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 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. 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)
 * 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)

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)
 * 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)

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 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)
 * 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)
 * 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)


 * The alpha carbon is carbon number 2, which is a little bit confusing. It is called "alpha" because it is the first carbon in the side chain, and called "2" because it is the second carbon in the longest carbon chain in the molecule. So it's actually true that the carboxyl group (but not "the carboxylic acid group", which might not even exist as a correct term) is attached to the alpha carbon in amino acids.
 * On the other hand, since *all* amino acids are like this, by definition, it makes little sense to say that this type of amino acid "has particular importance".
 * Searching the article for "particular importance" yielded nothing so it seems this error has been corrected. Polar Apposite (talk) 14:21, 20 November 2022 (UTC)
 * Amino acids need not be alpha. Beta-alanine is the simplest one that is not. But it's the alpha series that are especially important biochemically. DMacks (talk) 18:39, 20 November 2022 (UTC)
 * I think you're right. Thank you for educating me. Maybe I was a bit tired and in a rush when I wrote that comment, or confused by all the errors in the text I was commenting on. I mean, I think I knew that, but I forgot, for some reason.
 * Googling around, I see that my error is a common one, for example: https://bio.libretexts.org/Courses/University_of_California_Davis/BIS_2A%3A_Introductory_Biology_(Easlon)/Readings/04.3%3A_Amino_Acids has "Amino acids are the monomers that make up proteins. Each amino acid has the same core structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the alpha carbon known alternately as the R group, the variable group or the side-chain."
 * Also, https://www.britannica.com/science/amino-acid has "amino acid, any of a group of organic molecules that consist of a basic amino group (―NH2), an acidic carboxyl group (―COOH), and an organic R group (or side chain) that is unique to each amino acid. The term amino acid is short for α-amino [alpha-amino] carboxylic acid. Each molecule contains a central carbon (C) atom, called the α-carbon, to which both an amino and a carboxyl group are attached. The remaining two bonds of the α-carbon atom are generally satisfied by a hydrogen (H) atom and the R group." Polar Apposite (talk) 04:01, 21 November 2022 (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)? 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! ✅--Smokefoot (talk) 19:01, 13 June 2021 (UTC)
 * just me, or are the newly added image another image with D configuration? Christian75 (talk) 14:51, 24 August 2023 (UTC)

So much to do, so little time
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)


 * "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. &mdash; 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)
 * 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)
 * 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)
 * Now done: corrected file uploaded.  Athel cb (talk) 09:30, 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)


 * The distinction between -ate and acid is technically correct as there is a difference between the two terms, though it's usually still obvious from the pH what you mean if you use the wrong one. Aspartate and glutamate are the deprotonated forms of aspartic and glutamic acid. The deprotonated form (aspartate) is most common at physiological pH, but the protonated form (aspartic acid) exists in acidic environments. Since physiological pH is simply implied a lot of the time, colloquially the terms end up being used interchangeably.
 * I think the names should not be used interchangeably in the article, because people may mistakenly believe both forms are equivalent. It may also lead to awkward wording such as "anionic glutamate" when distinguishing between the two. In my opinion, "aspartate/glutamate" should be used as the default terms when discussing amino acids as they naturally occur, unless specifically referring to the protonated form. In the svg file of the 21 amino acids, they should definitely be labeled "Aspartate/Glutamate" and not "Aspartic/Glutamic Acid", as they're categorized as having charged side chains and only the prior is charged. 30103db (talk) 20:25, 3 October 2023 (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: &mdash; 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)

Please update with: "Prebiotic synthesis of α-amino acids and orotate from α-ketoacids potentiates transition to extant metabolic pathways" & info on relation to abiogenesis
I think it may be good to add at least very brief info from/about this study and/or similar articles to the article. It's currently featured in 2022 in science like so:

"Scientists report the discovery of chemical reactions by potential primordial soup components that produced amino acids and may be part of the origin of life on Earth."

More generally and beyond this study in specific, please add some info about how amino acids are thought to relate to the origin of life on Earth (abiogenesis) and are thought to originate, including with some brief info in the lead. I find it strange that this seems to be entirely missing in the article if I haven't only overlooked it.

Useful sources for this may include: "Amino acids and the origin of life on Earth", "The origin of the biologically coded amino acids", "Undefining life's biochemistry: implications for abiogenesis" and "Small Cofactors May Assist Protein Emergence from RNA World: Clues from RNA-Protein Complexes".

Prototyperspective (talk) 17:16, 2 September 2022 (UTC)
 * The article on amino acids is already long. It is appropriately focused on present day biochemistry.  Per WP:NOTNEWS, Wikipedia shies away from "hot papers", especially when they are somewhat tangential.  The targetted refs are WP:SECONDARY (reviews) and even better WP:TERTIARY (textbooks).  --Smokefoot (talk) 19:44, 2 September 2022 (UTC)
 * If the article on amino acids doesn't even at least mention abiogenesis / the origin of life with at least a few words (doesn't have to be long), something critical (basically right in the core of the article's topic), is very clearly missing.
 * Otherwise, that is / may be a fair point – however, you could also add this info via a review (or some reviews and/or textbooks) here and I also linked some as "Useful sources" above. Prototyperspective (talk) 20:57, 2 September 2022 (UTC)
 * Oh, I see your point. Sorry to seem obstructionist.  We definitely need something beyond a mere link to the Miller–Urey experiment.  There must be books and many reviews on this topic. I also will look around. --Smokefoot (talk) 22:13, 2 September 2022 (UTC)
 * Please take a look and improve!--Smokefoot (talk) 00:01, 3 September 2022 (UTC)
 * Done. Most striking to me was the lack of at least a wikilink to the abiogenesis article and that a mention was still missing in the lead. Some of the content I added may need some copyediting and I may have phrased some things a bit inadequately. That's partly why I asked about it on the Talk page anyway. Moreover, now I haven't used any of the sources I proposed here which somebody else may still find useful to add if the content can get condensed. Prototyperspective (talk) 21:15, 5 September 2022 (UTC)

The General Structure section diagram needs clarification.
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)

The side chains do not ionize *because* they contain only H and C?
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)


 * 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)

Hydrophobicity
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)

Grouped how?
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)

Section removed
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)