The explanation of the chemical properties table states that the reported mass of each amino acid "includes the mass of H2O". What does that mean? There's no discussion of water of hydration and I don't see any water molecules in the diagrams in the structures table earlier in the article. DMacks 05:08, 1 September 2006 (UTC)
I know wiki tables can be cumbersome to edit, so I'd be happy to hear any thoughts about the following thoughts before I go through and do them:
|
vs |
|
DMacks 05:42, 1 September 2006 (UTC)
Amino Acid | Abbrev. | |
---|---|---|
Alanine | A | Ala |
Amino Acid | Abbrev. | |
---|---|---|
Alanine | A | Ala |
I'd rather not have a net addition of columns to the second table—it's already off my screen. But also, the sidechain properties could be considered separately from the properties of the whole amino acid molecule. If you're interested in protein function, you really want to know size, hydrophobicity, and related properties, but don't have much reason to care about about mw or pKa of the NH2 or CO2H. Hrm, I'm starting to get confused about which idea of which table is which. So here's my thought:
General Chemical Properties
Amino Acid | Abbrev. | Mass (Da) | pI | pK1 (α-COOH) |
pK2 (α-+NH3) |
pKr (R) | |
---|---|---|---|---|---|---|---|
Alanine | A | Ala | 89.09 | 6.01 | 2.35 | 9.87 |
Sidechain-Related Effects
Amino Acid | Abbrev. | Side chain | Hydro- phobic |
Polar | Charged | Small | Tiny | Aromatic or Aliphatic |
van der Waals volume | |
---|---|---|---|---|---|---|---|---|---|---|
Alanine | A | Ala | -CH3 | X | - | - | X | X | - | 67 |
Gene Expression
Amino Acid | Abbrev. | Codon(s) | Occurrence in proteins (%) | |
---|---|---|---|---|
Alanine | A | Ala | GCU, GCC, GCA, GCG | 7.8 |
General Chit-Chat
Amino Acid | Abbrev. | Comments | |
---|---|---|---|
Alanine | A | Ala | Very abundant, very versatile. More stiff than glycine, but small enough to pose only small steric limits for the protein conformation. It behaves fairly neutrally, can be located in both hydrophilic regions on the protein outside and the hydrophobic areas inside. |
DMacks 18:44, 1 September 2006 (UTC)
Recent edits to this page added selenocysteine to the list; I'm somewhat of two minds on the matter. This is the list of standard amino acids, which would imply selenocysteine doesn't belong, but on the other hand it is one of the 22 naturally encoded amino acids and this list might be more useful with all of them. If that's the agreement then I'd suggest moving this page to list of naturally encoded amino acids, as the current title wouldn't be quite accurate. Opabinia regalis 23:51, 29 September 2006 (UTC)
My understanding is that J is used for isoleucine/leucine, as B is used for Asx and Z is used for Glx. Is this not correct? MAzari 02:25, 8 October 2006 (UTC)
It would be helpful to non-expert readers if there were some links or other hints as to the meaning of some of the qualities given. I was mystified by pK1, pK2 until I found the Protein pKa calculations link, which lead me to Acid dissociation constant, which clued me in to the general nature of the quantities in those columns. I never found pKr or pI (although I'd guess they were also acidic measures). "van der Waals volume" at least I could find by copying the text into the search box. If I had needed to look up "Da" in "Mass (Da)" it might have been difficult. Maybe appropriate links in the column heading would improve the situation. - R. S. Shaw 20:12, 17 October 2006 (UTC)
Don't have time to do it now, but I'm planning to import those values from the amino acid page, and add a table footnote explaining how the sign indicates hydrophilicity/hydrophobicity. Seems like the page here is well-suited for technical data. Maybe the other page should go to just a "hydrophobic" flag, since it's more of a layman's/overview page? DMacks 22:29, 2 February 2007 (UTC)
I was just wondering about the properties of the Van der Walls column. Is that the van der Waals volume of the side chain or the entire amino acid? Wouldn't the van der Waals volume of the entire amino acid be more useful? 87.243.196.213 09:05, 3 April 2007 (UTC)
Shouldn't Proteinogenic amino acid and List of standard amino acids be combined & maybe renamed Standard amino acids. Gregogil 20:23, 5 April 2007 (UTC)
In terms of naming, I think you should leave it as Standard amino acid, and leave proteinogenic to a subsection - when most people are searching for amino acids on wikipedia, they will not be looking for the term "proteinogenic". Biochemza 13:29, 1 November 2007 (UTC)
I would prefer to see List of standard amino acids remain intact, and at its current location. Could Proteinogenic amino acid just be merged into Amino acid?-- 69.118.143.107 ( talk) 19:26, 4 January 2008 (UTC)
The last column in the third wikitable says whether each amino acid is "essential in humans." The symbols are unclear. Instead, please write "yes" or "no."
