I have been learning about the chemical structure of RNA, but I can't understand why all hydrogen atoms disappear in the phosophodiester bond between the riboses of RNA.

Phosphoric acid is $H_3PO_4$:

Phosphoric acid

However, when it's connected to ribose the hydrogens disappear:

Phoshphodiester bond

Where did the hydrogens go and why?

  • $\begingroup$ I have edited your question and corrected your diagrams in a way that should answer your question. The valency of the oxygen in the original diagram of the phosphodiester bond was incorrect. Addition of the negative charge — shown in any book or web page — makes it clear that a H ion has been lost. This is such a basic question of chemistry that I would regard it as off topic for Biology SE. As you have accepted the answer from @anotherHomoSapiens I will now vote for it to be closed. $\endgroup$
    – David
    Commented Sep 13, 2016 at 20:59
  • $\begingroup$ @David good image resize edit. $\endgroup$
    – user25568
    Commented Sep 14, 2016 at 6:32
  • $\begingroup$ Hydrogenation depends on pH $\endgroup$
    – AliceD
    Commented Sep 14, 2016 at 12:03
  • $\begingroup$ @Christiaan correct, I read somewhere that at cellular pH (~6.8) DNA easily loses H and acquires -ve charge. $\endgroup$ Commented Sep 14, 2016 at 13:24

1 Answer 1


Generally hydrogen is not shown in DNA structure. I have made a simple diagram to show where all hydrogens go:


There are 3 hydrogens in phosphoric acid, each of them leaves as:

  • 1 H joins with 3' -OH of previous nucleotide to form H2O during DNA replication.

  • 1 OH joins with H of next nucleotide to form H2O during DNA replication.

  • 1 H is released as H+ (remember it was phosphoric acid), hence giving rise to the acidic character of DNA (remember it is DeoxyriboNucleic Acid).

I think you should first study DNA replication (if you haven't, yet) to get more thorough knowledge about the topic.

  • $\begingroup$ If this solves your problem, click the tick mark, below the down symbol to the left of my answer, to select it as correct. If it doesn't, ask your query here or improve the question. $\endgroup$ Commented Sep 13, 2016 at 13:25
  • 2
    $\begingroup$ @AnisSouames If hydrogen is not shown, then there a negative charge is shown on oxygen, like HCl--->H+ + Cl- ; the same way (H...PO4)---> H+ + (-)OPO3 . Due to THAT hydrogen, DNA is an ACID after all... Deoxribo-Nucleic-Acid. As well it is a "base" at the same time due to presence of "nitrogenous" (N-containing) bases that can give a lone pair of electron (Lewis base). Biological nitrogen-containing bases are more popular in another name "Alkaloid". $\endgroup$
    – user25568
    Commented Sep 13, 2016 at 19:58

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