Question

During a hypothetical 3' to 5' DNA polymerization, the energy necessary for the formation of the phosphodiester bond would come from the breaking of the high-energy P-P bond at the 5' end of the growing chain, BUT what happens if the last nucleotide (the triphosphate) was removed as part of proofreading?

Answer 1

During DNA polymerization, the energy for the formation of the phosphodiester bond comes from the breaking of the high-energy P-P bond at the 5' end of the growing chain. However, if the last nucleotide is removed as part of proofreading, the energy for phosphodiester bond formation comes from the hydrolysis of two phosphates (pyrophosphate) from the incoming nucleotide.

Step-by-step explanation:

During polymerization, a high-energy bond (the anhydride bond in the incoming NTP) is broken and a high-energy bond (the phosphodiester bond) is formed. The breaking of the pyrophosphate (PP) into two inorganic phosphates is what drives polymerization. Without this step, polymerization would not be energetically favorable.

However, if the last nucleotide (the triphosphate) is removed as part of proofreading, the energy for phosphodiester bond formation cannot come from the breaking of the high-energy P-P bond at the 5' end of the growing chain. Instead, the incorrect nucleotide is removed and replaced by the correct one.

Thus, in this scenario, the energy for phosphodiester bond formation would come from the hydrolysis of two phosphates (pyrophosphate) from the incoming nucleotide during the proofreading reaction.