginine | ||
CUG | (Leu/L) Leucine | CCG | (Pro/P) Proline | CAG | (Gln/Q) Glutamine | CGG | (Arg/R) Arginine | ||
A | AUU | (Ile/I) Isoleucine | ACU | (Thr/T) Threonine | AAU | (Asn/N) Asparagine | AGU | (Ser/S) Serine | |
AUC | (Ile/I) Isoleucine | ACC | (Thr/T) Threonine | AAC | (Asn/N) Asparagine | AGC | (Ser/S) Serine | ||
AUA | (Ile/I) Isoleucine | ACA | (Thr/T) Threonine | AAA | (Lys/K) Lysine | AGA | (Arg/R) Arginine | ||
AUG [A] | (Met/M) Methionine | ACG | (Thr/T) Threonine | AAG | (Lys/K) Lysine | AGG | (Arg/R) Arginine | ||
G | GUU | (Val/V) Valine | GCU | (Ala/A) Alanine | GAU | (Asp/D) Aspartic acid | GGU | (Gly/G) Glycine | |
GUC | (Val/V) Valine | GCC | (Ala/A) Alanine | GAC | (Asp/D) Aspartic acid | GGC | (Gly/G) Glycine | ||
GUA | (Val/V) Valine | GCA | (Ala/A) Alanine | GAA | (Glu/E) Glutamic acid | GGA | (Gly/G) Glycine | ||
GUG | (Val/V) Valine | GCG | (Ala/A) Alanine | GAG | (Glu/E) Glutamic acid | GGG | (Gly/G) Glycine |
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)
My recent edit here came up for discussion at Wikipedia talk:No original research: what you wrote 'the code is determined by' just doesn't make sense that I can see. And you have gone and stuck it in again. The code 'just is', it is interpreted to produce things, it is not determined by the proteins or enzymes it produces. Do you mean determines? by user:Dmcq
No, the code isn't "just is". The DNA sequence just is, but "the code" in this context isn't the DNA sequence. The genetic code is the correspondence by which three-letter codons in nucleic acid sequences yield amino acids in proteins.
When I say that it's determined by stuff coded for in the DNA, I mean that the aminoacyl-tRNA synthetases are ordinary proteins: they're produced from genes using the genetic code, same as any other protein. And that the tRNAs are, like any other RNA, produced by transcription from DNA (followed by processing, although I didn't mention that). It's hard to find a quote for the former. In most contexts, it would never occur to anyone to doubt that the synthetases are coded for in DNA just like any other protein. If you know enough to be talking about them in the first place, you don't need to be told that. The best I can find at the moment is a search listing lots of genes for aminoacyl tRNA synthetases: [6] Each entry tells what chromosome the gene is on, but it doesn't belabor the fact that it's DNA.
The fact that tRNAs are coded in DNA is much easier. Here's a quote for the it: "Transfer RNA molecules, like mRNA and other types of RNA, are transcribed from DNA templates." p 325, Biology, Neil A. Campbell ISBN 0-8053-1880-1 And for the fact that tRNAs are processed rather than having the original transcript be the final form: "tRNAs are covalently modified before they exit the nucleus", p 338 Molecular Biology of the Cell, Bruce Alberts et al., ISBN 0-8153-3218-1.
But to avoid running afoul of SYNTH, I would have to find those two statements together in the same source, making their implications at least as explicit as I did. Hard plus easy isn't somewhere in between, in this type of case. Hard plus easy is well-nigh impossible, so the article never gets improved in ways that are hard plus easy. I hate SYNTH. Suppose I took this "original research" to a journal that publishes original research. Would they vet it for correctness and then publish my article? No, they would assign an intern (if they felt sorry for me enough to waste the time) to explain to me that my supposed discovery was already obvious to everyone back in 1959. Here in WP, though, it's unverifiable original research. Did I mention that I hate SYNTH? (If anyone feels the need to answer that question, please do so at Wikipedia talk:No original research#I hate SYNTH.)
The problem in the article that got me to make the edit was that it said mRNA is produced directly by transcription, i.e. that there are no introns. I wrote, "In eucaryotes, the result of transcription is not mRNA itself, but pre-mRNA." Here's the corresponding statement in Campbell: "In bacteria, mRNAs are ready for translation as soon as they peel away from their DNA templates. In contrast, the RNA products of transcription in eukaryotes are processed before they leave the nucleus as mRNA." Campbell p 325 -- Dan Wylie-Sears 2 ( talk) 05:21, 23 May 2011 (UTC)
I don't see why the expanded genetic code section here should cover more than a few generalities from the linked article expanded genetic code. And I definitely do not think the link to that article should be removed. That article should be expanded rather than putting stuff in here at any detailed level. I have therefore reverted the changes being put in here to deal with the subject in greater depth. Dmcq ( talk) 17:54, 22 July 2011 (UTC)
(Copied from my user page where it shouldn't have been) Dmcq ( talk) 10:56, 24 July 2011 (UTC)
The problem here is that not all the new synthetic bases are analogs. For example, several synthetic bases are not analogs of A, C, G, T and U. For another example, Watson-Crick complements require A/T or A/U and C/G pairings; however, another synthetic base is X/X. X is its own Watson-Crick complement. None of the standard DNA or RNA bases are self-complementary. Thus, X is not an analog of anything previously discussed. Thus, adding the material as you require to Nucleic Acid Analogs would be incompatible with the actual research. While this refers to the research of Eric T. Kool (one such article appearing as xDNA in Wikipedia), Kool and other researchers have several more non-analog bases. I think it would be wrong to put factually-incorrect information under Nucleic Acid Analogs.
Typical codons are based on the standard DNA bases A, C, G and T, but if synthetic bases are used (such as X, which is not a nucleic acid analog) then the corresponding synthetic codons are entirely different. For example, a codon such as iso-C/X/G could hardly be included under a discussion of Nucleic Acid Analogs since once again X is not a nucleic acid analog. Just to be clear here, an analog usually is understood to mean a derivative of a standard base. X and other synthetic bases are not derivatives of A, C, G or T. This becomes even clearer when dealing with synthetic codons based on 4-bases. Thus the research based on "the 65th codon" certainly cannot come under standard codons of analogs of nucleic acids.
