Talk:Amino acid

About AA's catabolic pathways

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)

Zwiterionic AAs in the 21 AAs svg

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)

Sure. But see #A question regarding the formulas, drawings and renditions among many other such discussions. DMacks (talk) 06:35, 14 November 2016 (UTC)

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)

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)

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)

Missing positive charge on NH of imidazol ring of histidine

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)

The table says that its sidechain is 90% neutral, only 10% in the charged form. DMacks (talk) 06:34, 14 November 2016 (UTC)

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)

proline as an imino acid

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)

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)

@Double sharp: as a starting point, do you agree with the §General structure statements? DMacks (talk) 03:32, 27 November 2016 (UTC)

Yes, that looks fine to me. Double sharp (talk) 03:58, 27 November 2016 (UTC)

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Lede needs a good edit

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)

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)

d-Amino Acids: Toxic or Not?

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)

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)

This is entirely new to me (editing wikipedia). The section heading "D-amino acid natural abundance" is badly out of date. I recommend consulting a recent review article, Genchi, Giuseppe 2017. An overview on D-amino acids. Amino Acids, 49(9), pp.1521-1533. https://link.springer.com/article/10.1007/s00726-017-2459-5

It is open to the public and is very good. — Preceding unsigned comment added by Gary S. Hurd (talk • contribs) 18:31, 28 July 2019 (UTC)

@Gary S. Hurd: 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)

{Maybe that ref should go into D-Amino acid, which would benefit from some additional editing.--Smokefoot (talk) 02:08, 29 July 2019 (UTC)

Copyright violation?

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)

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)

Better words

May I suggest this improved version of the first sentence in the second paragraph that begins,'In biochemistry, amino acids having both the amine and the carboxylic acid groups attached to the first (alpha-) carbon atom have particular importance.'

In biochemistry, because amino acids have both the amine and carboxylic acid groups attached to the first (alph-) carbon atom they have particular importance.

Or better still,

Amino acids have both the amine and carboxylic acid groups attached to the first (alph-) carbon atom making them particularly importance in biochemistry.

I am not game to edit things directly, but a lot of Science articles are less well written than they could be. We live in a shockingly polarised world where people stream their education and end up either Literate or Numerate, but rarely both.

Of course, the second Paragraph begins with essentially the same content as the first, which is very poetic, but extends the article making it daunting to read. Yet it is of such fundamental importance. We are mostly made of two things and this is about one of them. There is so much to think about on so many levels and in so many dimensions. See!! I am not reading it now.

NaumTered 22:18, 28 August 2020 (UTC) — Preceding unsigned comment added by Norm Tered (talk • contribs)

Both of your suggestions change the meaning of the original sentence, which is wrong anyway. It claims that alpha amino acids have both groups on the same carbon, but the alpha carbon is in fact the one next to the carboxyl carbon. I'll change this. Further, you may claim that scientists are 'illiterate', but your prose contains basic errors. E.g. "begins,'In", "(alph-)", "(alph-)", "particularly importance". Zato123 (talk) 04:33, 14 September 2020 (UTC)

'amino acid residues' -- link more directly to what it means in this context?

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)

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)

Main figure should probably be an L-amino acid

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)

Excellent point!  Done--Smokefoot (talk) 19:01, 13 June 2021 (UTC)

So much to do, so little time

{{ping User:Smokefoot, User:Smokefoot, User:DMacks}} 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)

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)

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)

Toxicity: any suggested source?

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)

Cationic side-chains

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)

@99.165.76.203: "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)

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)

@Athel cb: 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)

@DMacks: 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)

For the moment I've just deleted the image as a stop-gap measure. Athel cb (talk) 08:33, 8 May 2022 (UTC)

Nomenclature description in lead section

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)

what

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)

You would seem to be correct. It seems to have been corrected. Arctic Gazelle (talk) 19:36, 25 April 2022 (UTC)

"Aspartic/Glutamic Acid" vs "Aspartate/Glutamate"

At certain points, the article becomes unusually passionate about this notion that the names "aspartic acid" and "glutamic acid" are incorrect (see the "Anionic side-chains" subsection) and that the only correct names are "aspartate" and "glutamate". It currrently says about the acid names: "Although the misnomer is so widespread as to be ineradicable, they should not be called acidic amino acids, because they act as Brønsted bases in all circumstances except for enzymes like pepsin that act in environments of very low pH like the mammalian stomach." (bold/italic emphasis already there in the article)

I'd like the opinion of other (bio)chemists on this. I call this overly pedantic. I want to point out that this choice is inconsistent with the names of their corresponding Wikipedia pages (currently Aspartic acid and Glutamic acid), and that the acid names are used regularly in the primary and secondary literature by (bio)chemists themselves without controversy. Also, many students are likely to encounter the acid names in their first exposures. We do not emphasize that "amino acids" are "ammonium carboxylates" at all physiological pH values or that "arginine" is "argininium", and I think these would be similarly correct-yet-too-pedantic changes to make.

In the meantime, I will edit the tone to be less aggressively "anti-acid" because I think it does not contribute to the helpfulness of the article more than a neutral discussion of nomenclature would. TungstenEinsteinium (talk) 18:30, 2 May 2022 (UTC)

Update needed for number of amino acids in genetic code

"More than 500 naturally occurring amino acids are known to constitute monomer units of peptides, including proteins, as of 2020 (though only 20^{[needs update]} appear in the genetic code, plus selenocysteine, which is encoded in a special way).

This sentence is outdated. Some sources there are actually 22 amino acids which participate in in-vivo protein synthesis, listed below:

—CrafterNova ^{[ TALK ]  [ CONT ]} 17:23, 7 May 2022 (UTC)

Comparing the article "20 appear in the genetic code" with your second ref "selenocysteine and pyrrolysine are considered the 21st and 22nd amino acids, respectively. They are more recently discovered amino acids that may become incorporated into protein chains during ribosomal protein synthesis", I think the appearance of contradiction is the result of a slight difference of words. Selenocysteine and pyrrolysine do not have their own DNA codons, but instead result from a different post-transcriptional handling of stop codons. So they are 22 proteinogenic amino acids, of which two are incorporated by processes other than the standard genetic code. However, your first ref does directly state that selenocysteine is "genetically encoded".

Pyrrolysine is only found in certain procaryotes. And synthetic biology has led to production of codons to incorporate amino acids that are not found in any ribosomally-produced proteins.

So first, we definitely need to add pyrrolysine as the 22nd when we mention selenocysteine as the 21st and clarify that we are talking about what's found currently in naturee, or else clarify that our discussion of 21 is based on certain categories of organisms found in nature. Second, we need to distinguish these two as slightly different from the other 20, while also keeping this key introduction understandable without needing to know technical terms. DMacks (talk) 17:54, 7 May 2022 (UTC)