link to model: https://media.pearsoncmg.com/bc/bc_0media_gen/jsmol/t7dnapol/t7dn

Question

link to model: https://media.pearsoncmg.com/bc/bc_0media_gen/jsmol/t7dnapol/t7dnapol.html

Identify the different components in this SN2 reaction.

A universal feature of nucleic acid polymerases is the use of two metal cations to catalyze the addition of new nucleotides to a growing chain. In the T7 DNA polymerase active site, two magnesium ions are positioned to facilitate the polymerization reaction. One cation interacts with the 3’ OH on the primer strand, whereas the other cation stabilizes the negative charges on all three phosphates of the incoming nucleotide.

Explanation / Answer

The above question is part of DNA synthesis.

Here the the daughter DNA strand is being built by polymerization of nucleotides.

When the DNA primer is extending, this hydroxyl oxygen binds with the alpha phosphorous atom of the incoming nucleotide by a SN2 mechanism.

SN2 mechanism is a substitution nucleophilic bimolecular mechanism which leads to the displacement of a group on a molecule, and its rate will depend on the active participation of two reactants.

So, here the two reactants are the oxygen and phosphorous atom which undergo SN2 mechanism. Which means the nucleophile is the alpha phosphorus atom in orange and the leaving group is the diphosphate which is dark blue in colour.

Thus, the answer is a.

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