Synthetic mRNA anti-codons must be treated similarly. Furthermore, synthetic tRNA also should not be treated under analogs of nucleic acids. Indeed, analogs of nucleic acids really should be treated entirely separately from codons, anti-codons, mRNA, tRNA and synthetic amino acids. The idea of putting all these things together under Nucleic Acids sounds very strange. No acceptable book in standard biochemistry has ever done this. Shadow600 ( talk) 05:44, 24 July 2011 (UTC)
yellow, nonpolar | g-Yellow, Trp | green-yellow, Tyr | green, polar | green-blue, His | blue, basic | red, acidic | (stop codon) |
2nd base | |||||||||
---|---|---|---|---|---|---|---|---|---|
T | C | A | G | ||||||
1st base | T | TTT 0.57 | Phe / F | TCT 0.11 | Ser / S | TAT 0.53 | Tyr / Y | TGT 0.42 | Cys / C |
TTC 0.43 | Phe / F | TCC 0.11 | Ser / S | TAC 0.47 | Tyr / Y | TGC 0.58 | Cys / C | ||
TTA 0.15 | Leu / L | TCA 0.15 | Ser / S | TAA 0.64 | Ochre | TGA 0.36 | Opal | ||
TTG 0.12 | Leu / L | TCG 0.16 | Ser / S | TAG 0.00 | Amber | TGG 1.00 | Trp / W | ||
C | CTT 0.12 | Leu / L | CCT 0.17 | Pro / P | CAT 0.55 | His / H | CGT 0.36 | Arg / R | |
CTC 0.10 | Leu / L | CCC 0.13 | Pro / P | CAC 0.45 | His / H | CGC 0.44 | Arg / R | ||
CTA 0.05 | Leu / L | CCA 0.14 | Pro / P | CAA 0.30 | Gln / Q | CGA 0.07 | Arg / R | ||
CTG 0.46 | Leu / L | CCG 0.55 | Pro / P | CAG 0.70 | Gln / Q | CGG 0.07 | Arg / R | ||
A | ATT 0.58 | Ile / I | ACT 0.16 | Thr / T | AAT 0.47 | Asn / N | AGT 0.14 | Ser / S | |
ATC 0.35 | Ile / I | ACC 0.47 | Thr / T | AAC 0.53 | Asn / N | AGC 0.33 | Ser / S | ||
ATA 0.07 | Ile / I | ACA 0.13 | Thr / T | AAA 0.73 | Lys / K | AGA 0.02 | Arg / R | ||
ATG [A] 1 | Met / M | ACG 0.24 | Thr / T | AAG 0.27 | Lys / K | AGG 0.03 | Arg / R | ||
G | GTT 0.25 | Val / V | GCT 0.11 | Ala / A | GAT 0.65 | Asp / D | GGT 0.29 | Gly / G | |
GTC 0.18 | Val / V | GCC 0.31 | Ala / A | GAC 0.35 | Asp / D | GGC 0.46 | Gly / G | ||
GTA 0.17 | Val / V | GCA 0.21 | Ala / A | GAA 0.70 | Glu / E | GGA 0.13 | Gly / G | ||
GTG 0.40 | Val / V | GCG 0.38 | Ala / A | GAG 0.30 | Glu / E | GGG 0.12 | Gly / G |
References
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20 small color-coded dots would be useful. A 4-color scheme could be used to coordinate these colored dots with the 4 major triplet groups. In this proposed drawing, one could see the extent of the spread of the amino acids through the H-M space. Unforetunately, the figure is too small to put the single letter code next to the dots. Youvan's biography has the same figure and it expands to a more complex figure that is fully labelled. Perhaps that is an option, but the expanded figure needs to be redrawn for rescaling and clarity. The choice of the colors was poor and the printed version is confusing because 2 of the colors are similar. Frank Layden ( talk) 17:48, 3 June 2013 (UTC)
One of my favorite fields of study is the Origin of the genetic code. At this time, I believe our ideas on Origin are highly speculative and something REALLY BIG is missing. Such discission belongs in a separate article. There we might also pick up some work on NP-hard problems. It is hard to imagine how the program (making protein) and the computer language (the genetic code) can evolve simultaneously and sustain life - by analogy. On the other hand, Redundancy is tabulated fact. There is a "take home" message for a student studying Redundancy: wobble at the 3rd position and hydropathy at the second position. So, in terms of editing this article, we have just removed a factual section (Redundancy) and added a speculative section (Origin). I am sorry to say this article was better one year ago. The current article reflects people's research interests, including mine, while the older article gave us more history and fact.
Can we vote?
Redundacy - IN; Origin - OUT Frank Layden ( talk) 16:17, 5 August 2013 (UTC)
There is an error in Figure 4: The top label should read "NGN". I am having it fixed by a graphic artist in the next few days. I am also having a vectorized version of the "expanded view" made for the hyperlink and for the subsection. Frank Layden ( talk) 01:02, 16 October 2013 (UTC)
There has been a lot of back and forth on Duons. We should come to con consensus before it goes into the main article.
My take on the whole this is summed up quite nicely in this article [1] basically the "duon" functionality is already well know and already has defined names like Regulatory DNA sequences, promoters, enhancers, termination sequences. These terms are already used in the Article and I don't think we should be using a term that basically boils down to a PR buzz word. it should not be in the introduction of the article, if at all. Ryftstarr ( talk) 14:29, 16 December 2013 (UTC)
This whole Duon stuff is obviously PR buzz and trying to make the fact that epigenetic modifications occur within protein sequences a novel finding AND a distinct phrase is quite laughable. Also, the even larger claim that non-coding selection on protein regions being unknown is even more unbelievable. For transcription factor binding sites within proteins check back to at LEAST 2001, http://nar.oxfordjournals.org/content/29/19/4070.long . This concept is not at all controversial for people in the specific field of epigenetics (modifications to DNA that do not change the underlying genetic code). Also ideas about optimal codons have been expressed since at least 1987 ( http://nar.oxfordjournals.org/content/15/3/1281).
Neglecting this background makes the recent insertion both shortsighted and also suspect in seeming to increase the tout of its scientific claims.
REGARDLESS, none of this discussion belongs in an introduction to the genetic code. At best it should be a distant footnote at the end linked to the more extensive discussion on codon usage. Were the editors not aware of this 30+ year research topic ( http://en.wikipedia.org/wiki/Codon_usage_bias)?
To be more specific, the last paragraph of the introduction is distracting to a general introduction of the genetic code, which is specifically about the translation of mRNA into a protein sequence. Trying to shoe-horn into some talk about how organisms are more than protein (I happen to agree with things being more than proteins) is obviously out of place and seems like proselytizing. Again, if you really want it to be there, mention it in the context of the main body, not 1/3 of the introduction.
99.174.80.45 ( talk) 04:45, 17 December 2013 (UTC)Thomas
I agree with both of those points DMacks. My main dispute was 1) overemphasis to a secondary point in the intro and 2) ignoring the rest of the extensive research on non-coding regions. I agree that the idea of DNA sequence=deterministic is misleading and worth mentioning, but as currently stated it seems to undercut the whole premise rather than the reality being more nuanced. A single sentence linking out to regulatory sequences and possibly codon usage seems like a good idea.
Though, I have to mention the overall misconception about the role most of these regulatory processes play. Most epigenetic modifications, be they transcription factors, DNA methylation, or histone modification, largely relate to changes in how MUCH of a given protein is produced, rather than WHAT protein is produced. There are some recent studies showing that histone/methylation can affect whether introns/exons are included/excluded thereby changing the protein sequence, but that does not (currently) seem to be a primary function. So again, the actual research is much less clear than is currently purported. As it stands, the last paragraph of the intro speaks more about the relevance of protein abundance evolution vs protein sequence evolution. I'm forgetting the more eloquent description of this debate, but it is a long-going discussion in the evolution literature. 99.174.80.45 ( talk) 05:15, 17 December 2013 (UTC) Thomas
Here is a rough draft of a replacement sentence: "While the genetic code determines the protein sequence for a given coding region, other genomic regions can influence when and where these proteins are produced" This sentence could be expanded to talk about further impact towards phenotype, but then in my opinion it starts to get bogged down in specifics that are tangential to the main article. 99.174.80.45 ( talk) 05:04, 18 December 2013 (UTC) Thomas
Genetic code graphic figure GeneticCode21-version-2.svg is confusing in this context. I may be confused myself (not a biologist), but this figure is from the catalog of a company that specializes in posttranslational modification, and makes heavy reference to various modifications, which as far as I can tell have no direct relation to the natural genetic code. My initial interpretation was "oh, so the redundant codons actually specify posttranslational modifications." I can understand the desire for a sexy graphic instead of boring tables, but IMO this page would be improved by simple deletion of that figure.
Robertmacl ( talk) 12:45, 13 May 2014 (UTC)
Descriptions of the genetic code have improved in the past ten years, but even a simple definition is still lacking. The old definition is no longer explicitly given - the genetic code is a transfer of linear information from DNA to protein - but it is still strongly implied in everything being said here. The net effect is that there is no working definition for molecular information, and molecular information is the purpose of genetic translations.
I think there is a simple, logical foundation for the genetic code. I think that the genetic code, if it is properly understood, is central to all processes in life. I think there is a phenomenal amount of molecular information stored in and translated by the genetic code, not just codons and amino acids.
I seem to be the only person on the planet that feels this way about it, and that's okay. But I'm a little bit surprised that after ten years these valid ideas are not even mentioned on a page like this. I think for the sake of debate, you should point them out if only to refute them, or tell people why they should reject them.
If anybody cares to understand this, they can start here: http://www.codefun.com/
I absolutely do not mean "genome." If you want to define the genetic code to be "essentially what a codon table shows" then I think that should be included as the first line in the page. Then I think you should explain exactly what a codon table is and exactly what it shows, because other than being defined that way, that is not what the genetic code is.
The basic problem is that "everybody knows" that the genetic code is something that translates "molecular information." Unfortunately, this represents nothing but a tautology in that molecular information is defined as that thing translated by the genetic code, and the genetic code is defined as essentially what a codon table shows.
My basic point is that a codon table is a very small part of what the genetic code actually is, and I am limiting this here specifically to the molecular information translated from nucleotide sequences to protein sequences. The genetic code at that level is still so many things that I think it is incumbent on any explanation like this to clearly define what it is explaining. Short of that, it does more to confuse people than actually clear things up.
