
#REDIRECT Genetic code
[[Image:RNA-codon.png|thumb|RNA codons.]] The genetic code is a set of rules, which mappings DNA sequences to proteins in the living cell (biology), and is employed in the process of protein biosynthesis. Nearly all living things use the same genetic code, called the standard genetic code, although a few organisms use minor variations of the standard code. ==Genome expression== The genetic information carried by an organism - its genome - is inscribed in one or more DNA molecules. Each functional portion of a DNA molecule is referred to as a gene. Each gene is transcription (genetics) into a short template molecule of the related polymer RNA, which is better suited for protein synthesis. This in turn is translation (genetics), by mediation of a machinery consisting of ribosomes and a set of transfer RNAs and associated enzymes, into an amino acid chain (peptide), which will then be folded into a protein. The gene sequence inscribed in DNA, and in RNA, is composed of tri-nucleotide units called codons, each coding for a single amino acid. Each nucleotide sub-unit consists of a phosphate, deoxyribose sugar and one of the 4 nitrogenous nucleotide bases grouped into 2 categories, purine and pyrimidine. The purine bases adenine (A) and guanine (G) are larger and consist of two aromatic rings . The pyrimidine bases cytosine (C) and thymine (T) are smaller and only consist of one aromatic ring. In RNA however, thymine (T) is substituted by uracil (U) and the deoxyribose is substituted by ribose. Overall, there are 43 = 64 different codon combinations. For example, the RNA sequence UUUAAACCC contains the codons UUU, AAA and CCC, each of which specifies one amino acid. So, this RNA sequence represents a protein sequence, three amino acids long. (DNA is also a sequence of nucleotide bases, but there thymine takes the place of uracil.) The standard genetic code is shown in the following tables. #Table 1: Codon Table shows what amino acid each of the 64 codons specifies. #Table 2: Reverse Codon Table shows what codons specify each of the 20 standard amino acids involved in translation. These are called forward and reverse codon tables, respectively. For example, the codon AAU represents the amino acid asparagine (Asp), and cysteine (Cys) is represented by UGU and by UGC. ==Table 1: RNA Codon table==
1The codon AUG both codes for methionine and serves as an initiation site: the first AUG in an mRNA's coding region is where translation into protein begins.
2This is a start codon for prokaryotes only. ==Table 2: Reverse codon table==
Marshall W. Nirenberg and his lab at the National Institutes of Health performed the experiments which first elucidated the correspondence between the codons and the amino acids for which they code. Har Gobind Khorana expanded on Nirenberg's work and found the codes for the amino acids that Nirenberg's methods could not. Khorana and Nirenberg won a share of the 1968 Nobel Prize in Physiology or Medicine for this work.
==Technical details==
=== Stop Codons ===
In classical genetics, the stop codons were given names: UAG was ''amber'', UGA was ''opal'', and UAA was ''ochre''. These names were originally the names of the specific genes in which mutation of each of these stop codons was first detected. Translation starts with a chain initiation codon (start codon). But unlike stop codons, these are not sufficient to begin the process; nearby initiation sequences are also required to induce transcription into mRNA and binding by ribosomes. The most notable start codon is AUG, which also codes for methionine. CUG and UUG, and in prokaryotes GUG and AUU, also work.
=== Degeneracy of the genetic code ===
Many codons are degenerate or redundant, meaning that two or more codons may code for the same amino acid. Degenerate codons typically differ in their third positions; e.g. both GAA and GAG code for the amino acid glutamic acid. A codon is said to be four-fold degenerate if any nucleotide at its third position specifies the same amino acid; it is said to be two-fold degenerate if only two of four possible nucleotides at its third position specify the same amino acid. In two-fold degenerate codons, the equivalent third position nucleotides are always either two purines (A/G) or two pyrimidines (C/T). The degeneracy of the genetic code is what accounts for the existence of silent mutations.
Degeneracy is required in order to produce enough different codons to code for 20 amino acids and a stop and start codon (at least 22 codons required). Because there are four different bases, triplet codons are the minimum number required to produce at least 22 different codes. For example if there were two bases per codon then only 16 amino acids could be coded for (4²=16). Because at least 22 codes are required, then 4³ gives 64, which is the minimum number of codons possible.
These properties of the genetic code make it more fault-tolerant for point mutations. For example, four-fold degenerate codons can tolerate any point mutation at the third position; two-fold degenerate codons can tolerate one out of the three possible point mutations at the third position. Since transition mutations (purine to purine or pyrimidine to pyrimidine mutations) are more likely than transversion (purine to pyrimidine or vice-versa) mutations, the equivalence of purines or that of pyrimidines at two-fold degenerate sites adds a further fault-tolerance.
A practical consequence of redundancy is that some errors in the genetic code either only causes a silent mutation or an error that would not affect the amino acid's hydrophilic/hydrophobic property, eg. a codon of XUX (where X = any nucleotide) tends to code for hydrophobic amino acids. Even so, it is a single point mutation which causes a modified haemoglobin molecule in sickle cell anaemia. The hydrophilic glutamate (Glu) is substituted by the hydrophobic valine (Val) which reduces the solubility of ß-globin. This causes haemoglobin to form linear polymers linked by the hydrophobic interaction between the valine groups causing sickle cell deformation of erythrocytes. Sickle cell anaemia is generally not caused by a ''de novo'' mutation. Rather it is selected for in malaria regions (in a similar way to thalassemia) as heterozygote people have some resistance to the malarial ''Plasmodium'' parasite (heterozygote advantage).
