1. The Development of the Operon Concept: What Cells Eat and When They Die (Berman et al.) The big idea: there are genes that control other genes! Bacterial growth curves

2. Exploring Regulatory Diversity Key point: We can work out the regulation factor for many other scenarios including other looping scenarios. Synergistic Activation Better census needed!

3. How Should We Think About Regulation Quantitatively? Wong, Gladney, and Keasling ‘03 Rate Equation Perspective “Thermodynamic Models” – Equilibrium Notions

4. The Lambda Switch: The Other Hydrogen Atom of Gene Regulation Roger Hendrix

5. Bacteriophage and Their Genomes http://www.biochem.wisc.edu/inman/empics/0020b.jpg

6. The Life Cycle of Bacteriophage Lambda

7. Physical Consequences of the Tight Squeeze in the Life Cycle of a Bacteriophage Rate of packing: 100bp/sec “Some assembly required” Self-assembly Rate of ejection: ≈ 100 - 1000bp/sec Construct a physical model of these processes. Forceful ejection

8. A Genetic Switch

9. The Lambda Genome

10. A More Detailed Example of the Parrts List

11. The Lambda Switch: Lysogenic State

12. The Lambda Switch: Lytic State

13. DNA Geography of the Switch

14. Binding of Transcription Factors

15. Synthetic Genetic Switch Collins et al. - see course website

16. Stable Solutions

17. Phase Portrait for the Switch

18. Synthetic Genetic Switch Collins et al. - see course website

19. Coupling of Genes in Networks