Question

Could anyone provide brief explanations to questions 1 through 7? My teacher doesn't provide the answers, and having an explanation will help me study. Please and thank you.

1) How do the metal ions in the active sites of DNA polymerases reduce the activation barrier to phosphoester bond formation? 2) Why is movement by the nascent DNA critical for the editing process as carried out by Pol I? 3) Explain, mechanistically, how the hydrolysis of ATP by the helicase DnaB, may be coupled to replication fork movement. Watch the replication animation from the Cold Spring Harbor Laboratories web site and make sure you can identify the following features on the figures below: lagging and leading strand DNA templates, DNA ahead of replication fork, helicase, primosome, sliding clamp, leading and lagging strand core polymerases, and clamp loader. 5) Explain the role of topoisomerases in DNA replication. If we had uracil in our DNA instead of thymine, how would the frequency of point mutations change? Why? 7) Alkylating agents such as ethylmethane sulfonate (EMS) tend to react quite readily with 06 of guanine, a strong nucleophile. Illustrate with a resonance structure why this carbonyl oxygen is unusually nucleophilic. 8) The following forms of DNA damage lead to changes in the templating specificity of the damaged bases: Methylation of G at 06, Deamination of C, Deamination of A. Draw the structures of these four damaged bases paired to their inappropriate partners. Your base pairs must have correct covalent structures and geometry.

Answer 1

1) The metal ions in the active sites of DNA polymerases activates the primer’s 3′-OH site for an attack on the α-phosphate of the deoxyribonucleotides. It has the role in assisting the exit of the pyrophosphate leaving the group and preventing the reverse reaction. The positively charged metal ion partially neutralizes the negatively charged leaving group and disfavors protonation reaction.

2) Te movement of nascent DNA is important for editing and proofreading by polymerase I because in this way both synthesis of DNA and proofread can occur simultaneously. The error in the sequence can be easily corrected or the process can be halted when both the process occurs simultaneously.