Lecture 5: RNA Structure and Transcription
After this lecture, you should be able to answer the following questions:1. What are introns? Exons? What are nucleosomes? Describe nucleosomes to your study partner. What property of histone proteins enables them to interact with DNA? How can histones be modified? What are the names of two enzymes that acetylate histone proteins? What is the net effect of histone acetylation? What about enzymes that de-acetylate histone proteins? What are they called? What is the net effect of histone de-acetylation on transcription?
2. What are the bases found in RNA? Are thymines present in RNA?
3. What are the different types of prokaryotic RNA? Decribe the structure of prokaryotic mRNA. What is a Shine-Delgarno sequence?
4. Describe promoter structure in prokaryotes. What is the -10 region? The -30 region?
5. Describe the prokaryotic RNA polymerase (the core polymerase) and its role in transcription. What do each of the subunits do? Which of the subunits of this multisubunit protein is the target of the antibiotic rifampicin? What is the role of the sigma factor (recall that core polymerase + sigma factor = ‘holoenzyme.”)
6. What is the lac operon? Explain why it represents a good example of transcriptional regulation in response to metabolic needs of bacteria.
7. What are the different types of eukaryotic RNA? How many eukaryotic RNA polymerase are there? Which eukarotic RNA polymerase is responsible for the synthesis of hnRNA/mRNA? Which of the eukaryotic RNA polymerases is most sensitive to alpha-amanitin?
8. Describe the structure of eukaryotic mRNA. How does it differ from the structure of prokaryotic mRNA?
9. Discuss the types of transcription and promoter elements in eukaryotic DNA.
10. What are the names and functions of the proteins that regulate mRNA synthesis in eukaryotes?
11. What is a transcription factor? Give an example of a basic-region leucine zipper (bZIP) transcription factor. Describe how binding of AP1 to DNA activates transcription.
Kit Corner:
1. Why is fluorescently-tagged Annexin V a good tool to use in the study of apoptosis? where does phosphatidylserine come into the picture?
2. HDAC inhibitors promote the continued acetylation of histones bu blocking histone deacetylase. What does that mean for DNA? Loose nucleosomes or tight ones?
3. Syber Green reagent is used in RT-PCR procedures such as the Shine Polo One Step RT-PCR kit. Why does the use of Syber Green in this assay eliminate the need for electrophoresis?
4. What effect would an inhibitor of P-gp have upon to the levels of NADH in the P-gp Drug Interaction Assay Kit (www.spibio.com)?
posted by Blase Billack, Ph.D. @ 2:56 PM
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