Bio 3709 Chapter 12 Replication Homework Sp18 PDF

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CHAPTER 12 – Homework Remember – not all of the answers are given. Use this homework as a study guide – most of the questions will come from these homeworks. True/False 1. DNA synthesis during replication is initiated from RNA primers. 2. DNA polymerases require both a template and a primer to initiate synthesis of new DNA. 3. DNA ligase forms covalent phosphodiester bonds between adjacent nucleotides. 4. DNA primase requires only a DNA template and RNA nucleotides to initiate RNA primer synthesis. 5. The proofreading function of DNA polymerases involves 5′  3′ exonuclease activity. (F) 6. DNA polymerases always synthesize new DNA by adding nucleotides on to the 5′ phosphate. (F) 7. Okazaki fragments are involved in both lagging and leading DNA strand synthesis. 8. Telomerase uses an inherent RNA template to synthesize new DNA. (T)

Multiple choices. 1. A portion of one strand of DNA has the sequence 5′ AATGGCTTA 3′. What is it’s complementary strand sequence? 2. DNA replication is initiated from _______. 3. To synthesize new DNA strands, DNA polymerase III requires ________ as a template. 4. DNA ligase forms ________ between adjacent nucleotides. 5. DNA polymerase always synthesizes new DNA by adding nucleotides onto the previous ______. 6. Okazaki fragments are involved in the synthesis of _______. 7. How many origins of replication are found in a prokaryotic cell? 8. How many origins of replication are found in a eukaryotic cell? 9. Where are primers found on the lagging strand during DNA synthesis?

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10.

What would happen if an organism’s telomerase were non-functional?

11. What is one difference between DNA replication in bacteria versus eukaryotes? a. Eukaryotic chromosomes are replicated bidirectionally, while bacterial chromosomes are replicated in one direction. b. Eukaryotic chromosomes have many origins of replication and replicate bidirectionally, while bacteria have only one origin of replication and replicate unidirectionally. c. Bacterial chromosomes are replicated bidirectionally, while eukaryotic chromosomes are replicated in one direction. d. Eukaryotic chromosomes have many origins of replication, while bacteria have only one origin of replication.* e. The process is identical in bacterial and eukaryotic DNA replication. 12.

During DNA replication in E. coli, what is the role of DnaA?

13. Which arrow(s) point(s) to the location of helicase in the diagram shown?

a. b. c. d. e.

A B C A and E B and D*

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14. If SSB is not present during DNA replication, what would you expect to see? 15. DNA helicase inhibitors are well studied as potential drug targets. What would you expect to see if DNA helicase activity is inhibited? a. The replisome complex would not assemble on the oriC region. b. The DNA cannot bend, so hydrogen bonds in the 13-mer region of oriC remain intact. c. Helicase catalyzes ATP hydrolysis and DNA strands separation, so the helix cannot be unwound and strands will not separate.* d. Helicase carries the SSB protein to the open region of DNA, so hydrolysis and strand separation will not occur. e. Helicase prevents reannealing of the separated strands, so strands would quickly reanneal and DNA replication cannot proceed. 16.

What is required for DNA polymerase to initiate DNA strand synthesis?

17. What enzyme(s) is/are responsible for removal of RNA primers and joining of Okazaki fragments? a. 18. You identify a cell in which DNA polymerase III is functional, but it seems to exhibit extremely low The extraordinary accuracy of the DNA polymerase III enzyme lies in its ability to "proofread" newly synthesized DNA, a function of the enzyme's ________. a. 19. Suppose that some cells are grown in culture in the presence of radioactive nucleotides for many generations, so that both strands of every DNA molecule are radioactive. The cells are then harvested and placed in new medium with nucleotides that are not radioactive, so that newly synthesized DNA will not be radioactive. What proportion of DNA molecules will be radioactive after two rounds of replication?

20. In the diagram below, which letter indicates the 5’ end of the leading strand? A)

21. In the diagram below, the arrow indicates the direction of movement of a replication fork.

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A B

C D Which strand is the leading strand? a. A b. B c. C d. D

Choose among the following choices for questions 22-25. A) DNA polymerase I B) single-stranded-binding protein C) helicase D) topoisomerase E) DNA polymerase III 22. _____ unwinds the double helix by breaking hydrogen bonds between the two strands at the replication fork. 23. _____ reduces DNA supercoiling and torsional stress that is created ahead of the replication fork. 24. _____ removes the RNA nucleotides of the primers and replaces them with DNA nucleotides. 25. _____ prevents the separated DNA strands from rewinding into a double helix. Fill In the Blank/Short Answer 26. In E. coli, which protein uses ATP to hydrolyze hydrogen bonds holding complementary strands together? Answer: DnaB 27. The large, complex aggregation of proteins and enzymes that assembles at the replication fork is known as the ________.

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Answer: replisome 28. Comparison of conserved sequences among related species usually leads to the identification of ________, which illustrate the nucleotides most often found at each position of DNA in the conserved region. Answer: consensus sequences 29. What is the term for the daughter strand synthesized continuously during DNA replication? Answer: leading strand 30. ________ is the term for multiprotein complexes in which a core enzyme is associated with additional protein components leading to its function. Answer: Holoenzyme

31.

What is semiconservative replication?

In semiconservative replication, the original two strands of the DNA double helix serve as templates for new strands of DNA. When replication is complete, two double-stranded DNA molecules will be present. Each will consist of one original template strand and one newly synthesized strand that is complementary to the template. 32. List the different proteins and/or enzymes taking part in bacterial DNA replication. Give the function of each in the bacterial DNA replication process (know at least five proteins and/or enzymes). DNA polymerase III is the primary DNA replication enzyme involved. It elongates a new DNA strand from the 3’ end of the primer. DNA polymerase I removes the RNA nucleotides of the RNA primers and replaces them with DNA nucleotides. DNA ligase connects Okazaki fragments by sealing nicks in the sugar-phosphate backbone. DNA primase synthesizes the RNA primers that provide the 3’–OH group needed for DNA polymerase III to initiate DNA synthesis. DNA helicase unwinds the DNA double helix by breaking hydrogen bonds between the two strands at the replication fork.

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DNA gyrase reduces DNA supercoiling and torsional strain that is created ahead of the replication fork by making double-stranded breaks in the DNA and resealing it. Gyrase is also called topoisomerase II. Initiator proteins bind to the replication origin and unwind short regions of DNA. Single-stranded binding protein (SSB protein) stabilizes single-stranded DNA prior to replication by binding to it, thus preventing the DNA from rewinding with its complementary sequences.

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