3. A DNA sequence to which RNA polymerase binds prior to initiation of transcription is called ______.
(A) Enhancer
(B) Riboswitch
(C) Promoter
(D) Operator
(E) Suppressor

4. Which of the following techniques is most useful in measuring the dissociation rate of the RNA polymerase-DNA complex? (A) DNase footprinting experiment. (B) Density gradient centrifugation. (C) Run-off transcription assay. (D) DMS footprinting experiment. (E) Filter binding assay.

5. Which of the following statements is     true     about a lac operon with this genotype? (: a mutant repressor gene whose product cannot bind inducer) (A) The mutation is recessive. (B) The operon is uninducible. (C) The mutation is trans-dominant. (D) The operon is nonrepressible. (E) None of the choices is correct.

6. Select the     correct     statement about Up elements? (A) They are proteins that promote transcription of RNA. (B) They stimulate the binding of repressor to DNA. (C) They are nonpromoter DNA elements. (D) They are recognized by the α-subunit C-terminal domain and allow extra strong interaction between polymerase and promoter. (E) They are usually found downstream of the genes they influence.

7. From the study of a crystal structure, a trigger loop is revealed in eukaryotic RNA polymerase II. What is the possible function of the trigger loop? (A) The trigger loop may initiate the dissociation of the RNA-DNA hybrid during transcription. (B) The trigger loop presumably stabilizes the substrate association with the active site of RNA polymerase II, and is involved in nucleotide selection against improper nucleotides. (C) The trigger loop is involved in maintaining dissociation of the RNA-DNA hybrid during transcription. (D) The trigger loop is used to maintain dissociation of template DNA (i.e. transcription bubble) during transcription. (E) The trigger loop is important for removing the misincorporated nucleotide during transcription.

8. Which statement is     true     for eukaryotic RNA polymerases? (A) RNA polymerase III is found in nucleolus to make precursor to tRNAs. (B) RNA polymerase II is insensitive to the toxin alpha-amanitin. (C) Yeast Rpb1, Rpb2 and Rpb7 are core subunits of RNA polymerase II, and are absolutely required for the enzyme activity. (D) In yeast, Rpb5 and Rpb6 are two of the common subunits that are found in all three RNA polymerases. (E) RNA polymerase I is responsible for making heterogeneous nuclear RNA (hnRNA).

9. Please choose one     correct     answer from the following statements related to general transcription factors in eukaryotes. (A) In eukaryotic transcription, TATA-box-binding protein (TBP) binds to the major groove of the TATA box and forces DNA to bend. (B) From structural studies on a TFIIB-RNA polymerase II complex, TFIIB binds to TBP at the TATA box via its C-terminal domain and to RNA polymerase II via its N-terminal domain. (C) Both TFIIE and TFIIH are required for transcription initiation and elongation, but not for promoter clearance. (D) TFIIS has a DNA helicase activity that is important for eukaryotic transcription initiation. (E) TBP is only required for transcription of genes regulated by RNA polymerase II.

10. Bacterial restriction and modification (RM) systems are important for performing DNA cloning. Please choose one     correct     answer for 4 different types of RM systems. (A) In the type II system, restriction and modification are mediated by the same enzyme with two different subunits, one for recognition and modification, and another one for DNA cleavage. (B) The type III system contains the methyltransferase and endonuclease that are encoded as two separate proteins and act independently. (C) The type I system contains two different enzymes; both of them recognize the same target DNA sequence and either cleave or modify the recognition sequence. (D) In the type II system, one enzyme contains several different subunits that are independently responsible for DNA recognition, cleavage or methylation. (E) The restriction enzymes in the Type II system do not need cofactors such as ATP; therefore, they are commonly used for DNA digestion in DNA cloning experiments.

11. Which is     true     for transcription in eukaryotes? (A) TFIIIA is a general transcription factor for RNA polymerase III, and contains a homeodomain DNA-binding motif. (B) In the absence of the hormone ligands, type II nuclear receptors (e.g. glucocorticoid receptor) reside in the cytoplasm, bound to another protein. (C) Insulators are DNA elements that can shield gene activation by enhancers or repression by silencers. (D) Enhancers are position- and orientation-dependent DNA elements that stimulate transcription. (E) Class II promoters for highly expressed genes tend to lack TATA box, whereas promoters for housekeeping tend to have TATA boxes.

12. Which of the following methods can be used to quantify the level of gene expression? (A) S1 mapping (B) Yeast one-hybrid analysis (C) Southern blot (D) Far western (E) Phage display

13. Eukaryotic DNA combines with basic protein molecules called histones to form structures known as nucleosomes. Which of the following histones is placed between two nucleosomes and serves as a linker histone? (A) H1 (B) H2A (C) H2B (D) H4 (E) H3

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