This fact is covered by the article but rather much hidden away. It is not represented in the lead. There are two critical steps. The FIRST step is the coupling of the Transfer RNA the the Amino Acid. This requires a specific enzyme, the amino asyl transfer RNA synthetase, for each amino acid. One can say the the DNA code for the AATRS embodies half of the genetic code. But this is not pointed out by the text. It has to be reasoned from the text. -- Ettrig ( talk) 12:59, 25 November 2014 (UTC)
I would say that tRNA is the molecule that does the translation from codon to amino acid. It is like a dictionary or something. You are correct, it is only because of the tRNA that AAA means Lysine. The translation from AAA to lysine has nothing to do with ribosomes. It is the tRNA and only the tRNA that translates codon to amino acid. "All" that the ribosome does is to get the correct tRNA to match the mRNA and then join the amino acids into a polypeptide. Note that the tRNA also provides the energy for the ribosome to move the mRNA by 3 bases as the mRNA is read. This probably should be clarified -- Lehasa ( talk) 13:51, 22 February 2015 (UTC)
Trying to use this data, I found it confusing. It's clearly not percent, since it sums to more than 100. I looked at the column heading, but was not familiar with the percent-like symbol. I hovered over the symbol, and it said "per mille", so I though it was per thousand, but was not sure in what language (I don't know Latin).
I went to the original reference cited in the section, which said "per thousand", which made sense. So I looked up per mille and found that I was not alone is not being familiar with this:
The term occurs so rarely in English that major dictionaries do not agree on the spelling or pronunciation even within a single dialect of English[10] and some major dictionaries such as Macmillan[11] and Longman[12] do not even contain an entry.
So I changed it, so now when you hover over the symbol it says "per thousand", which will be more helpful to the reader, I think. Other opinions are welcome. LouScheffer ( talk) 12:29, 17 October 2016 (UTC)
I'm wondering whether the amount of codons per gene varies, and if so, whether there is a minimum and maximum amount of codons per gene. Also, if there's a minimum/maximum amount of codons, is this amount a multiplication of 3 (i.e. 1³, 2³, 3³, ...). That way, we could also know the amount of possible genetic code variations per gene. KVDP ( talk) 16:10, 22 June 2017 (UTC)
I was wondering whether there has been any research in Decipherment of the DNA. For instance, there are various types of mutations of the same gene in the human population, which express themselves as differences in real life between the humans. [1]
Logically, each of these mutations is a code for a different message that conveys details on how to do something in the human body. My guess is that each of the 64 codons is a base building block in that code (so comparable to a letter in our own alphabet). Each gene (or hence sequence of codons) will (I think) convey a message to what type of tissue needs to be build (i.e. fat, bone, flesh, ...) and how long this strand of tissue needs to be, and its shape, and to what tissue it should connect). The thickness of the tissue is probably not specified directly, but rather specified by a seperate gene, perhaps via the "codon for specifying length". The latter, I assume because a disease like Talk:Sclerosteosis also exists.
The reason why this is useful to know is because, at present, for treating genetic diseases, we can only just use the genetic code of humans without that disease to overwrite the faulty gene in a person with the disease. However, as Stephen Friend from The Resilience Project found out, there are many versions of "good genetic code", and not all version will work on that person. We don't know why this is, and so every gene therapy that would be undertaken becomes a puzzle, and each gene therapy may need to be repeated several times. If we understand what message is in the gene, we might avoid all this.
KVDP ( talk) 09:13, 27 June 2017 (UTC)
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As described in my comment on Talk:Proteinogenic_amino_acid#Hydropathy_of_tyrosine, the table in this article in classifying tyrosine as polar and not hydrophobic is inconsistent with other statements in Wikipedia. Tyrosine's own article clarifies that it is near the borderline but "usually classified as" hydrophobic. This article's table should either be changed to match the sourced statements elsewhere, or itself sourced. 2607:FEA8:12A0:44D:0:0:0:C319 ( talk) 02:08, 24 May 2020 (UTC)
May I suggest that this image would be useful for our readers: [ [7]]
Charles Juvon ( talk) 22:21, 27 August 2020 (UTC)
H2mex ( talk) 03:03, 27 June 2021 (UTC)
Take a look at the new 3-D image and consider what is said in the article: "The reason may be that charge reversal (from a positive to a negative charge or vice versa) can only occur upon mutations in the first position, but never upon changes in the second position of a codon." Consider positive {R,K} <-> negative {D,E}. This statement is misleading. Please check me. Charles Juvon ( talk) 22:41, 9 September 2020 (UTC)
Both references to the 1.5 x 10^84 number are dead. One possible fix is to insert the actual equation: N[Abs[Sum[(-1)^j*Binomial[21,j]*j^64,{j,21}]],10] = 1.510109516 x 10^84 That's in Mathematica syntax. I'm no good in wiki markup for algebraic equations. N[_,10] is simply formatting. Charles Juvon ( talk) 19:11, 15 September 2020 (UTC)
Given the current last sentence of the Article and references 99 and 100, we might want to use this material from https://arxiv.org/ftp/arxiv/papers/1303/1303.6739.pdf : "Recent biotech achievements make it possible to employ genomic DNA as data storage more durable than any media currently used (Bancroft et al., 2001; Yachie et al., 2008; Ailenberg & Rotstein, 2009). Perhaps the most direct application for that was proposed even before the advent of synthetic biology. Considering alternative informational channels for SETI, Marx (1979) noted that genomes of living cells may provide a good instance for that. He also noted that even more durable is the genetic code. Exposed to strong negative selection, the code stays unchanged for billions of years, except for rare cases of minor variations (Knight et al., 2001) and context-dependent expansions (Yuan et al., 2010)." ---- Charles Juvon ( talk) 20:18, 5 November 2020 (UTC)
Unless someone has a better idea, we need to go back to the March 15, 2021 version. The top figure is an embarrassment. That editor is now in red letters. Charles Juvon ( talk) 01:45, 17 June 2021 (UTC)
"Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact, because the conventional wisdom avoids the question, there is little agreement as to whether the symmetrical nature actually even exists. A better understanding of symmetry and an appreciation for its essential role in the genetic code formation can improve our understanding of nature’s coding processes. Thus, it is worth formulating a new integrated symmetrical table for genetic codes, which is presented in this paper. It could be very useful to understand the Nobel laureate Crick’s wobble hypothesis — how one transfer ribonucleic acid can recognize two or more synonymous codons, which is an unsolved fundamental question in biological science."
H2mex ( talk) 19:25, 3 July 2021 (UTC)" Charles Juvon ( talk) 13:44, 12 July 2021 (UTC)
User 103.172.73.22 changed the image description at the top to say a codon is two nucleotides rather than three. Not clear why they would do that but it is clearly incorrect per other content already on the page. ArbitraryConstant ( talk) 21:29, 15 February 2023 (UTC)
Please consider this CC4.0 and use as you wish.
https://www.youtube.com/watch?v=eHZxMAZTFcY Doug youvan ( talk) 17:13, 9 September 2023 (UTC)
If another editor feels this would work in the article, please use it. Graph Construction: In our graph, vertices represent the 20 amino acids and the "Stop" signal. An edge connects two vertices if the amino acids they represent can be interchanged through a single point mutation in their corresponding codons. This graph is not just a visualization but an analytical tool, spotlighting the possible amino acid replacements due to minor genetic variations. Highlighting Mechanism: Using the computational capabilities of Mathematica, and with the expertise provided by Centaur Intelligence, each amino acid (and the Stop signal) is successively emphasized. When highlighted, all directly reachable amino acids through a single point mutation are illuminated, thus displaying the mutation landscape for each amino acid. Results: The resultant graph unravels the dense web of interconnections among amino acids based on single point mutations. As we animate through each amino acid, patterns emerge, revealing which amino acids can easily mutate into others and which remain more isolated.
