|
Winter 2007 |
| Instructor: | Prof. Terence Hwa; Urey 7246
phone: 4-7263 e-mail: hwa@ucsd.edu |
| Time: | TuTh
11am -- 12:20
pm (Jan 9 through March 15th) |
| Location: | Mayer 4322 (note: changed from original
schedule) |
| Class size: | no restriction |
| Office Hour: | After class or by appointment. |
| Course URL: | http://matisse.ucsd.edu/~hwa/class/w07
(this page) |
| Grade: | combination
of problem sets and 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
• Integrated models of gene expression and genetic
circuits
• Growth physiology and metabolic control
• Evolution of gene regulation
Course activity:
| date |
topics |
assignments |
|
| L1 | Tu,
Jan 9 |
overview I: of basic molecular biology and bacterial physiology | |
| L2 |
Th,
Jan 11 |
flow
of genetic information; gene regulation; comparison to eukaryotes |
|
| L3 |
Tu,
Jan 16 |
bacterial
growth physiology (Refs: bremer96, donachie68, neidhardt99) |
HW1 due 1/25 |
| L4 |
Th,
Jan 18 |
bacterial
growth physiology protein-DNA interaction: Intro (Refs: fields97, stormo98) |
|
| L5 |
Tu,
Jan 23 |
protein-DNA
interaction: thermodynamics (Refs: gerland02) |
|
| L6 |
Th,
Jan 25 |
protein-DNA interaction: kinetics [notes] | HW2 due 2/8 (Note new due date) |
| L7 |
Tu,
Jan 30 |
intro to transcription: RNA polymerase and sigma factors [notes] | Soln to HW 1 |
| L8 |
Th,
Feb 1 |
transcriptional
initiation control: basic model [notes] |
|
| L9 |
Tu,
Feb 6 |
transcriptional
initiation control: cooperative regulation [notes] |
|
| L10 |
Th,
Feb 8 |
transcriptional
initiation control: DNA looping [notes] |
HW3 due 2/22 |
| L11 |
Tu,
Feb 13 |
transcriptional initiation control: combinatorial regulation [notes] |
Soln to HW 2 |
| L12 | Th,
Feb 15 |
transcription termination, anti-termination, and elongation [notes] | |
| L13 |
Tu,
Feb 20 |
translation and its control [notes] | |
| L14 |
Th,
Feb 22 |
proteolysis and control
[notes] modeling gene expression [notes] |
term project oral: 3/12 |
| L15 |
Tu,
Feb 27 |
modeling genetic ciurcuit I [notes] |
|
| L16 |
Th,
Mar 1 |
modeling genetic circuit II [notes] |
Soln to HW 3 |
| L17 |
Tu,
Mar 6 |
stochasticity in gene expression [notes], [tutorial] | |
| L18 |
Th,
Mar 8 |
post-transcriptional control by small RNA [notes] | |
| M,
Mar 12 |
term project
presentation, 2:30 - 5:30pm, Urey 7130 |
report due 3/22 |
|
| L19 |
Tu,
Mar 13 |
control of bacteria growth [notes]
|
HW4 due 3/22 |
| L20 |
Th,
Mar 15 |
molecular
evolution [notes] |