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'{{ArticleHistory |action1=GAN |action1date=March 13, 2007 |action1link=Talk:Amino acid#GA-review |action1result=listed |action1oldid=114329311 |action2=GAR |action2date=18:17, 3 November 2008 |action2link=Talk:Amino acid/GAR |action2result=delisted |action2oldid=249460965 |action3=GAN |action3date=14:09, 18 November 2008 |action3link=Talk:Amino acid/GA2 |action3result=listed |action3oldid=252492874 |action4=GAR |action4date=17:27, 27 August 2009 (UTC) |action4link=Talk:Amino acid/GA3 |action4result=kept |action4oldid=310322485 |topic=Natsci |currentstatus=GA }} {{WikiProjectBannerShell| 1={{Wikiproject MCB|importance=Top|class=GA}} }} {{archives|search=yes|list=&#x20; * [[/Archive 1|Till end of 2004]] * [[/Archive 2|Till March 14, 2007]] }} ==non-standard aas== There is a problem in the section "non-standard amino acids": If the term "standard" applies to 22 aa's then it includes serenocysteine and pyrrolysine. The section needs to be re-written. I am tempted to say standard=20 aa's, as I believe this is still the common usage of this ill-defined term. [[User:Akita86|Akita86]] ([[User talk:Akita86|talk]]) 21:28, 17 September 2009 (UTC) *I have to second this. It was a bit disconcerting to have read this article before and seen twenty(20) standard amino acids, then a reference to the other two(2) aa's, then it has become twenty-two(22). This has gone further, to someone editing the article to have twenty-four standard aa's. I will assume the 'standard' term comes from those used by the ribosome to produce a polypeptide/protein. Note: the twenty(20) is reinforced by the named list which only has 20 aa's. [[Special:Contributions/206.116.0.55|206.116.0.55]] ([[User talk:206.116.0.55|talk]]) 05:57, 19 September 2009 (UTC) ::This problem still exists. It is rather strange to see selenocysteine and pyrrolysine listed as standard in one paragraph and as non-standard in the next. The problem rests on whether standard means "naturally occurring in proteins" or "directly encoded by DNA"; the first includes these two, the second excludes them. If there is no objection in the next week or so I will change the article to be consistent. [[User:Khajidha|Khajidha]] ([[User talk:Khajidha|talk]]) 17:14, 17 December 2009 (UTC) ::And this problem still exists! I think that selenocysteine in particular would not be regarded as a 'standard' amino acid by most scholars and rather as a 'non-standard' amino acid. I was very surprised and disappointed to see it referred to here. There are 20 amino acids coded by DNA and these are the 20 that should be included in a general discussion of amino acids. It is misleading to include selenocysteine and pyrrolysine in this article. In it's current form this cannot be regarded as a 'good article' by Wikipedia. It looks as if it has been written by a freshman biochemist. A qualified biochemist should correct this! J Pretty BSc(Hons) Chemistry. [[User:Johnpretty 010|Johnpretty 010]] March 2010 <small><span class="autosigned">—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[User:Johnpretty010|Johnpretty010]] ([[User talk:Johnpretty010|talk]] • [[Special:Contributions/Johnpretty010|contribs]]) 13:18, 11 March 2010 (UTC)</span></small><!-- Template:Unsigned --> <!--Autosigned by SineBot--> :::[[WP:Sofixit]]! Surely you don't think paid professionals contribute these articles? No articles are "by Wikipedia". [[User:GrahamColm|Graham Colm]] ([[User talk:GrahamColm|talk]]) 13:31, 11 March 2010 (UTC) ::lol, thanks Graham, yes I expect you are right. Nevertheless if I were a biochemist I wouldn't be happy to see this article. I've done some more research and need to revise my comments a little. It appears that both selenocysteine and pyrrolysine are encoded by DNA - but only under certain specific conditions, which is why I for one would argue that they should be regarded as 'non-standard'. This distinction ought to be made clear in this and other articles on the subject. It has to be said that the IUPAC has confused the issue by giving these two amino acids lettering and abbreviations that may imply that they are 'standard'. My copy (1995 Ed) of Lubert Stryer's highly respected textbook on Biochemistry does not include these two amino acids in it's general discussion and so again if biochemists now regard these two as standard, it should be made clear in discussion that their inclusion is a recent development. J Pretty BSc(Hons) Chemistry. [[User:Johnpretty 010|Johnpretty 010]] March 2010 :::I can't find my copy of Stryer—how can one lose something so big—but I fully believe you. But I have "Tropp, Burton. Molecular Biology. Oxford Oxfordshire: Oxford University Press, 2007" open behind me and the amino acids in question are not mentioned therein or in "Elliott, William and Daphne Elliott. Biochemistry and Molecular Biology. Oxford Oxfordshire: Oxford University Press, 1997". I would not regard them as standard, but I'm a virologist and not a biochemist. I'll have to look into this, but I am short of time at the moment.