https://www.youtube.com/watch?v=WsGw5w6tiyE
Doug youvan ( talk) 01:58, 29 September 2023 (UTC)
It's more accurate, but it would need some work by a graphic artist for scaling. Serine (S) is properly represented. CC 4.0. https://www.researchgate.net/publication/374911250_Amino_Acids_Are_Segregated_in_Hydropathy_-_Molar_Volume_Space_by_the_Second_Position_of_the_Codon Doug youvan ( talk) 01:27, 23 October 2023 (UTC)
https://www.researchgate.net/publication/374973672_Codon_Cluster_Analysis_With_Hydropathy_Written_by_GPT-4_in_Python Doug youvan ( talk) 19:38, 25 October 2023 (UTC)
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I couldn't find anywhere the answer to this: the DNA consists of 2 strands, which are complementary. Which strand is selected during gene expression? The choice cannot be random, since it would generate different proteins. For example, suppose one strand contains CTC, then the opposite strand will contain GAG. The first one will translate into mRNA GAG and encode for glutamic acid, the other one into CUC and generate Leucine. — Preceding unsigned comment added by 165.222.184.132 ( talk) 10:27, 22 September 2011 (UTC)
It seems rather redundant to have both - I undestand the reasons for setting up the table both ways but I don't think it adds much to the article to include the 2nd table. If there are no objection, I'll remove it. Hichris 18:49, 28 November 2006 (UTC)
It's not really redundant. For me (and hopefully for others) this table is a valuable resource that may be used for designing mutagenesis primers when exchanging amino acids by PCR. May I ask you to put it back, please? This message is encrypted! You'll need a brain to decode it. 14:53, 12 January 2007 (UTC)
Here's an alternative presentation, using the IUPAC abbreviations from DNA_sequence:
Ala | GCN | Leu | YUR, CUN |
---|---|---|---|
Arg | CGN, AGR (MGR) | Lys | AAR |
Asn | AAY | Met | AUG |
Asp | GAY | Phe | UUY |
Cys | UGY | Pro | CCN |
Gln | CAR | Ser | UCN, AGY |
Glu | GAR | Thr | ACN |
Gly | GGN | Trp | UGG |
His | CAY | Tyr | UAY |
Ile | AUY, AUA (AUH) | Val | GUN |
START | AUG | STOP | UAR, URA |
Currently, in section "RNA codon table", the header on the "Inverse table for the standard genetic code" table refers to "DNA codons", which should be "RNA codons". It looks like the same template is being used for both DNA and RNA codons, and the substitution T->U is made. However, the column name should be specific. Probably having separate tables would simplify things :) DeepCurl ( talk) 16:42, 24 March 2019 (UTC)
I just started reading the article so I am hitting points as I go. The age of the genetic code is estimated to be about as old as the earth itself.Eigen M, Lindemann BF, Tietze M, Winkler-Oswatitsch R, Dress A, von Haeseler A.How old is the genetic code? Statistical geometry of tRNA provides an answer. Science. 1989 May 12;244(4905):673-9. PMID: 2497522 [PubMed - indexed for MEDLINE]
The standard genetic code is universal but there are some modification in mitochondria, chloroplast, some organisms like yeast, etc. Oops! its already there. GetAgrippa 22:18, 17 January 2007 (UTC)
Now that I've read the article, kudos to the authors. Excellent article! GetAgrippa 05:46, 21 January 2007 (UTC)
...is being repeatedly added as an "alternative explanation" of how the genetic code came to be, and the explanation of why it should be added is based on editor bias or supression of alternative viewpoints. So let's figure it out:
Conclusion: does not belong. DMacks 19:57, 30 January 2007 (UTC)
Codon redirects here, but this is not very useful if you more or less know what the genetic code is and are wondering what the heck a codon is. I mean, is it a real physical structure, or is it just a scientific convention? in the first paragraph you get the idea that its a physical structure, later on you learn it can be read from any of three ways. If you chop a strand and have no start/stop sequence do its codons cease to exist? It could use its own article, even if its a short one. Brallan 17:59, 27 March 2007 (UTC)
This article should contain a reference to what ACGTU stand for. There's no obvious way to find the definitions of the symbols if you don't already know the basics. — Preceding unsigned comment added by 71.182.155.221 ( talk) 18:18, 9 February 2021 (UTC)
I thought it was strange that there was a hyperlink from the Introduction to a section later in the same article (the words "variant codes" linking to the section, "5 Variations to the standard genetic code"). Does anybody else agree? richard.decal ( talk) 07:05, 22 June 2010 (UTC)
I have written up my issues with Universal genetic code on its talk page. - Madeleine 21:02, 15 April 2007 (UTC)
I do not agree with the word "scientific". As this is a science related article, any theory provided here should be scientific in the first place. CharonZ 22:22, 25 April 2007 (UTC)
One of the "arguments" creationists often use is that the code is too complicated to have evolved on its own. I recently tried to see if the code could be condensed in order to simplify it. I simply placed the second base of the triplets in the middle of the code-sun, followed by the first, followed by the third. If you do that you manage to get all the codons for leucine, serine, arginine and stop together! Futhermore you can twist the codons in such a way that amino acids seem to cluster into structural/ functional groups (unpolar, polar, charged, intermediary, and special properties). If you are interested, please have a look at http://www.rna-game.org and leave comments. The Journal of Theoretical Biology seemed interested but they are known to take forever to process manuscripts. So, in the spirit of the opensource movement I went ahead and published a very rough first sketch on the net. Agabirhei 12:55, 18 July 2007 (UTC)
Is there the possibility to delete this particular talk section (Alternate representations of the genetic code)? The Journal of Theoretical Biology accepted my article and I have calmed down considerably after my initial shock at the results of playing sudoku with the genetic code. Apologies again for not following proper procedures. I don't know if I'm entitled to delete the section but I give my full consent to anyone who wishes and is entitled to do so. Agabirhei ( talk) 19:36, 4 July 2008 (UTC)
Popular accounts often misuse the phrase "genetic code" to mean "genome". See, for example, this Scientific American article: Genetic Code of Deadly Mosquito Cracked. Should the entry for "genetic code" or "genome" address this? — Tyrrell McAllister 09:57, 18 May 2007 (UTC)
Coming at this from a background of linguistics, I have a problem with using "code" to describe the subject matter of the article, as well as describing the codon as "transmitting information." The problem is that the codon describes the relatively circumscribed behavior of a limited series of chemical compounds, and the only "information" conveyed is the actual configuration of those chemical compounds. I recognize that a linguistic metaphor is useful, and possibly deemed essential by biologists in order to understand the workings of the codon and communicate it to others, but there should be a clear and unambiguous statement somewhere in the article that this is a heuristic device, and that the codon is not identical to a linguistic code. Digthepast ( talk) 15:19, 26 September 2011 (UTC)
What is the source of the codon usage statistics given in the picture? The values for Arginine in E. coli seem to contradict information given at http://www.biology.ualberta.ca/pilgrim.hp/links/codontable.html (which is apparently from Escherichia coli and Salmonella, Vol. 2, Ch. 114:2047-2066, 1996, Neidhardt FC ed., ASM press, Washington, D.C). It says in the image that the agg and aga codons are not used at all in E. coli, which seems to be wrong. Also, there is a very large difference according to the source I cited between usage of cgg and cgt, which the picture doesn't reflect. I haven't checked anything besides those, though. —Preceding unsigned comment added by 129.206.92.200 ( talk) 12:50, 24 January 2008 (UTC)
Doug Youvan ( talk) 02:04, 25 April 2008 (UTC)
Is this more understandable? OR-ish does not apply, because this is data already on WP, and I have published in the field.
Doug youvan ( talk) 16:43, 30 May 2008 (UTC)
Sorry - This out of sequence, but I now see Holley goes to Salk with Crick in 1968. Historical. Doug youvan ( talk) 02:39, 3 June 2008 (UTC)
Note: Exactly the same text as the current article with one sentence (bold) inserted with one or two references, and one small figure already on Commons:
U1 = UNN
A2 = NAN
C2 = NCN
U2 = NUN
Solubility -> Hydropathy
Size -> Molar Volume Doug youvan ( talk) 13:42, 3 June 2008 (UTC)
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].
