Talk:Amino acid

message: Regarding this piece: 
"After removal of one or more amino groups, the remainder of the molecule can sometimes be used to synthesize new amino acids, or it can be used for energy by entering glycolysis or the citric acid cycle, as detailed in image at right."
I think someone could add gluconeogenesis, at least, and maybe also the ketogenic pathways.
:In fact, "the image at the right" puts it, so maybe someone could set it straight between text and image.
I also wasn't aware of aminoacids entering glycolysis, unless it was for gluconegoenesis, and the image on the right also doesn't show any support to it. 
In the end, it would be like: citric acid cycle, (glycolysis), ketogenesis, and gluconeogenesis
I just won't edit it by my own decision, I suppose.
--Orangutan45 (talk) 05:03, 24 May 2016 (UTC)
thread_title:  About AA's catabolic pathways 

message: Why are all the amino acids not shown in their zwitterionic forms in the main svg? At physiological 7.4 pH, this is what they would be, right? Moine Bouddhiste (talk) 12:28, 12 November 2016 (UTC)
replies: text: Sure. But see #A question regarding the formulas, drawings and renditions among many other such discussions. DMacks (talk) 06:35, 14 November 2016 (UTC)
replies: text: I could not open the link for #A question. I do feel that the amino acids should be shown at physiological pH. Unionized amino acids are not naturally found. D.Bhandal (talk) 19:21, 21 January 2019 (UTC)
replies: text: The link is currently archived at Talk:Amino acid/Archive 3#A question regarding the formulas, drawings and renditions. Alexcalamaro (talk) 15:55, 22 August 2021 (UTC)
replies: text: This doesn't seem to be fixed despite the question being raised in 2016. Unfortunately all the diagrams ought to be changed, but I don't know if I have the skill or energy to do that. The zwitterion section is like a biochemistry textbook of the 1960s: zwitterions are mentioned, because a physical chemist has said that they ought to be, but then the authors make it clear that they don't believe a word of it by going back to wrong structures for the rest of the book.   Athel cb (talk) 11:59, 14 September 2021 (UTC)
replies: text: I added a note to the description stating it depicts the neutral instead of actual form, though ideally the file would be remade with the zwitterions. It's a bit weird when looking at the charged AAs', ie. Asp's side chain is deprotonated but the carboxyl group isn't, even though carboxyl's pKa is lower 30103db (talk) 19:13, 3 October 2023 (UTC)
thread_title:  Zwiterionic AAs in the 21 AAs svg 

message: Should there not be a positive charge on the NH of the imidazol ring of histidine at physiological pH?  — Preceding unsigned comment added by Moine Bouddhiste (talk • contribs) 14:08, 12 November 2016 (UTC)
replies: text: The table says that its sidechain is 90% neutral, only 10% in the charged form. DMacks (talk) 06:34, 14 November 2016 (UTC)
replies: text: If the table says that then the table is, I feel sure, wrong. However, "feel sure" isn't good enough, but so far I haven't found a reliable source. I'll continue looking. I have a Merck Index in my office, and maybe it's there.   Athel cb (talk) 08:29, 15 September 2021 (UTC)

text: The diagram shows it as a member of the group of amino acids that have a positively charged side chain along with arginine and lysine, which implies that there is a positive charge on the side chain. But none is to be seen. It seems to be a clear case of self-contradiction. Polar Apposite (talk) 12:17, 19 December 2022 (UTC)
thread_title:  Missing positive charge on NH of imidazol ring of histidine 

message: This is old terminology. According to the IUPAC Gold Book, an imino acid needs to have both imine and carboxyl functional groups. Proline instead has a secondary amine group. Double sharp (talk) 11:26, 26 November 2016 (UTC)
replies: text: Agreed, and Amino acid#General structure looks like a good explanation of current and historical details. The other sections need to be brought in line to relegate "imino" to a secondary detail. DMacks (talk) 03:20, 27 November 2016 (UTC)
replies: text:  as a starting point, do you agree with the §General structure statements? DMacks (talk) 03:32, 27 November 2016 (UTC)
replies: text: Yes, that looks fine to me. Double sharp (talk) 03:58, 27 November 2016 (UTC)
thread_title:  proline as an imino acid 

