W21: Quantitative Molecular Biology

Physics 176/276 

Instructor: Prof. Terry Hwa
TA/graders: Ghita Guessous; Chenhao Wu.
Time Wed/Fri 9:30 – 10:50 am 
[The lectures will be recorded and posted below]
Location offered synchronously via zoom [meeting id: 930-1588-0512];
authentication requires zoom login with ucsd domain name.
Office Hour: via zoom by appointment.
Course URL: this page (https://matisse.ucsd.edu/courses/w21-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

Student information entry

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

Course activity (tentative):

  Date Topics assignment
L1 Wed, Jan 6 Overview: intro to quantitative & systems biology; review of molecular microbiology [note] [recording HW1 due Fri Jan 15
L2 Fri, Jan 8 continuation of overview [note] [recording]  
L3 Wed, Jan 13 Protein-DNA interaction I:  
thermodynamics & specificity [note] [recording]
L4 Fri, Jan 15 Protein-DNA interaction II: kinetic accessibility [note]
Transcriptional regulation I: Intro [note] [recording]
HW2 due Fri Jan 29
L5 Wed, Jan 20 Transcriptional regulation II: [note] [recording]
Models of simple activation and repression 
L6 Fri, Jan 22 Transcriptional regulation III: [note] [recording]
Cooperative transcriptional control 
Solution to HW1
(password given in class)
L7 Wed, Jan 27 Transcriptional regulation IVa: [note] [recording]
Combinatorial transcriptional control (theory)
L8 Fri, Jan 29 Transcriptional regulation IVa (cont’d):
Combinatorial transcriptional control (theory)
Transcriptional regulation IVb: [note] [recording]
Combinatorial transcriptional control (expt)

HW3 due Wed Feb 17

L9 Wed, Feb 3 Transcriptional regulation IVb: [recording]
Combinatorial transcriptional control (expt)
Solution to HW2
L10 Fri, Feb 5 Post-transcriptional control I:
transcriptional termination [note] [recording]
L11 Wed, Feb 10 Post-transcriptional control II:
translation mechanisms [note] [recording]
L12 Fri, Feb 12 Post-transcriptional control II (cont’d):
gene silencing by small RNA 
Post-transcriptional control III:
proteolysis [note] [recording]
L13 Wed, Feb 17 Genetic Circuits I: [note] [recording]
positive and negative auto regulation
HW4 due Fri March 5
L14 Fri, Feb 19 Genetic Circuits I (cont’d): [recording]
positive and negative auto regulation
L15 Wed, Feb 24 Genetic Circuits II: [note] [recording]
stochastic gene expression
HW3 graded; ask TA for solution 
L16 Fri, Feb 26 Genetic Circuits III: [note] [recording]
metabolic control and feedback
L17 Wed, Mar 3 Growth Ia: [note] [recording]
Effect of cell growth on gene expression
L18 Fri, Mar 5 Growth Ib: [note] [recording]
Effect of cell growth on gene expression
L19 Wed, Mar 10 Growth IIa: [note] [recording]
control of gene expression by cell growth
HW5 due Thursday March 18
L20 Fri, Mar 12 Growth IIb: [note] [recording]
control of gene expression by cell growth