References
The Freeland et al. reference in this article links to an abstract at PubMed. As usual, further reading of the actual paper is blocked by copyright. However, there appears to be an on-line copy: http://www.evolvingcode.net/PDF/thecasefor.pdf . In fact, this verbose pdf paper supports the opposite view as what it is referenced to support in this genetic code article. The Freeland reference has excellent historical literature citations in mutational analyses, but nothing is cited in terms of an a priori mathematical analyses of the structure of the genetic code. Should we agree on how to fix this reference and the re-statement of its conclusion in this article? Doug youvan ( talk) 16:09, 1 June 2008 (UTC)
Image:GeneticCode21-version-2.svg needs replaced at higher resolution with a more common file format. Any ideas that aren't a copyvio? Doug youvan ( talk) 01:14, 3 June 2008 (UTC)
The following codon and the corresponding amino acid combinations do not occur in nature.
These combinations are found only in certain genetically modified clones and hypothetical proteins. To verify this (this won't take not more than a miniute):
I removed the following parenthetical statement from the "Transfer of information via the genetic code" section:
(Practically speaking, one would need at least 2 bits to represent a nucleotide, and 6 for a codon, in a typical computer.)
It's correct, but I think it's more information than the section needs, and it interrupts the flow of the article. No need to nitpick. James A. Stewart ( talk) 10:34, 7 October 2009 (UTC)
Codons appear to code for different amino acids in prokaryotic and eukaryotic cells—can someone add a table or at least a comprehensive list of differences? Bongo matic 06:21, 8 October 2009 (UTC)
Starting GA reassessment as part of the GA Sweeps process. Jezhotwells ( talk) 21:15, 26 February 2010 (UTC)
Could you provide some specific examples of where you consider the artcle's tone to be unencyclopedic? At first glance I don't notice any clear infringements of WP:NOTTEXTBOOK, like leading questions or systemic problem solutions as examples. Emw ( talk) 04:46, 1 March 2010 (UTC)
Here we can coordinate the collaboration of the month of this article. We need to find open points and unsolved issues and areas where be believe we can improve the article.
Open points / questions:
Greetings -- hroest 11:23, 4 March 2010 (UTC)
Just to add to the work list to remember (also for myself):
2. Section Genetic code#Sequence reading frame: Add the term Open reading frame = ORF. I will check some references since this article in WP is not well referenced as well. -- Firefly's luciferase ( talk) 03:14, 9 March 2010 (UTC) 3. Two details to be added: wobble base (for the base that is not necessary to determinate a particular amino acid. And, more details on Selenocysteine and Pyrrolysine, I think. -- Firefly's luciferase ( talk) 03:19, 9 March 2010 (UTC)
It's been proposed that Codon Dictionary be merged here; discussion is at Talk:Codon Dictionary. I note it here because there's only been one comment since the merge was proposed nearly a month ago. Adrian J. Hunter( talk• contribs) 16:25, 1 June 2010 (UTC)
Not sure when you guys changed the codon table, but it's be more useful to leave the table as a DNA codon table rather than a mRNA codon table. Reason is that there is a lot more people working at a DNA rather than at a mRNA level. I am going to change the uracils back to thymine. —Preceding unsigned comment added by 142.150.215.185 ( talk) 22:59, 9 September 2010 (UTC)
Hmm... It appears you are right. For some reason, I was under the impression that DNA codons have always been used but I could've confused this page with some other sites. You are right again in that a lot of biochem and genetics textbooks use an RNA codon table instead of a DNA codon table because that reflects the biochemistry of the process.
I made the change from the standpoint that RNA codons should be of less interest than DNA codons in practice. Unless a genome biologist is working exclusively with mRNA, he'd likely be much more interested in DNA codons than RNA codons. That stems partly from the fact that much of genes that are annotated are now stored as DNA sequences rather than RNA sequences.
If the consensus is that a RNA codon table is more appropriate, then I'd concede. However, I'd prefer to have a DNA codon table in this wiki so that people who are actually working with codons will be able to refer to those tables. Although of course... it's really just a matter of changing an U to a T, but that can be tedious depending on what one's using it for. —Preceding unsigned comment added by Bobthefish2 ( talk • contribs) 17:34, 10 September 2010 (UTC)
Textbooks I checked
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Until several weeks ago the codon table in this article looked like this:
2nd base | |||||
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U | C | A | G | ||
1st base |
U | UUU (Phe/F)
Phenylalanine UUC (Phe/F) Phenylalanine |
UCU (Ser/S)
Serine UCC (Ser/S) Serine |
UAU (Tyr/Y)
Tyrosine UAC (Tyr/Y) Tyrosine |
UGU (Cys/C)
Cysteine UGC (Cys/C) Cysteine |
UUA (Leu/L) Leucine | UCA (Ser/S) Serine | UAA Ochre (Stop) | UGA Opal (Stop) | ||
UUG (Leu/L) Leucine | UCG (Ser/S) Serine | UAG Amber (Stop) | UGG (Trp/W) Tryptophan | ||
C | CUU (Leu/L) Leucine CUC (Leu/L) Leucine |
CCU (Pro/P)
Proline CCC (Pro/P) Proline |
CAU (His/H)
Histidine CAC (His/H) Histidine |
CGU (Arg/R)
Arginine CGC (Arg/R) Arginine | |
CUA (Leu/L) Leucine CUG (Leu/L) Leucine |
CCA (Pro/P) Proline CCG (Pro/P) Proline |
CAA (Gln/Q)
Glutamine
CAG (Gln/Q) Glutamine |
CGA (Arg/R) Arginine CGG (Arg/R) Arginine | ||
A | AUU (Ile/I)
Isoleucine AUC (Ile/I) Isoleucine |
ACU (Thr/T)
Threonine ACC (Thr/T) Threonine |
AAU (Asn/N)
Asparagine AAC (Asn/N) Asparagine |
AGU (Ser/S) Serine AGC (Ser/S) Serine | |
AUA (Ile/I) Isoleucine | ACA (Thr/T) Threonine | AAA (Lys/K) Lysine | AGA (Arg/R) Arginine | ||
AUG
[A] (Met/M)
Methionine |
ACG (Thr/T) Threonine | AAG (Lys/K) Lysine | AGG (Arg/R) Arginine | ||
G | GUU (Val/V)
Valine GUC (Val/V) Valine |
GCU (Ala/A)
Alanine GCC (Ala/A) Alanine |
GAU (Asp/D)
Aspartic acid GAC (Asp/D) Aspartic acid |
GGU (Gly/G)
Glycine GGC (Gly/G) Glycine | |
GUA (Val/V) Valine GUG (Val/V) Valine |
GCA (Ala/A) Alanine GCG (Ala/A) Alanine |
GAA (Glu/E)
Glutamic acid GAG (Glu/E) Glutamic acid |
GGA (Gly/G) Glycine GGG (Gly/G) Glycine |
An IP changed it to the following:
2nd base | |||||||||||||||||||||||||||||||||||||
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U | C | A | G | ||||||||||||||||||||||||||||||||||
1st base |
U |
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C |
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A |
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G |
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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:
2nd base | |||||||||
---|---|---|---|---|---|---|---|---|---|
U | C | A | G | ||||||
1st base | U | UUU | (Phe/F) Phenylalanine | UCU | (Ser/S) Serine | UAU | (Tyr/Y) Tyrosine | UGU | (Cys/C) Cysteine |
UUC | (Phe/F) Phenylalanine | UCC | (Ser/S) Serine | UAC | (Tyr/Y) Tyrosine | UGC | (Cys/C) Cysteine | ||
UUA | (Leu/L) Leucine | UCA | (Ser/S) Serine | UAA | Ochre ( Stop) | UAG | Opal (Stop) | ||
UUG | (Leu/L) Leucine | UCG | (Ser/S) Serine | UAG | Amber (Stop) | UGG | (Trp/W) Tryptophan | ||
C | CUU | (Leu/L) Leucine | CCU | (Pro/P) Proline | CAU | (His/H) Histidine | CGU | (Arg/R) Arginine | |
CUC | (Leu/L) Leucine | CCC | (Pro/P) Proline | CAC | (His/H) Histidine | CGC | (Arg/R) Arginine | ||
CUA | (Leu/L) Leucine | CCA | (Pro/P) Proline | CAA | (Gln/Q) Glutamine | CGA | (Arg/R) Arginine | ||
CUG | (Leu/L) Leucine | CCG | (Pro/P) Proline | CAG | (Gln/Q) Glutamine | CGG | (Arg/R) Arginine | ||
A | AUU | (Ile/I) Isoleucine | ACU | (Thr/T) Threonine | AAU | (Asn/N) Asparagine | AGU | (Ser/S) Serine | |
AUC | (Ile/I) Isoleucine | ACC | (Thr/T) Threonine | AAC | (Asn/N) Asparagine | AGC | (Ser/S) Serine | ||
AUA | (Ile/I) Isoleucine | ACA | (Thr/T) Threonine | AAA | (Lys/K) Lysine | AGA | (Arg/R) Arginine | ||
AUG [A] | (Met/M) Methionine | ACG | (Thr/T) Threonine | AAG | (Lys/K) Lysine | AGG | (Arg/R) Arginine | ||
G | GUU | (Val/V) Valine | GCU | (Ala/A) Alanine | GAU | (Asp/D) Aspartic acid | GGU | (Gly/G) Glycine | |
GUC | (Val/V) Valine | GCC | (Ala/A) Alanine | GAC | (Asp/D) Aspartic acid | GGC | (Gly/G) Glycine | ||
GUA | (Val/V) Valine | GCA | (Ala/A) Alanine | GAA | (Glu/E) Glutamic acid | GGA | (Gly/G) Glycine | ||
GUG | (Val/V) Valine | GCG | (Ala/A) Alanine | GAG | (Glu/E) Glutamic acid | GGG | (Gly/G) Glycine |
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)
My recent edit here came up for discussion at Wikipedia talk:No original research: what you wrote 'the code is determined by' just doesn't make sense that I can see. And you have gone and stuck it in again. The code 'just is', it is interpreted to produce things, it is not determined by the proteins or enzymes it produces. Do you mean determines? by user:Dmcq
No, the code isn't "just is". The DNA sequence just is, but "the code" in this context isn't the DNA sequence. The genetic code is the correspondence by which three-letter codons in nucleic acid sequences yield amino acids in proteins.
