13. Which of the following is correct regarding the mechanism of RNA interference (RNAi)?
(A) RNAi is a gene silencing phenomenon triggered by single-stranded DNA (ssDNA) fragments.
(B) The Dicer enzyme is responsible for cleaving long double-stranded RNA into small siRNA fragments.
(C) The Slicer enzyme functions primarily to transport miRNA out of the nucleus into the cytoplasm.
(D) The RISC complex is primarily responsible for repairing damaged mRNA sequences in the ribosome.
(E) The RNAi phenomenon was originally discovered as an immune mechanism in bacterial cells.

14. Which statement concerning translation and the genetic code is accurate? (A) A codon is defined as a sequence of three nucleotides located on the tRNA molecule. (B) All types of RNA transcribed in the nucleus are eventually translated into proteins. (C) Aminoacyl-tRNA synthetases are responsible for attaching specific amino acids to the acceptor stem of tRNA. (D) Peptide bonds are the primary covalent bonds connecting the two strands of the DNA double helix. (E) Release factors function by increasing the efficiency of tRNA charging during elongation.

15. Which statement regarding the human genome structure or genomic techniques is correct? (A) Exon trapping relies on the presence of flanking splice sites to identify coding regions. (B) Protein-coding genes constitute the vast majority (over 90%) of the human genome sequence. (C) The bacterium E.coli possesses approximately 25,000 genes, similar to humans. (D) All plant genomes are significantly smaller in size compared to the human genome. (E) Radiation hybrids are defined as eukaryotic cells that have been infected with viral DNA.

16. What feature is critical for rho-independent termination? (A) Rut site (B) Strong rU-dA base pairs (C) Hairpin followed by weak rU-dA base pairs (D) NusA binding site (E) Fis sites

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.

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