Talk:Amino acid/Archive 3

picture of 21 amino acids
For the aminoacids Arginine, Lysine, Aspartic acid, and Glutamic acid the pictures given are for their corresponding ions. Protonated Arginine, Lysine and deprotonated Aspartic acid, Glutamic acid are given. This is very confusing for various reasons. For the first two cases at least the zwitterionic form can be presented, in this case the carboxyl proton should be removed. It would be nice if some one edits the picture and provides the neutral form of the amino acids. — Preceding unsigned comment added by Kitkarson (talk • contribs) 13:11, 22 May 2013 (UTC)

Showing 21 amino acids here is misleading. There are 20 canonical amino acids encoded in the genetic code; one or two other, special cases exist in which a stop codon is repurposed. A person being introduced to the concept of proteinogenic amino acids, however, should NOT be presented with 21 amino acids.Vmulligan (talk) 23:24, 13 September 2016 (UTC)

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. 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. 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. 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. Johnpretty 010 March 2010 —Preceding unsigned comment added by Johnpretty010 (talk • contribs) 13:18, 11 March 2010 (UTC)


 * WP:Sofixit! Surely you don't think paid professionals contribute these articles? No articles are "by Wikipedia". Graham Colm (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. 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.Graham Colm (talk) 14:18, 11 March 2010 (UTC)


 * No, I agree, these are not standard amino acids. Tim Vickers (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. Bcharles (talk) 15:05, 19 April 2010 (UTC)

Not sure where this should go but under [Occurrence and functions in biochemistry -> Essential amino acids] it states "Twenty-two amino acids are naturally incorporated into polypeptides and are called proteinogenic" then in the next subheading [Occurrence and functions in biochemistry -> Non-standard amino acids] it contradicts the previous statement with "Aside from the 23 proteinogenic amino acids" — Preceding unsigned comment added by 131.181.251.130 (talk) 01:12, 31 July 2014 (UTC)

I strongly, strongly agree: it is badly misleading and confusing, especially to students just being introduced to protein biochemistry, to start by suggesting that there are 21 standard amino acids. The genetic code, common to all life, encodes 20 canonical amino acids. We can have a section on the rare, special cases, in which a stop codon is repurposed to allow something unusual to be incorporated, but the figure and text at the start of the article should present 20 canonical amino acids. Selenocysteine should be omitted from the general description, and only discussed in a paragraph about special cases. Vmulligan (talk) 23:29, 13 September 2016 (UTC)
 * I agree that there is too much written about the two non-standard proteinogenic AAs, given how few proteins contain them. They appear in the introduction and sections "Proteinogenic amino acids" and "Non-standard amino acids" and have their own WP pages. I propose to remove this emphasis and return the focus to the standard 20 AAs and add a brief reference to the post-translationally modified forms of them commonly found in proteins and link to the relevant WP page. ChiBeta (talk) 06:07, 31 March 2017 (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? —Preceding unsigned comment added by 137.224.252.10 (talk) 13:57, 10 March 2009 (UTC)


 * Thank you. Added. Tim Vickers (talk) 15:34, 10 March 2009 (UTC)

GA-review
This was an easy promotion - great job. I really had no comments although I do see that this project is still evolving and being improved. I would suggest a peer review in a couple of months followed by an attempt for Featured article status.Peter Rehse 06:50, 14 March 2007 (UTC)

Dur I reverts lots.
Didn't see that Crazycomputers had already caught the vandalism when I reverted. Sorry. XD --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? 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. --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. --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? 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. 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? 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 mutations? This area seems fairly underdeveloped, in fact the genetic code is only mentioned a couple of times and not in any detail. Richard001 06:05, 29 July 2007 (UTC)

You can mention that DNA contains instructions for the construction of protein from amino acids.--71.247.34.248 (talk) 02:54, 15 December 2008 (UTC)
 * The article presently states:
 * "Twenty standard amino acids are used by 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). 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 (which was a source for a figure I remember from an advanced-level protein engineering class I took a few years ago). Any comments? 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". 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.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. —Preceding unsigned comment added by Niubrad (talk • contribs) 02:47, 28 February 2008 (UTC)