These variable codes for amino acids are possible because of modified bases in the first base of the anticodon, and the basepair formed is called a wobble base pair. The modified bases include inosine and the U-G basepair.
Only two amino acids are specified by a single codon; one of these is the amino-acid methionine, specified by the codon AUG, which also specifies the start of transcription; the other is tryptophan, specified by the codon UGG.
=== Phase or reading frame of a sequence ===
Note that a "codon" is entirely defined by your starting position. For example, the string GGGAAACCC, if read from the first position, contains the codons GGG, AAA and CCC. If read from the second position, it contains the codons GGA and AAC (partial codons being ignored). If read starting from the third position, GAA and ACC. Every DNA sequence can thus be read in three reading frames, each of which will produce a radically different amino acid sequence (in our example, Gly-Lys-Pro, Gly-Asp, and Glu-Thr, respectively). The actual frame a protein sequence is translated in is defined by a start codon, usually the first occurrence of AUG in the RNA sequence. Mutations that disrupt the reading frame (i.e. insertions or deletions of one or two nucleotide bases) severely impair the function of a protein and are thus exceedingly rare in ''in vivo'' protein-coding sequences, since they often lead to death before an organism is viable.
==Origin of the genetic code==
Numerous variations of the standard genetic code are found in mitochondrion, which are energy-producing organelles. Ciliate protozoa also have some variation in the genetic code: UAG and often UAA code for Glutamine (a variant also found in some green algae), or UGA codes for Cysteine. Another variant is found in some species of the yeast candida, where CUG codes for Serine. In some species of bacterium and archaea, a few non-standard amino acids are substituted for standard stop codons; UGA can code for selenocysteine and UAG can code for pyrrolysine. There may be other non-standard interpretations that are not known.
Despite these variations, 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.
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 other of the near-infinite set of 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.
Recent aptamer experiments have shown that amino acids have indeed a selective chemical affinity for the base triplets that code for them. This suggests that the current, complex transcription mechanism involving tRNA and associated enzymes is a later development, and that originally, protein sequences were directly templated on base sequences. Also, evidence has been found that originally the number of different amino acids used may have been considerably smaller than today.
== References ==
There are several books available online that go into great detail on this topic. They are available through the [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books NCBI Bookshelf], maintained by the National_Institutes_of_Health. In particular the following books would be useful to consult:
* Griffiths, Anthony J.F.; Miller, Jeffrey H.; Suzuki, David T.; Lewontin, Richard C.; Gelbart, William M. (1999). [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=iga.TOC ''Introduction to Genetic Analysis'' (7th ed.)]. New York: W. H. Freeman & Co. ISBN 0-7167-3771-X
* Alberts, Bruce; Johnson, Alexander; Lewis, Julian; Raff, Martin; Roberts, Keith; Walter, Peter. (2002). [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mboc4.TOC&depth=2 ''Molecular Biology of the Cell'' (4th ed.)]. New York: Garland Publishing. ISBN 0815332181
* Lodish, Harvey; Berk, Arnold; Zipursky, S. Lawrence; Matsudaira, Paul; Baltimore, David; Darnell, James E. (1999). [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mcb.TOC ''Molecular Cell Biology'' (4th ed.)]. New York: W. H. Freeman & Co. ISBN 0-7167-3706-X
==References==
Knight, R.D. and Landweber, L.F. (1998). [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9751648 Rhyme or reason: RNA-arginine interactions and the genetic code.] ''Chemistry & Biology'' 5(9), R215-R220. [http://bayes.colorado.edu/Papers/chmbio98.pdf PDF version of manuscript]
Brooks, Dawn J.; Fresco, Jacques R.; Lesk, Arthur M.; and Singh, Mona. (2002). [http://mbe.oupjournals.org/cgi/content/full/19/10/1645 Evolution of Amino Acid Frequencies in Proteins Over Deep Time: Inferred Order of Introduction of Amino Acids into the Genetic Code]. ''Molecular Biology and Evolution'' 19, 1645-1655.