[[User:GrahamColm|Graham Colm]] ([[User talk:GrahamColm|talk]]) 14:18, 11 March 2010 (UTC) ::No, I agree, these are not standard amino acids. [[User:TimVickers|Tim Vickers]] ([[User talk:TimVickers|talk]]) 17:53, 11 March 2010 (UTC) :I see this article being human/animal/eukaryote biased. Amino acids found in prokryotes and viruses should be given equal time. What variants or other amino acids are found in any species? :Reading at the top of "_The_ twenty-one amino acids found in eukaryotes" then seeing 22 mentioned, then several others produced by specific plants. Any reference to numbers of aa's should be fully qualified to indicate exactly what parameters the number refers to. There are several list of 21 aa's. At least one of these should be extended to list "nonstandard" and non-eukaryote aa's found in nature. [[User:Bcharles|Bcharles]] ([[User talk:Bcharles|talk]]) 15:05, 19 April 2010 (UTC) ==Hypusine== Sorry but Wikipedia doesn't allow me to add changes unless I'm a registered user. Could someone add hypusine as an amino acid originating from postranslational modification of initiation factor 5? <span style="font-size: smaller;" class="autosigned">—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/137.224.252.10|137.224.252.10]] ([[User talk:137.224.252.10|talk]]) 13:57, 10 March 2009 (UTC)</span><!-- Template:UnsignedIP --> <!--Autosigned by SineBot--> :Thank you. Added. [[User:TimVickers|Tim Vickers]] ([[User talk:TimVickers|talk]]) 15:34, 10 March 2009 (UTC) Fuck This SITE NA nD fUCK yALL wHO uSE itg YA some BITCHWS == Dur I reverts lots. == Didn't see that [[User:Crazycomputers|Crazycomputers]] had already caught the vandalism when I reverted. Sorry. XD --[[User:AgentCDE|AgentCDE]] 17:05, 22 March 2007 (UTC) == Proline == ''general formula NH2CHRCOOH'' IANABC (I Am Not A BioChemist) but the formula doesn't fit for proline with its secondary amine ... should it be changed? [[User:Daen|Daen]] 03:07, 25 March 2007 (UTC) :No. Proline's amine group cyclizes on the alpha carbon, true, but the general formula still holds if you think of one of nitrogen's hydrogens plus the rest of the ring as the R-group. --[[User:Cless Alvein|Cless Alvein]] 08:00, 30 March 2007 (UTC) :That general formula is not valid for proline. You can think of the R group in various ways, but proline simply doesn't have the NH2 that appears in the "general" formula. I'll add this as a footnote, since this level of detail could detract from the conciseness of the introduction. --[[User:Itub|Itub]] 08:34, 30 March 2007 (UTC) == Other Amino Acids == The article seems to be focused on "Life's Building Blocks". But what about the other amino acids? How many amino acids have been discovered? Besides life, what else builds, delivers, or uses amino acids? [[User:WynnSmith|WynnSmith]] 19:04, 16 April 2007 (UTC) :I can understand your first point, but what exactly do you expect to 'build' amino acids, or use them, besides life? They would be created by e.g. a lightning storm in the 'primordial soup' environment, but besides life, they certainly aren't going to be 'utilized' by anything else. [[User:Richard001|Richard001]] 01:31, 22 July 2007 (UTC) :In fact, there are many, many amino acids beyond those encoded by DNA, most of which are generated by post-translational processing of the standard 20 but some that arise from more esoteric biosynthetic processes. And many other amino acids are synthetic that have been incorporated into proteins or used for various purposes related to engineered enzymes. == BCAA == The branched chain amino acid paragraph is a little unusual - the aliphatic/hydrocarbon side chains are often just categorized as aliphatic side chains (Leu, Val, Ile). I've almost always heard branched amino acids used to refer to the beta-branched amino acids, which include Ile, Thr, and Val. This is a useful category because the branching affects the geometry of the protein backbone immediately surrounding the amino acids, and thus the protein structure. I don't know the history of the page - is there a reason that the branched chain aliphatic category was given precedence? [[User:Reesei|Reesei]] 19:30, 1 May 2007 (UTC) ==Genetic code== Perhaps there should be a little mention that many codons code for the same amino acid, and its implication for [[mutation]]s? This area seems fairly underdeveloped, in fact the genetic code is only mentioned a couple of times and not in any detail. [[User:Richard001|Richard001]] 06:05, 29 July 2007 (UTC) You can mention that DNA contains instructions for the construction of protein from amino acids.--[[Special:Contributions/71.247.34.248|71.247.34.248]] ([[User talk:71.247.34.248|talk]]) 02:54, 15 December 2008 (UTC) :The article presently states: ::"Twenty [[list of standard amino acids|standard amino acids]] are used by [[cell (biology)|cells]] in [[protein biosynthesis]], and these are specified by the general [[genetic code]]." :Your idea is reasonable but it's too casually worded to the point of being misleading. It's only the sequence that's specified by the DNA, not folding or post-translational modification info (i.e., all the things that make a protein actually functional). [[User:DMacks|DMacks]] ([[User talk:DMacks|talk]]) 03:21, 15 December 2008 (UTC) == Tyrosine polar/non-polar == It seems there have been a few edits back and forth mentioning Tyrosine as non-polar or polar. As far as I am aware, Tyrosine is considered a polar amino acid because of the hydroxyl group. One may also check the much-cited Venn-diagram found at EMBL [http://www.russell.embl-heidelberg.de/aas/](which was a source for a figure I remember from an advanced-level protein engineering class I took a few years ago). Any comments? [[User:Antorjal|Antorjal]] 03:25, 2 August 2007 (UTC) :I'll have a look at Chrighton ''Proteins'' when I get into work tomorrow. However, if you look at the hydropathy index in the table, it is about as polar as proline, which is also labelled as "non-polar". [[User:TimVickers|Tim Vickers]] 03:35, 2 August 2007 (UTC) ::With that I will agree with you 100%. Tyrosine was always one of the strange cases (along with good old tryptophan), where due to convention the amino acid was considered hydrophobic ''and'' polar. Go figure! In any case I'll go through "Fersht" tomorrow as well. :-) Have a nice night.