Wednesday, 20 December 2017

biochemistry - Chemistry of phosphodiester bond formation by DNA polymerase


As I'm teaching General Biology to my college students, I realized that I don't fully understand how a 3-P nucleotide like ATP is broken down to be incorporated into DNA during replication. How does this work??


In other words, what is the actual mechanism/reaction pathway for the following:


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What I know:


I understand that ATP is typically hydrolyzed to become dephosphorylated in other contexts. I also understand that a phosphate of one nucleotide is bonded to a deoxyribose of an adjacent nucleotide via dehydration synthesis from the joining of their hydroxyl groups to form DNA.


However, I cannot seem to find a good resource (online or in any of my [admittedly simple] general bio textbooks) that demonstrate how exactly both of these reactions take place during replication...



I'm assuming that DNA polymerase is taking advantage of the released phosphates from ATP (and the appropriate forms of GTP, CTP, TTP) to become activated?


Overall, what does this whole process look like on a chemical/molecular level?


I'd love a visual (especially a video) if you could provide such a resource in addition to a thorough explanation of what's going on here.




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