Reference no: EM132586507

Assignment - DNA replication Thought Questions

Part 1 -

Re-word and re-express the thoughts behind the famous sentence written by Watson and Crick in their molecular biology research article describing the structure of DNA: " It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material."

How did the manufacture of DNA by E.coli fed with heavy nitrogen nutrients help to verify that DNA replication is semi-conservative?

How would you describe the direction of DNA manufacture by DNA polymerase?

What is the solution to the problem at the replication fork in which only one of the strands can be lengthened by DNA polymerase in the same direction as the advancing replication fork?

If you are shown a portion of a replication fork showing the template strands and the newly synthesized strands, can you label the ends of each strand, making plain the polarity of every DNA molecule in the structure?

If you draw one replication bubble, how many replication forks have you drawn?

The number of replication bubbles that are opened to replicate a human genome is not known with much certainty. Make an estimate from the fact that it takes about 6 hours to replicate the genome and the fact that a eukaryotic replication fork advances at about 50 base pairs per second.

Why do replicating circular chromosomes (such as a replicating bacterial chromosome) resemble the Greek letter theta?

Part 2 -

What supplies the chemical energy, the driving force, for incorporating dNTP building blocks into a growing DNA strand?

Enzymes catalyze chemical reactions, i.e. they can be used over and over again to make the reaction happen more quickly. The suffix "-ase" is the designation of an enzyme, hence DNA polymerase is an enzyme. What chemical reaction does DNA polymerase catalyze?

To begin incorporating dNTP's, DNA polymerase needs a primer and a template. So what exactly is a primer, what is a template, and to which end of which of these are the dNTPs incorporated?

DNA polymerase I is composed of what type of folded chain?

Besides having the ability to catalyze the synthesis of DNA, DNA polymerase I can also actively trim the ends of DNA strands. Describe the direction and purpose of such "exonuclease" activities of DNA pol I.

Why and how is DNA proofread at the time of its synthesis?

How do we know that DNA pol I is not the replicative polymerase in E. coli cells?

How does DNA pol III achieve such a high degree of "processivity"?

A replisome is a complicated structure involving many molecular machines. What is the purpose of the following machines: topoisomerase, helicase, primase, single-strand binding proteins; and DNA ligase.

Describe an Okazaki fragment and explain why newly formed Okazaki fragments contain a stretch of RNA whereas less recently make Okazaki fragments contain no RNA.

If a replication mistake gets past the early proofreading, putting a newly incorporated base in a mismatched arrangement with the parental strand, how does the cellular machinery recognize which strand is the parental strand and which is the new strand? And after that recognition takes place, how is the newly synthesized strand fixed so that the mismatch is corrected?

Part 3 -

Name one of the major difference between the job of DNA replication in eukaryote as compared to prokaryotes?

Bacterial cells contain 3 kinds of DNA polymerase. Eukaryotic cells contain many more than that. Name one of the common purposes of DNA polymerases besides the replication of chromosomes.

Define "nucleosome" and explain why they are needed.

What happens to nucleosomes in the vicinity of the replisome?

Eukaryotic chromosomes have "telomeres". What is a telomere and why do bacterial chromosomes lack them entirely?

The ends of chromosomes present a problem for DNA replication in eukaryotes. Explain how RNA primers are the root of the problem.

How does telomerase counteract telomere shortening? What is the purpose of the RNA sequence carried by telomerase?

When an RNA sequence, such as telomerase RNA, is used to direct the manufacture of DNA, the information flow runs in the opposite direction dictated by the Central Dogma (which states that DNA directs the synthesis of RNA which directs the synthesis of protein). In what way does such "reverse transcriptase" activity come into play in the life cycle of retroviruses such as human HIV?