Homework #2 is due 10/17 Bonus #1 is due 10/24

1. Office hours: M 10/8 10-11:30am2-5pm in Bio 6 • Homework #2 is due 10/17 • Bonus #1 is due 10/24

2. Gene Expression is controlled at all of these steps: • DNA packaging • Transcription • RNA processing and transport • RNA degradation • Translation • Post-translational Fig 16.1

3. mRNA transport is an important regulatory step Molecular Biology of the Cell 4th ed. Alberts et al. Fig 6.40

4. mRNA can be localized to a specific parts of a cell (from Drosophila embryo) Molecular Biology of the Cell 4th ed. Alberts et al. Fig 7.52

5. At least 3 mechanisms are involved: Molecular Biology of the Cell 4th ed. Alberts et al. Fig 7.98 Directed transport via cytoskeleton Random diffusion and trapping Degradation and local protection

6. A processed mRNA ready for translation 5’ untranslatedregion 3’ untranslatedregion Protects from degradation/ recognition for ribosome Protects from degradation/ transport to cytoplasm

7. mRNA with 3’ UTR properly localized mRNA without 3’ UTR improperly localized Molecular Biology of the Cell 4th ed. Alberts et al. Fig 7.99

8. Gene Expression is controlled at all of these steps: • DNA packaging • Transcription • RNA processing and transport • RNA degradation • Translation • Post-translational Fig 16.1

9. Seeds germinated underground begin growing in darkness then emerge into light and begin photosynthesis energy from seed energy from sun

10. The level of this mRNA increases after plants are exposed to light. • How might the cell accomplish this?

11. The level of this mRNA increases after plants are exposed to light. • How might the cell accomplish this?Increased transcription and/or decreased mRNA degradation

12. Northern blot analysis: The level of this mRNA increases after plants are exposed to light. • How might the cell accomplish this? • Does this necessarily lead to increased protein production?

13. Gene Expression is controlled at all of these steps: • DNA packaging • Transcription • RNA processing and transport • RNA degradation • Translation • Post-translational Fig 16.1

14. C. elegans is commonly used to study development

15. C. elegans development

16. C. elegans mutants with cells that do not develop properly. Fig 12.25 and

17. C. elegans mutants with cells that do not develop properly. The product of these genes was found to be RNA?

18. MicroRNAs (miRNA) are ~22nt RNAs that play important regulatory roles Cell vol. 116, 281-297 2004

19. miRNA expressed How do microRNAs control gene expression? miRNA processed to ~22nt RNA Mature miRNA

20. A processed mRNA ready for translation: microRNAs inhibit translation by binding to the 3’ end of mRNA microRNA bind to 3’-UTR 5’-UTR 3’-UTR

21. miRNA expressed the 3’ end with attached microRNA interacts with the 5’ end, blocking translation miRNA processed to ~22nt RNA Mature miRNA

22. miRNAs can lead to methylation of DNA that leads to inhibition of transcription

23. microRNAs primarily target gene products that function during development Tbl 1

24. tissue specific expression of mouse microRNA PNAS vol. 101 #1 pg 360-365, 2004

25. Silencing RNAs (siRNA) are artificially induced dsRNA Fig 8.22

26. siRNA with exact matches to the target mRNA causes degradation of the mRNA Fig 8.21

27. microRNA siRNA mRNA degraded Translation inhibited

28. Fig 8.19

29. Gene Expression is controlled at all of these steps: • DNA packaging • Transcription • RNA processing and transport • RNA degradation • Translation • Post-translational Fig 16.1

30. Office hours: M 10/8 10-11:30am2-5pm in Bio 6 • Homework #2 is due 10/17 • Bonus #1 is due 10/24