LS3 MIDTERM I EXAM

INSTR: L. JOHNSON NAME:_________________________________ (last) (first) I.D. #__________________________________ Test Form B INSTRUCTIONS This exam is 9 pages long. Before starting make sure you have all the pages. Using a number 2 pencil, on the front of your scantron fill in the Instructor (Johnson), Class (LS3), Hour (12:00 or 1:00). Write and Bubble in your UID, your last name and first name. On the back of your scantron Write and Bubble in your UID and Test Form (see above). Feb. 1, 2013

1. Frederick Griffith was experimenting with Streptococcus pneumoniae in order to determine what made the S strain so virulent. With the discovery that the R strain could be transformed into the S strain in mice, he discovered that a) DNA could transform one bacterium into another. b) the R strain had to gain the ability to make a capsule in order to be virulent. c) the heat-killed S strain was toxic to mice. d) All of the above.

2. The graph above was taken from the Hershey Chase paper we discussed in class. Which of the following statements best describes what is happening at time 0. a) Most of the 32P and 35S are found inside the cell. b) Most of the labeled phage are still associated with the cell. c) The radioactive phage have not had time to inject their genetic material. d) The experiment has not yet started. 3. After 4 minutes 30% of the 32P is still found in the extracellular fraction. This can best be explained by a) Bacteria that were lysed by the blending and released the 32P labeled phage DNA. b) Bacteria that were lysed by the blending and released the 32P labeled bacterial DNA. c) 32P labeled phage that had not infected a bacterium so still retained its label. d) 32P labeled phage that had infected a bacterium so still retained its label. 4. Which of the following can be used to denature a DNA double helix? a) low temperature b) alkali c) high salt d) DNase e) All of the above

5. Which of the following is true about RNA structure: a) RNA is less versatile than DNA in its secondary and tertiary structure b) A single-stranded RNA cannot fold back on itself to form a hairpin loop. c) Double helical regions of RNA are found in a B-form helix. d) Unusual base pairs are some times found in RNA. e) All of the above. Consider the following RNA molecule.

6. Which base is at the 5 end? a) A b) G c) C d) U 7. Which base is at the 3 end? a) A b) G c) C d) U 8. Starting with a 600 bp plasmid and with two negative superhelical turns, which of the following statements about topology are correct (assume 10 bp/turn for standard B DNA): a) This plasmid is in equilibrium with a relaxed plasmid that has unwound 2 bp. b) The values of L, T and W for this plasmid are: 60, 58, -2 c) This plasmid will migrate faster through an agarose gel than a relaxed plasmid of the same size. d) b and c e) All of the above

 9. Which of the following is true about proteins? a) Proline cannot form a peptide bond because of the cyclical nature of its side chain. b) The plane of the peptide bond is rigid because of the resonance of its double bonds. c) A peptide with the sequence RRKAVDE has a net charge of -1. d) Disulfide bonds are commonly found in cytosolic proteins. e) All of the above. 10. How are the results of the Hershey-Chase experiment related to the Avery experiment? a) Both experiments demonstrate the DNA carries genetic information. b) Both experiments are aimed at determining the chemical nature of transformation. c) Both experiments utilize bacteriophage in their studies. d) All of the above. 11. Given the structure of guanosine below, what is the order of hydrogen bond acceptor and donors involved in base pairing (from top to bottom)? a) D,D,A b) A,D,D c) A,D,A d) D,A,D

12. Weak interactions hold DNA strands together in a B-form double helix that contains approximately 10 bases pairs per 34 AO turn. These forces include: a) Hydrogen bonding between water molecules and phosphodiester bonds. b) Hydrophobic stacking between bases on the same strands. c) Hydrogen bonding between bases on opposite strands. d) a and c e) b and c 13. Amino acids differ in the characteristics of their side chains. Which of the following statements are true: a) W and Q are single letter codes for tryptophan and glutamine. b) Arg and Lys are positively charged in cells and are considered basic amino acids. c) Glu and Asp are acidic amino acids. d) Tyrosine can be classified as an aromatic amino acid or polar uncharged. e) All of the above. 4

14. Which of the following is not characteristic of the bacterial genome? a) Genes are located close to one another. b) Multiple genes can be transcribed together into a single RNA molecule. c) Genes can be oriented in either direction. d) Genes are disrupted by intervening sequences. 15. Topoisomerases a) relax supercoiled DNA. b) result in a change in the linking number. c) make a covalent bond between a tyrosine and a phosphate in DNA to retain the energy associated with the phosphodiester bond d) a and c e) All of the above. 16. Nucleosomes a) are used to compact the DNA. b) can be post-translationally modified c) have two copies each of H1, H2, H3 and H4 d) a and b e) All of the above 17. Transcription a) involves polymerization of amino acids. b) takes place in the cytoplasm in eukaryotic cells. c) is catalyzed by reverse transcriptase. d) begins with the formation of a phosphodiester bond between two nucleoside triphosphates. e) All of the above 18. In E.coli, sigma factor a) can be considered an initiation factor b) is responsible for recognizing the promoter c) blocks the RNA exit channel d) a and b e) all of the above 19. Protein families refer to a) proteins that act in the same biochemical pathway b) proteins that are located in the same cellular compartment c) proteins that are similar in sequence and/or structure d) b and c e) All of the above 20. How many reading frames does a segment of DNA have? a) 4 b) 6 c) 3 d) 9

