W23: Quantitative Microbiology

Physics 176/276 

Instructor: Prof. Terry Hwa; Urey 7222
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.

Reference Books

Student information entry

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
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
Group project presentation