==See also==
*Anticodon
*Protein biosynthesis
*Operon
*lac operon
==External links==
*[http://www.geneseo.edu/~eshamb/php/dna.php Online DNA → Amino Acid Converter]
Molecular genetics
Gene expression
Someone should write about all exception from basic scheme. :Taw The article was kind of hard to read, so I'm doing some significant modifications. Let me know if these are ok. I'd really like to take the start codons out of the table, since they have considerably more variability than the rest of the code (differ between eukaryotes and prokaryotes), and aren't really sufficient for a start anyways. Also, why do we always capitalize STOP and START? ---- So DNA is not in "genetic code?" Also, DNA and genes are not organized into codons? This needs clarification; also, ought not the article to define intron and exon? User:Slrubenstein :Not sure what you mean by DNA not being in "genetic code", DNA is mentioned in the second paragraph and is the medium in which genetic encodings are written. Also, yes, DNA and genes are organized into codons; a codon is simply a group of three nucleotides, like the way a byte is a group of 8 ones and zeroes. As for introns and exons, they might be worth a mention but I don't think they're really directly relevant to an article about the genetic code. introns and exons are dealt with in "preprocessing", before RNA gets to the protein-translating machinery. User:Bryan Derksen The first sentence reads: :The genetic code is the code used to translation a sequence of RNA nucleotides into protein. Now, I assume that this is how biologists talk -- trust me, a non-biologist would eagerly look to the next sentence to find out what "translate" means in this context (or might just give up; remember, this is not a textbook, readers do not have professors or TA's to explain things, it has to be all here). So, not being sure what the technical meaning of translation is here, all I see is that there is no mention of DNA in the first sentence, only mention of RNA. Even knowing a fair amount of biology, this sentence leads me to think that the code is used in the RNA itself. There is nothing in the first sentence to suggest that the RNA is forming complementary bases from a strand of DNA which uses the same code. Look, I am not trying to be argumentative. I think the first sentence needs to be clear to leaypeople, and provide a good general definition. I really think a layperson would be pretty confused. Also, concerning codons, according to the first part of the article, codons are parts of RNA -- the implication is that they are not parts of DNA. Don't you see what I mean? The article may provide an accurate description of the process of transcription, which may be the main function of "genetic code," but it is not introducing the lay-person to what words like "genetic code" and "codon" mean in a clear way. User:Slrubenstein ---- :Translation starts with a chain initiation or START codon, but unlike STOP codons these are not sufficient by themselves to begin the process; nearby initiation sequences are also required to induce transcription into mRNA and binding by ribosomes What are "nearby initiation sequences"? Are we talking about cell processes that get DNA transcription/translating going, or are we talking about special sequences of codons? If the latter, why isn't it more accurate to drop talk about "start codons" and speak only of "start sequences" of codons? --User:Ryguasu 01:45 Jan 31, 2003 (UTC) ----- I edited the bit about redundancy a bit and removed the insinuation that met only has one codon because it is the start site; since the start site is recognized by a separate tRNA than the met-tRNA for normal elongation, it is not necessary that these two properties be coupled. That is, met could have redundant codons, and only one of them need specify the start site. User:Graft 18:30, 13 Jul 2004 (UTC) ==non-AUG START codons== ''(first moving material from above down here to a heading)'' What's with all these alternate starts? I can find one reference on pubmed that talks about GUG starts, in mtDNA. Nothing for CUG. Why are they given simply as 'start', with no annotation or caveats? For all practical purposes there's really only one start codon, the rest are basically just novelties, and the text ought to emphasize this. Unless someone has a reference saying otherwise? User:Graft 16:14, 9 Apr 2004 (UTC) :Wup. Never mind, found lots about alternate initiation. But I still think the text should emphasize that AUG is the norm. User:Graft 16:15, 9 Apr 2004 (UTC) ::I used to work on a family of mammalian transcription factors that are thought to initiate at a non-AUG codon (AUU=>I). There is evidence still lacking for a proof-positive concrete this-is-fact conclusion on that family, though, in particular amino-terminal peptide sequencing, exclusion of RNA-editing as a factor, and demonstration of either cross-recognition by a MET-encoding charged tRNA or the existence of a properly charged AUU anti-codon tRNA. I believe the evidence is concrete for plants, organelles, and microorganisms for known exceptions to their respective stereotypical START codons. For vertebrates (though I've been out of related research for going on 6 years) the hard-core biochemistry just isn't there to convince one that non-AUG initiation occurs ''in vivo''. I would suggest that the non-AUG options for vertebrates (and man) be included in th Translation (genetic) or a translation initiation article and to refer to that article. User:Ceyockey 03:07, 2005 Feb 11 (UTC) ==What are start and stop codons?== There is no explanation in the text. User:Gracefool |User talk:gracefool 01:56, 27 Sep 2004 (UTC) :The defintion is in the article, but rather implicit: ''Translation starts with a chain initiation codon (start codon). But unlike stop codons, these are not sufficient to begin the process; nearby initiation sequences are also required to induce transcription into mRNA and binding by ribosomes. The most notable start codon is AUG, which also codes for methionine. CUG and UUG, and in prokaryotes GUG and AUU, also work.'' :User:Pjacobi 11:08, 27 Sep 2004 (UTC) ==What does this mean?