Ch. 11 - DNA Replication and Recombination
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- In this chapter, we focused on how DNA is replicated and synthesized. We also discussed recombination at the DNA level. Along the way, we encountered many opportunities to consider how this information was acquired. On the basis of these discussions, what answers would you propose to the following fundamental questions? How was it demonstrated that DNA synthesis occurs under the direction of DNA polymerase III and not polymerase I?
Problem 1
- In this chapter, we focused on how DNA is replicated and synthesized. We also discussed recombination at the DNA level. Along the way, we encountered many opportunities to consider how this information was acquired. On the basis of these discussions, what answers would you propose to the following fundamental questions? How do we know that in vivo DNA synthesis occurs in the 5' to 3' direction?
Problem 1
- In this chapter, we focused on how DNA is replicated and synthesized. We also discussed recombination at the DNA level. Along the way, we encountered many opportunities to consider how this information was acquired. On the basis of these discussions, what answers would you propose to the following fundamental questions? How do we know that DNA synthesis is discontinuous on one of the two template strands?
Problem 1
- What observations reveal that a 'telomere problem' exists during eukaryotic DNA replication, and how did we learn of the solution to this problem?
Problem 1
- In this chapter, we focused on how DNA is replicated and synthesized. We also discussed recombination at the DNA level. Along the way, we encountered many opportunities to consider how this information was acquired. On the basis of these discussions, what answers would you propose to the following fundamental questions? What is the experimental basis for concluding that DNA replicates semiconservatively in both bacteria and eukaryotes?
Problem 1
- In this chapter, we focused on how DNA is organized at the chromosomal level. Along the way, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter, what answers would you propose to the following fundamental questions: How do we know that satellite DNA consists of repetitive sequences and has been derived from regions of the centromere?
Problem 1
- Write a short essay that distinguishes between the terms replication and synthesis, as applied to DNA. Which of the two is most closely allied with the field of biochemistry?
Problem 2
- Compare conservative, semiconservative, and dispersive modes of DNA replication.
Problem 3
- Describe the role of ¹⁵N in the Meselson–Stahl experiment.
Problem 4
- Predict the results of the experiment by Taylor, Woods, and Hughes if replication were (a) conservative and (b) dispersive.
Problem 5
- What are the requirements for in vitro synthesis of DNA under the direction of DNA polymerase I?
Problem 6
- In Kornberg's initial experiments, it was rumored that he grew E. coli in Anheuser-Busch beer vats. (Kornberg was working at Washington University in St. Louis.) Why do you think this might have been helpful to the experiment?
Problem 7
- How did Kornberg assess the fidelity of DNA polymerase I in copying a DNA template?
Problem 8
- Which characteristics of DNA polymerase I raised doubts that its in vivo function is the synthesis of DNA leading to complete replication?
Problem 9
- Kornberg showed that nucleotides are added to the 3' end of each growing DNA strand. In what way does an exposed 3'-OH group participate in strand elongation?
Problem 10
- What was the significance of the polA1 mutation?
Problem 11
- Summarize and compare the properties of DNA polymerase I, II, and III.
Problem 12
- List and describe the function of the ten subunits constituting DNA polymerase III. Distinguish between the holoenzyme and the core enzyme.
Problem 13
- Distinguish between (a) unidirectional and bidirectional synthesis, and (b) continuous and discontinuous synthesis of DNA.
Problem 14
- List the proteins that unwind DNA during in vivo DNA synthesis. How do they function?
Problem 15
- Define and indicate the significance of (a) Okazaki fragments, (b) DNA ligase, and (c) primer RNA during DNA replication.
Problem 16
- Outline the current model for DNA synthesis.
Problem 17
- Why is DNA synthesis expected to be more complex in eukaryotes than in bacteria? How is DNA synthesis similar in the two types of organisms?
Problem 18
- Suppose that E. coli synthesizes DNA at a rate of 100,000 nucleotides per minute and takes 40 minutes to replicate its chromosome. (a) How many base pairs are present in the entire E. coli chromosome? (b) What is the physical length of the chromosome in its helical configuration—that is, what is the circumference of the chromosome if it were opened into a circle?
Problem 19
Problem 20
DNA supercoiling, which occurs when coiling tension is generated ahead of the replication fork, is relieved by DNA gyrase. Supercoiling may also be involved in transcription regulation. Researchers discovered that enhancers operating over a long distance (2500 bp) are dependent on DNA supercoiling, while enhancers operating over shorter distances (110 bp) are not so dependent [Liu et al. (2001). Proc. Natl. Acad. Sci. USA 98:14,883–14,888]. Using a diagram, suggest a way in which supercoiling may positively influence enhancer activity over long distances.
- Several temperature-sensitive mutant strains of E. coli display the following characteristics. Predict what enzyme or function is being affected by each mutation. Newly synthesized DNA contains many mismatched base pairs.
Problem 20
- Several temperature-sensitive mutant strains of E. coli display the following characteristics. Predict what enzyme or function is being affected by each mutation. Okazaki fragments accumulate, and DNA synthesis is never completed.
Problem 20
- Several temperature-sensitive mutant strains of E. coli display the following characteristics. Predict what enzyme or function is being affected by each mutation. No initiation occurs.
Problem 20
- Several temperature-sensitive mutant strains of E. coli display the following characteristics. Predict what enzyme or function is being affected by each mutation. Synthesis is very slow.
Problem 20
- Several temperature-sensitive mutant strains of E. coli display the following characteristics. Predict what enzyme or function is being affected by each mutation. Supercoiled strands remain after replication, which is never completed.
Problem 20
