Talk:Phosphodiester bond

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Work in progress

I plan on doing a write-up for phosphodiester bonds with special emphasis on the biochemistry. --G3pro 9/9/04

Article title

I'm a Wikipedia newbie, but i think that the title of this article should be renamed to "Phosphodiester bond" to conform to other chemical bond names in Category:Chemical bonding. --Sergeymk 2005-10-31

I believe it should be called "Phosphodiester Linkage" but it is up for discussion. — Preceding unsigned comment added by 68.7.20.232 (talk) 06:20, 30 November 2005‎ (UTC)[reply]

"Very" negatively?

-Very negatively charged- No such thing as 'very negative', took 'very' away. —Preceding unsigned comment added by 87.110.241.142 (talk) 21:27, 20 March 2008 (UTC)[reply]

Image concern

Just a quick question about the image used. The third nucleoside is most definitely deoxythymidine, but why is the picture marked with U for uracil? It's very confusing. — Preceding unsigned comment added by 188.126.82.246 (talk) 19:53, 3 October 2011‎ (UTC)[reply]

Done (caption annotated a while ago, and now the image itself is fixed). DMacks (talk) 08:58, 10 August 2013 (UTC)[reply]

Not just for DNA and RNA

I noticed that this article includes only the the phosphodiester bond in DNA and RNA. It defines the bond as "...a group of strong covalent bonds between a phosphate group and two 5-carbon ring carbohydrates (pentoses) over two ester bonds." But as far as I know, a phosphodiester bond is more general than that-- it's when a phosphate connects two organic molecules via two bonds, each bond connecting one of the phosphate's oxygens to a carbon of the organic molecule. For example, a phospholipid has a phosphodiester bond. Right? (Here's one reference: synthesizing phospholipids using a phosphodiester bond: [1]) Marcipangris (talk) 21:38, 24 January 2011 (UTC)[reply]

That is indeed lacking here. The German-Wikipedia article de:Phosphodiesterbindung has a nice concise summary that might be a good lede here, before having major subsections for nucleosides vs other cases. DMacks (talk) 16:27, 8 August 2013 (UTC)[reply]

Moving comment from article

The following comment appeared within the article so I moved it here:

"on the side a structural formula is given to show the phosphodiaster bond which shows at the top uracil while down it is written that phosphate group is linked to thymine and two adinine bases. please rectify it" (added to article 22:17, 1 March 2012 by User:Shabz4life)

--Jameboy (talk) 06:00, 16 May 2012 (UTC)[reply]

Done. Jesanj (talk) 19:38, 18 May 2012 (UTC)[reply]

The image did appear to have thymine (with methyl group) but mislabeled it there as "U" (uracil, no methyl group)--these are deoxy's (DNA) so wouldn't make sense to have U, which is generally only in RNA anyway. I fixed the label in the image and adjusted the image-caption to sync with it. DMacks (talk) 08:58, 10 August 2013 (UTC)[reply]

Inaccurate or confusing

The article states that "when a single phosphate or two phosphates known as pyrophosphates break away and catalyze the reaction, the phosphodiester bond is formed". However, neither phosphates nor pyrophosphates catalyze the reaction; if anything, they are reactants and products of the reversible reaction, not catalysts. An appropriate enzyme would be the catalyst to the reaction, or maybe some other structure, such as those suggested by the PAH world hypothesis, but not phosphate nor pyrophosphate. Seeing how the sentence has already raised other concerns ("citation required"), I am moving it to this section. 62.37.5.52 (talk) 15:44, 31 August 2012 (UTC)[reply]

Note doesn't seem to make sense.

As far as I've ever heard prions don't directly depend on RNA for transmission. They do require new non-prion forms of the protein, which is synthesized in the usual manner (i.e. using ribosomes and tRNA to decode mRNA), but I don't see how any of this adds to this article. Tyersome (talk) 20:41, 16 November 2018 (UTC)[reply]

Organization

I think the second half of the opening section, and all of the "Enzyme Activity" could be better organized around "Breaking of the Phosphodiester Bond" or something similar. This could cover enzyme activity and alkaline hydrolysis, and make both more clearly distinct from the previous section about the nature (and formation) of the bond. Also, when addressing the bond in DNA and RNA, the usage of "sugar" and "monosaccharide" is unnecessarily general and unqualified, making it difficult to grasp, whereas "ribose" and "deoxyribose" would be both more precise and more clear. Diatomcymbella (talk) 04:19, 7 November 2023 (UTC)[reply]

See User:Diatomcymbella/sandbox for a sample edit in this vein. Diatomcymbella (talk) 04:22, 7 November 2023 (UTC)[reply]