== I'm not sure exactly what this means ([http://en.wikipedia.org/w/wiki.phtml?title=Genetic_code&diff=0&oldid=8670004 diff link]): : Note that if the number of amino acids coded for was eight or less, also the number of different bases needed would -- assuming a three base codon -- be only two: "generic purine" and "generic pyrimidine". Can anyone clarify? If so, I'll add it back into the article. --User:Bdesham 14:03, 21 Dec 2004 (UTC) : This means simply that we would have eight different codons: RRR RRY RYR RYY YRR YRY YYR and YYY. Enough to code eight different amino acids (R = purine, Y = pyrimidine). It would be a binary code, not base-4 as we have now. Note that purines are two-ring molecules and pyrimidines one-ring, so this is a strong geometric expression. Differences within these two groups are more subtle and would have been added to the code later in evolution. You can still see the "generic purine/pyrimidine" patterns in the code table... : If you now understand and agree that it is of interest, please explain it better on the page :-) - mv Tue Dec 21 18:01:15 EET 2004 == Yo! == Okay, there's some serious problems with what we're doing here. We have DNA, we have translation (genetics), we have codon, and we have genetic code. All of these are redundant to some extent, but far more than they need to be. This article is easily the most nested of the set; in order to grasp it, one must understand the information-storing nature of DNA, the basics of protein synthesis, and what a codon is. In its current form, the article attempts to recapitulate all this information. This seems the wrong attitude to take, especially as some of these are unwieldy topics that don't lend themselves to quick exposition. So, I propose that we simply take a hardass line and say up front, "Look, if you want to understand the genetic code, you MUST know what DNA is first. go read that article and when you grasp the information storage mechanism whereby DNA operates, come back here." (etc.) Such steps will prevent the article from filling up with useless and abbreviated twaddle, and will allow it to present the code itself succintly and discuss it in greater detail, as it deserves. User:Graft 04:01, 23 Dec 2004 (UTC) :Err, it seems codon is now a redirect here. Mentally amend the above paragraph as necessary. User:Graft 04:02, 23 Dec 2004 (UTC) : If you think you can make this better, then by all means. I tried myself and IMHO made it better, but not good. Still, remember that all articles have this problem: they all assume background knowledge that the reader may or may not have. Only in this case the knowledge is more technical and less likely to be found in any particular reader. :Putting a warning at the start to this effect may be a good idea. Still, even after that the article should remain self-contained in a meaningful way. So that somebody that is familiar with these backgrounds can read it and say 'ah yes, that's how it was'. - mv Fri Dec 24 02:01:41 GMT+2 2004 :User:Graft: yes, this looks clearly better! - mv Sat Dec 25 18:49:04 EET 2004 ---- Good job on this page guys. I just thought it would be a good idea, as suggested below, to have a list of exceptions. Also- it may be worth someones time to being to put in exceptions do different species, either on this page and like to the species or on the species page and like from here to there. Keep up the good work! --User:DavidMendoza == Dioxyribos == == Codon bias == A section should be added that talks about codon bias across organisms as an evolutionary change as well as codon bias between genes in one organsism as a subtle way of altering the rate of translation ([http://www.uky.edu/Classes/BIO/520/BIO520WWW/StudentPresent/grieser/ a short presentation that popped up as the #1 Google hit against "codon bias"]). I'll put it on my own list of things to do, but one of the others of you would likely get to it before me. User:Ceyockey 03:17, 2005 Feb 11 (UTC) == the real picture == After a quick perusal, I'd say this explanation is pretty good. What irritates me in media explanations of the genetic code is that they imply that the code is read exactly as such! (i.e. ATTCGG etc.) If I were 100% layperson hearing that I would be confused. They don't make clear that it is a sequence of amino acids which we then convert into letters. I've even heard reporters say something like "when they discovered the sequence of letters that make up the human genome"!! (as if there are small A's G's and T's visible somewhere! --User:62.254.0.38 17:33, 2 Apr 2005 (UTC) ==First sentence is wrong== ''The genetic code is a set of rules, which maps DNA sequences to proteins in the living cell, and is employed in the process of protein synthesis.'' This is an incorrect assertion. The code does not, in amy way shape or form, map anything (unless you have a strange definition of the word map). Surely it is more accurate to say that ''The genetic code is a set of instructions'' or even ''The genetic code is a set of rules''. One can then go on to explain that the instructions are used to make proteins, which provide structure and function. So the code is the set of instructions, written in triplets which tell the cell how to build proteins. There are many mistakes in this article. Note a gene is not the same as a cistron. Not everyone would agree that the definition of a gene is that it codes for one product (be it RNA or protein). Many would argue that a gene is a heritable unit. Try to use words which have a specific meaning, like cistron. I also think that it should be made apparent that there are other instructions which are not part of the code, no detail need be given, but it could be explained that they are similar to switches, turning genes on and off. It is difficult to explain concepts such as this to non biologists, but it is a technical article. I understand little of many othe technical pages, such as computer pages. One cannot be expected to go into the complexities of chemistry and protein structure/function in the same article, this is why articles are linked. For example if one wants to know what translation means to a biologist, then there should be a separate article about it. Alternatively this article could be the basis for one about protein synthesis and a link from genetic code to the article could be made. After all the genetic code is simply an explanation of how protein synthesis works ''in vivo'' This article seems to cover much irrelevant ground.