Study Guide We talked a lot about the scientists that performed the experiments we discussed in class. Be able to associate the scientists with specific experiments we discussed. Be able to describe and interpret all the experiments we discussed in class. Review all the handouts I passed out during class and be able to answer all the questions. This study guide is meant to help you think about the material. You will be responsible for all the material presented in lecture, even if it does not directly appear on this study guide. Think experimentally about these questions. Things like, how would you test this? What happens if the protein is disrupted? I have provided suggested readings on the syllabus. If we did not directly discuss the information in the readings, then I will not test you on that. Lecture 4 General Transcription 1. What are the four main steps of transcription? 2. How does RNA differ from DNA? 3. What is the primary function of RNA poly? 4. What regions of RNA polymerase are most conserved? Which regions of RNA poly are less conserved? Evolutionarily, why may this be? 5. There are four channels in RNA poly. Describe what goes in and out of these channels. Prokaryotic Transcription 1. How many versions of RNA poly do prokaryotes have? 2. Describe the prokaryotic promoter sequence. What is the significance of the 35 and 10 sequences 2. What are the two factors that sigma interacts with to promote transcription? 3. What region of DNA does sigma region 2 and 4 bind? What is the alpha CTD and what does it bind to? 4. What is the primary sigma factor in E. coli called? 5. What is a consensus sequence? How are consensus sequences discovered? 6. What does it mean to have a strong promoter sequence? 7. What is the role of sigma region 4 in promoter interactions? 8. What is the role of sigma region 2 in promoter interactions? 9. What is base flipping and how does this result in DNA melting? 10. What type of experiments determined that aromatic amino acids are important for melting DNA? 11. Describe the initiation of transcription in proks. What does the RNA poly need to do to initiate promoter escape? Is the initial transcribing complex efficient? 12. What type of interactions are broken for the elongation phase to begin? 13. Do you think there are proofreading mechanisms during transcription?