Lecture Notes

Here you can download pdf versions of my recent lecture notes.

Physical Chemistry of Biochemical Systems (CCB 342), Spring, 2012

1. Course syllabus.
2. Homework assignment #1, (due in class, Tuesday, Jan 31): Problems 1.12, 1.15, 1.26, 1.35 (a and b only), 1.46 and 1.47 (parts a,b,c,d only). Be sure to show your work.
3. Notes on the Boltzmann distribution.
4. Homework assignment #2, (due in class, Tuesday, Feb 7): Problems 2.3, 2.14, 2.16 and 2.21. As always, be sure to show your work.
5. Homework assignment #3, (due in class, Tuesday, Feb 14): Problems 3.14, 3.20, 3.25 and 3.34.
6. Homework assignment #4, (due in class, Tuesday, Feb 21): Problems 4.8, 4.15, 4.20, 4.37(a).
7. Study guide for exam 1. (Exam is on Friday, Feb. 24.) Exam key.
8. Stat. mech. approach to ligand binding.
9. Homework assignment #5, (due in class, Tuesday, Mar 6): Problems 5.8, 5.21, 5.22, 5.24(a).
10. Homework assignment #6, (due in class, Tuesday, Mar 20): Problems 6.13, 6.16, 6.27, 6.36.
11. Study guide for exam 2. (Exam is on Tuesday, Mar. 27.) Exam key.
12. Homework assignment #7, (due in class, Tuesday, Apr 10): Problems 9.22, 9.23, 9.32(a), 9.33.
13. Homework assignment #8, (due in class, Tuesday, Apr 24): Problems 11.32, 11.34, 11.35, 11.40.
14. Final exam will be Wednesday, May 9, 8am to 11am. Here is a study guide. I will be out of town from April 30 to May 3, but will be available to answer questions on May 4,6,7.

Genetic Systems and Structures, Spring 2012

1. Lac repressor structure, from Feb. 7,9, 2012
2. Notes on the Boltzmann distribution.
3. Notes on thermodynamics, from J.C. Slater, Introduction to Chemical Physics, chapters 2-4.
4. Intro. to molecular modeling of DNA.

Biophysical Chemistry I, (Introduction to Biomolecular Structure and Interactions), Fall 2010

1. Course syllabus.
2. Homework assignment #1: Download and install the VMD visualization program, and work through the Using VMD tutorial. There is nothing to hand in, but you will need to be able to use the program later in the course.
3. Basics of protein structure.
4. Homework assignment #2: (due Sept. 21) is here.
5. Thermodyanmics; protein-protein interactions.
   Notes on statistical mechanics, from J.C. Slater, Introduction to Chemical Physics, chapter 3.
6. Homework assignment #3: (due Sept. 30) is here.
7. Protein phosphorylation.
8. Protein folding (from Babis Kalodimos).
9. Basics of nucleic acid structure (Updated 10/14).
10. Homework assignment #4: (due Oct. 21) is here. Also available: the paper you need for question 5.
11. Protein-DNA interactions (from Babis Kalodimos).
12. Homework assignment #5: (due Nov. 9) is here.
13. Lipids and membrane proteins.
14. Enzymes and mechanisms. Also: reading material on blood substitutes.
15. Instructions for the final presentation and report are here.
16. Homework assignment #6: (due Nov. 23) is here.
17. The immune system.
18. Virus structures.

Biophysical Chemistry II (Methods in Molecular Biophysics), Spring 2010

1. Course syllabus.
2. Introduction, 1/19/10 (DAC).
3. Notes on thermodynamics, from J.C. Slater, Introduction to Chemical Physics, chapters 2-4.
4. Thermodynamics and calorimetry, 1/26/10 (BK).
5. Hydrodynamics and centrifugation, 2/2/10 (DAC).
6. Rotational motion, flucutations and fluorescence, 2/9/10 (DAC).
7. Crystallography and cryo-EM spectroscopy, 2/16/10 (DAC).
8. Biomolecular vibrational spectroscopy, 2/16/10 (DAC).
9. Molecular modeling and theory, 2/23/10, 3/2/10 (DAC).

Biophysical Chemistry I, (Introduction to Biomolecular Structure and Interactions), Fall 2009

1. Course syllabus.
2. Week 1, Introduction (Olson). (Homework assignment is on the final page.)
   Spreadsheet for PDB analysis.
   CA-only PDB file.
3. Lecture notes for weeks 2 and 3 (Case). [Updated on 9/17].
   Homework: Download and install the VMD visualization program, and work through the Using VMD tutorial. There is nothing to hand in, but you will need to be able to use the program later in the course.
4. Protein-protein interactions, (Olson, 9/22).
5. Phosphorylation, (Dr. Joachim Latzer, 9/24).
6. DNA structure, (Olson, 9/29, 10/1). Homework assignment is on the last page.
7. Protein/DNA interactions, (Olson, 10/6, 10/8).
8. DNA condensation and packaging, (Olson, 10/13, 10/15).
9. RNA and the ribosome, (Olson, 10/20, 10/22).
   Structural data for tRNA.
10. Lipids and membranes, (Case, 10/27, 10/29).
11. Membrane proteins, (Case, 11/10, 11/12).
12. Enzymes, (Case, 11/17, 11/19).
13. The immune system, (Case, 11/24, 12/1).
14. Virus structures, (Case, 12/3).
15. Final student presentations, 12/5, 12/8, 12/10.

Methods in Molecular Biophysics, Spring 2009

1. Introduction to Biophysics Methods, from Jan. 20, 2009. Lecture by Babis Kalodimos.
2. Thermodynamics, from Jan. 27, 2009. Lecture by Babis Kalodimos.
3. Hydrodynamics, from Feb. 3, 2009.
4. Rotational motion and fluorescence, from Feb. 10, 2009.
5. Biomolecular NMR, from Feb. 24, Mar. 3, 10, 24, 2009. Lectures by Babis Kalodimos.
6. Biomolecular NMR, from Mar. 24, 31, 2009. Lectures by Dave Case.
7. Protein vibrational spectroscopy, from Mar. 31, 2009.
8. Molecular dynamics simulations, from Apr. 7,14, 2009.
9. Dynamics from NMR, from Apr. 21, 2009. Lecture by Babis Kalodimos.
10. Cryo-electron microscopy, from Apr. 28, 2009.

Genetic Systems and Structures, Spring 2009

1. Lac repressor structure, from Jan. 27,29, 2009.
2. Intro. to modeling of DNA, from Feb. 10,12, 2009.
3. Notes on distance geometry, from Mar. 26, 2009.