--User:Wobble 11:07, 12 May 2005 (UTC) :Come on... no one uses the word "cistron" any more, except in idiosyncratic technical usages. Also, the use of the word "map" is the mathematical one. Borrowing a definition, a map is "The correspondence of elements in one set to elements in the same set or another set.", and "to map" is "To establish a mapping of (an element or a set)." With that definition the first sentence is perfectly fine. :Also, I'm not sure what you mean by "switches". Are you talking about gene regulation? If so, that's definitely out of the scope of this article. User:Graft 16:16, 12 May 2005 (UTC) So are you disputing that the code is a set of instructions? And is it not a more accessible way of defining it. This is not a mathematical article, so why use mathematical terminologies? I never said that gene regulation should be part of the article, just that it should be mentionned that the code is not the only purpose of DNA. I dispute the word gene because it is ambiguous. It does have different meanings in different disciplines. The word gene is as over used and as often misused as the word evolution. Being accurate leads to less confusion, and there seems to be plenty of confusion here. If no one uses the word cistron any more then more fool them, as it's a perfectly good word with an unambiguous meaning. Also the word map is used extensively already in molecular biology in terms of chromosome mapping, which will lead to even greater confusion.--User:Wobble 17:55, 12 May 2005 (UTC) :I don't dispute that the code is a set of instructions. But "mapping" precisely captures what the genetic code is: a relationship between two separate encodings or alphabets. Certainly, a mapping is also a set of instructions - "set of instructions" is a rather broad term. :I'm not particularly unhappy about the use of the word "gene" - most people understand what it means in specific contexts. "Cistron" is unnecessary jargon. User:Graft 18:26, 12 May 2005 (UTC) Well I disagree, I think the term map causes much confusion, and I disagree that it ''precisely captures what the genetic code is'', quite the reverse. But I don't want to get into a dispute about it, if people are generally happy then fine. Again with the word 'gene', if the consensus is that it's OK then fair enough, though people do use it to mean other things like 'allele' and 'locus' and even 'phenotype' (for example eye colour), it is over used and I was merely attempting to be more accurate. It is still true that much of what is in this article should really be in an article about protein synthesis. Remember that the article is about the genetic code, and not about transcription or translation, these should have their own articles. Also an article about protein synthesis (is ther one?) could include things like differences between prokaryote and eukaryote synthesis, how transcription and translation are linked in prokaryotes, but occur in seperately in eukaryotes. This is where there should be some mention of the differing roles of DNA and RNA in protein synthesis. After all the code is just one small part of protein synthesis, it merely allows us to predict a protein's primary structure from a citronic or mRNA sequence. What do you think?--User:Wobble 05:26, 13 May 2005 (UTC) ==Reasons for redundancy== ''The codons attempt to ensure that minor errors in the genetic code either only causes a silent mutation or an error that would not affect the amino acid's hydrophilic/hydrophobic property'' How can codons ''attempt'' to do anything, are they sentient? I will change this to ''A practical consequence of redundancy is that minor...etc'' as it seems more accurate to me. The code is redundant because it has to be, two bases are two few to code for all amino acids (4²=16), so it has to be three at a minimum (4³=64). One consequence of this is the occurence of silent mutations. --User:Wobble 06:34, 27 May 2005 (UTC) ''four-fold degenerate codons can tolerate any mutation at the third position; two-fold degenerate codons can tolerate one out of the three possible mutations at the third position'' This sentence is also clearly wrong. A four fold degenerate codon could not tolerate a deletion in the third position I have changed ''any mutation'' to ''any point mutation''--User:Wobble 06:49, 27 May 2005 (UTC)
See other meanings of words starting from letter:
Words begining with Genetic_code:
Genetic_Code
Genetic_code
Genetic_code
Genetic_code_(ATGC)
Genetic Code
#REDIRECT Genetic code
Genetic code
[[Image:RNA-codon.png|thumb|RNA codons.]] The genetic code is a set of rules, which mappings DNA sequences to proteins in the living cell (biology), and is employed in the process of protein biosynthesis. Nearly all living things use the same genetic code, called the standard genetic code, although a few organisms use minor variations of the standard code. ==Genome expression== The genetic information carried by an organism - its genome - is inscribed in one or more DNA molecules. Each functional portion of a DNA molecule is referred to as a gene. Each gene is transcription (genetics) into a short template molecule of the related polymer RNA, which is better suited for protein synthesis. This in turn is translation (genetics), by mediation of a machinery consisting of ribosomes and a set of transfer RNAs and associated enzymes, into an amino acid chain (peptide), which will then be folded into a protein. The gene sequence inscribed in DNA, and in RNA, is composed of tri-nucleotide units called codons, each coding for a single amino acid. Each nucleotide sub-unit consists of a phosphate, deoxyribose sugar and one of the 4 nitrogenous nucleotide bases grouped into 2 categories, purine and pyrimidine. The purine bases adenine (A) and guanine (G) are larger and consist of two aromatic rings . The pyrimidine bases cytosine (C) and thymine (T) are smaller and only consist of one aromatic ring. In RNA however, thymine (T) is substituted by uracil (U) and the deoxyribose is substituted by ribose. Overall, there are 43 = 64 different codon combinations. For example, the RNA sequence UUUAAACCC contains the codons UUU, AAA and CCC, each of which specifies one amino acid. So, this RNA sequence represents a protein sequence, three amino acids long. (DNA is also a sequence of nucleotide bases, but there thymine takes the place of uracil.) The standard genetic code is shown in the following tables. #Table 1: Codon Table shows what amino acid each of the 64 codons specifies. #Table 2: Reverse Codon Table shows what codons specify each of the 20 standard amino acids involved in translation. These are called forward and reverse codon tables, respectively. For example, the codon AAU represents the amino acid asparagine (Asp), and cysteine (Cys) is represented by UGU and by UGC. ==Table 1: RNA Codon table==