[[User:Antorjal|Antorjal]] 03:41, 2 August 2007 (UTC) ::: It is my understanding that Tyrosine is part of the grouping - polar uncharged. Because it's side chain amino acid has a pKr of 10.46, it has the possibility to become polar/charged in rare but possible cases of physiological pH, whereas proline and tryptophan have negligible pKr values for their side change. <small>—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[User:Niubrad|Niubrad]] ([[User talk:Niubrad|talk]] • [[Special:Contributions/Niubrad|contribs]]) 02:47, 28 February 2008 (UTC)</small><!-- Template:Unsigned --> <!--Autosigned by SineBot--> :::: According to my sources, the polar effect of the hydroxyl group is "overshadowed" by the non-polar nature of the benzene group. <span style="font-size: smaller;" class="autosigned">—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/70.24.169.208|70.24.169.208]] ([[User talk:70.24.169.208|talk]]) 03:36, 3 February 2009 (UTC)</span><!-- Template:UnsignedIP --> <!--Autosigned by SineBot--> :::It is mostly non-polar, with a split between non-plar and polar surface area (in a polypeptide) of 144 to 43, this compares to tryptophan with a 190 to 27. This data is cited in ''Crighton'' but comes from PMID 3681970 [[User:TimVickers|Tim Vickers]] ([[User talk:TimVickers|talk]]) 03:55, 3 February 2009 (UTC) :Since you guys know what you're talking about, can somebody change this on the Tyrosine article for the sake of consistency? Thanks. <span style="font-size: smaller;" class="autosigned">—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/204.140.154.86|204.140.154.86]] ([[User talk:204.140.154.86|talk]]) 03:08, 20 January 2011 (UTC)</span><!-- Template:UnsignedIP --> <!--Autosigned by SineBot--> ::Creighton actually lists two scales, hydrophobicity and hydrophilicity which are actually different properties, not different interpretations of the same property. The numeric values represent the free energies of transfer of between phases e.g. octanol-water for hydrophobicity and air-water for hydrophilicity as I recall (I don't have a copy of Creighton on hand). Anyhow Trp and Tyr are very hydrophobic but somewhat hydrophilic. Glycine is not very hydrophobic but not very hydrophilic either. Depending on which scale someone looks at trp and tyr come out very non-polar or not so non-polar. Hydropathy on the other hand is an empirical scale which is kind of a fudged composite of the two thermodynamic scales.[[Special:Contributions/96.54.32.44|96.54.32.44]] ([[User talk:96.54.32.44|talk]]) 06:35, 16 February 2011 (UTC) == Biological importance-Tyrosine/Tryptophan == Why do all biological proteins contain Tyrosine and Tryptophan?? Any specific reason?? :Not as far as I know, the chances of any string of amino acids not containing two of the twenty amino acids is pretty small, even if the sequence is just random. [[Collagen]] contains only a few Y/W residues and there might be some proteins with none, but I would expect them to be pretty rare. [[User:TimVickers|Tim Vickers]] 06:46, 5 August 2007 (UTC) :To add to [[User:TimVickers|Tim Vickers's]] excellent response, tyrosine is a lot more common that tryptophan, but even so, (depending on the species) more than 90% of proteins have at least one W.[[User:Antorjal|Antorjal]] 12:57, 5 August 2007 (UTC) ==Essential== i have a health book that says there are nine essential and 11 nonessential amino acids [[User:Soyseñorsnibbles|Soyseñorsnibbles]] 23:00, 28 September 2007 (UTC) :This seems surprisingly ill-defined and controversial. I've added a range of references. [[User:TimVickers|Tim Vickers]] 02:39, 29 September 2007 (UTC) == Cysteine == '''''Presentation College,'''''There is one querry that i have . Cystein , as an amino acid ... is it Polar ? I have a text book by Richard Kent which argues thet it is Non Polar ... <small>—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/190.58.4.66|190.58.4.66]] ([[User talk:190.58.4.66|talk]]) 04:40, 16 October 2007 (UTC)</small><!-- Template:UnsignedIP --> <!--Autosigned by SineBot--> :It is non-polar when protonated but polar when ionised. [[User:TimVickers|Tim Vickers]] 18:03, 4 December 2007 (UTC) :No, its not polar in its non-ionised form. S-H and C-H bond are pretty similar. [[User:Narayanese|Narayanese]] ([[User talk:Narayanese|talk]]) 21:42, 19 October 2008 (UTC) == Side chain polarity == I am going to have to strongly disagree with the assertion that the side chain of tyrosine is nonpolar. Although it can base stack and have hydrophobic interactions with its electrons above and below the plane of the aromatic ring, there is no conceivable way that you can tell me that it is nonpolar with the conspicuous hydrogen bonding phenolic oxygen <small>—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/68.242.170.102|68.242.170.102]] ([[User talk:68.242.170.102|talk]]) 16:25, 27 November 2007 (UTC)</small><!