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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)
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 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:
[1] cysteine behaves as a hydrophobic in proteins.
because it usually forms disulfide bridges. 218.102.218.18 10:00, 12 December 2005 (UTC)
Whether or not a cysteine residue is ionised depends on its pKa. When the cysteine is protonated it is hydrophobic, when it is in the thiolate form, it is hydrophillic. TimVickers 19:46, 13 March 2007 (UTC)
In derived substances you might want to consider adding Creatine and reviewing the Creatine entry. I don't really know enough myself to contribute. Steven Zenith 08:19, Jun 3, 2005 (UTC)
Those tables and that first images run of the screen on the right for people with a 800x600 screen. Can someone help to make it more accessible to those people (including me). Mgm| (talk) 22:02, Jun 3, 2005 (UTC)
The following are various physical data taken from D. R. Lide (Ed.), CRC Handbook of Chemistry and Physics (83rd Edn.), Boca Raton, Florida: CRC Press, 2002, ISBN 0-8493-0483-0.
Code | m.p. (°C) |
pKa1 (–COOH) |
pKa2 (–NH3+) |
pKa3 (side chain) |
Isoelectric point |
Solubility (g/100 g water) |
---|---|---|---|---|---|---|
Ala | 297 | 2.33 | 9.71 | 6.00 | 16.5 | |
Arg | 244 | 2.03 | 9.00 | 12.10 | 10.76 | 18.3 |
Asn | 235 | 2.16 | 8.73 | 5.41 | 2.5 | |
Asp | 270 | 1.95 | 9.66 | 3.71 | 2.77 | 0.5 |
Cys | 240 | 1.91 | 10.28 | 8.14 | 5.07 | v.s. |
Glu | 160 | 2.16 | 9.58 | 4.15 | 3.22 | 0.9 |
Gln | 185 | 2.18 | 9.00 | 5.65 | 4.2 | |
Gly | 290 | 2.34 | 9.58 | 5.97 | 25.1 | |
His | 287 | 1.70 | 9.09 | 6.04 | 7.59 | 4.4 |
Ile | 284 | 2.26 | 9.60 | 6.02 | 3.4 | |
Leu | 293 | 2.32 | 9.58 | 5.98 | 2.2 | |
Lys | 224 | 2.15 | 9.16 | 10.67 | 9.74 | 0.6 |
Met | 281 | 2.16 | 9.08 | 5.74 | 5.6 | |
Phe | 283 | 9.09 | 5.48 | 5.48 | 2.8 | |
Pro | 221 | 1.95 | 10.47 | 6.30 | 162.3 | |
Ser | 228 | 2.13 | 9.05 | 5.68 | 5.0 | |
Thr | 256 | 2.20 | 8.96 | 5.60 | 9.8 | |
Trp | 289 | 2.38 | 9.34 | 5.89 | 1.3 | |
Tyr | 343 | 2.24 | 9.04 | 10.10 | 5.66 | 0.05 |
Val | 315 | 2.27 | 9.52 | 5.96 | 8.9 |
Some of these values surprise me, to say the least. I have no problems with the small variations in quoted values of the dissociation constants, but other sources (eg Sigma-Aldrich) give quite different values for melting points (often with decomposition). As for solubility, 162 g proline soluble in 100 mL water? Only 50 mg tyrosine soluble in 100 mL water? Again, Sigma-Aldrich quotes different values for some amino acids.
Does anyone hvae comments or suggestions as to which data we should use for amino acid articles? Should we include a review of published data, as is done for chemical element articles? Physchim62 12:53, 15 July 2005 (UTC)
Code | Ala | Arg | Asn | Asp | Cys | Glu | Gln | Gly | His | Ile | Leu | Lys | Met | Phe | Pro | Ser | Thr | Trp | Tyr | Val |
Hydropathy index | 1.8 | -4.5 | -3.5 | -3.5 | 2.5 | -3.5 | -3.5 | -0.4 | -3.2 | 4.5 | 3.8 | -3.9 | 1.9 | 2.8 | 1.6 | -0.8 | -0.7 | -0.9 | -1.3 | 4.2 |
How do amino acids form in nature? Please elaborate in article - Roy Boy 800 05:54, 16 August 2005 (UTC)
R group appears to be the correct term, at least for the proteinogenic amino acids. -- Bubbachuck 16:46, 21 August 2005 (UTC)
Have amino acids been observed to form spontaneously in nature? Or have all the "primordial soup" experiments been caused through human experimentation? If they have been observed, where can I find this information?