| 2nd base | |||||
|---|---|---|---|---|---|
| U | C | A | G | ||
| 1st base |
U |
UUU (Phe/F)Phenylalanine UUC (Phe/F)Phenylalanine UUA (Leu/L)Leucine UUG (Leu/L)Leucine, ''Start'' |
UCU (Ser/S)Serine UCC (Ser/S)Serine UCA (Ser/S)Serine UCG (Ser/S)Serine |
UAU (Tyr/Y)Tyrosine UAC (Tyr/Y)Tyrosine UAA Ochre (''Stop'') UAG Amber (''Stop'') |
UGU (Cys/C)Cysteine UGC (Cys/C)Cysteine UGA Opal (''Stop'') UGG (Trp/W)Tryptophan |
| C |
CUU (Leu/L)Leucine CUC (Leu/L)Leucine CUA (Leu/L)Leucine CUG (Leu/L)Leucine, ''Start'' |
CCU (Pro/P)Proline CCC (Pro/P)Proline CCA (Pro/P)Proline CCG (Pro/P)Proline |
CAU (His/H)Histidine CAC (His/H)Histidine CAA (Gln/Q)Glutamine CAG (Gln/Q)Glutamine |
CGU (Arg/R)Arginine CGC (Arg/R)Arginine CGA (Arg/R)Arginine CGG (Arg/R)Arginine |
|
| A |
AUU (Ile/I)Isoleucine, ''Start''2 AUC (Ile/I)Isoleucine AUA (Ile/I)Isoleucine AUG (Met/M)Methionine, ''Start''1 |
ACU (Thr/T)Threonine ACC (Thr/T)Threonine ACA (Thr/T)Threonine ACG (Thr/T)Threonine |
AAU (Asn/N)Asparagine AAC (Asn/N)Asparagine AAA (Lys/K)Lysine AAG (Lys/K)Lysine |
AGU (Ser/S)Serine AGC (Ser/S)Serine AGA (Arg/R)Arginine AGG (Arg/R)Arginine |
|
| G |
GUU (Val/V)Valine GUC (Val/V)Valine GUA (Val/V)Valine GUG (Val/V)Valine, ''Start''2 |
GCU (Ala/A)Alanine GCC (Ala/A)Alanine GCA (Ala/A)Alanine GCG (Ala/A)Alanine |
GAU (Asp/D)Aspartic acid GAC (Asp/D)Aspartic acid GAA (Glu/E)Glutamic acid GAG (Glu/E)Glutamic acid |
GGU (Gly/G)Glycine GGC (Gly/G)Glycine GGA (Gly/G)Glycine GGG (Gly/G)Glycine |
|
2This is a start codon for prokaryotes only. ==Table 2: Reverse codon table==
| Ala | A | GCU, GCC, GCA, GCG | Leu | L | UUA, UUG, CUU, CUC, CUA, CUG |
| Arg | R | CGU, CGC, CGA, CGG, AGA, AGG | Lys | K | AAA, AAG |
| Asn | N | AAU, AAC | Met | M | AUG |
| Asp | D | GAU, GAC | Phe | F | UUU, UUC |
| Cys | C | UGU, UGC | Pro | P | CCU, CCC, CCA, CCG |
| Gln | Q | CAA, CAG | Ser | S | UCU, UCC, UCA, UCG, AGU,AGC |
| Glu | E | GAA, GAG | Thr | T | ACU, ACC, ACA, ACG |
| Gly | G | GGU, GGC, GGA, GGG | Trp | W | UGG |
| His | H | CAU, CAC | Tyr | Y | UAU, UAC |
| Ile | I | AUU, AUC, AUA | Val | V | GUU, GUC, GUA, GUG |
| ''Start'' | AUG, GUG | ''Stop'' | UAG, UGA, UAA |
Genetic code
Someone should write about all exception from basic scheme. :Taw The article was kind of hard to read, so I'm doing some significant modifications. Let me know if these are ok. I'd really like to take the start codons out of the table, since they have considerably more variability than the rest of the code (differ between eukaryotes and prokaryotes), and aren't really sufficient for a start anyways. Also, why do we always capitalize STOP and START? ---- So DNA is not in "genetic code?" Also, DNA and genes are not organized into codons? This needs clarification; also, ought not the article to define intron and exon? User:Slrubenstein :Not sure what you mean by DNA not being in "genetic code", DNA is mentioned in the second paragraph and is the medium in which genetic encodings are written. Also, yes, DNA and genes are organized into codons; a codon is simply a group of three nucleotides, like the way a byte is a group of 8 ones and zeroes. As for introns and exons, they might be worth a mention but I don't think they're really directly relevant to an article about the genetic code. introns and exons are dealt with in "preprocessing", before RNA gets to the protein-translating machinery. User:Bryan Derksen The first sentence reads: :The genetic code is the code used to translation a sequence of RNA nucleotides into protein. Now, I assume that this is how biologists talk -- trust me, a non-biologist would eagerly look to the next sentence to find out what "translate" means in this context (or might just give up; remember, this is not a textbook, readers do not have professors or TA's to explain things, it has to be all here). So, not being sure what the technical meaning of translation is here, all I see is that there is no mention of DNA in the first sentence, only mention of RNA. Even knowing a fair amount of biology, this sentence leads me to think that the code is used in the RNA itself. There is nothing in the first sentence to suggest that the RNA is forming complementary bases from a strand of DNA which uses the same code. Look, I am not trying to be argumentative. I think the first sentence needs to be clear to leaypeople, and provide a good general definition. I really think a layperson would be pretty confused. Also, concerning codons, according to the first part of the article, codons are parts of RNA -- the implication is that they are not parts of DNA. Don't you see what I mean? The article may provide an accurate description of the process of transcription, which may be the main function of "genetic code," but it is not introducing the lay-person to what words like "genetic code" and "codon" mean in a clear way. User:Slrubenstein ---- :Translation starts with a chain initiation or START codon, but unlike STOP codons these are not sufficient by themselves to begin the process; nearby initiation sequences are also required to induce transcription into mRNA and binding by ribosomes What are "nearby initiation sequences"? Are we talking about cell processes that get DNA transcription/translating going, or are we talking about special sequences of codons? If the latter, why isn't it more accurate to drop talk about "start codons" and speak only of "start sequences" of codons? --User:Ryguasu 01:45 Jan 31, 2003 (UTC) ----- I edited the bit about redundancy a bit and removed the insinuation that met only has one codon because it is the start site; since the start site is recognized by a separate tRNA than the met-tRNA for normal elongation, it is not necessary that these two properties be coupled. That is, met could have redundant codons, and only one of them need specify the start site. User:Graft 18:30, 13 Jul 2004 (UTC) ==non-AUG START codons== ''(first moving material from above down here to a heading)'' What's with all these alternate starts? I can find one reference on pubmed that talks about GUG starts, in mtDNA. Nothing for CUG. Why are they given simply as 'start', with no annotation or caveats? For all practical purposes there's really only one start codon, the rest are basically just novelties, and the text ought to emphasize this. Unless someone has a reference saying otherwise? User:Graft 16:14, 