BIOL 5304 Molecular Biology Fall 2018 Name. Homework #1 Due Monday, September 10 at 10:00 AM. 80 points - 1 -

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1 BIOL 5304 Molecular Biology Fall 2018 ame omework #1 Due Monday, September 10 at 10:00 AM 80 points - 1 -

2 1. (20 points-maximum) For each item at the left, find all the descriptions on the right that apply to it, and write the appropriate letters in the blanks. There are at least 30 correct responses. Score 1 point for a correct response, and (-1) for an incorrect response. All proteins listed are from E. coli. A. DA Polymerase I B. DA Polymerase III (core) C. Single strand binding protein (SSB) D. Primase (DnaG) E. Sliding Clamp F. t protein G. DnaA. Replication elicase (DnaB) I. Clamp loader (g complex) J. Topoisomerase I K. DA gyrase L. DA ligase M. Dam methylase 2-3 copies occur in the functional unit as 6 identical subunits Requires ATP Binds to the replication helicase Binds specific sequences of double-strand DA as 3 exonuclease activity as 5 exonuclease activity Requires all 4 types of ribonucleotide triphosphates Component of DA polymerase III holoenzyme Makes and seals single-strand breaks in DA Binds to the clamp loader Binds non-specific sequences of single-strand DA Requires deoxyribonucleotide triphosphates Drives the movement of the replication fork Interacts with the clamp Introduces negative supercoils Closes single-strand breaks in DA Opens the duplex DA at the origin of replication 2. (4 points) ow is a T:G mismatch repaired in duplex DA? - 2 -

3 3. (4 points) Inside cells, RA molecules are highly structured, with significant basepairing. Describe some of the structural features that are found in such molecules. 4. (4 points) Which of the following would serve as an effective telomerase? (View the Interactive Animation: Action of Telomerase, if you need help.) (Each contains a curved ribonucleic acid. The linear DA is shown below.) A B Draw an intermediate to show how the correct telomerase would work

4 5. (9 points) Consider a circular, duplex DA of 4725 bp entirely in B-form (10.5 bp/turn) a) What are Tw and Lk 0? b) If this circular DA is isolated from a cell, with a typical superhelical density, δ = , (where δ = Lk/Lk 0 ) while remaining in B-form, what are Lk, Tw, and Wr? c) If a dye is added to visualize the DA from part b), and it causes the DA to have 25 bp/turn, on average, what are the new values of Lk, Tw, and Wr? d) What is the new value of δ in step c)? Is the DA negatively-supercoiled, positivelysupercoiled, or totally relaxed? - 4 -

5 6. (5 points) Below are the chemical structures of guanine and adenine bases as nucleosides. On the right draw the structure of a deaminated form of the adenine base, and an -alkylated form of the guanine base. Would Watson-Crick hydrogen bonding in a duplex be affected by either of your modifications? Which ones? 2 O O O O O 2 O O 7. (6 points) Describe the nucleotide excision repair pathway in E. coli

6 8. (6 points) Briefly describe the disassembly and assembly of nucleosomes that occurs during DA replication. (Look at the ucleosome Assembly Interactive Animation, Chapter 8. It s only an exercise, no questions involved.) 9. (6 points) Describe how Compound X could be tested in the Ames test to determine if it were mutagenic, and potentially carcinogenic

7 10. (16 points) Play the following animated exercises found at the publisher s website. Write answers (A, B, etc, is sufficient) to the questions that are found in the section called Apply Your Knowledge. Chapter Animation umber of Questions 4 DA Topology: Twist and Writhe 8 4 Topoisomerase I Activity 8 9 DA Polymerization 7-7 -

BIOCHEMISTRY REVIEW. Overview of Biomolecules. Chapter 11 DNA Replication

BIOCHEMISTRY REVIEW. Overview of Biomolecules. Chapter 11 DNA Replication BIOCHEMISTRY REVIEW Overview of Biomolecules Chapter 11 DNA Replication 2 3 4 5 6 7 8 9 Are You Getting It?? Which characteristics will be part of semi-conservative replication? (multiple answers) a) The