W15: Quantitative Molecular Biology

Physics 176/276 

Lecturer: Prof. Terry Hwa; Urey 7246
phone: 4-7263; e-mail: hwa@ucsd.edu
Time/Location: W F 11:00am – 12:20pm; Mayer Hall 5301(no class on Friday Feb 13th)
Office Hour: After class or by appointment.
Course URL: this page (http://matisse.ucsd.edu/winter-2015-physics-176276-quantitative-molecular-biology/)
Grade 4-5 problem sets (to be posted below); a term project or final.
Prerequisite: 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

Course activity:


Date Topics assignment
L1 Wed, Jan 7 Overview: intro to quantitative biology; basic biochemistry; central dogma; macromolecular machineries;
L2 Fri, Jan 9 overview: gene regulation & signaling; mutations & recombination; quantitative/physical aspects; eukaryotes and systems biology.  HW1 due Friday Jan 16
L3 Wed, Jan 14 Protein-DNA interaction I: introduction and thermodynamics 
L4 Fri, Jan 16 Protein-DNA interaction II: specificity   HW2 due Friday Jan 30
L5 Wed, Jan 21 Protein-DNA interaction III: kinetic accessibility; 1D/3D search  
L6 Fri, Jan 23 Transcriptional regulation I: Intro to molecules and interactions;
L7 Wed, Jan 28 Transcriptional regulation II: Models of simple activation and repression Soln to HW1
L8 Fri, Jan 30 Transcriptional regulation III: Cooperative transcriptional control, DNA looping HW3 due Wed Feb 11(can turn in on Feb 18)
L9 Wed, Feb 4 Transcriptional regulation IVa: Combinatorial transcriptional control (theory)
L10 Fri, Feb 6 Transcriptional regulation IVb: Combinatorial transcriptional control (expt) Soln to HW2
L11 Wed, Feb 11 post-transcriptional control: elongation and anti-termination
Fri, Feb 13 no class
L12 Wed, Feb 18 translational machineries and mechanisms HW4 due Wed March 4
L13 Fri, Feb 20 translational control by sRNAproteolysisgenetics circuits: introduction Soln to HW3
L14 Mon, Feb 23(same time and location) genetic circuits: positive and negative auto-regulation; nonlinear effects of small RNA and proteolysis
L15 Fri, Feb 27 genetic circuits: stochastic gene expression HW5 due Mon March 16(typos corrected Mar 11)
L16 Wed, Mar 4 genetic circuits: metabolic control
L17 Fri, May 6 metabolic feedback;bacterial growth I Soln to HW4(soln posted)
L18 Wed, Mar 11 bacterial growth II
L19 Fri, Mar 13 bacterial growth III