9 Apr 2004 (UTC) :Wup. Never mind, found lots about alternate initiation. But I still think the text should emphasize that AUG is the norm. User:Graft 16:15, 9 Apr 2004 (UTC) ::I used to work on a family of mammalian transcription factors that are thought to initiate at a non-AUG codon (AUU=>I). There is evidence still lacking for a proof-positive concrete this-is-fact conclusion on that family, though, in particular amino-terminal peptide sequencing, exclusion of RNA-editing as a factor, and demonstration of either cross-recognition by a MET-encoding charged tRNA or the existence of a properly charged AUU anti-codon tRNA. I believe the evidence is concrete for plants, organelles, and microorganisms for known exceptions to their respective stereotypical START codons. For vertebrates (though I've been out of related research for going on 6 years) the hard-core biochemistry just isn't there to convince one that non-AUG initiation occurs ''in vivo''. I would suggest that the non-AUG options for vertebrates (and man) be included in th Translation (genetic) or a translation initiation article and to refer to that article. User:Ceyockey 03:07, 2005 Feb 11 (UTC) ==What are start and stop codons?== There is no explanation in the text. User:Gracefool |User talk:gracefool 01:56, 27 Sep 2004 (UTC) :The defintion is in the article, but rather implicit: ''Translation starts with a chain initiation codon (start codon). But unlike stop codons, these are not sufficient to begin the process; nearby initiation sequences are also required to induce transcription into mRNA and binding by ribosomes. The most notable start codon is AUG, which also codes for methionine. CUG and UUG, and in prokaryotes GUG and AUU, also work.'' :User:Pjacobi 11:08, 27 Sep 2004 (UTC) ==What does this mean?== I'm not sure exactly what this means ([http://en.wikipedia.org/w/wiki.phtml?title=Genetic_code&diff=0&oldid=8670004 diff link]): : Note that if the number of amino acids coded for was eight or less, also the number of different bases needed would -- assuming a three base codon -- be only two: "generic purine" and "generic pyrimidine". Can anyone clarify? If so, I'll add it back into the article. --User:Bdesham 14:03, 21 Dec 2004 (UTC) : This means simply that we would have eight different codons: RRR RRY RYR RYY YRR YRY YYR and YYY. Enough to code eight different amino acids (R = purine, Y = pyrimidine). It would be a binary code, not base-4 as we have now. Note that purines are two-ring molecules and pyrimidines one-ring, so this is a strong geometric expression. Differences within these two groups are more subtle and would have been added to the code later in evolution. You can still see the "generic purine/pyrimidine" patterns in the code table... : If you now understand and agree that it is of interest, please explain it better on the page :-) - mv Tue Dec 21 18:01:15 EET 2004 == Yo! == Okay, there's some serious problems with what we're doing here. We have DNA, we have translation (genetics), we have codon, and we have genetic code. All of these are redundant to some extent, but far more than they need to be. This article is easily the most nested of the set; in order to grasp it, one must understand the information-storing nature of DNA, the basics of protein synthesis, and what a codon is. In its current form, the article attempts to recapitulate all this information. This seems the wrong attitude to take, especially as some of these are unwieldy topics that don't lend themselves to quick exposition. So, I propose that we simply take a hardass line and say up front, "Look, if you want to understand the genetic code, you MUST know what DNA is first. go read that article and when you grasp the information storage mechanism whereby DNA operates, come back here." (etc.) Such steps will prevent the article from filling up with useless and abbreviated twaddle, and will allow it to present the code itself succintly and discuss it in greater detail, as it deserves. User:Graft 04:01, 23 Dec 2004 (UTC) :Err, it seems codon is now a redirect here. Mentally amend the above paragraph as necessary. User:Graft 04:02, 23 Dec 2004 (UTC) : If you think you can make this better, then by all means. I tried myself and IMHO made it better, but not good. Still, remember that all articles have this problem: they all assume background knowledge that the reader may or may not have. Only in this case the knowledge is more technical and less likely to be found in any particular reader. :Putting a warning at the start to this effect may be a good idea. Still, even after that the article should remain self-contained in a meaningful way. So that somebody that is familiar with these backgrounds can read it and say 'ah yes, that's how it was'. - mv Fri Dec 24 02:01:41 GMT+2 2004 :User:Graft: yes, this looks clearly better! - mv Sat Dec 25 18:49:04 EET 2004 ---- Good job on this page guys. I just thought it would be a good idea, as suggested below, to have a list of exceptions. Also- it may be worth someones time to being to put in exceptions do different species, either on this page and like to the species or on the species page and like from here to there. Keep up the good work! --User:DavidMendoza == Dioxyribos == == Codon bias == A section should be added that talks about codon bias across organisms as an evolutionary change as well as codon bias between genes in one organsism as a subtle way of altering the rate of translation ([http://www.uky.edu/Classes/BIO/520/BIO520WWW/StudentPresent/grieser/ a short presentation that popped up as the #1 Google hit against "codon bias"]). I'll put it on my own list of things to do, but one of the others of you would likely get to it before me. User:Ceyockey 03:17, 2005 Feb 11 (UTC) == the real picture == After a quick perusal, I'd say this explanation is pretty good. What irritates me in media explanations of the genetic code is that they imply that the code is read exactly as such! (i.e. ATTCGG etc.) If I were 100% layperson hearing that I would be confused. They don't make clear that it is a sequence of amino acids which we then convert into letters. I've even heard reporters say something like "when they discovered the sequence of letters that make up the human genome"!! (as if there are small A's G's and T's visible somewhere! --User:62.254.0.38 17:33, 2 Apr 2005 (UTC) ==First sentence is wrong== ''The genetic code is a set of rules, which maps DNA sequences to proteins in