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- Cell cultures can be synchronized, or brought into the same phase of the cell cycle, by various means. For example, adding thymidine to a cell culture causes all cells to become arrested early in S phase. What is the mechanism by which thymidine treatment blocks DNA replication?If deoxyribonucleotides that lack the 3’-OH groups are added during the replication process, what do you expect will occur? Describe what happens when a nonsense mutation is introduced into the gene encoding transposase within a transposon. A pure culture of an unknown bacterium was streaked onto plates of a variety of media. You notice that the colony morphology is strikingly different on plates of minimal media with glucose compared to that seen on trypticase soy agar plates. How can you explain these differences in colony morphology?You examine DNA replication in an E. coli mutant, which has a partially defective DNA polymerase. In vitro experiments using the mutant DNA polymerase gives an error rate of 10-3, as compared to the expected error rate of 10-6. Which of the following activities is the mutant polymerase likely to be missing, as compared to the normal polymerase? Explain your answer.
- Ultraviolet light can cause covalent linkages between consecutive pyrimidine bases in DNA (up to 100 per second in a single cell in sunlight!). These bulky lesions (i.e. cyclobutane pyrimidine dimers and 6-4 photoproducts), which inhibit DNA and RNA polymerases, are mostly reversed by CPD photolyase when light >300 nm is available to power the reaction. In the dark, however, which DNA repair system is best able to correct these errors? a) non-homologous end-joining b) mismatch repairc) nucleotide-excision repaird) base-excision repair e) homology-directed repairBelow is a diagram of DNA replication as currently believed to occur in E. coli. From specific points, arrows are provided that lead to numbers. Answer the questions below relating to the locations specified by the numbers. (02) What end (5’ or 3’) of the molecule is here? (State which) What enzyme is probably functioning here to deal with supercoils in the DNA? What enzyme is probably functioning here to unwind the DNA? What nucleic acid is probably depicted here? What are these short DNA fragments usually called? What enzyme probably functions here to couple these two newly synthesized fragments of DNA? Is this strand the leading or lagging strand? What end (5’ or 3’) of the molecule is here? (State which)Briefly discuss the pros and cons of having a nucleoid (as bacteria do) versus a double nuclear membrane surrounding the DNA (as in eukaryotes). List and explain three reasons why DNA replication is very accurate.
- Imagine a bacterial cell with a mutation that renders helicase completely nonfunctional (note that this would be a lethal mutation). What, precisely, would go wrong with replication in this cell? Please describe what goes wrong, as well as all downstream effects.In eukaryotes, the Replication factor C (RFC) is a clamp loader. In the absence of RFC, what would be the consequences to the outcome of DNA replication? Explain.Whether the statement "In E. coli, where the replication fork travels at 500 nucleotide pairs per second, the DNA ahead of the fork-in the absence of topoisomerase-would have to rotate at nearly 3000 revolutions per minute" is true or false.
- Many of the gene products involved in DNA synthesis wereinitially defined by studying mutant E. coli strains that could notsynthesize DNA. Question: The dnaE gene encodes the a subunit of DNA polymeraseIII. What effect is expected from a mutation in this gene?How could the mutant strain be maintained?The experiment below is from a seminal set of experiments in the 1960s that illustrated the role of various repair pathways for DNA damage caused by UV radiation. In this experiment, the scientists isolated E coli strains that are mutant in the Rec A gene, the UvrA gene or both. They then irradiated cultures of each strain with increasing doses of UV light and measured the effect on cell viability. Answer the following questions about this data. A. Which DNA repair pathway and repair activity is inhibited by the Rec A mutant? B. Which DNA repair pathway and repair function is inhibited by UvrA mutant? C. Why is the UvrA/RecA double mutant so much more senitive to UV light than either mutant alone?It is desired to isolate genomic DNA from liquid culture of S. cerevisiae yeast. A commercial kit will be used to isolate genomic DNA from this liquid culture. Answer the following questions to understand the strategy used by commercial kits for genomic DNA isolation. a) List all the steps from cell pellet preparation to DNA elution. b) With which feature can the membrane in the column that comes with the commercial kit bind DNA? c) Which component in the kit would you use to recover the DNA from the membrane of the column to which the DNA was attached?