When I say that it's determined by stuff coded for in the DNA, I mean that the aminoacyl-tRNA synthetases are ordinary proteins: they're produced from genes using the genetic code, same as any other protein. And that the tRNAs are, like any other RNA, produced by transcription from DNA (followed by processing, although I didn't mention that). It's hard to find a quote for the former. In most contexts, it would never occur to anyone to doubt that the synthetases are coded for in DNA just like any other protein. If you know enough to be talking about them in the first place, you don't need to be told that. The best I can find at the moment is a search listing lots of genes for aminoacyl tRNA synthetases: [6] Each entry tells what chromosome the gene is on, but it doesn't belabor the fact that it's DNA.
The fact that tRNAs are coded in DNA is much easier. Here's a quote for the it: "Transfer RNA molecules, like mRNA and other types of RNA, are transcribed from DNA templates." p 325, Biology, Neil A. Campbell ISBN 0-8053-1880-1 And for the fact that tRNAs are processed rather than having the original transcript be the final form: "tRNAs are covalently modified before they exit the nucleus", p 338 Molecular Biology of the Cell, Bruce Alberts et al., ISBN 0-8153-3218-1.
But to avoid running afoul of SYNTH, I would have to find those two statements together in the same source, making their implications at least as explicit as I did. Hard plus easy isn't somewhere in between, in this type of case. Hard plus easy is well-nigh impossible, so the article never gets improved in ways that are hard plus easy. I hate SYNTH. Suppose I took this "original research" to a journal that publishes original research. Would they vet it for correctness and then publish my article? No, they would assign an intern (if they felt sorry for me enough to waste the time) to explain to me that my supposed discovery was already obvious to everyone back in 1959. Here in WP, though, it's unverifiable original research. Did I mention that I hate SYNTH? (If anyone feels the need to answer that question, please do so at Wikipedia talk:No original research#I hate SYNTH.)
The problem in the article that got me to make the edit was that it said mRNA is produced directly by transcription, i.e. that there are no introns. I wrote, "In eucaryotes, the result of transcription is not mRNA itself, but pre-mRNA." Here's the corresponding statement in Campbell: "In bacteria, mRNAs are ready for translation as soon as they peel away from their DNA templates. In contrast, the RNA products of transcription in eukaryotes are processed before they leave the nucleus as mRNA." Campbell p 325 -- Dan Wylie-Sears 2 ( talk) 05:21, 23 May 2011 (UTC)
I don't see why the expanded genetic code section here should cover more than a few generalities from the linked article expanded genetic code. And I definitely do not think the link to that article should be removed. That article should be expanded rather than putting stuff in here at any detailed level. I have therefore reverted the changes being put in here to deal with the subject in greater depth. Dmcq ( talk) 17:54, 22 July 2011 (UTC)
(Copied from my user page where it shouldn't have been) Dmcq ( talk) 10:56, 24 July 2011 (UTC)
The problem here is that not all the new synthetic bases are analogs. For example, several synthetic bases are not analogs of A, C, G, T and U. For another example, Watson-Crick complements require A/T or A/U and C/G pairings; however, another synthetic base is X/X. X is its own Watson-Crick complement. None of the standard DNA or RNA bases are self-complementary. Thus, X is not an analog of anything previously discussed. Thus, adding the material as you require to Nucleic Acid Analogs would be incompatible with the actual research. While this refers to the research of Eric T. Kool (one such article appearing as xDNA in Wikipedia), Kool and other researchers have several more non-analog bases. I think it would be wrong to put factually-incorrect information under Nucleic Acid Analogs.
Typical codons are based on the standard DNA bases A, C, G and T, but if synthetic bases are used (such as X, which is not a nucleic acid analog) then the corresponding synthetic codons are entirely different. For example, a codon such as iso-C/X/G could hardly be included under a discussion of Nucleic Acid Analogs since once again X is not a nucleic acid analog. Just to be clear here, an analog usually is understood to mean a derivative of a standard base. X and other synthetic bases are not derivatives of A, C, G or T. This becomes even clearer when dealing with synthetic codons based on 4-bases. Thus the research based on "the 65th codon" certainly cannot come under standard codons of analogs of nucleic acids.
Synthetic mRNA anti-codons must be treated similarly. Furthermore, synthetic tRNA also should not be treated under analogs of nucleic acids. Indeed, analogs of nucleic acids really should be treated entirely separately from codons, anti-codons, mRNA, tRNA and synthetic amino acids. The idea of putting all these things together under Nucleic Acids sounds very strange. No acceptable book in standard biochemistry has ever done this. Shadow600 ( talk) 05:44, 24 July 2011 (UTC)
yellow, nonpolar | g-Yellow, Trp | green-yellow, Tyr | green, polar | green-blue, His | blue, basic | red, acidic | (stop codon) |
2nd base | |||||||||
---|---|---|---|---|---|---|---|---|---|
T | C | A | G | ||||||
1st base | T | TTT 0.57 | Phe / F | TCT 0.11 | Ser / S | TAT 0.53 | Tyr / Y | TGT 0.42 | Cys / C |
TTC 0.43 | Phe / F | TCC 0.11 | Ser / S | TAC 0.47 | Tyr / Y | TGC 0.58 | Cys / C | ||
TTA 0.15 | Leu / L | TCA 0.15 | Ser / S | TAA 0.64 | Ochre | TGA 0.36 | Opal | ||
TTG 0.12 | Leu / L | TCG 0.16 | Ser / S | TAG 0.00 | Amber | TGG 1.00 | Trp / W | ||
C | CTT 0.12 | Leu / L | CCT 0.17 | Pro / P | CAT 0.55 | His / H | CGT 0.36 | Arg / R | |
CTC 0.10 | Leu / L | CCC 0.13 | Pro / P | CAC 0.45 | His / H | CGC 0.44 | Arg / R | ||
CTA 0.05 | Leu / L | CCA 0.14 | Pro / P | CAA 0.30 | Gln / Q | CGA 0.07 | Arg / R | ||
CTG 0.46 | Leu / L | CCG 0.55 | Pro / P | CAG 0.70 | Gln / Q | CGG 0.07 | Arg / R | ||
A | ATT 0.58 | Ile / I | ACT 0.16 | Thr / T | AAT 0.47 | Asn / N | AGT 0.14 | Ser / S | |
ATC 0.35 | Ile / I | ACC 0.47 | Thr / T | AAC 0.53 | Asn / N | AGC 0.33 | Ser / S | ||
ATA 0.07 | Ile / I | ACA 0.13 | Thr / T | AAA 0.73 | Lys / K | AGA 0.02 | Arg / R | ||
ATG [A] 1 | Met / M | ACG 0.24 | Thr / T | AAG 0.27 | Lys / K | AGG 0.03 | Arg / R | ||
G | GTT 0.25 | Val / V | GCT 0.11 | Ala / A | GAT 0.65 | Asp / D | GGT 0.29 | Gly / G | |
GTC 0.18 | Val / V | GCC 0.31 | Ala / A | GAC 0.35 | Asp / D | GGC 0.46 | Gly / G | ||
GTA 0.17 | Val / V | GCA 0.21 | Ala / A | GAA 0.70 | Glu / E | GGA 0.13 | Gly / G | ||
GTG 0.40 | Val / V | GCG 0.38 | Ala / A | GAG 0.30 | Glu / E | GGG 0.12 | Gly / G |
References
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20 small color-coded dots would be useful. A 4-color scheme could be used to coordinate these colored dots with the 4 major triplet groups. In this proposed drawing, one could see the extent of the spread of the amino acids through the H-M space. Unforetunately, the figure is too small to put the single letter code next to the dots. Youvan's biography has the same figure and it expands to a more complex figure that is fully labelled. Perhaps that is an option, but the expanded figure needs to be redrawn for rescaling and clarity. The choice of the colors was poor and the printed version is confusing because 2 of the colors are similar. Frank Layden ( talk) 17:48, 3 June 2013 (UTC)
One of my favorite fields of study is the Origin of the genetic code. At this time, I believe our ideas on Origin are highly speculative and something REALLY BIG is missing. Such discission belongs in a separate article. There we might also pick up some work on NP-hard problems. It is hard to imagine how the program (making protein) and the computer language (the genetic code) can evolve simultaneously and sustain life - by analogy. On the other hand, Redundancy is tabulated fact. There is a "take home" message for a student studying Redundancy: wobble at the 3rd position and hydropathy at the second position. So, in terms of editing this article, we have just removed a factual section (Redundancy) and added a speculative section (Origin). I am sorry to say this article was better one year ago. The current article reflects people's research interests, including mine, while the older article gave us more history and fact.