 * According to my sources, the polar effect of the hydroxyl group is "overshadowed" by the non-polar nature of the benzene group. —Preceding unsigned comment added by 70.24.169.208 (talk) 03:36, 3 February 2009 (UTC)


 * 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 Tim Vickers (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. —Preceding unsigned comment added by 204.140.154.86 (talk) 03:08, 20 January 2011 (UTC)


 * 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.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. Tim Vickers 06:46, 5 August 2007 (UTC)
 * To add to 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.Antorjal 12:57, 5 August 2007 (UTC)

Essential
i have a health book that says there are nine essential and 11 nonessential amino acids Soyseñorsnibbles 23:00, 28 September 2007 (UTC)


 * This seems surprisingly ill-defined and controversial. I've added a range of references. 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 ... —Preceding unsigned comment added by 190.58.4.66 (talk) 04:40, 16 October 2007 (UTC)


 * It is non-polar when protonated but polar when ionised. 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. 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 —Preceding unsigned comment added by 68.242.170.102 (talk) 16:25, 27 November 2007 (UTC)


 * This is one on the boundary, it has both polar and nonpolar characteristics and does not easily fit into a black/white classification. Tim Vickers 18:04, 4 December 2007 (UTC)


 * Its both. The term is "amphipathic" —Preceding unsigned comment added by 163.1.143.145 (talk) 07:36, 30 September 2008 (UTC)

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. -- 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." —Preceding unsigned comment added by 208.233.39.21 (talk)

SVG version of Protein-primary-structure.png ?
I went to the source of 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. (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) —Preceding unsigned comment added by Mdanziger (talk • contribs)
 * Couldn't get the svg to work either. But it does work to make it bigger (transform->scale) and then export as bitmap. Narayanese (talk) 17:38, 16 October 2008 (UTC)

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 this paper for a discussion of the terms "essential" and "non-essential" and this paper for a relatively recent review on the topic. Tim Vickers (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. —Preceding unsigned comment added by 140.193.67.28 (talk) 21:57, 28 February 2009 (UTC)
 * 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. 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. Tim Vickers (talk) 17:08, 2 December 2008 (UTC)

Amino Acids . animation
http://francoislafontaine.com/story/moment/amino255.html

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 peptides. 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.--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. —Preceding unsigned comment added by Cubathy (talk • contribs) 09:07, 21 December 2009 (UTC)

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 —Preceding unsigned comment added by Rusconi (talk • contribs) 19:58, 29 January 2010 (UTC)


 * Fixed. 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. 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). --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". —Preceding unsigned comment added by 87.168.181.47 (talk) 14:32, 14 January 2011 (UTC)
 * 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. DMacks (talk) 15:47, 14 January 2011 (UTC)
 * He fixed it. 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. — Preceding unsigned comment added by KathosValor (talk • contribs) 08:09, 28 January 2011 (UTC)
 * 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. 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.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").  148.177.1.210 (talk) 20:33, 16 February 2011 (UTC)
 * So Wikipedia is an encyclopedia that subscribes to inaccuracy?96.54.32.44 (talk) 19:05, 17 February 2011 (UTC)
 * If reliable sources describe the world inaccurately, then yes, so do we. Verifiability, not truth.  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. Biophys (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. 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.Biophys (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. 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. 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 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.  -- Ed (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.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. 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.\ 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". 96.54.32.44 (talk) 08:44, 20 February 2011 (UTC)


 * To me, that looks like an excellent revision. Many thanks, 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.). Biophys (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 + pKaR), where pKaR is the side chain pKa. Cysteine also has potentially negative side chain with pKaR = 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(pKaR + 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. 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.Biophys (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. 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 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). — Preceding unsigned comment added by 149.171.197.22 (talk) 01:48, 16 August 2011 (UTC)
 * The primary CIP priority check is highest one attachment, not the total of all attachments (check Cahn–Ingold–Prelog priority rules #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. 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? 122.106.52.228 (talk) 09:12, 16 August 2011 (UTC)