-- Template:UnsignedIP --> <!--Autosigned by SineBot--> :This is one on the boundary, it has both polar and nonpolar characteristics and does not easily fit into a black/white classification. [[User:TimVickers|Tim Vickers]] 18:04, 4 December 2007 (UTC) ::Its both. The term is "amphipathic" <span style="font-size: smaller;" class="autosigned">—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/163.1.143.145|163.1.143.145]] ([[User talk:163.1.143.145|talk]]) 07:36, 30 September 2008 (UTC)</span><!-- Template:UnsignedIP --> <!--Autosigned by SineBot--> == Origins and evolution == This article could benefit from a section on the origins and evolution of amino acids. I'm thinking in particular of the [[Miller-Urey experiment]] and the question of handedness.[http://www.npr.org/templates/story/story.php?storyId=5448305] -- [[User:Beland|Beland]] ([[User talk:Beland|talk]]) 01:10, 4 January 2008 (UTC) == Comment removed from article text == "I hate how semi-complicated things like this could be explained a lot easier if people didn't resort to overly complicated words." <small>—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/208.233.39.21|208.233.39.21]] ([[User talk:208.233.39.21|talk]]) </small><!-- Template:UnsignedIP --> == SVG version of Protein-primary-structure.png ? == I went to [http://www.genome.gov/Pages/Hyperion/DIR/VIP/Glossary/Illustration/amino_acid.cfm?key=amino%20acids the source] of [http://en.wikipedia.org/wiki/Image:Protein-primary-structure.png this image] to try and get a higher res version for a paper I'm writing. I downloaded the pdf there, opened it in [[Inkscape]] and saved it as an svg. Unfortunately, the image got a bit messed up as you can see [http://en.wikipedia.org/wiki/Image:Protein-primary-structure.svg here]. (It looks ok on its own page but a shrunken version on the article page looks hideous.) It would seem that an svg image would be preferable to a png for an image like this one, especially given the low resolution of the png. I have very little experience with images on Wikipedia. I think that if someone who knew what they were doing would look at the picture, they could make it work. 15:12, 16 October 2008 (UTC) <small><span class="autosigned">—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[User:Mdanziger|Mdanziger]] ([[User talk:Mdanziger|talk]] • [[Special:Contributions/Mdanziger|contribs]]) </span></small><!-- Template:Unsigned --> <!--Autosigned by SineBot--> :Couldn't get the svg to work either. But it does work to make it bigger (transform->scale) and then export as bitmap. [[User:Narayanese|Narayanese]] ([[User talk:Narayanese|talk]]) 17:38, 16 October 2008 (UTC) {{Talk:Amino acid/GA1}} ==Essential amino acids?== !! 8 Amino Acids or 9 ?? The article states that there are only 8 animo acids that the body does not produce. However, a Cornell article discussing the properties of cow milk, states that there are nine essential amino acids that the human body does not produce, (milk providing all 9). http://www.milkfacts.info/Milk%20Composition/Protein.htm Which is correct? Thank you for your attention. abubasir, Seoul South Korea :See [http://jn.nutrition.org/cgi/content/full/130/7/1835S this paper] for a discussion of the terms "essential" and "non-essential" and [http://jn.nutrition.org/cgi/reprint/124/8_Suppl/1517S.pdf this paper] for a relatively recent review on the topic. [[User:TimVickers|Tim Vickers]] ([[User talk:TimVickers|talk]]) 19:26, 19 November 2008 (UTC) This article mentions 8 essential amino acids then later give mneumonics for remembering the 10 amino acids. Please consider editing this section. <span style="font-size: smaller;" class="autosigned">—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/140.193.67.28|140.193.67.28]] ([[User talk:140.193.67.28|talk]]) 21:57, 28 February 2009 (UTC)</span><!-- Template:UnsignedIP --> <!--Autosigned by SineBot--> :Even worse: one of the three mnemonics has ''11'' words! But the whole problem is different ideas of "essential when?". As mentioned in the previous sentences, it's age-dependent, and 8 or 10 are both reasonable counts for the number of essential ones. Reworded to avoid looking so silly. [[User:DMacks|DMacks]] ([[User talk:DMacks|talk]]) 23:37, 28 February 2009 (UTC) == Histidine Charge == Could anyone explain why histidine is listed as charged at neutral pH in the data table? I assume it's not a mistake, but my understanding is that it's non-charged. :The side-chain imidazole ring has a pKa of about 6, so at pH 7 it will be partially ionized. [[User:TimVickers|Tim Vickers]] ([[User talk:TimVickers|talk]]) 17:08, 2 December 2008 (UTC) == Amino Acids . animation == http://francoislafontaine.com/story/moment/amino255.html {{Talk:Amino acid/GA3}} ==App's== The report claims some applications that may not exist or are only used in ultra-specialized research labs. It would be great if anyone can identify a synthetic catalyst that has amino acid component. The report also has a sizeable section on "Biodegradable plastics." I guess biodegradable plastics ''could'' be made from amino acids, but probably none are made that way, so this section is a tangential and probably belongs in the article on [[peptide]]s. So I was thinking of making that move. From the industrial production data, it appears taht the applications are pretty prosaic. Mankind main use of amino acids is to make food spicy. Or to fatten cows, pigs, and chickens.