Shalom (
Hello •
Peace)
23:55, 21 October 2007 (UTC)
Is there a one letter abbreviation for gamma glutamic acid? i think the 3 is Gla? Benkeboy ( talk) 16:32, 6 May 2008 (UTC)
The explanation of the chemical properties table states that the reported mass of each amino acid "includes the mass of H2O". What does that mean? There's no discussion of water of hydration and I don't see any water molecules in the diagrams in the structures table earlier in the article. DMacks 05:08, 1 September 2006 (UTC)
I know wiki tables can be cumbersome to edit, so I'd be happy to hear any thoughts about the following thoughts before I go through and do them:
|
vs |
|
DMacks 05:42, 1 September 2006 (UTC)
Amino Acid | Abbrev. | |
---|---|---|
Alanine | A | Ala |
Amino Acid | Abbrev. | |
---|---|---|
Alanine | A | Ala |
I'd rather not have a net addition of columns to the second table—it's already off my screen. But also, the sidechain properties could be considered separately from the properties of the whole amino acid molecule. If you're interested in protein function, you really want to know size, hydrophobicity, and related properties, but don't have much reason to care about about mw or pKa of the NH2 or CO2H. Hrm, I'm starting to get confused about which idea of which table is which. So here's my thought:
General Chemical Properties
Amino Acid | Abbrev. | Mass (Da) | pI | pK1 (α-COOH) |
pK2 (α-+NH3) |
pKr (R) | |
---|---|---|---|---|---|---|---|
Alanine | A | Ala | 89.09 | 6.01 | 2.35 | 9.87 |
Sidechain-Related Effects
Amino Acid | Abbrev. | Side chain | Hydro- phobic |
Polar | Charged | Small | Tiny | Aromatic or Aliphatic |
van der Waals volume | |
---|---|---|---|---|---|---|---|---|---|---|
Alanine | A | Ala | -CH3 | X | - | - | X | X | - | 67 |
Gene Expression
Amino Acid | Abbrev. | Codon(s) | Occurrence in proteins (%) | |
---|---|---|---|---|
Alanine | A | Ala | GCU, GCC, GCA, GCG | 7.8 |
General Chit-Chat
Amino Acid | Abbrev. | Comments | |
---|---|---|---|
Alanine | A | Ala | Very abundant, very versatile. More stiff than glycine, but small enough to pose only small steric limits for the protein conformation. It behaves fairly neutrally, can be located in both hydrophilic regions on the protein outside and the hydrophobic areas inside. |
DMacks 18:44, 1 September 2006 (UTC)
Recent edits to this page added selenocysteine to the list; I'm somewhat of two minds on the matter. This is the list of standard amino acids, which would imply selenocysteine doesn't belong, but on the other hand it is one of the 22 naturally encoded amino acids and this list might be more useful with all of them. If that's the agreement then I'd suggest moving this page to list of naturally encoded amino acids, as the current title wouldn't be quite accurate. Opabinia regalis 23:51, 29 September 2006 (UTC)
My understanding is that J is used for isoleucine/leucine, as B is used for Asx and Z is used for Glx. Is this not correct? MAzari 02:25, 8 October 2006 (UTC)
It would be helpful to non-expert readers if there were some links or other hints as to the meaning of some of the qualities given. I was mystified by pK1, pK2 until I found the Protein pKa calculations link, which lead me to Acid dissociation constant, which clued me in to the general nature of the quantities in those columns. I never found pKr or pI (although I'd guess they were also acidic measures). "van der Waals volume" at least I could find by copying the text into the search box. If I had needed to look up "Da" in "Mass (Da)" it might have been difficult. Maybe appropriate links in the column heading would improve the situation. - R. S. Shaw 20:12, 17 October 2006 (UTC)
Don't have time to do it now, but I'm planning to import those values from the amino acid page, and add a table footnote explaining how the sign indicates hydrophilicity/hydrophobicity. Seems like the page here is well-suited for technical data. Maybe the other page should go to just a "hydrophobic" flag, since it's more of a layman's/overview page? DMacks 22:29, 2 February 2007 (UTC)
I was just wondering about the properties of the Van der Walls column. Is that the van der Waals volume of the side chain or the entire amino acid? Wouldn't the van der Waals volume of the entire amino acid be more useful? 87.243.196.213 09:05, 3 April 2007 (UTC)
Shouldn't Proteinogenic amino acid and List of standard amino acids be combined & maybe renamed Standard amino acids. Gregogil 20:23, 5 April 2007 (UTC)
In terms of naming, I think you should leave it as Standard amino acid, and leave proteinogenic to a subsection - when most people are searching for amino acids on wikipedia, they will not be looking for the term "proteinogenic". Biochemza 13:29, 1 November 2007 (UTC)
I would prefer to see List of standard amino acids remain intact, and at its current location. Could Proteinogenic amino acid just be merged into Amino acid?-- 69.118.143.107 ( talk) 19:26, 4 January 2008 (UTC)
The last column in the third wikitable says whether each amino acid is "essential in humans." The symbols are unclear. Instead, please write "yes" or "no."
Shalom (
Hello •
Peace)
23:55, 21 October 2007 (UTC)
Is there a one letter abbreviation for gamma glutamic acid? i think the 3 is Gla? Benkeboy ( talk) 16:32, 6 May 2008 (UTC)