1. Homework #2 is due 10/18
Bonus #1 is due 10/25
Exam key is online

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. Eukaryotic transcription must be activated by binding of transcription factors

4. Enhancers are regulatory regions located some distance away from the promoter

5. Proteins that help bend DNA can play an important role in transcription
Fig 11.14

6. DNA bends to bring different areas in to close contact.

7. Enhancer-blocking insulators prevent enhancer activation
Fig 11.17

8. Insulators block the folding of DNA preventing enhancers from interacting with the promoter
Fig 11.18

9. How do eukaryotic cells jointly express several proteins (without operons)?

10. Promoter sequences where transcription factors can bind activating multiple gene in response to the environment

11. Combinations of regulatory transcription factors regulate expression of different genes
Fig 11.16

12. Promoters typically have several regulatory sequences

13. Steroid response element

14. Steroids bind to receptors/transcription factors inside cell
get translocated to the nucleus
bind to promoters and activate transcription.
cytoplasm

15. Steroid response element

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

17. Alternate Splicing in Drosophila sex determination
Fig 12.23

18. Sex determination is fruit flies
Fig 12.23

19. Alternate splicing leads to sex determination in fruit flies
Fig 12.23

20. Mammalian mRNA Splice-Isoform Selection Is Tightly Controlled
Jennifer L. Chisa and David T. Burke
Genetics, Vol. 175: , March 2007
Regulation of gene expression is often in response to a changing environment.
But how stable can alternative splicing be, and does it play a role in maintaining homeostasis?

21. Alternative splicing modifies at least half of all primary mRNA transcripts in mammals.
More than one alternative splice isoform can be maintained concurrently in the steady state mRNA pool of a single tissue or cell type, and changes in the ratios of isoforms have been associated with physiological variation and susceptibility to disease.
Splice isoforms with opposing functions can be generated; for example, different isoforms of Bcl-x have pro-apoptotic and anti-apoptotic function.
Chisa, J. L. et al. Genetics 2007;175: Fig. 1

22. Using RT-PCR alternatively spliced versions of different genes were identified
Chisa, J. L. et al. Genetics 2007;175: Fig. 1

23. variation in splice-isoform ratios is conserved in two genetically diverse mouse populations
Black= genetically heterogeneous population UMHET3
Red= a population of hybrid females
Chisa, J. L. et al. Genetics 2007;175: Fig. 4

24. In different individuals splice isoforms in different tissues are conserved
Chisa, J. L. et al. Genetics 2007;175: Fig. 5

25. Splice-isoform ratios differ between young and old animals (different environments)
Chisa, J. L. et al. Genetics 2007;175: Fig. 6

26. Conclusions:
Differences are observed in different tissues and at different ages, but there was always tight control of the relative amounts of the different splice-isoforms.
Slight differences in alternative splicing may be indicative of abnormalities (disease).

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

28. 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

29. 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

30. A processed mRNA ready for translation
5’ untranslated region
3’ untranslated region
Protects from degradation/ recognition for ribosome
Protects from degradation/ transport to cytoplasm

31. 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

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

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

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

35. 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

36. 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?

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