--[[User:Smokefoot|Smokefoot]] ([[User talk:Smokefoot|talk]]) 17:25, 22 August 2009 (UTC) == Table of abbreviations out of date? == I've just rolled back an IP edit in the "Table of standard amino acid abbreviations and side chain properties" section reading: '''The data shown here are outdated. The hydropathy scale is currently devised on the space a amino acid takes when present inside a tertiary protein, and based on that, Phenylalanine, tyrosine and tryptophan that have a benzene ring in their side group have maximum hydrophobicity. My reference is the book "Genes V" by Benzamin Lewin. I don't have much time now, otherwise I could give you the related research paper. Kindly update.''' Can someone with a bit more knowledge take a look whether this needs looking at. <small><span class="autosigned">—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[User:Cubathy|Cubathy]] ([[User talk:Cubathy|talk]] • [[Special:Contributions/Cubathy|contribs]]) 09:07, 21 December 2009 (UTC)</span></small><!-- Template:Unsigned --> ==Error in the formula of Arginine, in the Figure Amino_acids.png== As I do not own the source of the Amino acids.png file, I cannot modify it. Please fix the error present on the Arginine (R) formula, the first nitrogen present on the side chain should be -NH-, not -N-. Thank you. Filippo Rusconi <small><span class="autosigned">—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[User:Rusconi|Rusconi]] ([[User talk:Rusconi|talk]] • [[Special:Contributions/Rusconi|contribs]]) 19:58, 29 January 2010 (UTC)</span></small><!-- Template:Unsigned --> <!--Autosigned by SineBot--> :Fixed. [[User:DMacks|DMacks]] ([[User talk:DMacks|talk]]) 20:33, 29 January 2010 (UTC) ==Placement of the AA figure and the "Hydrophilic/hydrophobic" section == The large figure with all the amino acids, grouped by their physical properties [Aa.svg] is in a weird spot. It is crammed into the intro section and the information the figure contains makes much more sense later in the article. I propose we move into to the "Hydrophilic and hydrophobic amino acids" section. Further, I think it is strange that the section about polarity is alone and so far down the article. I think it should be the first subsection of "General Structure" (the text in that section already has a paragraph on polarity). This is also nice for people (like me) who often visit the AA article as a reference for the sidechain structure, because the figure will remain close to the top of the article. [[User:Richard.decal|richard.decal]] ([[User talk:Richard.decal|talk]]) 06:30, 23 June 2010 (UTC) == Expanded genetic code == I have added expanded genetic code by copy paste from genetic code, but I have not mentioned the letter codes used for the amino acids as they are non-iupac and author specific and re-use the other non-20 ), which gets confusing (non ascii capital letters ([[Þ]], [[Ð]], [[Ü]] etc) cannot be used for various encoding reasons). --[[User:Squidonius|Squidonius]] ([[User talk:Squidonius|talk]]) 21:42, 14 July 2010 (UTC) == Typo in Aa.svg == File Aa.svg: Headline of Section A should read "Electrically" and not "Electricaly". <span style="font-size: smaller;" class="autosigned">—Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/87.168.181.47|87.168.181.47]] ([[User talk:87.168.181.47|talk]]) 14:32, 14 January 2011 (UTC)</span><!-- Template:UnsignedIP --> <!--Autosigned by SineBot--> :I sent a comment to editor who made that image. If it doesn't get fixed in a few days, will try to do it myself. [[User:DMacks|DMacks]] ([[User talk:DMacks|talk]]) 15:47, 14 January 2011 (UTC) ::He fixed it. [[User:DMacks|DMacks]] ([[User talk:DMacks|talk]]) 15:00, 28 January 2011 (UTC) ==Typo in Aa.svg; an error in the abbreviated name for tyrosine== File:aa.svg - This should be Tyr not Try. Previous version was correct. <small><span class="autosigned">— Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[User:KathosValor|KathosValor]] ([[User talk:KathosValor|talk]] • [[Special:Contributions/KathosValor|contribs]]) 08:09, 28 January 2011 (UTC)</span></small><!-- Template:Unsigned --> :I sent a comment to editor who made that image. If it doesn't get fixed in a few days, will try to do it myself. [[User:DMacks|DMacks]] ([[User talk:DMacks|talk]]) 15:07, 28 January 2011 (UTC) == Overemphasis of the neutral form == Practically all the figures in this article show neutral amino and carboxylic acid on the same molecule. Zwitterions are mentioned, but almost as an aside. In reality, amino acids in neutral aqueous solution and in crystalline solid state are zwitterions. The ratio of zwitterion to neutral at pH 7 is about 10^7 to one. At more acidic pH, the carboxylate becomes protonated, but so is the amino group. At high pH the amino group is deprotonated, but so is the carboxylate. Nowhere on the pH scale are there significant concentrations of the neutral carboxylic acid and neutral amino group on the same molecule.