As far as I know, spontaneous formation has only been observed when initiated by human experimentation. The conditions on most of the planet today would probably prohibit the chemical reactions necessary from occuring. The early earth had very different conditions though, which the experiments try to replicate as accurately as possible.
An ammino isn't any molecule with both carboxilic acid and amine functional groups as the first paragraph implies they both need to be on the same carbon as in the general formualar.
The amino acid and carboxylate functionalities can't be on the same carbon, can they? I think the alpha amino acid terminology refers to a molecule where the amine is on the alpha-carbon to the carbonyl. If they were both on the same carbon you would have COOH-C-NH3 which leaves no place for the functional group. Can somebody clarify this for me?
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!
Can somebody tell me, why glycin is supposed to be hydrophobic. It's soluble in water, isn't it.
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 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)
I thought it is 22 not 20?
20 is the number of proteinogenic amino acids generally given. Post-translational modifications occur after translation so the amino acids modified in this way arguably aren't amino acids anymore (they have no amino or carboxylic acid function), they're really amino acid residues. It might be more correct to say there are 20 proteinogenic amino acids (in most organisms), but considerable more when their modified residues are considered.
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)
What about Glucogenic and Ketogenic Amino acids seperation. Could there be a paragraph on that. Also is hypoglycine in this article and it causing Jamaican Vomiting sickness. I would read the whole thing but im lazy and revising for exams...telesforos
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) .
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)
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)
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)
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)
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)
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)
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)
![]() | This is an archive of past discussions. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk page. |
Archive 1 | Archive 2 | Archive 3 |
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)
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 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:
[1] cysteine behaves as a hydrophobic in proteins.
because it usually forms disulfide bridges. 218.102.218.18 10:00, 12 December 2005 (UTC)
Whether or not a cysteine residue is ionised depends on its pKa. When the cysteine is protonated it is hydrophobic, when it is in the thiolate form, it is hydrophillic. TimVickers 19:46, 13 March 2007 (UTC)
In derived substances you might want to consider adding Creatine and reviewing the Creatine entry. I don't really know enough myself to contribute. Steven Zenith 08:19, Jun 3, 2005 (UTC)
Those tables and that first images run of the screen on the right for people with a 800x600 screen. Can someone help to make it more accessible to those people (including me). Mgm| (talk) 22:02, Jun 3, 2005 (UTC)
The following are various physical data taken from D. R. Lide (Ed.), CRC Handbook of Chemistry and Physics (83rd Edn.), Boca Raton, Florida: CRC Press, 2002, ISBN 0-8493-0483-0.