Can we vote?
Redundacy - IN; Origin - OUT Frank Layden ( talk) 16:17, 5 August 2013 (UTC)
There is an error in Figure 4: The top label should read "NGN". I am having it fixed by a graphic artist in the next few days. I am also having a vectorized version of the "expanded view" made for the hyperlink and for the subsection. Frank Layden ( talk) 01:02, 16 October 2013 (UTC)
There has been a lot of back and forth on Duons. We should come to con consensus before it goes into the main article.
My take on the whole this is summed up quite nicely in this article [1] basically the "duon" functionality is already well know and already has defined names like Regulatory DNA sequences, promoters, enhancers, termination sequences. These terms are already used in the Article and I don't think we should be using a term that basically boils down to a PR buzz word. it should not be in the introduction of the article, if at all. Ryftstarr ( talk) 14:29, 16 December 2013 (UTC)
This whole Duon stuff is obviously PR buzz and trying to make the fact that epigenetic modifications occur within protein sequences a novel finding AND a distinct phrase is quite laughable. Also, the even larger claim that non-coding selection on protein regions being unknown is even more unbelievable. For transcription factor binding sites within proteins check back to at LEAST 2001, http://nar.oxfordjournals.org/content/29/19/4070.long . This concept is not at all controversial for people in the specific field of epigenetics (modifications to DNA that do not change the underlying genetic code). Also ideas about optimal codons have been expressed since at least 1987 ( http://nar.oxfordjournals.org/content/15/3/1281).
Neglecting this background makes the recent insertion both shortsighted and also suspect in seeming to increase the tout of its scientific claims.
REGARDLESS, none of this discussion belongs in an introduction to the genetic code. At best it should be a distant footnote at the end linked to the more extensive discussion on codon usage. Were the editors not aware of this 30+ year research topic ( http://en.wikipedia.org/wiki/Codon_usage_bias)?
To be more specific, the last paragraph of the introduction is distracting to a general introduction of the genetic code, which is specifically about the translation of mRNA into a protein sequence. Trying to shoe-horn into some talk about how organisms are more than protein (I happen to agree with things being more than proteins) is obviously out of place and seems like proselytizing. Again, if you really want it to be there, mention it in the context of the main body, not 1/3 of the introduction.
99.174.80.45 ( talk) 04:45, 17 December 2013 (UTC)Thomas
I agree with both of those points DMacks. My main dispute was 1) overemphasis to a secondary point in the intro and 2) ignoring the rest of the extensive research on non-coding regions. I agree that the idea of DNA sequence=deterministic is misleading and worth mentioning, but as currently stated it seems to undercut the whole premise rather than the reality being more nuanced. A single sentence linking out to regulatory sequences and possibly codon usage seems like a good idea.
Though, I have to mention the overall misconception about the role most of these regulatory processes play. Most epigenetic modifications, be they transcription factors, DNA methylation, or histone modification, largely relate to changes in how MUCH of a given protein is produced, rather than WHAT protein is produced. There are some recent studies showing that histone/methylation can affect whether introns/exons are included/excluded thereby changing the protein sequence, but that does not (currently) seem to be a primary function. So again, the actual research is much less clear than is currently purported. As it stands, the last paragraph of the intro speaks more about the relevance of protein abundance evolution vs protein sequence evolution. I'm forgetting the more eloquent description of this debate, but it is a long-going discussion in the evolution literature. 99.174.80.45 ( talk) 05:15, 17 December 2013 (UTC) Thomas
Here is a rough draft of a replacement sentence: "While the genetic code determines the protein sequence for a given coding region, other genomic regions can influence when and where these proteins are produced" This sentence could be expanded to talk about further impact towards phenotype, but then in my opinion it starts to get bogged down in specifics that are tangential to the main article. 99.174.80.45 ( talk) 05:04, 18 December 2013 (UTC) Thomas
Genetic code graphic figure GeneticCode21-version-2.svg is confusing in this context. I may be confused myself (not a biologist), but this figure is from the catalog of a company that specializes in posttranslational modification, and makes heavy reference to various modifications, which as far as I can tell have no direct relation to the natural genetic code. My initial interpretation was "oh, so the redundant codons actually specify posttranslational modifications." I can understand the desire for a sexy graphic instead of boring tables, but IMO this page would be improved by simple deletion of that figure.
Robertmacl ( talk) 12:45, 13 May 2014 (UTC)
Descriptions of the genetic code have improved in the past ten years, but even a simple definition is still lacking. The old definition is no longer explicitly given - the genetic code is a transfer of linear information from DNA to protein - but it is still strongly implied in everything being said here. The net effect is that there is no working definition for molecular information, and molecular information is the purpose of genetic translations.
I think there is a simple, logical foundation for the genetic code. I think that the genetic code, if it is properly understood, is central to all processes in life. I think there is a phenomenal amount of molecular information stored in and translated by the genetic code, not just codons and amino acids.
I seem to be the only person on the planet that feels this way about it, and that's okay. But I'm a little bit surprised that after ten years these valid ideas are not even mentioned on a page like this. I think for the sake of debate, you should point them out if only to refute them, or tell people why they should reject them.
If anybody cares to understand this, they can start here: http://www.codefun.com/
I absolutely do not mean "genome." If you want to define the genetic code to be "essentially what a codon table shows" then I think that should be included as the first line in the page. Then I think you should explain exactly what a codon table is and exactly what it shows, because other than being defined that way, that is not what the genetic code is.
The basic problem is that "everybody knows" that the genetic code is something that translates "molecular information." Unfortunately, this represents nothing but a tautology in that molecular information is defined as that thing translated by the genetic code, and the genetic code is defined as essentially what a codon table shows.
My basic point is that a codon table is a very small part of what the genetic code actually is, and I am limiting this here specifically to the molecular information translated from nucleotide sequences to protein sequences. The genetic code at that level is still so many things that I think it is incumbent on any explanation like this to clearly define what it is explaining. Short of that, it does more to confuse people than actually clear things up.