[[Special:Contributions/96.54.32.44|96.54.32.44]] ([[User talk:96.54.32.44|talk]]) 06:52, 16 February 2011 (UTC) :It all comes down to convention. Amino acids are very widely depicted in the scientific literature in their neutral forms, and Wikipedia's role is to report on what others write. We shouldn't aim to defy convention in order to be technically more accurate. We are writing about "amino acids", after all, not "ammonium carboxylates". If anything needs to be changed, I would suggest adding further discussion of their true chemical structure, more than the current degree ("almost as an aside"). [[Special:Contributions/148.177.1.210|148.177.1.210]] ([[User talk:148.177.1.210|talk]]) 20:33, 16 February 2011 (UTC) ::So Wikipedia is an encyclopedia that subscribes to inaccuracy?[[Special:Contributions/96.54.32.44|96.54.32.44]] ([[User talk:96.54.32.44|talk]]) 19:05, 17 February 2011 (UTC) :::If reliable sources describe the world inaccurately, then yes, so do we. [[Wikipedia:Verifiability, not truth]]. [[Special:Contributions/148.177.1.210|148.177.1.210]] ([[User talk:148.177.1.210|talk]]) 19:13, 17 February 2011 (UTC) ::::Interesting discussion. The fully uncharged form can exist in nonpolar solvents (e.g. cyclohexane), hence the picture is not an error, generally speaking. [[User:Hodja Nasreddin|Biophys]] ([[User talk:Hodja Nasreddin|talk]]) 20:55, 17 February 2011 (UTC) :::::The zwitterion form is depicted in many textbooks, e.g. Fersht, Structure and Mechanism in Protein Science, 3rd Ed.(1999) pp.2-3. The biochemical standard state is described as aqueous solution, pH 7, 1 atm pressure 298 K (Tinoco, Sauer and Wang, Physical Chemistry, Principles and and Application in Biological Sciences, 3rd Ed (1995) p.139. If we are to consider amino acids in terms of biochemistry, that should be the defining state. Moreover, amino acids are barely soluble in non polar solvents precisely because of the huge thermodynamic penalty of either desolvating the zwitterion or converting to the neutral form. [[Special:Contributions/96.54.32.44|96.54.32.44]] ([[User talk:96.54.32.44|talk]]) 00:33, 18 February 2011 (UTC) ::::::Of course it would be better to use a good picture with zwitterionic form if we have it.[[User:Hodja Nasreddin|Biophys]] ([[User talk:Hodja Nasreddin|talk]]) 04:32, 18 February 2011 (UTC) :There are already a couple of images showing the zwitterion. The problem is that they appear as an aside, while the virtually non-existent neutral form is emphasized in 24images, including the main table of structures. Ironically, the structures show aspartate and glutamate with deprotonated side-chain carboxylates despite the fact that the pKa values dictate that alpha-carboxylic acid will deprotonate before the side chain does. There are indeed plenty of sources with all the amino acids in zwitterion form, the only issue being copyright of images. Most of the amino acids were discovered prior to the formulation of [[Brønsted-Lowry]] description of acid/base behaviour, hence older texts adhered to the older convention. [[Special:Contributions/96.54.32.44|96.54.32.44]] ([[User talk:96.54.32.44|talk]]) 19:05, 19 February 2011 (UTC) :I asked [[WP:Chemicals]] for input, since this is a fundamental question to presenting the diagrams of these types of structures in many articles. [[User:DMacks|DMacks]] ([[User talk:DMacks|talk]]) 19:19, 19 February 2011 (UTC) ::For what its worth, I checked three textbooks that I have; one biology, one biochemistry, and one organic chemistry (all from the mid 1990s). They all depict amino acids as the neutral compounds. Looking at [http://www.britannica.com/EBchecked/topic/20691/amino-acid Encyclopedia Britannica] I see the same. So the suggestion that this is the standard convention seems accurate. Because the protonation state of each amino group and each carboxylic acid group is going to vary depending on conditions (solvent, pH, etc.), defaulting to all neutral representations makes sense, despite the fact that zwitterions and various other charged states are going to be the predominant forms under typical conditions. -- [[User:Edgar181|Ed]] ([[User talk:Edgar181|Edgar181]]) 21:05, 19 February 2011 (UTC) :::I agree with you all that the zwitterion is an acceptable form in physiological PH (Conributor 96.54.32.44). What form you Wiki guys want to use is up to you all. I agree the neutral form cannot exist at physiological PHs. This fact does not prevent the neutral form's existence. The molecule could exist, due to equilibrium, at low, possibly undetectable, concentrations. If people here come to an agreement on what ionized form to show, can someone do the following? I only wish the contradicting views in the main Amino Acid page be corrected. Please, someone with the authority to edit the Amino acid page edit the All Caps sentence in the first paragraph. The sentence looks bad. I assume the author of all-caps sentence meant amino acids cannot exist at physiological PHs in a neutral form. An outright declaration of contradicting views on a main Wikipedia page is confusing to the general public.[[Special:Contributions/69.229.121.10|69.229.121.10]] ([[User talk:69.229.121.10|talk]]) 05:21, 20 February 2011 (UTC) ::::The only all-caps sentence I see in recent article history was inserted and then removed 6 seconds later a few hours ago. [[User:DMacks|DMacks]] ([[User talk:DMacks|talk]]) 09:44, 20 February 2011 (UTC) :I don't necessarily suggest that all the figures be changed, but rather am concerned that the zwitterion form, which is the predominant form under biochemical conditions is barely mentioned, and one might expect the subject of amino acids to be of interests to biochemists or individuals trying to learn something of biochemistry. :The paragraph labelled '''Zwitterion''' digresses into discussing isoelectric points, saying the following: :"''The amine and carboxylic acid functional groups found in amino acids allow it to have amphiprotic properties.