I've spent some hours trying to understand what exactly is a phosphoester bond, but I'm still confused and at this point I just want to throw myself out of the window. I've already read that post which treats the question but it doesn't really help me since, according to the link given by WYSIWYG♦:

A phosphoester bond is a bond between the phosphorous atom of a phosphate group and an oxygen atom.

But considering the answer of electronpusher:

Each nucleotide contains one phosphoester bond (between a phosphate O and sugar 5'-C).

It doesn't really make sense to me, since such a bond (in a nucleotide) is not exactly a bond between the phosphorous atom of the phosphate group and an oxygen atom (that is, it's a O-C bond, not a P-O bond).

So, what is exactly a phosphoester bond? Is it a O-glycosidic bond between the sugar (ribose or 2'-deoxyribose, in a nucleotide) and the phosphate group? Or is it the bond that there is between the phosphorous atom of a phosphate group and an oxygen atom of the same phosphate group?

I'm really confused and desperate by all this, so any help would be greatly appreciated. Thanks in advance!

  • $\begingroup$ You can find a diagram of the structure of a phospho diester bond in any biochemistry text eg. Lodish et al. and the definition: "A covalent bond in which two hydroxyl groups form ester linkages to the same phosphate group; joins adjacent nucleotides in DNA and RNA". So the question is do you know what an ester linkage is and do you know what a phosphate group is? If not you should try WIkipedia or a basic chemistry book. I shall vote to move to SE Chemistry but you should be able to answer this yourself. $\endgroup$
    – David
    Commented Aug 9, 2017 at 19:01

1 Answer 1


A phosphoester bond is in fact a bond between the phosphorus atom of a phosphate group and an oxygen atom. Your confusion comes from the fact that electronpusher's statement is inaccurate.

Instead, electronpusher should have said:

Each nucleotide contains one phosphodiester bond (between a phosphate O & a 5'-C on one sugar belonging to one nucleotide, and then another bond between a phosphate O & a 3'-C on another sugar belonging to another nucleotide).

More elegantly put, "a phosphodiester bond occurs when two of the hydroxyl groups in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds" (source).

The resulting bond is between O-C because the hydroxyl groups react with each other and transesterification occurs. The OH from the phosphate interacts with the OH (attached to the carbon) from the sugar, transesterification occurs, thus leaving only 1 oxygen, of which is the oxygen in the P-O-C bond sequence, exhibited in the following image.

Phosphodiester bonds between three nucleotides

The next image is a simplification of the reaction mechanism. Dehydration does not actually occur (transesterification does, as mentioned), but instead, this image is provided as to more easily identify which entities are involved in the reaction, as to more directly address the concerns expressed by the OP. The true reaction mechanism can be found here.

Phosphoester bond reaction mechanism

  • $\begingroup$ Thanks a lot for your answer! However, I still don't see why the bonds we are talking about are phosphoester (or phosphodiester) bonds, since they are both O-C bonds and not O-P bonds... :/ $\endgroup$
    – justdoit
    Commented Aug 9, 2017 at 18:58
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    $\begingroup$ You're quite welcome! Study smart, not hard ;) $\endgroup$
    – user22020
    Commented Aug 9, 2017 at 19:15
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    $\begingroup$ Good answer, I would just say that the condensation reaction shown is thermodynamically unfavourable. In realty, nucleotides are joined together by transesterfication. See this question and answers: biology.stackexchange.com/questions/61319/… $\endgroup$
    – canadianer
    Commented Aug 9, 2017 at 19:38
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    $\begingroup$ @canadianer Thanks for that. I've updated my answer to include and reference this. $\endgroup$
    – user22020
    Commented Aug 9, 2017 at 19:57
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    $\begingroup$ @Charles - Nice job, and great attitude. I never heard of a phosphoester bond (only diester) until just now. $\endgroup$ Commented Aug 9, 2017 at 20:54

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