Introduction is too technical.
I can't understand the introduction at all, is there a simple way of writing the opening paragraph that does not include technical terms? I came here looking for a tiny bit more detailed information on dietary requirements and feel the introduction is aimed at a more technically aware group of people. 101.173.195.52 (talk) 07:22, 1 February 2012 (UTC)
 * Have you seen Protein (nutrient)? Graham Colm (talk) 07:34, 1 February 2012 (UTC)

repeating
"these include nucleophilic addition, amide bond formation and imine formation for the amine group and esterification, amide bond formation and decarboxylation for the carboxylic acid group". 109.160.135.18 (talk) —Preceding undated comment added 07:10, 3 July 2012 (UTC)
 * Right. First it is one among a list "...for the amine group" and the other among a different list that happens to include this same item "...for the carboxylic acid group". It's a comparison of the two separate parts, and you correctly noted that one reaction applies to both: it's the reaction that allows linking consecutive amino acids to each other to form the peptide chains found in all protein structures. DMacks (talk) 07:22, 3 July 2012 (UTC)
 * thanks 109.160.135.18 (talk) 09:21, 3 July 2012 (UTC)

What a mess the lede is
For a general article on Amino Acids, the lede slips back and forth between categories and terms without discrimination: all amino acids, standard amino acids, alpha-amino acids, the 22-total-or-21-human proteinogenic amino acids and the rest. The lede poorly delineates these so it's wrong in too many places ("amino acids serve as the building blocks of proteins"? Not in my textbook. Some do, some don't; if it means the 21-or-is-it-22-who-knows proteinogenic amino acids it doesn't say clearly and the wiki title is about amino acids generally, so it's incorrect). We also never find out if "standard", "alpha-amino" or "proteinogenic" amino acids are the same thing or if not their differences (sources differ), so we are left to guess the differences and which one the lede means at any point it discusses "amino acids" without a qualifier.

What a mess. I'm going to try and clean it. Can someone check I got it right, fix or add good cites, and not be too hard on me if it's not perfect. James 173 — Preceding unsigned comment added by James 173 (talk • contribs) 00:37, 9 September 2012 (UTC)


 * I applaud your effort, but I'm afraid you're overcomplicating it. The lede of an article like this should be at least broadly accessible to an intelligent high school student.  A high school student shouldn't necessarily be able to understand all of it, but should at least come away with a clear grasp of the most essential facts, which as I see it are (1) proteins are chains of amino acids; (2) an amino acid consists of a central carbon atom with four things attached to it:  an H, an amine group, an acid group, and a variable "payload"; (3) amino acids can be chained together by means of peptide bonds, which bind the amine group of one to the acid group of another.  Concerning cites, my feeling is that for basic textbook material of this sort they are not so essential -- they are crucial if something comes into dispute, but otherwise it is more important to be correct and understandable than to have everything rigorously sourced.  In many Wikipedia articles the convention is that things in the lede don't need to be cited at all -- they should be repeated in more detail in the body, and cited there. Regards, Looie496 (talk) 03:33, 9 September 2012 (UTC)


 * The cites explanation reassures me. It should be accurate too, the old one was wrong because it didn't do what the page says. Wikipedia:Manual of Style/Lede section says an "introduction to the article" and a "summary of its most important aspects" that can "stand alone as a concise overview" and "summarize the most important points".


 * For amino acids this means mentioning: (4) amino acids are an important component in the human body, being its 2nd most major component after water; (5) brief touch on major amino acid categorisations or families [this has "stand alone importance" & is also essential as context for subsequent alpha-amino acid mention]; (6) "amino acid" is often used as a reference for an extremely narrow subgroup, just 20-22 of the 500+ "full range" of amino acids [major confusion point for understanding]; (7) stereoisomerism is an important aspect of amino acids [although anything beyond a brief mention is too much]; (8) correct clear distinction of alpha (et al)-amino acid, proteinogenic amino acid, standard amino acid, and essential [& hence conditionally e.] amino acid; (9) be clear amino acids' biologically importance is not limited to protein, they have "stand alone" non-protein importance too; (10) not limited to alpha and standard amino acids, non-standard and non-alpha amino acids perform crucial roles too [and some examples of those roles]; (11) not limited to one function each [monofunction], standard and non-standard amino acids can both have multiple bodily roles [and proteinogenic/standard amino acids can be important non-proteinogenically]; (12) amino acids have exogenous relevance in the wider commercial & scientific worlds.