[9]''" No problem. :"''At a certain pH, known as the isoelectric point, an amino acid has no overall charge since the number of protonated ammonia groups (positive charges) and deprotonated carboxylate groups (negative charges) are equal.[18] The amino acids all have different isoelectric points. The ions produced at the isoelectric point have both positive and negative charges and are known as a zwitterion, which comes from the German word Zwitter meaning "hermaphrodite" or "hybrid".[19]''" One could be misled to understand that the zwitterion only occurs at the isoelectric point, whereas it is actually present as the major form from ~pH 2.2 (mean alpha-carboxylic acid pKa) through to ~pH 9.4 (mean pKa of the alpha-ammonium ion). At pH < 2.2, the positive ion predominates, and at pH > 9.4 the negative ion predominates. :"''Amino acids '''can''' exist as zwitterions in solids and in polar solutions such as water, but not in the gas phase.[20] Zwitterions have minimal solubility at their isolectric point''" True enough, except the "can" implies other possibilities without specifying what they are. Given all the information presented in the structure figures, one might think that the zwitterion is a special case rather than the major form present. :"''and an amino acid can be isolated by precipitating it from water by adjusting the pH to its particular isoelectric point.''" which is only really true for the hydrophobic amino acids; more polar amino acids reach a minimum point in their pH/solubility curve, but are still relatively quite soluble. What I suggest is a rewrite, dividing into two paragraphs: '''Zwitterions''' The α-amino and carboxylic acid functional groups found in amino acids allow them to have amphiprotic properties.[9] Carboxylic acid groups can be deprotonated to become negative carboxylates, and α-amino groups can be protonated to become positive α-ammonium groups. At pH values greater than the [[pKa]] of the carboxylic acid group (mean for the 20 common amino acids is about 2.2, see the table of amino acid structures above), the negative carboxylate ion predominates. At pH values lower than the pKa of the α-ammonium group (mean for the 20 common α-amino acids is about 9.4) the nitrogen is predominantly protonated as a positively charged α-ammonium group. Thus at pH between 2.2 and 9.4, the predominant form adopted by α-amino acids contains a negative carboxylate and a positive α-ammonium group as shown in structure (2) on the right, so is net zero charge. This molecular state is known as a zwitterion, which comes from the German word Zwitter meaning "hermaphrodite" or "hybrid".[19] Below pH 2.2, the predominant form will have a neutral carboxylic acid group and a positive α-ammonium ion (net charge +1), and above pH 9.4, a negative carboxylate and neutral α-amino group (net charge -1). The fully neutral form (structure (1) on the right) is a very minor species in aqueous solution throughout the pH range (less than 1 part in 10^7). Amino acids also exist as zwitterions in the solid phase, and crystallize with salt-like properties unlike typical organic acids or amines. '''Isoelectric point''' At pH values between the two pKa values, the zwitterion predominates, but coexists in dynamic equilibrium with small amounts of net negative and net positive ions. At the exact midpoint between the two pKa values, the trace amount of net negative and trace of net positive ions exactly balance, so that average net charge of all forms present is zero.[18] This pH is known as the [[isoelectric point]] pI, so pI = (pKa1 + pKa2) / 2. The individual amino acids all have slightly different pKa values, so have different isoelectric points. Amino acids have zero mobility in [[electrophoresis]] at their isoelectric point, although this behaviour is more usually exploited for peptides and proteins than single amino acids. Zwitterions have minimum solubility at their isolectric point and some amino acids (particularly with non-polar side chains) can be isolated by precipitation from water by adjusting the pH to the required isoelectric point. "but not in the gas phase.[20]" Reference cited does not really say this. It's based on theoretical calculations for certain metal complexes of glycine, so "gas phase" exists as a computational state rather than one that can be experimentally achieved.