|
Fall 2009 |
| Instructor: | Prof. Terence Hwa; Urey 7246
phone: 4-7263 e-mail: hwa@ucsd.edu |
| Time: | MW
9:30am -- 10:50 am (Sept 28th through Dec 2nd; no class Wed Nov
11) |
| Location: | Note of room
change: Mayer Hall 5301 |
| Class size: | no restriction |
| Office Hour: | After class or by appointment. |
| Course URL: | http://matisse.ucsd.edu/~hwa/class/f09
(this page) |
| Grade: | combination
of problem sets and final or term project report |
| Homework: | to be posted below |
| Prerequisite: | undergraduate thermodynamics and statistical mechanics and introductory molecular biology, or consent of instructor |
Course outline
•
Introduction and overview: central dogma, gene regulation, genetic
circuits
• Molecular interaction: kinetics, equilibrium,
cooperativity; protein-DNA interaction
• Transcriptional control by activators and
repressors; cooperativity and combinatorial control
• Post-transcriptional control: attenuation,
termination, and degradation
• Simple genetic circuits with feedback: bistability
and oscillation
• Stochastic gene expression
• Metabolic control and
growth physiology
Course activity:
| date |
topics |
assignments |
|
| L1 | Mon,
Sept 28 |
overview:
intro to quantitation; basic biochemistry and molecular biology |
|
| L2 |
Wed,
Sept 30 |
overview:
flow
of genetic information; gene regulation; comparison to eukaryotes |
HW1
due Oct 7 |
| L3 |
Mon,
Oct 5 |
protein-DNA
interaction: intro and thermodynamics |
|
| L4 |
Wed,
Oct 7 |
protein-DNA
interaction: thermodynamics and kinetics |
HW2 due Oct 21 |
| L5 |
Mon,
Oct 12 |
introduction
to transcriptional control: machinery and mechanisms |
|
| L6 |
Wed,
Oct 14 |
transcriptional
control: basic models |
|
| L7 |
Mon,
Oct 19 |
transcriptional
control: cooperativity |
soln to HW1 |
| L8 |
Wed,
Oct 21 |
transcriptional
control: DNA looping, combinatorial regulation |
HW3 due Nov 4 |
| L9 |
Mon,
Oct 26 |
transcriptoinal
control: combinatorial regulation |
|
| L10 |
Wed, Oct 28 | case
study: combinatorial control of the lac operon |
|
| L11 |
Mon,
Nov 2 |
transcriptional
elongation, termination, and anti-termination |
soln to HW2 |
| L12 |
Wed,
Nov 4 |
translation
and translational mechanims |
HW4 due Nov 18 |
| L13 |
Mon,
Nov 9 |
translational
control; proteolysis |
|
| Wed,
Nov 11 |
Veteran's
Day (no class) |
||
| L14 |
Mon,
Nov 16 |
genetic
circuit I |
|
| L15 |
Wed,
Nov 18 |
genetic
circuit II |