21. Transcription initiation involves a series of ordered steps. What is the correct order of the following steps? 1. Abortive initiation 2. Open complex formation 3. Promoter escape 4. Closed complex formation a) 2, 1, 3, 4 b) 4, 2, 3, 1 c) 4, 2, 1, 3 d) 2, 4, 1, 3 e) 2, 4, 3, 1 22. Which of the following is not true about prokaryotic transcription? a) The 5 end of the RNA is always a triphosphate. b) Rho-independent termination occurs at sites where stem-loop structures can form in the RNA and are followed by a series of Us. c) The transcription bubble is about 12-14 nucleotides long. d) Formation of RNA from nucleoside monophosphates is an energetically favorable reaction. e) Eukaryotic and prokaryotic RNA polymerases have similar structures. 23. tRNAs a) with a covalently attached amino acid are said to be charged. b) all form the same three dimensional shape. c) base pair with the mRNA at the codon loop. d) a and b e) All of the above. 24. Which of the following stabilizes both alpha-helices and beta-sheets? a) H-bonding between the peptide bonds in one strand with a second strand. b) H-bonding between donors and acceptors in the backbone. c) Hydrophobic interactions between the side chains. d) H-bonding between the polar uncharged amino acid side chains. e) All of the above. 25. The helix-loop-helix motif a) is a structural domain. b) always functions to bind Ca2+. c) is said to be a supersecondary structure. d) b and c e) All of the above.

 26. In the above graph, relative absorbance at 260 nm is plotted against temperature for three different DNAs (A, B and C). If the length of the DNAs were the same, which DNA has the highest GC content? a) A b) B c) C d) They all have the same GC content e) There is not enough information in this graph to answer the question. 27. Suppose now that the GC content was the same in each of the DNAs, but the length varied. Which DNA is the shortest? a) A b) B c) C d) They all have the same length. e) There is not enough information in this graph to answer the question. 28. What is the Tm of the three DNAs? a) 50, 60 and 90 (for A, B, and C) b) 90, 100 and 110 c) 70, 85 and 110 d) There is not enough information in this graph to answer the question.

29. Consider the diagram above, where the top line represents a DNA fragment cut into three pieces (2, 4 and 8 kilobases long). Probe A can hybridize to the 4 kb fragment and Probe B can hybridize to the 8 kb fragment. If you do a Southern blot using these DNA fragments, how many bands will you see if you use Probe A as your probe? a) 1 b) 2 c) 3 d) none

 30. In the diagram shown above, which end of the RNA is base pairing to the DNA? a) 5 end b) 3 end 31. Which strand has the same sequence as the RNA? a) Template strand b) Coding strand 32. The dissociation constant, Kd, represents a) the salt concentration at which a ligand dissociates from a protein. b) the affinity a protein has for a ligand. c) the concentration of the ligand when fifty percent of the protein is found in a complex. d) b and c e) All of the above 33. Which of the following statements is not true. a) Specific DNA binding proteins bind to defined DNA sequences. b) Specific DNA binding proteins can distinguish between the base pairs through H-bonding in the major groove of DNA. c) Non-specific DNA binding proteins frequently interact with the phosphodiester backbone. d) Non-specific DNA binding proteins are not very abundant in eukaryotic cells. e) All of the above are true. 34. RNA synthesis is directional because a) the 5 phosphate attacks the 3 OH to form a phosphodiester bond. b) the 3 OH attacks the 5 phosphate to form a phosphodiester bond c) pyrophosphate is released making the reaction irreversible d) a and c e) b and c 35. What types of post-translational modifications can occur on lysines? a) Methylation b) Phosphorylation c) Acetylation d) a and c e) All of the above

36. Which types of modifications do not change the charge of the protein? a) Methylation b) Phosphorylation c) Acetylation d) Adenylylation e) All of the modifications result in a change in charge. 37. How do enzymes speed up reactions? a) Reduce the free energy of the reaction b) Increase the free energy of the substrates c) Increase the free energy of the transition state d) Reduce the activation energy e) None of the above.

38. Consider the results shown above for an in vitro transcription assay where all four nucleoside triphosphates are added but only the one indicated is radioactive. Based on these results, which of the following DNA molecules could have been used as template. a) CTGCTGCTGCTG b) TCTCTCTCTCTC c) AGAGAGAGAGA d) TATATATATAT e) AGCAGCAGCAG 39. For the 32P to become incorporated into the RNA in the reaction above, which position must the 32P be in? a) Alpha b) Beta c) Gamma d) Any position. 40. Which of the following is not true about antibodies? a) They are composed of beta-sheets and loops. b) They can be considered hetero-tetramers. c) They have two binding sites for the antigen. d) They are held together by disulfide bonds. e) All of the statements are true.