 * None of these is minor or expendable to summarise amino acids' "most important points" or provide a "concise stand-alone overview". I tried, that's the minimum it comes down to. It's a big topic, those 12 cover it. PS The lede was happy to spend 30 words on how big side-chains are but not mention amino acids act as neurotransmitters. I think it's secondary & a waste of space in the lede [mention of side chains suffices] but I can't figure if removing breaks a rule. Does it? James 173. James 173 (talk) 08:52, 9 September 2012 (UTC)


 * I removed that sentence, it looks much better without. James James 173 (talk) 10:20, 9 September 2012 (UTC)


 * Agree with James 173. The lede should be more of a summary; most of those points should be relocated below the TOC, if they are not already duplicated there. Kortoso (talk) 23:43, 13 December 2013 (UTC)

more info please
hello!

please include in the aminoacid table, info like: acidic basic

acyclic cyclic

buried???

aliphatic aromatic

hydrophilic hydrophobic

size

surface???

molecular weight

saturared??? — Preceding unsigned comment added by 195.251.115.2 (talk) 13:03, 26 October 2012 (UTC)

D-, L- isomers
Could someone clarify the origin and importance of D- and L- designations as applied to amino acids? I realize that they are ambiguous, and almost always conform to R and S, but as a non-chemist I would like to understand what utility they have in biochemistry. Specifically, I don't get the supposed correspondence to D- and L- isomers of glyceraldehyde - what am I missing? lifeform (talk) 22:20, 1 May 2014 (UTC)
 * Whatever terminology one uses to identify them, the chemical fact is that there are two different 3D geometric forms: they are mirror images of each other (like your hands are the same as each other in terms of local shape, finger order, knuckle direction, etc. except for being completely opposite as whole objects. Most biological molecules have this property, including amino acids (and by extension the proteins made from them) and the enzymes and other molecules that bind to them. If the AA has two forms and the enzyme has two forms, there is a "matched" and a "mismatched" pairing (like putting your left and right gloves on correctly or getting them mixed up). Only one way works, because the other way the AA doesn't fit right (either it doesn't fit at all, or it winds up forming a mis-shapen or non-functional complex). So once you have one AA or enzyme, it requires the "right" binding partner, which means other things that bind to it must also match, which means other things that bind to that must match it, etc etc, and suddenly we wind up with virtually every case of a given class of molecules having the same left or right form so that they all can inter-operate.


 * Glyceraldehyde is another example of a molecule that has two geometric forms (the technical term for them is "stereoisomer"s, or more specifically, "enantiomers"). For consistency, scientists like to use the same terminology as much as possible, or at least in many analogous cases. For whatever reason, D/L had been used to identify the two different enantiomers of glyceraldehyde so someone said "hey, both of these have a central chiral carbon, with a carbonyl, a single-bonded O/N, an H, and another carbon (with possibly other things beyond that)". Serine is the closest relationship: the only differences are whether the carbonyl is an aldehyde vs acid group, and whether the single-bonded atom is O vs N. DMacks (talk) 01:39, 2 May 2014 (UTC)


 * Thanks for that, DMacks. I'm starting to see that the D- and L- concepts are more pertinent to life processes than R and S - e.g. L-cysteine (like L-serine) fits biochemically, even though its R rather than S. Thanks. lifeform (talk) 07:07, 2 May 2014 (UTC)

