Physics 176/276
| Instructor: | Prof. Terry Hwa; Urey 7222 e-mail: TA/graders: Ghita Guessous. |
| Time | Tu/Th 2:00 – 3:20 pm (occasional additional lectures as needed) |
| Location | Mayer Hall Annex 2623 |
| Office Hour: | after class or by appointment. |
| Course URL: | this page (https://matisse.ucsd.edu/courses/w23-quant-microb/) |
| Grade | 4 problem sets (to be posted below); final group project (3-6pm, Thur Mar 23) |
| Prerequisite: | math through ordinary differential equation; undergrad thermodynamics & statistical mechanics; intro to molecular biology; or consent of instructor. |
Course outline
- Intro: central dogma, bacterial gene regulation, and physiology
- Protein-DNA interactions: equilibrium and kinetic characteristics
- Transcriptional control; cooperativity and combinatorial control
- Post-transcriptional control and simple genetic circuits
- Bacterial growth physiology: growth laws and growth control,
catabolite repression, diauxic shift, metabolic overflow
Course activity (tentative):
| Date | Topics | assignment | |
| L1 | Tu, Jan 10 | Intro to quantitative systems biology; review of molecular microbiology [note] |
|
| L2 | Th, Jan 12 | Protein-DNA interaction I: thermodynamics & specificity [note] refs: Berg & von Hippel, 1986; 1987; 1988; Fields et al, 1997; Gerland et al, 2002; |
|
| L3 | Fri, Jan 13 (makeup, MHA2623) |
Protein-DNA interaction II: kinetic accessibility [note: see L2] [recording] refs: Berg, Winter, von Hippel, 1981; Winter, Berg, von Hippel, 1981 |
HW1 on L1-L3 due Fri Jan 27 |
| Tu, Jan 17 | no class | ||
| Th, Jan 19 | no class | ||
| L4 | Tu, Jan 24 | Transcriptional regulation I: Intro; simple models of activation & repression [note] [Bintu et al, 2005a][Bintu et al, 2005b] |
|
| L5 | Th, Jan 26 | Transcriptional regulation II: Cooperative control [note] |
HW2 on L4-L7 due Fri Feb 10 |
| L6 | Tu, Jan 31 | Transcriptional regulation III: Combinatorial control (theory) [note] [Buchler et al, 2003] |
HW1 solution |
| L7 | Th, Feb 2 | Transcriptional regulation IV: Combinatorial control (expt) [note] [Kuhlman et al, 2007] |
|
| L8 | Tu, Feb 7 | Post-transcriptional control I: tax termination & tsl initiation [note] |
|
| L9 | Th, Feb 9 | Post-transcriptional control II: gene-silencing by small RNA and proteolysis [note] [Levine et al, 2007] [Buchler et al, 2005] |
HW3a on L8-L12 due Th Mar 2 |
| L10 | Tu, Feb 14 | Genetic circuits I: -ve & +ve auto-regulation, switches, and oscillators [modified note] |
HW2 solution |
| L11 | Th, Feb 16 | Genetic circuits II: stochastic gene expression [note] |
|
| L12 | Tu, Feb 21 | Genetic circuits III: metabolic control & feedback [note] [recording] |
|
| L13 | Th, Feb 23 | Bacterial growth physiology [note] [recording] |
|
| L14 | Tu, Feb 28 | Quantitative Central Dogma [note] [recording] [Balakrishnan et al, 2022] |
|
| L15 | Th, Mar 2 | Global proteome allocation [note] [recording] [Scott et al, 2010] [Scott & TH, 2022] |
HW4 on L13-15 due Tu Mar 14 |
| Tu, Mar 7 |
no class | ||
| L16 | Th, Mar 9 | ppGpp signaling and growth control [note] [recording] [Scott et al, 2014][Dai et al, 2017][Wu et al, 2022] |
|
| L17 | Fri, Mar 10 (same time, same room) |
ppGpp signaling (cont’d) [note] [recording] |
|
| L18 | Tu, Mar 14 | Carbon catabolite repression [note] [You et al, 2013][Scott & TH, 2022] |
group project due Th Mar 23 |
| L19 | Th, Mar 16 | Carbon co-utilization and diauxic shift [note] [Hermsen et al, 2015] [Okano et al, 2020] [Erickson et al, 2017] |
|
| Th, Mar 23 3-6pm |
Group project presentation |