Problem : How does the 3' to 5' proof-reading exonuclease work?

The proof-reading exonuclease scans the newly synthesized DNA strand in the opposite direction of DNA replication for errors in base pairing. When it finds an error, it cuts the incorrect base pair from the newly synthesized strand out and the entire replication holoenzyme backs up and attempts to introduce the correct base all over again.

Problem : Where does the exonuclease cut the daughter strand to remove an improperly paired base?

The exonuclease cleaves the phosphodiester bond that is located between the phosphate group of the incorrect base and the 3' –OH of the previous base on the daughter strand.

Problem : What are the three main sources of DNA damage?

The three main sources are hydrolysis, chemical damage, and radiation damage.

Problem : Thymine dimer mutations are corrected by what DNA repair system?

Short-patch excision repair system.

Problem : In the mismatch repair system, how does the exonuclease distinguish which base is the correct one?

Adenine bases that are located on the original or parent DNA strand are methylated during replication. When the mismatch repair exonuclease finds a mismatched base pair, it removes the base that is on the strand that lacks methylated adenines.