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thread_title:  External links modified 

message: It's huge -- 555 words. That's surely too long. I don't have the interest or expertise, but hope someone else does. 60.248.185.19 (talk) 05:16, 1 June 2018 (UTC)
replies: text: I have moved a large part of it to the biochemistry section, but it can probably be improved.  Athel cb (talk) 12:28, 17 September 2021 (UTC)
thread_title:  Lede needs a good edit 

message: I'm not sure how or where to put it, but some explanation of how d-amino acids interact with multi-cellular biochemistry should be included.  I have found various references to "d-amino acids are toxic to humans" on the internet, but none of them explain how.  The sources I have found that say that are mostly abstracts for biochemical papers, so I assume they know what they are talking about.  Nevertheless, this article does not even contain the statement "D-amino acids are toxic to most life" or its converse "d-amino acids are benign to most life". 66.219.236.172 (talk) 07:11, 8 July 2018 (UTC)
replies: text: Neither of those statements is blanket true, and we certainly couldn't say so without a cite to a reliable source. Some D-amino acids might be toxic by certain routes of exposure. There is comparably little of it in our diet (based on low occurance due to difficulty in biosynthesis). But some D-amino acids are found naturally in us as part of major biochemical processes (as discussed in the article). Feel free to post links to some abstracts. DMacks (talk) 14:00, 8 July 2018 (UTC)

text: welcome to Wikipedia! Please feel free to edit the article itself to update that section. In the mean time, I left a note there that the current content is not up-to-date. DMacks (talk) 20:07, 28 July 2019 (UTC)
replies: text: {Maybe that ref should go into D-Amino acid, which would benefit from some additional editing.--Smokefoot (talk) 02:08, 29 July 2019 (UTC)
thread_title:  d-Amino Acids: Toxic or Not? 

message: Some Human Genetic Disorders Affecting Amino Acid Catabolism is a recently created subsection with a table, under Catabolism. Is it possible that the table was copied verbatim from the reference: Jain, J. L. Fundamentals of biochemistry. New Delhi: S. Chand and Co. ISBN 8121903432. OCLC 818809626. David notMD (talk) 09:24, 25 September 2019 (UTC)
replies: text: One of a pool of presumably student editors, with poor contribution habits. I object editorially, as being too specialized/detailed for this main "amino acid" article, so I'm removing it. DMacks (talk) 03:35, 9 December 2019 (UTC)
thread_title:  Copyright violation? 

message: In the lead, in the sentence, "In the form of proteins, amino acid residues form the second-largest component...", would it be ok to link the whole term 'amino acid residues' (as I have done here) to the specific sub-section in the chemistry article which does eventually explain 'residue' in a biochemical/protein context, instead of as it is currently, which just links the single word 'residues' to the whole chemistry article about residues in general? That article starts by giving a more general definition of 'residue', which general definition could initially be confusing to some. Further on down in that article is the relevant sub-section which defines residue in a more protein-relevant manner, and that's what I would think to link directly to.  UnderEducatedGeezer (talk) 04:36, 28 December 2020 (UTC)
replies: text: Unless it might be better to link the phrase to the sub-section immediately before the biochem sub-section, Residue_(chemistry)#Characteristic_units_within_a_molecule? UnderEducatedGeezer (talk) 04:41, 28 December 2020 (UTC)
thread_title:  'amino acid residues' -- link more directly to what it means in this context? 

