Talk:Proteinogenic amino acid

message: Shouldn't Proteinogenic amino acid and List of standard amino acids be combined & maybe renamed Standard amino acids. Gregogil 20:22, 5 April 2007 (UTC)
replies: text: I don't see why not, but Standard amino acid might be preferable given the convention of singular article names. I've added the merge tags to both articles now.--Eloil 03:15, 19 April 2007 (UTC)
replies: text: Yes merge. --Sadi Carnot 05:04, 4 June 2007 (UTC)

text: I agree with Reesei for the same reasons. Let's not forget the non-standard proteinogenic amino acids. Antorjal 19:49, 2 August 2007 (UTC)
thread_title:  Combining 

message: I would like to propose that the 22 amino acids be listed as proteinogenic amino acids.  This would make the most sense as a page header.  I do agree that the 20 listed could be considered "standard" amino acids in the proteinogenic amino acid page.  Therefore the standard amino acid page should be removed as it has been.  I think "canonical" is a better descriptor in this case as found in a recent review.  This review also supports 22 proteinogenic amino acids. 
This article now asserts that there are '22 standard amino acids'. Surely there are 20 standard amino acids? The standard amino acids are those that are directly encoded by the genetic code. Nature is full of proteins containing modified amino acids. Pyrrolysine in particular is not found in eukaryotes. Well it's hardly a 'standard' amino acid then is it? Selenocysteine is a modified amino acid. While technically it may be correct to say that there are 22 'proteinogenic' amino acids, they are not at the same time 'standard' and I feel that the article should be redrafted to reflect this.
Johnpretty010 (talk) 21:55, 17 June 2011 (UTC)
thread_title: 22 proteinogenic amino acids

message: The "Remarks" section at the end discusses the properties of each amino acid in protein, but also says whether each is "Essential in humans".  This information is redundant with the previous table, to the extent it matches (it doesn't: see Histidine).  And the two types of information don't really fit together anyway.  If it were expanding on the previous table, it might make sense, but it actually has less information (nothing about conditionals).  I'll remove it if no one objects.  —Preceding unsigned comment added by Bennetto (talk • contribs) 23:44, 21 June 2008 (UTC)
replies: text: Yes, the "Remarks" seems to be just a dumping-ground of info. I say feel free to do anything to merge or organize/separate out any of it into its own discussion/table. The (bio)chemical information in this section does seem useful but would be better to push it all somewhere else (maybe each amino-acid's own page?) instead of some cherry-picked highlights here (it's less "hard-facts" than the other data tables). DMacks (talk) 06:38, 23 June 2008 (UTC)
thread_title:  Remarks 

message: The MW for Selenocysteine given here, 169.06, does not match page http://en.wikipedia.org/wiki/Selenocysteine 168.053 g/mol  —Preceding unsigned comment added by 84.68.181.173 (talk) 16:46, 20 July 2008 (UTC)
replies: text: Corrected to 168.053. I wonder if the former value was for some ionic form (though would probably require pH much lower than physiologic to get protonated)? DMacks (talk) 18:43, 20 July 2008 (UTC)

text: Fixed --Kkmurray (talk) 15:20, 8 January 2010 (UTC)
thread_title:  Molecular weights 

message: Cysteine is not acidic, it's neutral.  Who thought it was acidic, why, and can someone remove the incorrect information? 132.198.84.83 (talk) 19:36, 18 September 2008 (UTC)
replies: text: Cys has a pKa of ~8, so could be considered acidic.  Inside the cell it is not, since it is involved in disulfide bond formation, which is affected by disulfide exchange by glutathione and thioredoxin more than pH.  This is why biochemistry books don't list it as acidic. Qchristensen (talk) 01:42, 20 March 2009 (UTC)
replies: text: There's a reducing environment inside most cells, so intracellular Cys tends to be in the -SH form.  Disulfides are found primarily in extracellular proteins where an oxidizing environment exists. It's a historical accident that the first two proteins to be sequenced were insulin and ribonuclease, both extracellular, and as a result the disulfide bond gets overemphasised in some textbooks.96.54.32.44 (talk) 06:11, 16 February 2011 (UTC)
thread_title:  cysteine 

message: I added a table of residue masses for mass spectrometry. --Kkmurray (talk) 20:01, 6 January 2009 (UTC)
thread_title:  Amino acid residue masses 

message: Hydroxyproline is given as an example of a non-proteinogen, but on the hydroxyproline it is called a proteinogen. Correct one of them someone?  —Preceding unsigned comment added by 212.248.169.208 (talk) 18:40, 16 August 2009 (UTC)
replies: text: Hydroxyproline and hydroxylysine are formed by in situ hydroxylation of Pro and Lys respectively after they have been incorporated into the polypeptide chain.96.54.32.44 (talk) 06:07, 16 February 2011 (UTC)
thread_title: Hydroxyproline

message: Given the pKas of alpha amino and alpha carboxylate groups, the zwitterion form is by far and away the predominant form in aqueous pH 7 and crystalline states. The ratio of zwitterion to neutral is about 10^7 : 1.96.54.32.44 (talk) 06:18, 16 February 2011 (UTC)
thread_title:  What, no zwitterions? 

message: I couldn't see a reference to the source of information about occurrence in human proteins (Gene expression and biochemistry section).   I assume these percentages are molar fractions, rather than by mass.  
Robin Whittle (talk) 11:39, 14 February 2013 (UTC)
thread_title:  Occurrence in human proteins - molar or mass? 

