Physics 176/276
| Instructor: | Prof. Terry Hwa; Urey 7222 e-mail: grader: Shiqi Liu |
| 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 (4-520 pm) |
Transcriptional regulation IV: Combinatorial control (expt) [note] [Kuhlman et al, 2007] |
|
| L8 | Tu, Feb 4 | post-transcriptional control I: transcription termination, anti-termination, and translational mechanisms [note] [Dai et al, 2016] | HW1 soln |
| L9 | Fri, Feb 7 (4-520 pm) |
post-transcriptional control II: gene-silencing by small RNA; proteolysis [note] [recording] [Levine et al, 2007] [Buchler et al, 2005] | |
| L10 | Tu, Feb 11 | Genetic circuits I: -ve & +ve feedback; switches and oscillators [note] [Gao et al, 2022] | |
| L11 | Th, Feb 13 | Genetic circuits II: stochastic gene expression [note] [recording] |
HW3 on L8-L12 due Th Feb 27 |
| L12 | Tu, Feb 18 | Genetic circuits III: metabolic control & feedback [note][recording] | HW2 soln |
| L13 | Th, Feb 20 | Bacterial growth physiology [note] [recording] | |
| L14 | Tu, Feb 25 | Quantitative Central Dogma [note] [recording] [Balakrishnan et al, 2022] | |
| L15 | Th, Feb 27 | Global proteome allocation [note] [recording] [Scott et al, 2010] | HW4 on L13-18 due Th March 13 |
| L16 | Tu, Mar 4 | Growth control by ppGpp [note] [recording] [Wu et al, 2022] |
|
| L17 | Th, Mar 6 | Catabolite repression and proteome allocation [note] [You et al, 2013] | |
| L18 | Tu, Mar 11 | diauxic growth and metabolic overflow [note] [recording] [Basan et al, 2015] | |
| L19 | Th, Mar 13 | gene expression and growth kinetics [note] [recording] [Erickson et al, 2017] |