Talk:List of standard amino acids

From Wikipedia, the free encyclopedia

You have new messages (last change).

Contents

[edit] Weights explanation

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 assume that means the amino acid molecule itself, not the residue in a polypeptide chain. You're right that it's unclear though. I don't have a copy of Lehninger but Voet&Voet gives residue masses that are 18Da lower than these, which makes sense. Opabinia regalis 06:12, 1 September 2006 (UTC)

[edit] Chemical properties tables need some work

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:

  • Need to standardize the row-label columns with respect to name, 3-letter code, 1-letter code.
Abbrev. Full Name
A Ala Alanine
vs
Amino acid Abbrev.
Alanine Ala, A
  • The majority of the types of data are general/organic chemistry. However, the "Remarks" column of the first table and the "Codon" and "Occurrence in proteins (%)" columns in the second table are biochemistry or biology/genetics. Should those be moved into their own new table? That would avoid having that Remarks line-broken after every third word, making the first table less sparse vertically, and would also reduce the need for side-scrolling these fairly wide tables.
  • There is a side-chain type (hydrophobic, etc.) column in both tables. I think it's better in the second table. That's the only property in the first table that is qualitative and primarily about the side-chain, whereas the second table has lots of qualitative side-chain information.
  • The genetic code page (which is also a redirect from Codon) already contains the codons for each amino acid in a nicely compact table. And they also have the standard "3D-ish" codon→residue map. Should we just link to theirs?

DMacks 05:42, 1 September 2006 (UTC)

I think the two tables are kind of redundant - they look like two different users compiled them and couldn't decide which one to use, so they went with both. They're inconsistent in formatting and naming (aspartate vs aspartic acid), and the "remarks" section is wordy and often unsourced (unless all of this came from Lehninger).
I think I like a combined form of the abbreviation methods:
Amino Acid Abbrev.
Alanine A Ala
Agreed that the side chain information should go in the second table. I don't know how well this would work formatting-wise, especially at lower resolution, but I'd propose moving the masses, pI's, and pKa's to the second table, and moving the codons and protein occurrences to the first. That way there's a table for physical properties and a table for functional properties. What do you think? Opabinia regalis 06:12, 1 September 2006 (UTC)
That row-label looks nice! Maybe even make the full name a title cell?
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)

Hm, the first table is the fat one on my screen, I assume because of text wrapping, but definitely we should keep them all viewable at lower resolution, down to 800x600 if possible. Putting all the pKa's together is intuitive but I have to think the R-group pKa should go with the side chain information, no? Other than that I think your split looks pretty good. I'm not sure the "remarks" are really necessary - at best they should be shortened, and maybe then could go in the side chain table, since most of them are about side chain properties.
I think this list should probably also include a note for which amino acids are essential in humans (not sure which table that fits best under) and possibly a wikilink to the article on the enzyme that synthesizes them. Opabinia regalis 02:34, 2 September 2006 (UTC)
Late addendum: I don't think we have sufficiently systematic articles on biosynthetic pathways to implement my last idea, so scratch that. Opabinia regalis 03:41, 4 September 2006 (UTC)
Essential is a good idea. Rename the "Gene Expression" table to "Biochemistry" and add an "Essential" column to it?
Thinking of sidechains, yeah, gotta decide if the names should be "aspartic acid" or "aspartate", etc. I vote the former, so that the structure can be drawn that way (protonated carboxylate) to match the name and to match the amino acid molecule itself, not "its prefered state at physiological pH. Then the mw makes sense and we don't have to worry about which counterion to use.
The "charged" column in the sidechains table is weird. It says that aspartate is "negative", which is only true under physiological pH. A more generic/intrinsic description might be "acidic" or "basic" (wikilinked), which is applicable to the molecule itself, and it's a given that acids sometimes ionize to form a deprotonated species. Then putting the pKr column adjacent in that table makes sense.
I wish there was a way to rotate column headings 90 ° without resorting to graphical labels, so that the checkboxish columns weren't so wide:( Since "charged" is a subset of "polar", would it be clearer to merge those columns? Call it "polarity", and give each row a single word from among "nonpolar", "polar", "positive", "negative" (though not sure how to handle the alternative "acidic"/"basic" way)? DMacks 17:26, 13 September 2006 (UTC)
I just rearranged the tables, pretty closely following the suggestions above. One potential issue is that I've left them arranged in alphabetical order by one-letter code, but the first element in the table is now the amino acid name.
The "checkbox" columns do seem wide but their width is determined by the table headers, and rotating the table to put the amino acids on the horizontal axis would just make it wider. I think merging "polar" and "charged" is reasonable, though there's the implicit expectation that readers know that acidic/basic implies polarity and suggests charge under some conditions. Opabinia regalis 06:45, 16 September 2006 (UTC)

[edit] Selenocysteine?

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)

[edit] J is not used?

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)

Good catch, you're right - see [1] for the UniProt/EBI list, citing IUPAC. Opabinia regalis 03:14, 8 October 2006 (UTC)

[edit] Hints if not definitions?

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)

I just linked "pI" and "pK" in the table headers. DMacks 20:22, 17 October 2006 (UTC)

[edit] Hydropathy index

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)

Retrieved from "http://en.wikipedia.org../../../l/i/s/Talk%7EList_of_standard_amino_acids_22df.html"