Code | m.p. (°C) |
pKa1 (–COOH) |
pKa2 (–NH3+) |
pKa3 (side chain) |
Isoelectric point |
Solubility (g/100 g water) |
---|---|---|---|---|---|---|
Ala | 297 | 2.33 | 9.71 | 6.00 | 16.5 | |
Arg | 244 | 2.03 | 9.00 | 12.10 | 10.76 | 18.3 |
Asn | 235 | 2.16 | 8.73 | 5.41 | 2.5 | |
Asp | 270 | 1.95 | 9.66 | 3.71 | 2.77 | 0.5 |
Cys | 240 | 1.91 | 10.28 | 8.14 | 5.07 | v.s. |
Glu | 160 | 2.16 | 9.58 | 4.15 | 3.22 | 0.9 |
Gln | 185 | 2.18 | 9.00 | 5.65 | 4.2 | |
Gly | 290 | 2.34 | 9.58 | 5.97 | 25.1 | |
His | 287 | 1.70 | 9.09 | 6.04 | 7.59 | 4.4 |
Ile | 284 | 2.26 | 9.60 | 6.02 | 3.4 | |
Leu | 293 | 2.32 | 9.58 | 5.98 | 2.2 | |
Lys | 224 | 2.15 | 9.16 | 10.67 | 9.74 | 0.6 |
Met | 281 | 2.16 | 9.08 | 5.74 | 5.6 | |
Phe | 283 | 9.09 | 5.48 | 5.48 | 2.8 | |
Pro | 221 | 1.95 | 10.47 | 6.30 | 162.3 | |
Ser | 228 | 2.13 | 9.05 | 5.68 | 5.0 | |
Thr | 256 | 2.20 | 8.96 | 5.60 | 9.8 | |
Trp | 289 | 2.38 | 9.34 | 5.89 | 1.3 | |
Tyr | 343 | 2.24 | 9.04 | 10.10 | 5.66 | 0.05 |
Val | 315 | 2.27 | 9.52 | 5.96 | 8.9 |
Some of these values surprise me, to say the least. I have no problems with the small variations in quoted values of the dissociation constants, but other sources (eg Sigma-Aldrich) give quite different values for melting points (often with decomposition). As for solubility, 162 g proline soluble in 100 mL water? Only 50 mg tyrosine soluble in 100 mL water? Again, Sigma-Aldrich quotes different values for some amino acids.
Does anyone hvae comments or suggestions as to which data we should use for amino acid articles? Should we include a review of published data, as is done for chemical element articles? Physchim62 12:53, 15 July 2005 (UTC)
Code | Ala | Arg | Asn | Asp | Cys | Glu | Gln | Gly | His | Ile | Leu | Lys | Met | Phe | Pro | Ser | Thr | Trp | Tyr | Val |
Hydropathy index | 1.8 | -4.5 | -3.5 | -3.5 | 2.5 | -3.5 | -3.5 | -0.4 | -3.2 | 4.5 | 3.8 | -3.9 | 1.9 | 2.8 | 1.6 | -0.8 | -0.7 | -0.9 | -1.3 | 4.2 |
How do amino acids form in nature? Please elaborate in article - Roy Boy 800 05:54, 16 August 2005 (UTC)
R group appears to be the correct term, at least for the proteinogenic amino acids. -- Bubbachuck 16:46, 21 August 2005 (UTC)
Have amino acids been observed to form spontaneously in nature? Or have all the "primordial soup" experiments been caused through human experimentation? If they have been observed, where can I find this information?
As far as I know, spontaneous formation has only been observed when initiated by human experimentation. The conditions on most of the planet today would probably prohibit the chemical reactions necessary from occuring. The early earth had very different conditions though, which the experiments try to replicate as accurately as possible.
An ammino isn't any molecule with both carboxilic acid and amine functional groups as the first paragraph implies they both need to be on the same carbon as in the general formualar.
The amino acid and carboxylate functionalities can't be on the same carbon, can they? I think the alpha amino acid terminology refers to a molecule where the amine is on the alpha-carbon to the carbonyl. If they were both on the same carbon you would have COOH-C-NH3 which leaves no place for the functional group. Can somebody clarify this for me?
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!
Can somebody tell me, why glycin is supposed to be hydrophobic. It's soluble in water, isn't it.
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 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)
I thought it is 22 not 20?
20 is the number of proteinogenic amino acids generally given. Post-translational modifications occur after translation so the amino acids modified in this way arguably aren't amino acids anymore (they have no amino or carboxylic acid function), they're really amino acid residues. It might be more correct to say there are 20 proteinogenic amino acids (in most organisms), but considerable more when their modified residues are considered.
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)
What about Glucogenic and Ketogenic Amino acids seperation. Could there be a paragraph on that. Also is hypoglycine in this article and it causing Jamaican Vomiting sickness. I would read the whole thing but im lazy and revising for exams...telesforos
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) .
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)
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)
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)
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)
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)
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)
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)