This fact is covered by the article but rather much hidden away. It is not represented in the lead. There are two critical steps. The FIRST step is the coupling of the Transfer RNA the the Amino Acid. This requires a specific enzyme, the amino asyl transfer RNA synthetase, for each amino acid. One can say the the DNA code for the AATRS embodies half of the genetic code. But this is not pointed out by the text. It has to be reasoned from the text. -- Ettrig ( talk) 12:59, 25 November 2014 (UTC)
I would say that tRNA is the molecule that does the translation from codon to amino acid. It is like a dictionary or something. You are correct, it is only because of the tRNA that AAA means Lysine. The translation from AAA to lysine has nothing to do with ribosomes. It is the tRNA and only the tRNA that translates codon to amino acid. "All" that the ribosome does is to get the correct tRNA to match the mRNA and then join the amino acids into a polypeptide. Note that the tRNA also provides the energy for the ribosome to move the mRNA by 3 bases as the mRNA is read. This probably should be clarified -- Lehasa ( talk) 13:51, 22 February 2015 (UTC)
Trying to use this data, I found it confusing. It's clearly not percent, since it sums to more than 100. I looked at the column heading, but was not familiar with the percent-like symbol. I hovered over the symbol, and it said "per mille", so I though it was per thousand, but was not sure in what language (I don't know Latin).
I went to the original reference cited in the section, which said "per thousand", which made sense. So I looked up per mille and found that I was not alone is not being familiar with this:
The term occurs so rarely in English that major dictionaries do not agree on the spelling or pronunciation even within a single dialect of English[10] and some major dictionaries such as Macmillan[11] and Longman[12] do not even contain an entry.
So I changed it, so now when you hover over the symbol it says "per thousand", which will be more helpful to the reader, I think. Other opinions are welcome. LouScheffer ( talk) 12:29, 17 October 2016 (UTC)
I'm wondering whether the amount of codons per gene varies, and if so, whether there is a minimum and maximum amount of codons per gene. Also, if there's a minimum/maximum amount of codons, is this amount a multiplication of 3 (i.e. 1³, 2³, 3³, ...). That way, we could also know the amount of possible genetic code variations per gene. KVDP ( talk) 16:10, 22 June 2017 (UTC)
I was wondering whether there has been any research in Decipherment of the DNA. For instance, there are various types of mutations of the same gene in the human population, which express themselves as differences in real life between the humans. [1]
Logically, each of these mutations is a code for a different message that conveys details on how to do something in the human body. My guess is that each of the 64 codons is a base building block in that code (so comparable to a letter in our own alphabet). Each gene (or hence sequence of codons) will (I think) convey a message to what type of tissue needs to be build (i.e. fat, bone, flesh, ...) and how long this strand of tissue needs to be, and its shape, and to what tissue it should connect). The thickness of the tissue is probably not specified directly, but rather specified by a seperate gene, perhaps via the "codon for specifying length". The latter, I assume because a disease like Talk:Sclerosteosis also exists.
The reason why this is useful to know is because, at present, for treating genetic diseases, we can only just use the genetic code of humans without that disease to overwrite the faulty gene in a person with the disease. However, as Stephen Friend from The Resilience Project found out, there are many versions of "good genetic code", and not all version will work on that person. We don't know why this is, and so every gene therapy that would be undertaken becomes a puzzle, and each gene therapy may need to be repeated several times. If we understand what message is in the gene, we might avoid all this.
KVDP ( talk) 09:13, 27 June 2017 (UTC)
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As described in my comment on Talk:Proteinogenic_amino_acid#Hydropathy_of_tyrosine, the table in this article in classifying tyrosine as polar and not hydrophobic is inconsistent with other statements in Wikipedia. Tyrosine's own article clarifies that it is near the borderline but "usually classified as" hydrophobic. This article's table should either be changed to match the sourced statements elsewhere, or itself sourced. 2607:FEA8:12A0:44D:0:0:0:C319 ( talk) 02:08, 24 May 2020 (UTC)
May I suggest that this image would be useful for our readers: [ [7]]
Charles Juvon ( talk) 22:21, 27 August 2020 (UTC)
H2mex ( talk) 03:03, 27 June 2021 (UTC)
Take a look at the new 3-D image and consider what is said in the article: "The reason may be that charge reversal (from a positive to a negative charge or vice versa) can only occur upon mutations in the first position, but never upon changes in the second position of a codon." Consider positive {R,K} <-> negative {D,E}. This statement is misleading. Please check me. Charles Juvon ( talk) 22:41, 9 September 2020 (UTC)
Both references to the 1.5 x 10^84 number are dead. One possible fix is to insert the actual equation: N[Abs[Sum[(-1)^j*Binomial[21,j]*j^64,{j,21}]],10] = 1.510109516 x 10^84 That's in Mathematica syntax. I'm no good in wiki markup for algebraic equations. N[_,10] is simply formatting. Charles Juvon ( talk) 19:11, 15 September 2020 (UTC)
Given the current last sentence of the Article and references 99 and 100, we might want to use this material from https://arxiv.org/ftp/arxiv/papers/1303/1303.6739.pdf : "Recent biotech achievements make it possible to employ genomic DNA as data storage more durable than any media currently used (Bancroft et al., 2001; Yachie et al., 2008; Ailenberg & Rotstein, 2009). Perhaps the most direct application for that was proposed even before the advent of synthetic biology. Considering alternative informational channels for SETI, Marx (1979) noted that genomes of living cells may provide a good instance for that. He also noted that even more durable is the genetic code. Exposed to strong negative selection, the code stays unchanged for billions of years, except for rare cases of minor variations (Knight et al., 2001) and context-dependent expansions (Yuan et al., 2010)." ---- Charles Juvon ( talk) 20:18, 5 November 2020 (UTC)
Unless someone has a better idea, we need to go back to the March 15, 2021 version. The top figure is an embarrassment. That editor is now in red letters. Charles Juvon ( talk) 01:45, 17 June 2021 (UTC)
"Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact, because the conventional wisdom avoids the question, there is little agreement as to whether the symmetrical nature actually even exists. A better understanding of symmetry and an appreciation for its essential role in the genetic code formation can improve our understanding of nature’s coding processes. Thus, it is worth formulating a new integrated symmetrical table for genetic codes, which is presented in this paper. It could be very useful to understand the Nobel laureate Crick’s wobble hypothesis — how one transfer ribonucleic acid can recognize two or more synonymous codons, which is an unsolved fundamental question in biological science."
H2mex ( talk) 19:25, 3 July 2021 (UTC)" Charles Juvon ( talk) 13:44, 12 July 2021 (UTC)
User 103.172.73.22 changed the image description at the top to say a codon is two nucleotides rather than three. Not clear why they would do that but it is clearly incorrect per other content already on the page. ArbitraryConstant ( talk) 21:29, 15 February 2023 (UTC)
Please consider this CC4.0 and use as you wish.
https://www.youtube.com/watch?v=eHZxMAZTFcY Doug youvan ( talk) 17:13, 9 September 2023 (UTC)
If another editor feels this would work in the article, please use it. Graph Construction: In our graph, vertices represent the 20 amino acids and the "Stop" signal. An edge connects two vertices if the amino acids they represent can be interchanged through a single point mutation in their corresponding codons. This graph is not just a visualization but an analytical tool, spotlighting the possible amino acid replacements due to minor genetic variations. Highlighting Mechanism: Using the computational capabilities of Mathematica, and with the expertise provided by Centaur Intelligence, each amino acid (and the Stop signal) is successively emphasized. When highlighted, all directly reachable amino acids through a single point mutation are illuminated, thus displaying the mutation landscape for each amino acid. Results: The resultant graph unravels the dense web of interconnections among amino acids based on single point mutations. As we animate through each amino acid, patterns emerge, revealing which amino acids can easily mutate into others and which remain more isolated.
https://www.youtube.com/watch?v=WsGw5w6tiyE
Doug youvan ( talk) 01:58, 29 September 2023 (UTC)
It's more accurate, but it would need some work by a graphic artist for scaling. Serine (S) is properly represented. CC 4.0. https://www.researchgate.net/publication/374911250_Amino_Acids_Are_Segregated_in_Hydropathy_-_Molar_Volume_Space_by_the_Second_Position_of_the_Codon Doug youvan ( talk) 01:27, 23 October 2023 (UTC)
https://www.researchgate.net/publication/374973672_Codon_Cluster_Analysis_With_Hydropathy_Written_by_GPT-4_in_Python Doug youvan ( talk) 19:38, 25 October 2023 (UTC)
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