Talk:Amino acid/Archive 2

message: Some of the data in the two tables are same. I feel it is better to merge both and present a unified table listing all the properties. For those requiring 'Yes' or 'No' could we use numeric of '1' or '0'. This will greatly enable custom programming for protein sequences.
Nattu 23:11, 26 May 2006 (UTC)
thread_title: Need to combine the two 'property' tables

message: It looks like the arginine picture here and in the arginine article has an extra hydrogen atom.  Shouldn't the imine group be =NH rather than =NH2 ?
:The =NH2 would be correct if the protonated form (which will predominate at neutral pH) were intended, but in this case there should be a "+" to indicate the positive charge.  It looks like all of the sidechains (other than this ambiguous, wrong one) are shown un-ionized, but the alpha-amino and alpha-carboxyl groups are shown ionized, which strikes me as a strange decision. Josh Cherry 00:53, 24 Jan 2005 (UTC)
replies: text: If you guys don't mind, I'm going to redraw all these in ISIS/Draw and regularize this.  I'm going to draw them as they are ionized at pH 7.0, in the style of the chart on p. 79 of Lehninger.  Also, I'd like to actually make two forms of each image; one with a size corresponding to the current one (so it sits well in the infoboxes for individual amino acids) and one with a standard image size, so we don't have that slightly annoying "thumbnailed" look in some of the the amino acids in the chart.  That way, they should all come out at the same size.  Comments? John Sheu 02:12, 18 February 2006 (UTC)
replies: text: Makes us a sample, or two - say the aas that you think need most work  - post them on Wikipedia_talk:WikiProject_Chemicals and we (the guys who work on WikiProject_Molecular_and_Cellular_Biology, those who work on WikiProject_Chemicals, yourself, etc.) will discuss the whole thing. As for the ionization - we try not to draw them like that in the info table. It's another story if you want to show what groups are ionized inside the cell at pH 7.0, but then you should make another image, put it in the appropriate section, and add some text explaining why these and not other groups get ionized and how. -- Boris 09:58, 18 February 2006 (UTC)
thread_title:  Arginine picture incorrect? 

message: The hydrophobic nature of Cys_SH seems to conflict with the polarized nature of the sulfhydryl group. However, we need to consider the fact that the sulfhydryl group is inactive toward water molecules.
According to:
 cysteine behaves as a hydrophobic in proteins.
because it usually forms disulfide bridges. 218.102.218.18 10:00, 12 December 2005 (UTC)
replies: text: The majority of cys residues are NOT in disulfide bridges. Disulphide bridges (as a rule of thumb) will only form in oxidising environments, such as in extracellular and pericellular environments. To find a disulphide bridge in a intracellular protein is rare (although not unheard of). In protein structures, Cys residues can co-ordinate metal ions (eg Zinc-finger proteins) and are negatively charged at physiological pH. Bassophile 13:22, 3 January 2007 (UTC)
thread_title:  Cysteine - hydrophobic 

message: How do amino acids form in nature? Please elaborate in article - RoyBoy 800 05:54, 16 August 2005 (UTC)
thread_title:  Form naturally 

message: R group appears to be the correct term, at least for the proteinogenic amino acids. -- Bubbachuck 16:46, 21 August 2005 (UTC)
thread_title:  R group vs. side chain 

message: I would like 'amino acids' to also have a "layman" definition. What does it mean for the common person? How can they include amino acids into their diet? I looked up amino acids on wiki, realizing it is an important part of my nutrition, but everything I read here sounds like mumbojumbo. Is someone willing to provide a definition to human nutrition that meets the common man's understanding? A paragraph or something!
:If you're interested in nutritional issues, there's a whole section on this page and listed in the table of contents titled "Nutritional importance". That section then has an additional link to Protein in nutrition, a page that seems to be a fairly lay-accessible page. Maybe we should have a
:
:at the top of the Amino acid page? DMacks 04:09, 4 January 2007 (UTC)
thread_title: Need lay definition

message: Can somebody tell me, why glycin is supposed to be hydrophobic. It's soluble in water, isn't it.
*Yes, free glycine is soluble in water, but when it forms part of a peptide chain, the polar portions are used for bonding and only the hydrogens are left exposed to water: as such, it does nothing to increase the water-affinity of the protein (unlike, say, glutamic acid where a free -COOH group is left dangling off the peptide backbone). Physchim62 12:33, 20 October 2005 (UTC)
thread_title:  Glycin - hydrophobic????? 