message: The amino acid in the main figure had D configuration. This might be confusing for some readers as mostly L-amino acids are used in biology, industry, research etc. I myself tried to figure if the stereoisomer I drew is in the correct configuration by comparing to that image. Luckily I compared also with other sources. 185.175.34.246 (talk) 12:03, 13 June 2021 (UTC)
replies: text: Excellent point! --Smokefoot (talk) 19:01, 13 June 2021 (UTC)
replies: text:  just me, or are the newly added image another image with D configuration? Christian75 (talk) 14:51, 24 August 2023 (UTC)
thread_title:  Main figure should probably be an L-amino acid 

message:  There are a great many things to be corrected in this article and I plan to do some serious editing in the next few days or weeks. I'm mentioning it here because some experts will disagree with my edits, and I want to give them the opportunity to say so. Ideally, many of the figures should be redrawn, but I'm not sure that I have the skill for that.  Athel cb (talk) 09:18, 15 September 2021 (UTC)
replies: text: What are some of the big problems?  Given the generality of the topic, we should rely on secondary or even tertiary sources, like textbooks.--Smokefoot (talk) 13:43, 16 September 2021 (UTC)
replies: text: The most serious problems concern ionization, a topic vital for understanding amino acid chemistry, but which the author of the section on zwitterions clearly did not understand. Unfortunately this affects the whole article, including most of the figures.   Athel cb (talk) 11:38, 17 September 2021 (UTC)
thread_title:  So much to do, so little time 

message: Stimulated by the question above about toxicity of D-amino acids I have been searching for a reliable source of information. I have located my Merck Index, but it does not include systematic information about that. Likewise the Rubber Book and two encyclopaedias of biochemistry that I have. I have searched Web of Science for "LD-50" AND "amino acid" and similar search strings, but although I get vast numbers of hits I haven't found anything useful. Yet there has to be a table somewhere on LD-50 values. Any suggestions?   Athel cb (talk) 13:29, 21 September 2021 (UTC)
thread_title: Toxicity: any suggested source?

message: In the figure for cationic side-chains, the fixed cation on the arginine side chain should read H2N+= rather than H3N+=. Citation: Wikipedia's own Arginine entry, among many others.  — Preceding unsigned comment added by 99.165.76.203 (talk) 14:44, 9 November 2021 (UTC)
replies: text: "NH2+" doesn't exist. Nitrogen in NH2 can have positive charge only if it accepts a proton, since the amino group acts as a small Brønsted base, thereby becoming the Ammonium (NH3+) cation. This is just simple acid-base theory. —CrafterNova [ TALK ]  [ CONT ] 17:48, 7 May 2022 (UTC)
replies: text: IP 99 is actually correct here. They state correctly that the N in question in :File:Side-chains of His, Lys and Arg.png is the one with a double-bond to the central C, the iminium-like portion. I think you are reading it to be about the N with one bond, the ammonium-like portion? An N with two bonds and 3 H would exceed octet; an iminium only has two H. DMacks (talk) 19:42, 7 May 2022 (UTC)

text:  this is your image, and is consistent with several others of yours, such as :File:Ionization of groups in proteins.png. Any thoughts? DMacks (talk) 19:45, 7 May 2022 (UTC)
replies: text:  Yes, you're right. I need to change the image. (I hope that won't mean redrawing it completely, as I don't know if I have the original file somewhere.) Maddeningly, I had it correct in the 4th edition of Fundamentals of Enzyme Kinetics -- the error must have arisen in converting the monochrome version to colour.  Athel cb (talk) 08:22, 8 May 2022 (UTC)
replies: text: For the moment I've just deleted the image as a stop-gap measure.   Athel cb (talk) 08:33, 8 May 2022 (UTC)
replies: text: Now done: corrected file uploaded.   Athel cb (talk) 09:30, 8 May 2022 (UTC)
thread_title: Cationic side-chains

message: Beginning at the second paragraph, there's a fairly editorial description of UIPAC naming convention that puts too much weight on the rarity of the structure in nature. Especially the word "fictitious," use of scare quotes, and repeating part of a probably unnecessary quote. Same bias seems to affect the caption. This may be an important issue, but deserves at most a brief mention in the lead. At least that's how it struck me. Yellowdesk60 (talk) 17:43, 2 January 2022 (UTC)
thread_title:  Nomenclature description in lead section 

