1. Describe three types of post-transcriptional regulation of protein-coding genes.

2. True or false?: The CTD is responsible for mRNA-processing steps that are specific for mRNA and not for other forms of RNA. Explain why you chose true or false.

3. There are a number of conserved sequences found in an mRNA that dictate where splicing occurs. Where are these sequences found relative to the exon-intron junctions? What is the significance of these sequences in the splicing process? One of these important regions is the branch-point A found in the intron. What is the role of the branch-point A in the splicing process, and can this be accomplished with the OH group on either the 2′ or the 3′ carbon?

4. What are the differences between hnRNAs, snRNAs, miRNAs, siRNAs, and snoRNAs?

5. 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?

6. 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 polyadenylation site. To test whether both polyadenylation sites are used, you isolate mRNA and find a longer transcript from muscle tissue and a shorter transcript from all other tissues. Speculate about the mechanism involved in the production of these different transcripts.

7. RNA editing is a common process in the mitochondria of trypanosomes and plants as well as in chloroplasts, and in rare cases it occurs in higher eukaryotes. What is RNA editing, and what benefit does it demonstrate in the documented example of ApoB in humans?

8. Because DNA is found in the nucleus, transcription is a nuclear-localized process. Ribosomes responsible for protein synthesis are found in the cytoplasm. Why is hnRNP trafficking to the cytoplasm restricted to the nuclear pore complexes?

9. A protein complex in the nucleus is responsible for transporting mRNA molecules into the cytoplasm. Describe the proteins that form this exporter. What two protein groups are probably behind the mechanism involved in the directional movement of the mRNP and exporter into the cytosol?

10. RNA knockdown has become a powerful tool in the arsenal of methods used to repress gene expression. Briefly describe how gene expression can be knocked down. What effect would introducing siRNAs to TSC1 have on human cells?

11. Speculate about why plants deficient in Dicer activity show increased sensitivity to infection by RNA viruses.

12. mRNA stability is a key regulator of protein levels in a cell. Briefly describe the three mRNA degradation pathways. Suppose that a yeast cell has a mutation in the DCP1 gene, resulting in decreased uncapping activity. Would you expect to see a change in the P bodies found in this mutant cell?

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13. mRNA localization now appears to be a common phenomenon. What benefit does mRNA localization have for a cell? What is the evidence that some mRNAs are directed to accumulate in specific subcellular locations?