Macromolecules (Biochemistry 200A) Fall 2016
http://macromolecules.ucsf.edu/
Course Directors:
Dyche Mullins
Jonathan Weissman
Course Lecturers:
David Agard
Steve Altschuler
Yifan Chen
John Gross
Bo Huang
JJ Miranda
Dyche Mullins
Geeta Narlikar
Jonathan Weissman
[email protected]
[email protected]
Course TAs: Victoria Cheung <[email protected]>
Kelsey Hickey <[email protected]>
Mitchell Lopez <[email protected]>
Rebecca McGillivary <[email protected]>
Discussion Leaders: Leor Weinberger, Seemay Chou, Joe Bondy-Denomy, JJ Miranda,
Sy Redding, Bassem Al-Sady, Matt Thompson, Shawn Douglas (coordinator)
Course Time and Location: Lecture will be held Mondays and Wednesdays from 9am-10:30am
in BH-212. Discussion sections will be held every Friday in GH-204, GH-261, and GH-S271.
TA led review session will be held Monday evenings from 5:30pm-7:30pm, with dinner
provided. In addition, three TA led workshops will be held throughout the semester for
additional practice problems and review (see schedule below).
Grading: Grades will be determined by:
20% discussion section attendance and participation
40% problem sets
40% final project
Holidays/Events: NSF application deadline – October 24; Veteran’s Day - November 11;
Thanksgiving - November 24; ASCB Annual Meeting (San Francisco) - 12/3-7; BBC
Retreat - ??
Week 1: September 26, 28
Lecture 1: Dyche Mullins
Understanding molecular motion: diffusion and random walks
Lecture 2: JJ Miranda
Structure of macromolecules I
Discussion 9/30, Paper: Guo et al., random walks in the cytoplasm.
Week 2: October 3, 5
Lecture 3: Geeta Narlikar
Lecture 4: Geeta Narlikar
Molecular interactions
Thermodynamics I
Discussion 10/7, Papers: Li et al., multivalent interactions and “phase transitions”
Week 3: October 10, 12
Lecture 5: Dyche Mullins
Pre-steady state kinetics
Lecture 6: Geeta Narlikar
Thermodynamics II
TA Kinetics Workshop: 5:30 pm in S201
Discussion 10/14, Papers: Peluso et al. and Sohl et al., pre-steady state kinetics
Week 4: October 17, 19
Lecture 7: Bo Huang
Fluorescence spectroscopy
Lecture 8: Dyche Mullins
Purifying and working with proteins
Discussion 10/21, Papers: Hua et al. and Yildiz et al., single-molecule biophysics
Problem Set 1: due 10/21
Week 5: October 24, 26
Lecture 9: Geeta Narlikar
Enzyme kinetics
Lecture 10: JJ Miranda
Structure of Macromolecules II
TA Thermo Workshop:
Discussion 10/28, Papers: Hopfield and Yamane & Hopfield, kinetic proofreading
October 24 - NSF application deadline
Start serious work on final course projects: circa 11/1.
Week 6: October 31, November 2
Lecture 11: Geeta Narlikar Binding and cooperativity I
Lecture 12: Geeta Narlikar Binding and cooperativity II
Discussion 11/4, Papers: Johnson et al., cooperativity in repressor/DNA interactions
TA/Gross NMR Workshop: Wednesday 5:30 pm
Problem Set 2: TBD (to be determined)
Week 7: November 7, 9 (Veterans Day 11/11)
Lecture 13: David Agard
X-ray crystallography I
Lecture 14: David Agard
X-ray crystallography II
Discussion 11/10, Papers: Zhou et al. and Liao et al., structural biology of ion channels
Week 8: November 14, 16
Lecture 15: John Gross
The power of NMR Spectroscopy
Lecture 16: Yifan Chen
Determining molecular structure by electron microscopy
Discussion 11/18, Papers: Morrison et al., NMR spectroscopy
TA Structure Workshop:
Week 9: November 21, 23 (Thanksgiving 11/24)
Lecture 17: Steve Altschuler
Modeling complex biological systems
(no lecture on 11/23 no discussion on 11/25 – Thanksgiving break)
Week 10: November 28, 30
Lecture 18: Jonathan Weissman
Systems Biology
Lecture 19: Jonathan Weissman
Mass Spectrometry (double check)
TA Course Review:
Discussion 10/31, Papers: Gardner et al. and Bagowski et al., systems biology
(ASCB 12/3 - 12/7)
Week 11: December 5, 7
Lecture 20: Lecture 22: Miranda/ Mullins
(No lecture on December 7)
Final course symposium
Friday, December 9 – 2:00 – 5:00 pm
Second Floor Teaching Lab
Extreme Macro