message: from the article: The three-letter symbol Asx or one-letter symbol B means the amino acid is either asparagine??? or aspartic acid, whereas Glx or Z means either glutamic acid or glutamine.
Isnt it Asn. And do these B/Z refer to the acid form (i.e. not the ion), if so, then this should be made clear in the article. But in proteins they will ionize or not depending on pH, so what's the actual point? (again, explain in the article please).
ALSO,
why is there so much information in the table? Shouldn't there just be links to the individual articles (but it would be replicated anyway), and perhaps reorganize the diagrams of the strucutre? Does anyone agree with me?
: The B/Z degeneracy codes date back to the earlier days of protein analysis. If you turn a protein into amino acids by cleaving peptide bonds, you lose the Asn/Asp and Gln/Glu distinction because the peptide bond in the sidechain gets converted to a carboxylic acid (it's a peptide too). Thus, when you report the amino acid composition, you can't tell how much of the Asp was originally Asn, so you just report the amount of 'Asx' in the protein. They were also useful in early crystallography, because at low resolution, it is hard to tell the oxygen electron density from the nitrogen. Modern techniques have mostly eliminated the need for those degeneracy codes. -- 20:22, 21 December 2005 (UTC)
thread_title:  the table 

message: The imidazole ring in your table doesn't have the pi-bonds located in the right orientation.  The biochemistry book that I have in front of me (Lehninger, "Principles of Biochemistry", p. 79) shows a different orientation.  Just wanted to let you know, aside from that, everything else looked correct.
Pjlmac 03:56, 6 January 2006 (UTC)
replies: text: The structure you see in Lehninger's book and the one here are the two His tautomeric forms  (scroll down to the second image). You should pay more attention to the organic chemistry classes, where they teach about resonance structures and π-clouds. -- Boris 06:25, 6 January 2006 (UTC)
thread_title:  Histidine picture isn't correct 

message: I thought it is 22 not 20?
:If you are talking about the amino acids that have their own tRNA - the correct number is 21, the usual ones plus Selenocystein. If you are talking about the amino acids that make up the proteins - at least 50 - the usual ones plus their non-revirsable covalent postranslational modifications such as 4-OH-Pro, 4-OH-Lys, γ-carboxy-glutamate, Cittruline, etc., i'm pretty sure these modifications result in number greater than the mentioned but these are the most common. If you are talkin about all the amino acids that are naturally synthesized - probably several hundred. -- Boris 14:35, 20 January 2006 (UTC)
replies: text: There are 20 common amino acids and 22 naturally genetically encoded amino acids (counting selenocysteine and pyrrolysine) so yes you are right. As of Sept. 21st 2006, there are 22 that are naturally genetically encoded "proteinogenic" amino acids. --Antorjal 07:31, 21 September 2006 (UTC)
thread_title:  How many are there? 

message: I'm moving this comment left by 72.224.127.74 in the article to here: "STRUCTURE OF ARGINIE IS SHOWN WRONG IN THE TABLE...DOUBLE BOND WITH -NH2 IS SHOWN AND SINGLE WITH -NH..SHOULD BE JUST OPPOSITE".  I agree that one of the nitrogens of the guanidine has one too many hydrogens.  (Or, depending on pH, that nitrogen should have a positive charge.) Edgar181 19:13, 27 January 2006 (UTC)
thread_title:  Structure of arginine 

message: These two molecules look the same.  Is the Alanine molecule having an extra carbon attached to the same carbon the amino group is?
To me it looks like the hydrogens are declared specifically in Alanine, but implied in Glycine.  Maybe I do not know how to read the structure. —The preceding unsigned comment was added by 12.10.127.58 (talk • contribs) .
:Organic structures often omit the explicit "C" label for carbons; a line that ends with no label thus means there's a carbon there (with as many hydrogens as appropriate for standard valence). Thus, alanine has a proton and a methyl attached to the backbone carbon, whereas glycine has two protons. DMacks 20:42, 1 June 2006 (UTC)
replies: text: You mean, hydrogen not proton? -- Boris 00:28, 2 June 2006 (UTC)
replies: text: The standard hydrogen nucleus is just a proton:) But yes, to be pedantic, hydrogen. DMacks 15:02, 2 June 2006 (UTC)
replies: text: Alanine indeed has an extra methyl group on the alpha-carbon. The 2 C-alpha hydrogens are not declared specifically in Gly as it is non-chiral. Bassophile 13:16, 3 January 2007 (UTC)
thread_title:  Alanine/Glycine 

