Physics 176/276
| Instructor: | Prof. Terry Hwa; Urey 7222 e-mail: TA/graders: TBA |
| Time | Tu/Th 2:00 – 3:20 pm (one make-up lecture the week of Jan 27) |
| Location | Urey Hall |
| Office Hour: | after class or by appointment. |
| Course URL: | this page (https://matisse.ucsd.edu/courses/w25-quant-microb/) |
| Grade | 4 problem sets (to be posted below); a possible final project |
| Prerequisite: | math through ordinary differential equation; undergrad thermodynamics & statistical mechanics; intro to molecular biology; or consent of instructor. |
Course outline
- Intro: central dogma, gene regulatory network, and bacterial physiology
- Protein-DNA interactions: equilibrium, kinetic, cooperatively
- Gene regulation: cooperativity and combinatorial regulation
- stochastic gene expression; genetic circuits with feedback
- Bacterial growth physiology: growth laws, growth and size control
- Bacterial metabolism: catabolite repression, diauxic shift, metabolic overflow
- Bacterial motility and chemotaxis
Course activity (tentative):
| Date | Topics | assignment | |
| L1 | Tu, Jan 7 | Intro to quantitative biology; review of molecular microbiology [note] ref: Monod, 1949 |
|
| L2 | Th, Jan 9 | Protein-DNA interaction I: thermodynamics & specificity [note] refs: Berg & von Hippel, 1986; 1987; 1988; Fields et al, 1997; Gerland et al, 2002; |
HW1 on L1-L3 due Tu Jan 28 |
| L3 | Tu, Jan 14 | Protein-DNA interaction II: kinetic accessibility [note]; intro to bacterial transcription [note] refs: Berg, Winter, von Hippel, 1981; Winter, Berg, von Hippel, 1981 |
|
| L4 | Th, Jan 16 | Transcriptional regulation I: simple models of activation & repression [note] [Bintu et al, 2005a][Bintu et al, 2005b] |
|
| Tu, Jan 21 | no class | ||
| Th, Jan 23 | no class | ||
| L5 | Tu, Jan 28 | Transcriptional regulation II: Cooperative control [note] |
|
| L6 | Th, Jan 30 | Transcriptional regulation III: Combinatorial control (theory) [note] [Buchler et al, 2003] |
HW2 on L4-L7 due Th Feb 13 |
| L7 | Fri, Jan 31 (tentative) |
Transcriptional regulation IV: Combinatorial control (expt) [note] [Kuhlman et al, 2007] |