problem set 6 mbb

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Simon Fraser University *

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Biology

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Feb 20, 2024

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Problem set 6 MBB 222 Fall 2023 (King) Answer the questions to the best of your ability. Fill in your answers in this document in spaces below. Save the document with your answers and submit it to CANVAS before the deadline (Sunday Nov. 12 th , 2023, midnight) . 1. Review questions 4, 6, 7, 9 at the end of Chapter 3 in your textbook (pp. 152-153). 4. The topological properties of DNA are linking number, twist, and writhe. They are related to each other by Linking #= twist + writhe. Twist and writhe can change if linking number stays constant. 6. Type I topoisomerases cleave 1 strand on the DNA and type II topoisomerases cleave both DNA strands. 7. Topoisomerases are involved in the process of chromatin formation and DNA replication because both processes involve the winding or unwinding of DNA which leads to positive supercoiling and topological strain. Topoisomerases relieve the positive supercoiling so that the strain does not stop the unwinding. 9. The hyperchromic effect is the increase in light absorbance at 260nm when DNA strands separate.

2. Challenge problem 24 at the end of Chapter 3 in your textbook (p. 153). 3. Review question 10-13 at the end of Chapter 20 in your textbook (p. 1051). 10. During cytosine deamination cytosine can be deaminated spontaneously and produces uracil. The uracil is then removed by uracil DNA glycosylase and that removal produces an abasic site that is repaired by base excision repair which causes a nick in the DNA created by AP endonuclease. The nucleotide is replaced by a short patch repair while a short section of multiple nucleotides is replaced by long patch repair. 11. If left unrepaired: cyclobutene pyrimidine dimers can distort the DNA helix and cause a roadblock for access to individual bases. At these roadblocks, the replication fork during DNA replication stalls and skips over these sections and places an incorrect nucleotide. RNA polymerase also does the same thing.

12. The 3 types of mutations are  Silent mutations which do not change the coded amino acid and have no effect on the protein  Nonsense mutations which result in an early stop of codons and make nonfictional proteins  Missense mutations which put the wrong amino acids into the protein which also makes non-functional proteins. 13. O6-methylguanine-DNA methyltransferase is needed to remove O6-methylguanine. It is not considered an enzyme because it is irreversibly modified during the process. A cysteine in the active site performs a nucleophilic attack upon the methyl group which removes it from the guanine and converts it to cysteine to homocysteine. Lastly, the protein is degraded to metabolize homosysteine. 4. Compare DNA polymerases I and III with respect to their structures (i.e. how big, how many subunits? functional domains) and roles in DNA replication. DNA pol I DNA pol III structure  Single subunit  Smaller in size  2 functional domains  Grabs DNA like a hand  Multisubunit  Larger in size  2 core polymerase subunits are held together by the clamp loading complex  Functional dimer roles in rep’n  acts on the Okazaki fragments  5’-3’ exonuclease activity - degrades/removes RNA primer  5’-3’ polymerase activity - adds dNTPs to the 3’ ends of the Okazaki fragments, extending them as the RNA primer of the adjacent Okazaki fragment gets  main strand extension polymerase  adds deoxynucleotides to bother leading and lagging strands at replication fork  beta clamps allow each core polymerase to encircle DNA and add thousands of nucleotides before polymerase complex dissociates  highly processive  has 3’-5’ activity

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