17. Which experimental method is commonly used to determine the binding site of a protein on DNA?
(A) Western blot
(B) DNase I footprinting
(C) Nitrocellulose filter-binding assay
(D) Gel-shift (EMSA) assay
(E) Heparin competition assay

18. Which of the following statements best describes the lac repressor (LacI)? (A) It binds to the CAP-binding site and prevents transcription. (B) It binds directly to RNA polymerase to inhibit open complex formation. (C) It degrades lactose to allolactose. (D) It activates the lac promoter when glucose is absent. (E) It is a tetramer that binds to the operator sequence to repress transcription.

19. During λ phage infection, immediate early genes are transcribed by: (A) Phage-encoded RNA polymerase (B) RNA polymerase lacking σ (C) RNA polymerase with σ38 (D) Host RNA polymerase holoenzyme (E) RNA polymerase bound to Q

20. What role does the alarmone ppGpp play at the molecular level in transcriptional regulation? (A) Enhances promoter melting (B) Stabilizes open promoter complexes (C) Binds RNA polymerase and destabilizes open promoter complexes (D) Stimulates σ factor release (E) Increases elongation rate

21. Which is incorrect for eukaryotic promoters? (A) Class I promoters generally consists of a core element surrounding the transcription start site and an upstream promoter element (UPE). (B) In the 5S and 7SL RNA genes, the promoters are located entirely within the genes themselves. (C) For class III genes, type II promoters found in tRNA genes contain two regions, Box A and Box B, which are recognized by TFIIIC. (D) Proximal promoter elements of class II genes act in an orientation-dependent yet position-independent manner. (E) In class II genes, TATA-less promoters are common in both housekeeping and developmentally regulated genes.

22. Choose a correct statement about eukaryotic RNA polymerases (RNAPS) I, II and III? (A) Rpb5, Rpb7, Rpb9, Rpb11 and Rpb12 are common subunits for all three RNAPS. (B) Three loops extending from the clamp of RNAP II--the zipper, lid and rudder--are revealed by crystal structure, and the zipper initiates RNA-DNA hybrid dissociation. (C) RNAP containing the IIO subunit is involved in the formation of pre-initiation complex, while RNAP with the IIA subunit contributes to transcription elongation. (D) In RNAP, flexing of the bridge helix is crucial for translocation during transcription, while the trigger loop ensures correct nucleotide selection and positioning. (E) RNAP II is located in the nucleolus and is highly sensitive to alpha-amanitin, which inhibits RNAP translocation but does not block phosphodiester bond formation.

23. Which of the following is true for eukaryotic Class I and III general transcription factors, except: (A) TFIIIB and TFIIIC are required for all "classical" class III genes. (B) TFIIIC is an assembly factor that helps TFIIIB to bind to a region just upstream of the transcription start site. (C) Human SL1 is an assembly factor that helps the UPE-binding factor of RNA polymerase I to bind to the core promoter element. (D) TFIIIA is a zinc finger protein & is required for transcription of the 5S rRNA genes, but not the tRNA genes. (E) For the class I transcription, human SL1 consists of TATA-binding protein (TBP) and TBP-associated factors (TAFs), which are different from TAFs found in TFIID.

24. Which of the following statement is correct in eukaryotic transcription? (A) Yeast Gcn4 controls amino acid metabolism, containing a domain using the basic region to bind to DNA and helix-loop-helix to form a protein dimer. (B) The carboxyl-terminal domain of RNA polymerase is phosphorylated prior to the formation of the initiation complex. (C) By adding of excess acetyltransferase to in vitro transcription assay, it is likely lead to a tighter association of histone with DNA, resulting in reduced transcription. (D) TAF1 of the general transcription factor TFIID is a helicase and a histone acetyltransferase. (E) The high mobility group protein (HMG I(Y)) plays a role in interferon-ẞ (IFN-ẞ) transcription by bending the DNA, causing more activators to bind and interact with each other to enhance transcription.

25. Which of the following statement is correct related to general and gene-specific transcription factors in eukaryotes? (A) TATA-box-binding protein (TBP) binds to the minor groove of DNA, bends the consensus TATA DNA, and is required for most members of class I, II and III genes. (B) For RNAP III, TBP is a component of the general transcription factor TFIIIC. (C) The bZIP transcription factors dimerize through a basic domain and bind to target DNA through a leucine zipper. (D) TFIIE and TFIIH are essential for promoter clearance and transcription elongation. (E) The Cys2His2-zinc finger of TFIIIA is composed of an antiparallel beta-sheet followed by an alpha-helix, and the beta-sheet recognizes and binds to specific DNA sequences in the major groove.

1. Why are action potentials usually conducted in one direction? (A) The nodes of Ranvier conduct potentials in one direction. (B) The brief refractory period prevents reopening of voltage-gated sodium channels. (C) The axon hillock has a higher membrane potential than the terminals of the axon. (D) Voltage-gated channels for both Na+ and K+ open in only one direction.

2. Which of the following statements is an important consequence of the first law of thermodynamics for a living organism? (A) The energy content of an organism is constant. (B) An organism ultimately must obtain all of the necessary energy for life from its environment. (C) The entropy of an organism decreases with time as the organism grows in complexity. (D) Organisms grow by converting energy into organic matter.

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