W20: Quantitative Molecular Biology

Physics 176/276 

Instructor: Prof. Terry Hwa; Urey 7222
phone: 4-7263; e-mail: 
grader: Ghita Guessous; NSB 2121,  
Time/Location: Tu Th 12:30 – 1:50Pm; Mayer Hall Annex 2702
(occasional make-up lectures; time and location TBA)
Office Hour: After class or by appointment.
Course URL: this page (https://matisse.ucsd.edu/courses/w20-quantitative-molecular-biology/)
Grade 4-5 problem sets (to be posted below); a term project or final.
Prerequisite: math through ordinary differential equation;
undergraduate thermodynamics and statistical mechanics;
intro to molecular biology; or consent of instructor.

Course description

Reference Books

Course outline

  • Introduction and overview: central dogma, gene regulation, genetic circuits
  • Molecular interactions: kinetics, equilibrium, cooperativity; protein-DNA interaction
  • Transcriptional control by activators and repressors; cooperativityand combinatorial control
  • Post-transcriptional control: attenuation, termination, and degradation
  • Simple genetic circuits with feedback: bistabilityand oscillation
  • Stochastic gene expression
  • Metabolic control and growth physiology

A follow-up course on population dynamics, evolution, and ecological interactions will be offered in Spring 2020

Course activity:

  Date Topics assignment
L1 Tu, Jan 7 Overview: intro to quantitative & systems biology; review of molecular microbiology HW1 due Th Jan 16
L2 Th, Jan 9 Protein-DNA interaction I:  thermodynamics & specificity
  TBA TA review of basic math
(pls email Ghita if interested)
L3 Tu, Jan 14 Protein-DNA interaction II: kinetic accessibility  
L4 Th, Jan 16 Transcriptional regulation I:
Intro to molecules and interactions
HW2 due Tu, Jan 28 
L5 Tu, Jan 21 Transcriptional regulation II:
Models of simple activation and repression
L6 Th, Jan 23 Transcriptional regulation III:
Cooperative transcriptional control
solution to HW1
ask TA for password
L7 Tu, Jan 28 Transcriptional regulation III: DNA looping
Transcriptional regulation IVa:
Combinatorial transcriptional control (theory)
L8 Th, Jan 30 Transcriptional regulation IVa:
Combinatorial transcriptional control (theory)
L9 Tu, Feb 4 Transcriptional regulation IVb:
Combinatorial transcriptional control (expt)
HW3 due Th Feb 13
L10 Th, Feb 6 Post-transcriptional control I:
transcriptional termination
solution to HW2
L11 Tu, Feb 11 Post-transcriptional control II:
gene silencing by small RNA
L12 Th, Feb 13 Post-transcriptional control III: proteolysis  
L13 Tu, Feb 18 Genetic Circuits Ia:
positive and negative auto regulation
HW4 due Tu Mar 3
  ??? TA review of nonlinear dynamics  
L14 Th, Feb 20 Genetic Circuits Ib:
positive and negative auto regulation
L15 Tu, Feb 25 Genetic Circuits II: stochastic gene expression  
L16 Th, Feb 27 Genetic Circuits III:
metabolic control and feedback
L17 Tu, Mar 3 Growth Ia: Effect of cell growth on gene expression  
L18 Th, Mar 5 Growth Ib:Effect of cell growth on gene expression HW5 due Th Mar 19
(prob #3 slightly revised on March 6th)
L19 Tu, Mar 10

Growth IIa: control of gene expression by cell growth
new location (for this class only): 4322 Mayer Hall

L20 Th, Mar 12 Growth IIb: control of gene expression by cell growth