Talk:Deoxyribose

Links needed
I think there needs to be more information available, perhaps by a link, about the chemistry and stereochemistry of sugars. It is a very important point that there are a lot of pentoses with the same chemical formula, and that ribose is the name of one particular configuration. Also, the discussion could be improved by giving readers a clue to the numbering conventions, perhaps in the diagram. The 3 and 5 positions are important too. It would even be helpful if a student could learn why and when the nomenclature for the third carbon changes from 3 to 3'.

Sugars form polymers in many ways, it is a fascinating and difficult subject area. The author here, though, seems to have in mind the particular way that ribose sugars are polymerized in nucleic acids. A crucial distinction between nucleic acid polymers and ordinary polysacharides is the 3'-5' phospho linkage. The phosphate deriviatives of ribose are not mentioned.

In discussing ribose there should be room for linkages to related important concepts such as ATP, ADP, AMP, cyclic-AMP, pyrophosphate, GTP, etc. There could also be useful links to its systhesis and metabolism. There are other scientifically important synthetic derivatives, etc.
 * We're in the process of simplifying the information in the article. --G3pro 21:45, 9 Sep 2004 (UTC)
 * I believe that numbering of carbon atoms will assist reader understanding. Such things are normally included in typical textbooks.  Also, the images presented in this, and related bio-chemistry articles, will also increase reader comprehension, especially if they show the sequence of intermediate conformations.  For instance, it is difficult for non-specialists to see how ribose can assume linear and ring formation, especially if the bonding changes are not well presented.  William R. Buckley (talk) 23:32, 13 November 2009 (UTC)

Out-of-place Information
There's a lot of stuff here that doesn't belong in an article on deoxyribose, for example all that information about RNA, and in fact most of the information about DNA. This should not try to cover nucleic acids in general; that information is covered in several other articles. So, unless there are loud objections, I plan on removing much of this. Josh Cherry 01:39, 9 Sep 2004 (UTC)


 * I totally agree with you. I definitely have plans for this article and I'll try to get something coherent in the next few days.  I've been working on getting chemical structures and models in most of these related articles and making the existing ones pretty.  I'll see what I can do, but don't start removing yet.  I want to see what I can salvage and what we can definitely throw away.  We should post our plans and discuss here.  --G3pro


 * Wow, I just read over the article and everything past the 1/3 point is really garbage material. --G3pro


 * I deleted what was very unnecessary, but there is still a lot of information on Nucleotides which really does not belong in the article on deoxyribose. Yet, the difference between deoxyribose and ribose is critical to the functions of RNA and DNA.  It's a tough call.  I'm totally in favor of strictly discussing deoxyribose and a possible contrast to ribose, and to merge the other information with a nucleotide article if that information is not already in there.  --G3pro 21:45, 9 Sep 2004 (UTC)


 * I read on the ribose article that this page is meant to discuss the contrasts between the molecules. I'll go with that.  --G3pro 21:58, 9 Sep 2004 (UTC)

I have no objection to moving information to a different article, but I am glad you kept the observations about the significance of the 2' deoxy form apparently being able to form larger helices. I am not aware that this is discussed anywhere else. I think it is relevant to the question, "Why is it biologically necessary to have both ribose and deoxyribose?"

As to the paragraphs you removed, well, there are a lot of edit wars going on. This seemed like a good place to remind readers that there is no shortage of unanswered questions and that our knowledge of biology is still quite limited. I am not sure that message about deoxyribose chemistry and biology is clearly stated anywhere else either. I do think such messages can help inspire the next generation of scientists. I am not sure that it is out of place. --AJim 16:52, 11 Sep 2004 (UTC)


 * What I found out of place was generic information about DNA base-pairing and nucleotides which really has no place in an article dedicated to the sugar. I kept the information directly related to the differences between ribose and deoxyribose and the significace those differences are to the cell.  --G3pro 17:50, 11 Sep 2004 (UTC)

Long Helices and RNA
The article says that
 * In contrast, very similar molecules, containing ribose instead of deoxyribose, and known generically as RNA, are only known to form relatively short double helical complementary base paired structures. These are well known, for instance, in ribosomal RNA molecules and in transfer RNA (tRNA), where so called hairpin structures form from palindromic sequences within one molecule.

RNA is certainly capable of forming double helices much longer than those found in tRNAs and rRNAs. Double-stranded RNA viruses contain double-stranded RNAs that are thousands of basepairs long. Pehaps there's an issue for much longer things--I don't know much about this--but I think the above is misleading. Josh Cherry 23:23, 30 Jan 2005 (UTC)

Aldehyde
I don't see the aldehyde (H-C=O) in the picture. Sorry??
 * 1) Might need to look at the linear version Adenosine | Talk 08:54, 26 April 2006 (UTC)

No all i see is hydroxide groups, a quick google pulls up no results for an aldehyde on a ribose, im confused? --86.0.124.62 (talk) 21:59, 15 January 2008 (UTC)joe!
 * Deoxyribose, like many sugars, intercoverts rapidly between multiple forms. See the image labelled "Chemical equilibrium".  The middle structure has an aldehyde functional group.  -- Ed (Edgar181) 22:03, 15 January 2008 (UTC)

Got it... There is an aldehyde in the linear version...

H-C=O <-here bonds to.. | H-C-OH H-C-OH H-C-OH <- ..here H-C-H |  OH

When it is in the ring structure, the double bond oxygen in the aldehyde becomes an alcohol group, and the alcohol group on the fourth carbon becomes the ether, the Oxygen in the ring.

The page is very misleading with the 'aldehyde' next to the ring structure.--86.0.124.62 (talk) 22:11, 15 January 2008 (UTC) joe!

MERGE!
Merge quickly, these articles should not be separated any longer! Adenosine | Talk 08:55, 26 April 2006 (UTC)

Done! Paul D. Anderson 01:26, 16 September 2006 (UTC)

Aqueous Solution - why is C2'-endo form preferred?
This is not a homework question! (although it might make a good one.. I don't know..)

Is there an accepted explanation of why the C2'-endo ring form is preferred? I would (wildly) guess that a ring form would be preferred to a linear form because conversion from linear to ring form takes less energy than the reverse - or perhaps is exothermic. But why it would have to do with is the 5-carbon ring preferred over the 6-carbon ring? I'd imagine this might have to do with have two lone pairs versus one at the carbon adjacent to the oxygen, but have no idea what.

216.9.142.231 (talk) 16:57, 23 September 2011 (UTC)Jim

And what does 'favoured for ribose' actually mean ? :- "In aqueous solution, deoxyribose primarily exists as a mixture of three structures: the linear form H−(C=O)−(CH2)−(CHOH)3−H and two ring forms, deoxyribofuranose ("C3′-endo"), with a five-membered ring, and deoxyribopyranose ("C2′-endo"), with a six-membered ring. The latter form is predominant (whereas the C3′-endo form is favored for ribose)." Andrewg4oep (talk) — Preceding undated comment added 08:26, 17 July 2022 (UTC)

Assessment comment
Substituted at 13:14, 29 April 2016 (UTC)