the living cell, and is employed in the process of protein synthesis.'' This is an incorrect assertion. The code does not, in amy way shape or form, map anything (unless you have a strange definition of the word map). Surely it is more accurate to say that ''The genetic code is a set of instructions'' or even ''The genetic code is a set of rules''. One can then go on to explain that the instructions are used to make proteins, which provide structure and function. So the code is the set of instructions, written in triplets which tell the cell how to build proteins. There are many mistakes in this article. Note a gene is not the same as a cistron. Not everyone would agree that the definition of a gene is that it codes for one product (be it RNA or protein). Many would argue that a gene is a heritable unit. Try to use words which have a specific meaning, like cistron. I also think that it should be made apparent that there are other instructions which are not part of the code, no detail need be given, but it could be explained that they are similar to switches, turning genes on and off. It is difficult to explain concepts such as this to non biologists, but it is a technical article. I understand little of many othe technical pages, such as computer pages. One cannot be expected to go into the complexities of chemistry and protein structure/function in the same article, this is why articles are linked. For example if one wants to know what translation means to a biologist, then there should be a separate article about it. Alternatively this article could be the basis for one about protein synthesis and a link from genetic code to the article could be made. After all the genetic code is simply an explanation of how protein synthesis works ''in vivo'' This article seems to cover much irrelevant ground.--User:Wobble 11:07, 12 May 2005 (UTC) :Come on... no one uses the word "cistron" any more, except in idiosyncratic technical usages. Also, the use of the word "map" is the mathematical one. Borrowing a definition, a map is "The correspondence of elements in one set to elements in the same set or another set.", and "to map" is "To establish a mapping of (an element or a set)." With that definition the first sentence is perfectly fine. :Also, I'm not sure what you mean by "switches". Are you talking about gene regulation? If so, that's definitely out of the scope of this article. User:Graft 16:16, 12 May 2005 (UTC) So are you disputing that the code is a set of instructions? And is it not a more accessible way of defining it. This is not a mathematical article, so why use mathematical terminologies? I never said that gene regulation should be part of the article, just that it should be mentionned that the code is not the only purpose of DNA. I dispute the word gene because it is ambiguous. It does have different meanings in different disciplines. The word gene is as over used and as often misused as the word evolution. Being accurate leads to less confusion, and there seems to be plenty of confusion here. If no one uses the word cistron any more then more fool them, as it's a perfectly good word with an unambiguous meaning. Also the word map is used extensively already in molecular biology in terms of chromosome mapping, which will lead to even greater confusion.--User:Wobble 17:55, 12 May 2005 (UTC) :I don't dispute that the code is a set of instructions. But "mapping" precisely captures what the genetic code is: a relationship between two separate encodings or alphabets. Certainly, a mapping is also a set of instructions - "set of instructions" is a rather broad term. :I'm not particularly unhappy about the use of the word "gene" - most people understand what it means in specific contexts. "Cistron" is unnecessary jargon. User:Graft 18:26, 12 May 2005 (UTC) Well I disagree, I think the term map causes much confusion, and I disagree that it ''precisely captures what the genetic code is'', quite the reverse. But I don't want to get into a dispute about it, if people are generally happy then fine. Again with the word 'gene', if the consensus is that it's OK then fair enough, though people do use it to mean other things like 'allele' and 'locus' and even 'phenotype' (for example eye colour), it is over used and I was merely attempting to be more accurate. It is still true that much of what is in this article should really be in an article about protein synthesis. Remember that the article is about the genetic code, and not about transcription or translation, these should have their own articles. Also an article about protein synthesis (is ther one?) could include things like differences between prokaryote and eukaryote synthesis, how transcription and translation are linked in prokaryotes, but occur in seperately in eukaryotes. This is where there should be some mention of the differing roles of DNA and RNA in protein synthesis. After all the code is just one small part of protein synthesis, it merely allows us to predict a protein's primary structure from a citronic or mRNA sequence. What do you think?--User:Wobble 05:26, 13 May 2005 (UTC) ==Reasons for redundancy== ''The codons attempt to ensure that minor errors in the genetic code either only causes a silent mutation or an error that would not affect the amino acid's hydrophilic/hydrophobic property'' How can codons ''attempt'' to do anything, are they sentient? I will change this to ''A practical consequence of redundancy is that minor...etc'' as it seems more accurate to me. The code is redundant because it has to be, two bases are two few to code for all amino acids (4²=16), so it has to be three at a minimum (4³=64). One consequence of this is the occurence of silent mutations. --User:Wobble 06:34, 27 May 2005 (UTC) ''four-fold degenerate codons can tolerate any mutation at the third position; two-fold degenerate codons can tolerate one out of the three possible mutations at the third position'' This sentence is also clearly wrong. A four fold degenerate codon could not tolerate a deletion in the third position I have changed ''any mutation'' to ''any point mutation''--User:Wobble 06:49, 27 May 2005 (UTC)
See other meanings of words starting from letter:
G
GA | GB | GC | GD | GE | GF | GH | GI | GJ | GK | GL | GM | GN | GO | GP | GR | GS | GT | GU | GW | GX | GY | GZ |Words begining with Genetic_code:
Genetic_Code
Genetic_code
Genetic_code
Genetic_code_(ATGC)
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