Question

Which one of the following serves as the nucleophilic attacker in the DNA polymerase mechanism of action?

a) DNA template strand
b) DNA primer
c) Incoming dNTP (deoxynucleotide triphosphate)
d) RNA primer

Answer 1

The incoming dNTP acts as the nucleophile in the DNA polymerase reaction, attacking the alpha-phosphorous to form a new phosphodiester bond in the presence of divalent metal ions.

Step-by-step explanation:

The nucleophilic attacker in the DNA polymerase mechanism of action is the incoming dNTP (deoxynucleotide triphosphate). During DNA synthesis, the enzyme DNA polymerase utilizes a template strand to form a new complementary strand. The current growing chain of DNA provides a 3'-OH group which acts as a nucleophile. This nucleophile attacks the alpha-phosphorous atom of the incoming dNTP. The reaction is a nucleophilic substitution where the release of pyrophosphate (PP) occurs, facilitating the formation of the new phosphodiester bond.

To catalyze the formation of the phosphodiester bond, divalent metal ions, typically Mg2+, are necessary. This metal ion is crucial for proper positioning and stability of the nucleophilic 3'-OH group as well as the incoming dNTP.

DNA polymerase requires a primer to begin DNA synthesis, and this primer can be an RNA primer synthesized by a primase. However, the primer itself does not act as the nucleophile; rather, the nucleophile is the 3'-OH group that comes from the primer or the previous nucleotide in the growing DNA chain.