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Some months ago, I asked what was a phosphoester bond, because I didn't really understand the following picture and explanations provided in the "Molecular biology of the gene" from Watson, Baker, Bell and al. (7th edition).

enter image description here

The explanation is the following:

We can think of how the base is joined to 2'-deoxyribose by imagining the removal of a molecule of water between the hydroxyl on the 1' carbon of the sugar and the base to form a glycosidic bond (Fig. 4-2). The sugar and base alone are called a nucleoside. Likewise, we can imagine linking the phosphate to 2'-deoxyribose by removing a water molecule from between the phosphate and the hydroxyl on the 5' carbon to make a 5' phosphomonoester. Adding a phosphate (or more than one phosphate) to a nucleoside creates a nucleotide.

Thus, by making a glycosidic bond between the base and the sugar, and by making a phosphoester bond between the sugar and the phosphoric acid, we have created a nucleotide.

What I didn't understand months ago was, to resume, "why is the bond between the phosphate group and the 2'-deoxyribose called a phosphoester bond since the phosphoester bond (which is, by definition, a P-O bond) already exists before the bonding between the phosphate group and the sugar?"

While this question is still bothering me (I was not entirely satisfied with the answers I got back then, because the synthesis of a single strand of DNA is something which is probably different from the synthesis of nucleotides themselves), the question I'm asking myself right now is: "why do general biology books always talk about condensation reactions, while this article and this book do not mention it in the biosynthesis pathways of nucleotides?"

What I mean is: it seems like the biosynthesis of nucleotides is far more complicated than just being two condensation reactions. Furthermore, when I look at the 10th step of this picture (which comes from the article I mentioned above), I see a condensation reaction at the end of the pathway, but it does not occur where the book from Watson and al. suggests it should:

enter image description here

So, after months of wondering and researchs about all this, my final question about this is, as mentioned above:

Why do biology books always mention condensation reactions while, apparently, it doesn't have a lot to do with the manner in which the nucleotides are synthesized?

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    $\begingroup$ I'm voting to close this question as off-topic because this list is about biology, not the motives of authors of texts, which in any case can only be a matter of speculation. $\endgroup$
    – David
    Dec 6, 2017 at 19:26

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A condensation reaction is defined on Wikipedia as

a reaction in which two molecules or moieties, often functional groups, combine to form a larger molecule, together with the loss of a small molecule. Possible small molecules that are lost include water, acetic acid, hydrogen chloride, or methanol, but most commonly in biological reactions it is water.

It doesn't say anything about the number of steps required to reach the final compound, nor about the type of bonds formed. Following this definition, the nucleotide synthesis occurs via condensation reactions.

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  • $\begingroup$ Thanks a lot for your answer. However, it still does not explain why the book from Watson and al. talk about the loss of two water molecules, and it doesn't explain either why that same book explains the synthesis of nucleotides in such a simplistic way, while it is apparently way more complicated than just a phosphoester and a glycosidic bond... $\endgroup$
    – justdoit
    Dec 6, 2017 at 13:36
  • $\begingroup$ It is a simplification but it is correct. You start with 3 molecules, you end up with one via 2 condensation reactions and you lose 2 H2O in total. What is the problem? the schematic is pretty straightforward. $\endgroup$
    – alec_djinn
    Dec 6, 2017 at 13:42
  • $\begingroup$ If it is really what happens, then there is no problem anymore. The last thing that is still bothering me is that phosphoester bond thing. $\endgroup$
    – justdoit
    Dec 6, 2017 at 13:55

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