1. BIO409/509 Cell and Molecular Biology

2. You don’t need to hand in corrected answers for Exam #2.

3. SECOND Methods paper assignment due Wed., 4/20 (you don’t do this assignment if you are in the 4H STEM Ambassador Program) Assignment: Choose a SECOND method in Molecular Biology or Cell Biology and write 2-3 page paper about the following: 1)Describe the steps done in the method 2)Explain the “highlight” steps: What are the key “tricks” in the method. 3)Describe two different applications of the method to help demonstrate how the method is valuable. On an extra page, include a bibliography with any resources you used: Our textbook, web sites, personal communications, journal articles, etc.

4. BIO409/509 Cell and Molecular Biology We will skip Chapter 7 DNA Replication and never cover it. Chapter 8 RNA Synthesis this week. Chapter 8 Protein Synthesis next week.

5. RNA Synthesis and Processing 8

7. Figure 8.25 Structure of transcriptional activators

8. Figure 8.11 RNA polymerase II/Mediator complexes and transcription initiation

9. Figure 8.17 Action of enhancers (Part 1)

10. Figure 8.17 Action of enhancers (Part 2)

11. Figure 8.19 The immunoglobulin enhancer

12. Figure 8.14 Identification of eukaryotic regulatory sequences

13. Figure 8.21 Electrophoreticmobility shift assay

14. Figure 8.24 Purification of Sp1 by DNA-affinity chromatography

15. Figure 8.23 Chromatin immunoprecipitation (Part 1)

16. Figure 8.23 Chromatin immunoprecipitation (Part 2)

17. Figure 8.25 Structure of transcriptional activators

18. Figure 8.26 Examples of DNA-binding domains (Part 1)

19. Regulation of Transcription in Eukaryotes DNA binding domains: 1. Zinc finger domain: binds zinc ions and folds into loops (“fingers”) that bind DNA. Steroid hormone receptors have zinc fingers; they regulate gene transcription in response to hormones such as estrogen and testosterone.

20. Figure 8.22 Representative transcription factor binding sites

23. Figure 8.25 Structure of transcriptional activators

24. Regulation of Transcription in Eukaryotes Activation domains of transcription factors are not as well characterized. They stimulate transcription by two mechanisms: Interact with Mediator proteins and general transcription factors Interact with coactivators to modify chromatin structure.

25. Figure 8.27 Action of transcriptional activators

26. Figure 8.29 Regulation of transcriptional elongation (Part 2)

27. Figure 8.31 Histone acetylation (Part 2)

28. Chromatin and Epigenetics Chromatin remodeling factors are protein complexes that alter contacts between DNA and histones. They can reposition nucleosomes, change conformation of nucleosomes, or eject nucleosomes from the DNA.

29. Figure 8.36 Polychrome proteins

30. Figure 8.41 Action of lncRNAs (Part 1)

31. epigenetic inheritance

32. Figure 8.37 DNA methylation

33. Figure 8.38 Maintenance of methylation patterns

35. Figure 8.44 Processing of eukaryotic messenger RNAs (Part 1)

36. Exam #2 Distribution 89 * A 88 ** A 87 * A 86 ** A 85 84 ** A- 83 ** A- 82 81 80 79 * B+ 78 * B+ 77 76 75 74 * B 73 *** B 72 71 * B- 70 * B- 69 68 67 66 * C+ 65 64 63 62 61 60 59 * C- 58 57 56 41 * F 39 * F 37 * F