message: I quote:
* The first few amino acids were discovered in the early 1900s.[6][7] In 1806, French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound from asparagus that was subsequently named asparagine, the first amino acid to be discovered.[8][9] Cystine was discovered in 1810,[10] although its monomer, cysteine, remained undiscovered until 1884.[11][9][b] Glycine and leucine were discovered in 1820.[12]
Isn't that an immediate contradiction? How could "the first few" amino acids have been discovered in the "early 1900s" when several were discovered in the previous century? --123.243.244.238 (talk) 10:24, 3 March 2022 (UTC)
replies: text: You would seem to be correct. It seems to have been corrected. Arctic Gazelle (talk) 19:36, 25 April 2022 (UTC)
thread_title:  what 

message: The diagram shows histadine without a charge on its side chain, but it is lumped in with Group A. Conversely, selenocysteine is shown with a charge on its side chain and yet is *not* in Group A. I would like to know why, and I think a lot of readers would. Also, I'd like to know what "Special Cases" (defining Group C) means. How about clarification regarding this in the caption to the diagram? Polar Apposite (talk) 10:12, 15 November 2022 (UTC)
thread_title:  The General Structure section diagram needs clarification. 

message: I edited the aliphatic side-chains section. I added "therefore" to "do not ionize", reversed the positions of isoleucine and leucine to match the General Structure chart, and added phenylalanine. I am a layman so I would appreciate a chemist checking my work here. Polar Apposite (talk) 17:29, 17 November 2022 (UTC)
replies: text: Is it supposed to say that the amino acids do not ionize, or the side chains do not ionize? Polar Apposite (talk) 17:38, 17 November 2022 (UTC)
thread_title:  The side chains do not ionize *because* they contain only H and C? 

message: It says, "The water-soluble proteins tend to have their hydrophobic residues (Leu, Ile, Val, Phe, and Trp) buried in the middle of the protein, whereas hydrophilic side chains are exposed to the aqueous solvent." 
1. Shouldn't the full names rather than the three-letter symbols be used?
2. Can a residue with a hydrophobic side chain not be hydrophobic? If so, is like being compared to like when a list of residues is contrasted with a type of side chain?
3. Is it the hydrophobic side chain that tends to be buried in the middle of the protein, or the whole residue?
4. The diagram near the top of the article lists *eight* hydrophobic (with a hydrophobic side chain, if that's different) amino acids, so is that list of five correct? Polar Apposite (talk) 18:15, 19 December 2022 (UTC)
thread_title:  Hydrophobicity 

message: It says in the caption to the color chart,"The 21 proteinogenic α-amino acids found in eukaryotes, grouped according to their side chains' pKa values and charges carried at physiological pH (7.4)" but the pKa values of most of the side chains of the alpha-amino acids are not shown, and it very much looks to me that they are grouped according to hydrophobicity, and so on, as it says in the chart and ordered according to increasing complexity going from left to right, at least in the section containing the eight amino acids classified as having a hydrophobic side chain. Furthermore, in the few cases where the pKa value of the side chain is shown, there is no grouping according pKa value that I can see. Arg, His, and Lys are in the one group but the pKa value of the side chain is 12.10, 6.04, 10.67 respectively, while Tyr, which has a side chain pKa of 10.10, which would seem to indicate that it should be grouped with those three is instead in another group. Polar Apposite (talk) 16:55, 10 January 2023 (UTC)
thread_title:  Grouped how? 

message: The following section was removed because it did not appear to fit in with the main theme, amino acids, but maybe I am mistaken:
Dietary exposure to the nonstandard amino acid BMAA has been linked to human neurodegenerative diseases, including ALS.
--Smokefoot (talk) 18:15, 29 September 2023 (UTC)
thread_title: Section removed