Revised September 6, 2000
Lecture 04: Transcription, Polymerases, Promoters, Initiation
1. What are the differences between DNA and RNA?
2. Distinguish between the sense and antisense strands of double-stranded DNA in a manner that makes it clear you know what each is and how they differ.
3. Describe the major features of transcription that are applicable both to prokaryotic cells and eukaryotic cells.
4. What role is played by the antisense strand of the double stranded DNA during the process of transcription?
5. What is the source of the energy that drives RNA synthesis (transcription)?
6. How does the nucleotide sequence of the sense strand of double-stranded DNA differ from the nucleotide sequence of the corresponding messenger RNA?
7. What is a promoter sequence and why is it important?
8. Describe the major elements of a typical prokaryotic promoter.
9. How does the RNA polymerase core enzyme differ from the RNA polymerase holoenzyme. Answer both in terms of structure and in terms of function.
10. What is the special significance of the sigma-subunit of prokaryotic RNA polymerase?
11. Is all of the DNA in a genome transcribed? Explain the reasoning behind your answer.
12. Describe the differences that exist between prokaryotic and eukaryotic cells with regard to the temporal and spatial relationship between transcription and translation.
13. Identify the three types of RNA polymerase found in eukaryotic cells and briefly describe the function of each.
14. What are transcription factors and how are they beleived to function?
15. What is the role of the TATA box in promoters that have one?
16. What role is played by the TATA-binding protein in the initiation of transcription from promoters that contain a TATA box?
17. What is an enhancer and what are the special properties that distinguish it from cis-acting sequences that are directly a part of the promoter.
18. How is a distant enhancer site believed to activate transcription? (What mechanism allows it to exert its effect over a considerable distance?)
19. Enhancers are sometimes found to be located within the introns of the gene whose expression they regulate. Why does the removal of the intron during message splicing not interfere with the regulatory function of the enhancer?
20. What are the major components of the class II preinitiation complex and how is it assembled. What component is added first? What is the role of that component?
21. What aspects of the overall life cycles of eukaryotic organisms make it necessary to have more complex controls over gene expression than are found in prokaryotic cells?
22. Enhancers are known to work at a distance of thousands of base pairs from the promoter whose transcription they enhance.
a. What is the actual distance (measured along the DNA backbone) between two points of a DNA double helix separated by 1000 base pairs.
b. How can an enhancer exert an effect on transcription over such a distance.
c. Based on your answer to part b, speculate on how an enhancer might still be able to function with its polarity reversed in the double stranded DNA.
d. Enahncers are part of the chromosomal DNA, such that every cell in the body that does not have an altered genome contains the same enhancers. Speculate on why the transcription of the genes they are associated with these enhancers is enhanced in some types of cells and not in others.
e. What effect would you expect a mutation in an enhancer that prevented it from binding its activation factor to have on transcription of the gene it is associated with?
f. Would you expect the effect in part e to be the same in all of the cells in the organism with the mutation?
23. Summarize the overall organization of a typical eukaryotic gene and the RNA that is initially transcribed from it.
24. Describe three distinctly different ways in which eukaryotic messenger RNA is modified after the gene is transcribed.
25. Describe the "cap" that is added to the 5'-end of eukaryotic mRNA molecules. What unusual features does it have?
26. What role or roles are believed to be played by the 5'-cap on eukaryotic mRNAs?
27. What modification occurs at the 3'-end of most eukarytoic mRNAs? What is the signal that causes the modification to be made?
28. What is a snRNP, and what is its significance to message processing?
29. Summarize the major steps involved in removing introns from hnRNA, including the signals that are involved in determining what sequences are to be removed.
30. Describe the formation of a "lariat loop" during the removal of an intron. What is unusual about the bond that closes the loop?
31. How do ribosomal RNAs differ from their initial transcript?
32. Describe the steps involved in the flow of genetic information from DNA to protein in an eukaryotic cell. How does the overall process differ in prokaryotic cells?
33. Describe all of the parts of a full-length eukaryotic mRNA that do not code for amino acids.
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