5-Briefly summarize the palm, thumb, and finger domains of DNA polymerase III, a

Question

5-Briefly summarize the palm, thumb, and finger domains of DNA polymerase III, and explain how they contribute to replication. What is the role of the metal ions in the palm's activity?

6-Okazaki discovered the fragments named after him by briefly exposing replicating DNA to radioactively-labeled nucleotides and then separating the labeled DNA fragments by size. Using this method, he identified two populations of fragments. Describe what these two populations must have looked like. Why was it important to use a short exposure to the radioactive label rather than a longer one?

7-How is the DNA unwound at the replication fork? What effect does this have on the DNA upstream of the fork, and how does the cell deal with this effect?

8-How is methylation involved in the control of timing of replication origin firing in E. coli? What effect does a loss-of-function mutation in the gene encoding dam methylase have on replication timing?

9-Explain why the replication machinery is incapable of completely replicating the ends of the chromosomes. What is the practical effect of this? How do eukaryotic cells get around this problem?

Explanation / Answer

5) DNA polymerase is a replicative enzyme, which replicate or duplicate the DNA. DNA polymerase-III is the main replication enzyme in prokaryotes with processivity and fidelity. The structure of DNA polymerase-III has three main domains called thumb, and finger.   

Palm has the catalytic site, fingers that position the template, a thumb that binds DNA and is important in processivity, an exonuclease domain with its own active site, and an N-terminal domain.

7) The DNA unwound at the replication fork by using the enzyme helicase, it breaks the hydrogen bonds between the two DNA strands.  

8) Methylation of DNA is occurring by the enzyme Dam methylase. The oric site contains a sequence of 5'-GATC-3', this sequence is hemimethylated by Dam methylase and sequestered for a period of time. Only after this, the oriC is released and must be fully methylated by Dam methylase before DnaA binding occurs.

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