Recitation8_2023

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Due November 8, 2023 Recitation 8 (10 total questions, total 19 points) Question 1: Answer the following based on the ribonucleotide structure below: (2 pts) a. Box the part that is added to a growing chain of nucleic acid. b. Star the atom(s) that can form a hydrogen bond with the complementary nitrogenous base. c. Circle the part of the molecule that decreases the stability of RNA as compared to DNA. d. How does DNA polymerase derive the energy required to catalyze the joining of nucleotides? Question 2: What does deamination of cytosine produce? Why does DNA contain thymine instead of uracil? Briefly explain. (2 pts) Question 3: The following two questions pertain to DNA ligase: (2 pts) a. If a chemical inhibitor of DNA ligase was added to bacterial cells after DNA replication initiation, the outcome would be: A) elongation of both strands would not occur without ligase to join new nucleotides together. B) elongation would occur, but Okazaki fragments would not be joined together. C) elongation of the lagging strand, but not the leading strand would occur. D) normal replication would proceed as DNA ligase is not required for this process. E) too many supercoils would build up in the DNA, resulting in a halting of elongation. b. Which of the following statements is true of a DNA ligase? A) It forms a phosphodiester bond at a single-strand break in DNA, between a 3 ′ -OH group and a 5 ′ -triphosphate B) It forms a phosphodiester bond at a single-strand break in DNA, between a 3 ′ -OH group and a 5 ′ -monophosphate C) It forms a glycosidic bond at a single-strand break in DNA, between a 3 ′ -OH group and a nitrogenous base D) DNA ligase requires ATP for its activity during replication.
Question 4: The drawing below shows an origin of DNA replication. Answer the following. (2 pts) a. Show how the new strands would be synthesized, using rectangles to represent RNA primers and arrows to represent new DNA being made. Label the leading and lagging strands and their 3 ′ and 5 ′ ends. b. Label/identify the enzyme (filled black circle) that helps in unwinding the parental DNA strands at the ends of the replication bubble as replication continues. Name the type of bond broken by this enzyme. Question 5 : A portion of one DNA strand of the human gene responsible for cystic fibrosis is: 5 ′ ..... ATAGCAGAGCACCATTCTG ..... 3 ′ Write the sequence of the corresponding region of the other DNA strand of this gene, noting the polarity. What do the dots before and after the given sequence represent? (1 pt) Question 6: Imagine you have three test tubes containing identical solutions of purified, double-stranded human DNA. (3 pt) You expose the DNA in tube 1 to an agent that breaks the sugar-phosphate (phosphodiester) bonds. You expose the DNA in tube 2 to an agent that breaks the bonds that attach the bases to the sugars. You expose the DNA in tube 3 to an agent that breaks the hydrogen bonds. After treatment, how would the structures of the molecules in the three tubes differ? Question 7: Which of the following structural characteristics is NOT normally observed in a DNA duplex? (1 pt) a. purine–pyrimidine pairs b. sugar–phosphate backbone c. uniform left-handed twist
d. antiparallel strands Question 8: The eukaryotic genomes are much larger than the prokaryotic genomes. What is the one major difference in eukaryotic vs. prokaryotic replication that reduces the total time required for the whole eukaryotic genome to replicate. (1 pt) Question 9: The structure of the replicating DNA molecule is shown. Answer the following. (2 pts) a. If the origin of replication is in region B, where (region A, C, or D) is the replication expected to terminate? b. What is the problem encountered during the separation of newly segregated DNA from the parental DNA? How is this problem resolved? Question 10: You are a virologist interested in studying the evolution of viral genomes. You are studying two newly isolated viral strains and have sequenced their genomes. You find that the genome of strain 1 contains 25% A, 55% G, 20% C, and 10% T. You report that you have isolated a virus with a single-stranded DNA genome. Based on what evidence can you make this conclusion? (1 pt) a. because single-stranded genomes always have a large percentage of purines b. by using the formula G - A = C + T c. because double-stranded genomes have equal amounts of A and T d. because single-stranded genomes have a higher rate of mutation Question 11: An RNA molecule has the following sequence (see below). Parts of region 1 can form a stem-loop with region 2 or with region 3. (2 pts) a. Which stem-loop would you predict to be more stable: a region 1/region 2 interaction or a region 1/region 3 interaction? Explain your choice. b. Can region 2 form a stem-loop with region 3? Why or why not?
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