message: I wonder why N-formylmethionine is not considered a proteinogenic amino acid (or amino acid derivative). The AUG codon codes it in a normal way, and it has its own specific tRNA. It is used in protein biosynthesis in bacteria, mitochondria and chloroplast (so also in eukaryotes) but not in archaea. Technically, it is a amino acid derivative rather than a normal amino acid, but it is coded in the genetic code and added into proteins by the normal mechanism. Therefore, there would be 23 proteinogenic amino acids. I think the case of N-formylmethionine should be explained in the article either it is considered amino acid or just a derivative.--Miguelferig (talk) 19:10, 2 June 2013 (UTC)
replies: text: Its own article calls it a proteinogenic AA and explains how it's encoded and involved in translation/transcription. But that article also says it's usually removed as part of the protein synthesis process, so it might be outside the definition of "proteinogenic" as used in the article here? This whole business of counting is pretty crazy and subject to interpretation/context (whose genetic code? etc.), I've only ever seen high-school and freshman-college teachers care. See also the next section. DMacks (talk) 21:16, 10 July 2013 (UTC)
replies: text: The main argument to say that N-formylmethionine is a proteinogenic amino acid is that the AUG codon codes it. However, the AUG codon is the only codon for Methionine; this means that, if we accept N-formylmethionine as a proteinogenic AA for this reason, then Methionine isn't a proteinogenic AA anymore: only one of them can meet this condition at the same time. In either case, there are 22 AA, not 23. I'm not a specialist, so that's just what I understand by myself, but what do you think about it? --Grelot-de-Bois (talk) 03:29, 7 September 2014 (UTC)

text: N-Formylmethionine says that it "plays a crucial part in the protein synthesis of bacteria, mitochondria and chloroplasts. It is not used in cytosolic protein synthesis of eukaryotes".  My reading of various snippets is "there are 21 proteinogenic AAs in eukaryotes" and "there are 23 proteinogenic AAs in prokaryotes".  If that reading is correct, it seems like we should change the numbers listed in this article to include N-formylmethionine or change its title and wording to make it clear that it's referring primarliy to eukaryotes and delineate the references to prokaryotes. --Wcoole (talk) 00:45, 27 October 2015 (UTC)
thread_title: N-formylmethionine

message: The introduction is one of the best written I have had the pleasure of reading. It is just what all Wikipedia science articles should be, but many fail at. It is a sterling example of how a collaborative writing effort can lead to clear, concise, complete prose. Thanks to all who contributed. Nick Beeson (talk) 14:13, 27 June 2013 (UTC)
thread_title:  Beautifully Said 

message: In the Proteinogenic amino acid#Side chain properties§Side chain properties table, there are columns for pKa and pH. The former is a value, and the latter is either blank or a word/phrase such as strongly/weakly acidic/basic. But the pKa value trends don't agree with the pH descriptors. Values 3.90–8.18 are "acidic" and 10.46 is "weakly acidic", but 6.04/10.54/12.48 are "weakly basic"/"basic"/"strongly basic" respectively. That is, the "weakly acidic" value is well beyond the "weakly basic" one and almost the same as the "basic" one, and the "weakly basic" one is in the middle of the range of "acidic" ones. I assume the senses of acidic and basic aren't direct opposite equilibrium-constant ideas (not literally predominance of one or the other side of the same equilibrium equation), but this really needs to be explained clearly. DMacks (talk) 05:01, 12 December 2016 (UTC)
replies: text: I've made changes and quoted values determined for residues within alanine pentapeptides, or at least with blocked N- & C-termini, and in dilute salt solution. These seem the best to represent typical values for the amino-acid residues in an unfolded protein under aqueous conditions.ChiBeta (talk) 01:18, 2 February 2017 (UTC)
thread_title:  Side-chain pKa vs pH 

message: I'm having a hard time to find a source for the side-chain van-der-Waals volumes in the table of this page mentioned in the subject. To search, I use the AAindex database which I think one could see as canonical source for all things related to amino acid values. More specifically, I use the aaindex1 file which is downloadable from the ftp server.
The format of the aaindex1 file makes it easy to search for values for alanine (or leucine) starting with, e.g., "6" via the Unix command line: rgrep "^[ ]\+6"
Example: the van-der-Waals volume for alanine is said to be "67" in the Wikipedia table. However, the grep given above does not find a single line in the aaindex1 file which has the required "   67" entry. Lot's of "6.x" entries, one "60." entry, one "685." entry, but no "67".
To account for multiples of ten and rounding, I also looked for lines which values would approximately match the alanine and arginine values: "67  148", as they are side by side in the aaindex file. E.g.: 'rgrep "^[ ]\+6[^ ]\+1" ' would find a line starting with "  6.6 14.8". But there, too, no luck.
The edit which brought the table into this Wikipedia entry was made by a merger in 2008 (here), but after that I cannot trace back further.
Ideas?  — Preceding unsigned comment added by BaChev (talk • contribs) 19:54, 14 December 2017 (UTC)
thread_title:  Source for van-der-Waals volume of side-chains? 

message: Tyrosine is listed in the table of properties here, and in the table of the mRNA genetic code in that article, as a polar (i.e. hydrophilic) amino acid; but the illustration in the "Structures" section of this article, and the description in the compound's own article, both classify it as hydrophobic.  The real issue is that there's no hard line between hydrophilic and hydrophobic, and tyrosine is less hydrophobic than others while still being basically more hydrophobic than hydrophilic.  But if we're going to do a binary classification, we ought to do it consistently - and the tyrosine article, and the illustration in this article, both are cited, while the tables seem not to be cited. 2607:FEA8:12A0:44D:0:0:0:C319 (talk) 02:03, 24 May 2020 (UTC)
thread_title:  Hydropathy of tyrosine