\ [[Special:Contributions/96.54.32.44|96.54.32.44]] ([[User talk:96.54.32.44|talk]]) 08:37, 20 February 2011 (UTC) I'm sorry, I don't have any of my basic biochemistry textbooks on hand to cite chapter and verse, but I'm sure you will find this discussed in Metzler, or Creighton, or Lehninger, particularly the old Blue Lehninger (1975) rather than the newer Ouija board versions of "Lehninger". [[Special:Contributions/96.54.32.44|96.54.32.44]] ([[User talk:96.54.32.44|talk]]) 08:44, 20 February 2011 (UTC) :To me, that looks like an excellent revision. Many thanks, [[User:Walkerma|Walkerma]] ([[User talk:Walkerma|talk]]) 03:41, 21 February 2011 (UTC) ::Sounds like improvement. "Gas phase" may refer to something observed by [[Mass spectrometry]]. Do not forget that isolectric points also depend on the presence of side-chain charge (Arg, Lys, His, Asp, Glu, etc.). [[User:Hodja Nasreddin|Biophys]] ([[User talk:Hodja Nasreddin|talk]]) 20:38, 21 February 2011 (UTC) :::Reference (20) discusses transition metal complexes of amino acids, where the amino rather than the ammonium group acts as the ligand, thus metal complex formation significantly alters the normal pKas of the free amino acid. It may be interesting chemistry, but is straying far away from typical biochemical behaviour of the amino acids. Mass spec, as far as I know, always deals in ions so that they can be accelerated and deflected by electric and magnetic fields and detected by deposition of charge at the detecting anode. In conventional mass spec, amino acids are usually derivatized to enhance their volatility. Gas phase infra-red spectroscopy should be able to tell the difference between zwitterion and neutral molecule, but I'm not aware of any literature on the topic. :::I did not go into the isoelectric points of amino acids with charged side chains in order to keep things straightforward, but if you like they could be included, as in following paragraph: '''Isoelectric point''' At pH values between the two pKa values, the zwitterion predominates, but coexists in dynamic equilibrium with small amounts of net negative and net positive ions. At the exact midpoint between the two pKa values, the trace amount of net negative and trace of net positive ions exactly balance, so that average net charge of all forms present is zero.[18] This pH is known as the [[isoelectric point]] pI, so pI = ½(pKa₁ + pKa₂). The individual amino acids all have slightly different pKa values, so have different isoelectric points. For amino acids with charged side chains, the pKa of the side chain is involved. Thus for Asp, Glu with negative side chains, pI = ½(pKa₁ + pKa_R), where pKa_R is the side chain pKa. Cysteine also has potentially negative side chain with pKa_R = 8.14, so pI should be calculated as for Asp and Glu, even though the side chain is not significantly charged at neutral pH. For His, Lys and Arg with positive side chains, pI = ½(pKa_R + pKa₂). Amino acids have zero mobility in [[electrophoresis]] at their isoelectric point, although this behaviour is more usually exploited for peptides and proteins than single amino acids. Zwitterions have minimum solubility at their isolectric point and some amino acids (particularly with non-polar side chains) can be isolated by precipitation from water by adjusting the pH to the required isoelectric point. :::Then of course, I could add an explanation of why the particular pKas are chosen for calculation of pI and so on. I personally prefer the simpler version but either would do. [[Special:Contributions/96.54.32.44|96.54.32.44]] ([[User talk:96.54.32.44|talk]]) 22:53, 21 February 2011 (UTC) ::::I think you should simply go ahead and make the changes you prefer. If others disagree on details, they would fix your text a little.[[User:Hodja Nasreddin|Biophys]] ([[User talk:Hodja Nasreddin|talk]]) 17:49, 22 February 2011 (UTC) :::::OK, I have put the two paragraphs into the main page. I dropped the old ref 20: the article simply did not support the statement in the original text. [[Special:Contributions/96.54.32.44|96.54.32.44]] ([[User talk:96.54.32.44|talk]]) 01:35, 25 February 2011 (UTC) == Isomerism == Could someone please explain to me why L-Cysteine is allegedly R? Under the rules I was taught, and as listed on [[Cahn–Ingold–Prelog_priority_rules | Wikipedia]], mass only comes into it when they are the same element just different isotopes (such as Deuterium and Hydrogen). Also, double bonds are treated as 2 bonds to the same atom. Therefore, C=OO counts as having 3 oxygen atoms and thus has a priority of 3*8 or 24. The side chain has a sulphur and 2 hydrogens, giving a priority of 2*1+16 or 18. This is still well below the 24 of the carboxyl group, and thus the carboxyl group has a higher priority, and thus the L form should still be the S form, not the R form. The one which the L form is the R form is selenocysteine, which has selenium in the place of sulfur, giving that chain a priority of 32+2 or 34, making it higher than the carboxyl group. Unless I get a satisfactory explanation, I will change it in a week (and on its page). <span style="font-size: smaller;" class="autosigned">— Preceding [[Wikipedia:Signatures|unsigned]] comment added by [[Special:Contributions/149.171.197.22|149.171.197.22]] ([[User talk:149.171.197.22|talk]]) 01:48, 16 August 2011 (UTC)</span><!-- Template:Unsigned IP --> <!--Autosigned by SineBot--> :The primary CIP priority check is highest one attachment, not the total of all attachments (check [[Cahn–Ingold–Prelog priority rules#Assignment of priorities]] #1). Therefore C–S beats C=OO because S > O and the fact that there are 2 O (or three O group equivalents) does not matter. [[User:DMacks|DMacks]] ([[User talk:DMacks|talk]]) 01:57, 16 August 2011 (UTC) Thanks for clearing that up for me. Seems uni professors aren't that great at describing things properly. Could atomic mass be replaced with atomic number, as the rules do state that? [[Special:Contributions/122.106.52.228|122.106.52.228]] ([[User talk:122.106.52.228|talk]]) 09:12, 16 August 2011 (UTC)'