A question regarding the formulas, drawings and renditions
A reader wrote into Wikimedia raising an issue about the amino acids articles. I don't have the subject matter expertise to know whether this observation is accurate or not so I asked for permission to post the observation to the talk page. I hope others can weigh in on whether this observation is valid. I provided a link to this page to the person the road in and encouraged them to contribute.-- S Philbrick (Talk)  19:31, 17 September 2014 (UTC) The backbone structure of the amino acid had what I feel is an impossible conformation. At any pH it is impossible (at least to the best of my knowledge) for a primary amino group to be deprotonated (C-NH2, instead of C-NH3+) and the carboxyl group be protonated (CO2H instead of CO2-). This is primarily because the difference between their pKa's is roughly 5 (the Amino group being ~8 and the Carboxyl group being ~3, which makes the carboxyl group many orders of magnitude more acidic, and thus, prone to lose a proton), which means short of some very extenuating circumstances there should be no circumstance in which the carboxyl group is protonated and the amino group is not. As such I would suggest all renditions be replaced with either the zwitterion (NH3+ and CO2-) form found typically at pH of 7, or the fully protonated, or fully deprotonated forms as the standard across the pages.

This problem I have found is present in literally every one of your pages on the 20 amino acids (http://en.wikipedia.org/wiki/Histidine, http://en.wikipedia.org/wiki/Isoleucine , etc.) and the primary landing page for the amino acids in general (http://en.wikipedia.org/wiki/Amino_acid). This problem is in the chemical formula, structure drawings, and computerized renditions in the system. As such I would like to request either that they all be fixed, or that I be informed as to why they are correct and I am not.

This chemical analysis is correct (and may even be more complicated for cases where the sidechain is also able to be protonated or deprotonated). This is in agreement with, for example, Amino acid in the article (compare to the lede-thumb image that is explicitly identified as "un-ionized form", suggesting that this detail is somehow noteworthy about the diagram). I just checked a few chem/biochem textbooks, and they often do represent them in the zwitterionic form, especially when discussing chemical behavior. However, they also do sometimes use "each site neutral" diagrams (some books often, some only occasionally). That's in keeping with the names "amino" and "acid" (the non-ionized groups) vs for example "ammonium" and "carboxylate". IUPAC doesn't seem to define "amino acid" itself, but the White Book (formally from IUBMB, linked from the IUPAC Gold Book) does have "amino-acid residue in a polypeptide", which uses solely the neutral groups when discussing these sections of them (a polypeptide is a multi-component chain that still runs from an amino on one end to an acid on the other).

Looking into wider reference material, I am often seeing them as all-neutral, for example, Sigma's full table (and every one of its catalog entries for the individual chemicals). I checked the links to external databases in the alanine infobox, and every one exclusively uses diagrams and terminology for the all-neutral form.

WikiProject Chemicals set the standard of representing all sorts of chemicals in their neutral forms in general (including amino acids and other acid–base mixtures). I can't find the formal guideline itself, but here are two discussions mentioning it. DMacks (talk) 20:14, 17 September 2014 (UTC)

pakki
pakki is a sonki pakki is a monki pakki is sinki pakki is a panki''' — Preceding unsigned comment added by 175.157.82.216 (talk) 15:11, 2 February 2015 (UTC)
 * So which is it? Double sharp (talk) 06:48, 22 September 2015 (UTC)

Double counting selenocysteine?
Right now it says there are 23 proteinogenic amino acids on the page. 21 naturally synthesized and 2 specially synthesized, but both groups contain selenocysteine. Could someone change that to 22? Thanks — Preceding unsigned comment added by 173.48.0.247 (talk) 15:13, 28 August 2015 (UTC)

Detailed Information on How Amino Acids are produced in production needed
Detailed Information on How Free Form Amino Acids are produced for the health food industry is needed very much to improve the articles on each amino acid. I have read that a certain amino acid is produced by fermenting chicken feathers. I have also read that L-Cysteine that is an ingredient in some breads as a dough conditioner is made from Chinese people's hair. I have read that a GMO bacteria is used to increase the production of L-Tryptophan by certain manufacturers. The articles due mention that fermentation is used in the production of amino acids but lacks detailed information on how this is done and the organic materials that are used that are fermented. This information is needed very much to improve the articles for each one of the amino acids. 64.132.187.90 (talk) 22:15, 1 February 2016 (UTC)