1. Describe three types of post-transcriptional regulation of protein-coding genes.
2. What is the evidence that transcription termination by RNA polymerase II is coupled to polyadenylation?
3. It has been suggested that manipulation of HIV anti-termination might provide for effective therapies in combatting AIDS. What effect would a mutation in the TAR sequence that abolishes Tat binding have on HIV transcription after HIV infection and why? A mutation in Cdk9 that abolishes activity?
4. Some heat shock genes encode proteins that act rapidly to protect other proteins from harsh conditions. Describe the mechanism that has evolved to regulate the expression of such genes.
5. You are investigating the transcriptional regulation of genes from a recently discovered eukaryotic organism. You find that this organism has three RNA polymerase-like enzymes and that genes encoding proteins are transcribed using an RNA polymerase II-like enzyme. When examining the full-length mRNAs produced, you find that there is no 5' structure (i.e., cap). Are you surprised? Why/why not?
6. Why do researchers believe that the fragile-X disorder involves an aberration in RNA binding?
7. What is the difference between hnRNAs, snRNAs, miRNAs, siRNAs, and snoRNAs?
8. Describe how the discovery that introns are removed during splicing was made. How are the locations of exon-intron junctions predicted?
9. What are the mechanistic similarities between Group II intron self-splicing and spliceosomal splicing? What is the evidence that there may be an evolutionary relationship between the two?
10. Where do researchers believe most transcription and RNA-processing events occur? What is the evidence to support this?
11. You obtain the sequence of a gene containing 10 exons, 9 introns, and a 3' UTR containing a polyadenylation consensus sequence. The fifth intron also contains a polyadenyl-ation site. To test whether both polyadenylation sites are used, you isolate mRNA and find a longer transcript from muscle tissue and a shorter mRNA transcript from all other tissues. Speculate about the mechanism involved in the production of these two transcripts.
12. What is the evidence that an mRNA exporter directs mRNPs through nuclear pores? What is the evidence that most vertebrates also utilize such an exporter?
13. Why is localization of Ran GAP in the nucleus and Ran nucleotide exchange factor (RCC1) in the cytoplasm necessary for unidirectional transport of cargo proteins containing an NES?
14. Speculate about why plants deficient in Dicer activity show increased sensitivity to infection by RNA viruses.
15. What is the evidence that some mRNAs are directed to accumulate in specific subcellular locations?
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