1. Chapter 11 Molecular Mechanisms of Gene regulation Jones and Bartlett Publishers © 2005

2. The 4 critical sequences in the lac operon bound by CRP, RNA polymerase, repressor and the ribosome

3. See Figure 11.8. lac operon repression loop.

4. Binding of tryptophan (the co-repressor) activates an inactive repressor into an active form capable of binding to the trp operator site

5. The terminal region of the trp attenuator sequence.

6. Structure of the leader polypeptide in the trp operon The two tandem tryptophans in the leader peptide act as “stalling sequences” in the absence of tryptophan in the cell

7. Alternative conformations that the trp leader RNA can assume which are important in attenuation

8. Other operons with repeated amino acid sequences that act as “stalling sequence” during attenuation Other amino acid operons using attenuation: leucine and isoleucine,

9. TRAP B. subtilis utilizes a different way of controlling the expression of trp operon. trp operon is not repressible in B. subtilis. No aporepressor, no short leader polypeptide sequence. TRAP: trp RNA-binding attenuation protein. Each monomer binds a tryptophan molecule. 11-mer radially-symmetric TRAP is active form. Binds to regions 1+2 in figure 11.13.

11. Riboswitches A 5’ untranslated leader mRNA can have a small molecule bind to it to change its conformation between two states: Antiterminator Terminator yitL gene in B. subtilis methionine biosynthesis

12. Riboswitch regulation of transcription termination

13. The genetic map of bacteriophage

14. Control of transcription in bacteriophage life cycle by the anti-terminators N and Q proteins, the activator C II protein and the repressor/activator C I protein

15. cI and cro proteins function as a genetic switch: cI turns on lysogeny. cro turns on the lytic cycle.

16. Transcriptional regulation in eukaryotes Many housekeeping genes are expressed constitutively. Levels of expression can be 2-10 fold different in induced vs. uninduced genes. Galactose metabolism in yeast is a good case study.

17. GAL pathway in yeast Extensively studied system. Eight genes of this pathway are involved in galactose metabolism and regulation. Five genes (GAL2, MEL1, GAL4, GAL80, and GAL5) are on different chromosomes. Three genes are clustered on chromosome II (GAL7, GAL10, GAL1).

18. The steps and enzymes involved in the utilization of the sugar galactose in the yeast Saccharomyces

19. Function of the yeast GAL genes GAL3, GAL4, and GAL80 are regulatory genes.

20. The transcriptional orientation of the 3 genes coding for enzymes important in galactose utilization in Saccharomyces Their synthesis is regulated by the transcription activator Gal4 protein.

21. Regulation of the yeast GAL genes

23. Transcriptional Activator Proteins Two broad types of transcriptional activator proteins: helix-turn-helix motif, so it fits into grooves of DNA zinc finger motif, because zinc ions are involved.

24. Transcriptional Activator Proteins

25. Transcriptional Enhancers (Silencers – opposite of enhancers)

26. Deletion scanning

27. Transcriptional Enhancers (Silencers – opposite of enhancers)

28. Deletion scanning

30. Transcriptional activation by recruitment

31. Chromatin remodeling complexes

32. Alternative promoters