8. Which of the following agents causes DNA damage by forming pyrimidine dimers?
(A) X-rays
(B) γ-radiation
(C) UV radiation
(D) alkylating agents
(E) ethidium bromide

9. Which of the following repair mechanisms is a damage bypass mechanism, not an actual repair mechanism? (A) DNA photolyase (B) base excision repair (C) nonhomologous end joining (D) mismatch repair (E) recombination repair

10. Which of the following statement is     not true   ? (A) DRB sensitivity inducing factor (DSIF) and negative elongation factor (NELF) can help eukaryotic RNA polymerase II in the paused state. (B) TFIIH can catalyze phosphorylation of the carboxyl-terminal domain of RNA polymerase II and is required for promoter clearance, but is not needed for transcription elongation. (C) The signal for RNA polymerase II to leave the paused state is delivered by the positive elongation factor-b (P-TEFb). (D) P-TEFb phosphorylates RNA polymerase II, DSIF and NELF. Next, DSIF leaves the paused complex, but NELF remains to stimulate transcription elongation. (E) TFIIB binds to TATA-binding protein via its C-terminal domain (TFIIBC) and can determine the start site of transcription.

11. Which of the following statement regarding eukaryotic RNA polymerase II is     not true    ? (A) The zipper of Rpb1 collaborates with the lid to initiate dissociation of the DNA-RNA hybrid. (B) The lid of Rpbl interacts with DNA-RNA hybrid & maintains the hybrid dissociation. (C) The pore 1 of RNA polymerase II is the place for extrusion of the 3'end of RNA when RNA polymerase II backtracks. (D) Alpha-amanitin blocks translocation after a phosphodiester bond forms in transcription, without blocking nucleotide entry. (E) Bridge helix lies next to the active center of RNA polymerase II & flexing this helix may function in translocation during transcription.

12. What is the effect on the activity of eukaryotic     RNA polymerase I     if     TAF1 is        deleted     from the promoter? (A) Polymerase I will not form the preinitiation complex. (B) Phosphorylation of the DNA-binding domain will be impaired. (C) Transcription elongation will be slowed. (D) Polymerase I will not form the preinitiation complex and phosphorylation of the DNA-binding domain will be impaired are correct. (E) None of the choices is correct.

13. The Klenow (large) fragment of E. coli DNA polymerase I contains which of the following enzymatic activities? (A) DNA polymerase and 3' to 5' exonuclease (B) DNA polymerase and 5' to 3' exonuclease (C) DNA polymerase and both 3' to 5' and 5' to 3' exonucleases (D) only DNA polymerase (E) only 5' to 3' exonuclease

14. Which of the following regarding structural basis of eukaryotic RNA polymerase II and its nucleotide selection is     not true    ? (A) Structure of yeast RNA polymerase II shows a deep cleft that is lined with basic amino acids and can accept a linear DNA template. (B) From structure of yeast RNA polymerase II, there is a funnel-shaped pore in the bottom of the enzyme and this pore may serve as the exit point for extruding the 3'-end of the nascent RNA. (C) To understand how RNA polymerase II can discriminate against dNTPs, Kornberg and colleagues found that the enzyme incorporated ribonucleotides at a much slower rate than it did deoxyribonucleotides. (D) When a correct nucleotide occupies the nucleotide-binding "A" site, the trigger loop of Rpbl makes several important contacts with that nucleotide to presumably stabilize the nucleotide's association with the active site. (E) The metal B enters the active site of RNA polymerase II by forming complex with the incoming nucleotide.

15. Which of the following is     not true     for heterogeneity of the Rpb1 subunit in eukaryotic RNA polymerase II? (A) RNA polymerase II from plasmacytoma showed heterogeneity in its largest subunit. (B) Subunit Ila is un-phosphorylated and is the primary product to join the preinitiation complex of yeast RNA polymerase II. (C) The carboxyl-terminal domain of RNA polymerase II is phosphorylated prior to the formation of the initiation complex. (D) Phosphorylation of Ila is occurred on its carboxyl-terminal domain. (E) RNA polymerase II with IIo is involved in transcription elongation.

16. Which of the following is     not     a part of the eukaryotic core class II promoter? (A) TATA box. (B) Upstream elements. (C) TFIIB recognition element (BRE). (D) Downstream promoter element (DPE). (E) Initiator (Inr).

17. An experiment was designed to obtain nonspecific transcription from both strands of a DNA molecule. Which of the following strategies would be most effective in achieving this? (A) Use intact DNA. (B) Add the CAP protein. (C) Remove the sigma-factor from RNA polymerase. (D) Include the RNA holoenzyme in the reaction. (E) Enrich the preparation with sigma subunit.

18. Which of the following statements is     not true     about the cro gene? (A) It must be stimulated during the lytic cycle. (B) Its product represses λ repressor activity. (C) It is adjacent to the cII gene. (D) It codes for a repressor of the cI gene. (E) cro activation is necessary for lysogeny.

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