I understand that in phosphodiester bond formation, two hydroxl groups on the phosphate molecule bind to the 3' and 5' OH groups on two independent pentose sugars. This is a condensation reaction, so two molecules of water are released.

I am just confused about the hydroxl groups on the phosphate. From what I know, the phosphate molecule looks like this.

enter image description here

How is phosphate able to do a condensation reaction with two pentose sugars if it has no hydroxide groups?

Thanks a lot

  • $\begingroup$ It's catalyzed by a ligase, e.g. DNA ligase It's not a one-step process. $\endgroup$
    – Fizz
    Mar 30 '19 at 8:34
  • $\begingroup$ Orthophosphate is not involved in phosophodiester bond formation, but deoxynucleotide triphosphates and the 3'-OH on a deoxyribose of a growing polynucleotide chain. Consult a text book to see the actual reaction, as you are expected to do before posting here. $\endgroup$
    – David
    Mar 30 '19 at 16:30
  • $\begingroup$ @David I read this resource teaching.ncl.ac.uk/bms/wiki/index.php/Phosphodiester_bond which stated that "In phosphodiester formation, two hydroxyl (OH) groups on the phosphate molecule bind to the 3’ and 5’ carbons on two independent pentose sugars." But isn't there only one hydroxide on each phosphate? Thanks $\endgroup$ Mar 30 '19 at 21:58
  • $\begingroup$ I said a text book. Berg et al. on NCBI Bookshelf is a reputable source. Read about the DNA Ligase reaction there, especially Figure 27.28 and 27.29. The DNA polymerase reaction (which forms most of the phosphodiester bonds) is described in terms of the enzyme mechanism, but the reacting species are shown correctly in Figure 27.12. Explore the rest of this book if you need more context. $\endgroup$
    – David
    Mar 30 '19 at 23:47

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