message: In the overview section, the list of 8 essential amino acids plus histidine and arginine (conditionally essential?) agrees with most sources I have seen.
Under the heading 'Nutrition' there is a list of 9 essential amino acids that includes histidine as essential and then mentions alanine as sometimes essential. I've never seen alanine included as essential anywhere else. The Nutrition section actually seems redundant so perhaps should be removed. Or at least changed to agree with the rest of the article. Obvious1 02:08, 4 July 2006 (UTC)
thread_title:  Essential amino acids 

message: The table specifies asparagine and glutamine as neutralized versions of aspartic and glutamic acids. Is seems to me that the difference is not in neutralization, but replacement of the carboxyl with an amide. I realize that the amide is not as good an electron donor as the carboxyl it replaces, but is neutralization really a good description of this process?Tuckerekcut 18:36, 12 August 2006 (UTC)
thread_title:  ASP/ASN and GLU/GTN 

message: In working on the protein article and some related tasks, I was surprised to find we don't have a list of standard amino acids or similar article. The inclusion of all 20 structures and the large amount of tabular data here break up the prose of this article but would serve their purpose well on a separate data page. Any opinions on moving them and prominently linking from here? Opabinia regalis 05:06, 26 August 2006 (UTC)
thread_title:  Separate tabular data to its own page? 

message: I noticed that there wasn't anything about them in the article. Should a section be added on them, should they be added to an existing section or are they not worth mentioning? - Bisected8 14:35, 6 December 2006 (UTC)
replies: text: Come to think of it, it's actually quite bad that the only mention of zwitterions in this article is in an image caption; this should definitely have a short paragraph somewhere. If you're interested in writing one, feel free! Opabinia regalis 00:49, 7 December 2006 (UTC)
replies: text:  I've added a bit as a subection of the section Reactions - Bisected8 21:19, 7 December 2006 (UTC)
thread_title:  Should a section on zwiterions and isoelectric points be added? 

message: I'm considering moving values to List of standard amino acids table and leaving just a "hydrophobic?" flag here on the Amino acid table. Comments? DMacks 22:34, 2 February 2007 (UTC)
replies: text: The number refers only to an amino acid residue in a protein, so strictly should not be in a table dealing with amino acids without further explanation. Also if we don't give pKas for the side chains, I don't see why we should give this number. Either both or neither. TimVickers 22:46, 2 February 2007 (UTC)
replies: text: It's just that I was wondering about the hydropathy index and there was no article in wikipedia. So I looked it up and wrote it here too. I did not really think about where to put the values. I just thought, it might be good to have them somewhere. FelixP 23:13, 2 February 2007 (UTC)
replies: text: Thanks Felix, it's good to have them, but I think DMacks is right that they belong on the page with the more numerical data. Actually I really thought they were on that page already. Opabinia regalis 00:31, 3 February 2007 (UTC)
thread_title:  Hydropathy index in AA table 

message: BCAA redirects here but it is not in the article text. The text "BCAA" should be mentioned somewhere in the article, or the redirect removed. What is BCAA? ··gracefool |☺ 23:26, 4 February 2007 (UTC)
replies: text: "Branched Chain Amino Acid" I'll add it somewhere. TimVickers 01:07, 5 February 2007 (UTC)
thread_title:  BCAA 

message: Personally, I feel that a better understanding of amino acids can be reached if they are presented in their zwitterionic forms, as the vast majority of conditions under which they exist has the dominant form being the zwitterion. Some textbooks note that this is true under physiologcal conditions, but this may lead readers to think that they are uncharged outside of a living organism, when in fact, even when extracted, amino acids exist as a salt. (see http://bip.cnrs-mrs.fr/bip10/zwitter.htm). Cless Alvein 01:03, 5 February 2007 (UTC)
thread_title:  Most pictures currently represent amino acids in their uncharged forms