MWF 1:00 – 2:30 Room M112
To truly understand biological processes we must understand the macromolecules that carry out biological function. Regardless of one's particular areas of research, this knowledge allows better design and evaluation of experiments and deeper appreciation of the essence of biology. This course provides a rigorous background that will allow students to glean information from protein structures and to use and evaluate thermodynamic and kinetic concepts to understand biological function.
Concepts of thermodynamics, molecular forces, and kinetics of enzymatic and diffusional processes will be introduced and related to their practical application in experimental design and interpretation. Principles of protein structure, packing and protein•ligand interactions will be developed through lectures, discussions and problem sets. The use of these concepts to understand biological function and the level of individual molecular interactions and at the level of complex processes will be demonstrated through case studies from the literature.
Course Director: Bill Weis
Dan Kraut (dkraut@stanford)
Office hours Thursdays from 4-6 in Beckman B477 (5-6763)
Stefan Larson (smlarson@stanford)
Office hours Tuesdays from 3-4:30 in Keck 316
Rebecca Piskorowski (rapisko@stanford)
Office hours Wednesdays from 5-7 in Beckman B177 (3-7557)
Steven Block phone: 724-4046 e-mail: sblock@stanford
Dan Herschlag phone: 723-9442 e-mail: herschla@cmgm
Karla Kirkegaard phone: 498-7075 e-mail: karlak@stanford
Joseph Puglisi phone: 498-4397 e-mail: puglisi@stanford
Bill Weis phone: 725-4623 e-mail: bill.weis@stanford
• Lectures will be scheduled for 80 min, but lecturers are encouraged to not fill all of this time, to leave generous time for questions and for ensuring that the important, new concepts are conveyed to students at all levels
• There will be five problem sets through the course. They are due at the start of class on the specified day. The final problem set will entail describing a molecular approach to a problem of interest to you.
• Grades will be based solely on these problem sets.
• Notes will be handed out at the start of each lecture.
• Students are encouraged to ask questions at the beginning and throughout each lecture. Ample time has been allotted for questions within the schedule.
• Do not hesitate to contact any of the instructors or the TA with any questions related to the course and material covered.
Recommended (available at Stanford Bookstore):
Random Walks in Biology Berg
Proteins: Structures and Molecular Properties Creighton
Structures and Mechanism in Protein Science Fersht
On Reserve at Lane Library:
1. Introduction to Protein Structure Branden &Tooze
2. Biophysical Chemistry Cantor & Schimmel
3. Physical Chemistry Eisenberg & Crothers
4. Physical Chemistry Tinoco, Sauer, and Wang
5. Catalysis in Chemistry and Enzymology Jencks
The recommended texts are also on reserve.
Date Topic Lecturer Problem Sets
Sept 26 (Wed) I. Introduction to Thermodynamics &
Molecular Forces Puglisi
Sept 28 (Fri) cont'd Puglisi #1 out
Oct 1 (Mon) cont'd Puglisi
Oct 3 (Wed) cont’d Puglisi
Oct 5 (Fri) II. Protein Structure Weis #2 out #1 due
Oct 8 (Mon) cont'd Weis
Oct 10 (Wed) cont'd Weis
Oct 12 (Fri) cont'd Weis
Oct 15 (Mon) cont’d Weis
III.Rates of Biological Processes
Oct 17 (Wed) A. Diffusion and Biology Block #3 out #2 due
Oct 19 (Fri) con’td Block
Oct 22 (Mon) B. Enzymes: basic concepts of kinetics,
Catalysis & energetics Herschlag
Oct 24(Wed) cont’d Herschlag
Oct 26 (Fri) Kinetic simulation workshop
Oct 29 (Mon) cont’d Herschlag #4out #3 due
Oct 31(Wed) cont'd Herschlag
Nov 2 (Fri) cont’d Herschlag
Nov 5 (Mon) cont’d Herschlag
Nov 7 (Wed) cont’d Herschlag
Nov. 9 (Fri) IV. Allostery/Molecular transducers Block #5 out #4 due
Nov 12 (Mon) cont’d Block
V. Protein. Protein Interaction and
Nov 14 (Wed) Biochemical approaches Herschlag
Nov 16 (Fri) cont’d Kirkegaard
Nov 19 (Mon) cont’d Kirkegaard
Nov 21 (Wed) TBA
Nov 26 (Mon) cont’d Kirkegaard #5 due
Nov 28(Wed) VI. Single molecule approaches Block
Nov 30 (Fri) cont’d Block
Dec 3-7(Mon) Student research presentations
Dec 10 - 14 FINALS WEEK
Homework set 2:
Homework set 4a (Kinetic Modeling):
You may find it useful/necessary to download the class handout (containing the problem set), a short guide to modeling with Berkeley Madonna, the entire BM users guide, and the Lorsch & Herschlag article necessary to complete the homework.
So do we understand how enzymes work? (David Blow)
Proteins. (Linda Jen-Jacobson)
Pyle1990 (scanned in)
Pyle1991 (scanned in)