THIS WEB SITE IS UNDER CONSTRUCTION FOR 2006
Section 1 Aug 31- Sept 21: Proteins
& Motifs Homework I
Section 2 Sept 26-Oct 24: Forces & Folding
Homework II
Section 3 Sept 26-Dec 12: Transmembrane
electron & proton transfer proteins Reading
III
The course is divided into 3 sections.
(1) The basics of protein structure.
Using web resources to analyze the relationships between proteins.
(2) The forces that determine protein
structure and function.
Hydrophobicity; Electrostatics; van der Waals interactions etc
(3) Analysis of bioenergetic proteins. These allow us to study protein function combining biochemistry, structural biology, physics, and engineering principles. We will study bioenergetic proteins that use store energy to make ATP. Some initial references here
Course Requirements. Each person will be given one protein
as the basis for a ≈20 page paper. You will show your understanding
of the course material in your analysis of the paper. How
to write your paper.
In addition, there will be homework to be handed
in most weeks. The grade will be on class participation + the paper. While
the homework is pass/fail - you must hand it in at a satisfactory level
to pass the class.
This class is for advanced undergraduates and graduate students. Students with diverse backgrounds in biology, chemistry, biochemistry, physics, and engineering are welcome. The fall will be mostly for students from biology and biochemistry while the spring semester is more for students with a background in the physical sciences.
Please bring to class all handouts for the section on which we are working.
Schedule
Molecular visualization: Rasmol
& PYMOL & Swiss
Pdb Viewer
Protein Data Bank
1-Thurs, Aug 1: Class
outline; basic definitions; Mitochondria.
Before doing anything Please send me an email
so I have youre email address.
Name:
Major and year:
Highest Bio, Chem and Physics classes you have taken:
What kind of internet access you have
What you hope to get out of this class:
Homework & Reading-1.
2-Tues Sept 5: Lecture: Mitochondria and biological energy
overview; proton transfers; cofactors
Homework & Reading-2.
3-Thurs, Sept 7: Lecture: Amino acid properties; peptide bonds
Homework & Reading-3.
(hand in Homework-1
lecture 1)
4-Tues Sept 12: Lecture: Protein Motifs; 1°,2°,3° structures;
visualization
Homework & Reading-4
5-Thurs Sept 14: Lecture: Protein folds and families
Homework & Reading-5.
(hand in Homework 2,3)
6-Tues Sept 19: Matching primary sequences
Homework & Reading 6.
Web site with a good overview of forces
8-Thurs Sept 21: Thermodynamics
I
Reading & homework-8 (hand
in Homework 4,5)
7-Tues Sept 26: Structure and sequences of transmembrane
proteins: our proteins.
You will give a brief talk about the structure of your protein, pointing out
the important residues and cofactors, and telling us what reaction is carried
out. Email me 1-3 powerpoint pictures if you want ahead of time.
No homework (hand in Homework 4,5)
9-Thurs Sept 28: Thermodynamics II (hand in Homework
lecture 6,7)
Reading
& homework-8 Thermo I & II have same homework (hand in Homework
6 (7 was talk))
10-Thurs Oct 5: Dr. Koder on where protein structures come from.
11-Tues Oct 10: Hydrogen bonds; Lennard Jones Interactions
& Molecular Volume & Packing
Reading & homework-11
(hand in Homework 8-9)
12-Thurs Oct 12: Solvation of ions.
Thermodynamic homework due today.
Reading & homework-12
13-Tues Oct 17: Hydrophobicity
Reading & homework-13.
(hand in Homework 10,11)
14-Thurs Oct 19: pKs and stat. mech
Reading & homework-14.
15-Tues Oct 24: Electrochemistry and pKs-Thermodynamic boxes
Reading & homework-15.
(hand in Homework 12,13)
16-Thurs Oct 26:Sums of small forces
Reading & homework-16.
17-Tues Oct 31 Your second short talk. Describe the
reaction your protein carries out. Focus on the energetics, what the free
energy difference between reactants and products,under standard conditions
and in the cell. What forces are most important in helping your protein work.
Description of
short talk for today (hand in Homework 14,15)
18-Thurs Nov 2:Electron transfer chains
Reading & homework-18 .
19-Tues Nov 7: .Electron transfer I: electrons
Reading & homework-19 (hand in Homework lecture 17)
20-Thurs Nov 9: Electron Transfer II: nuclei
Reading & homework-20
21-Tues Nov 14: Photosynthetic proteins
Reading & homework-21 (hand in homework 18, 19)
22-Thurs Nov 16: Pure Proton pumps: bacteriorhodopsin
Reading & homework-22
23-Tues Nov 21: ATPase: protons and motors
Reading & homework-23
Thurs Nov 23 - Thanksgiving
24-Tues Nov 28: Succinate DH and others
Reading & homework-24
25-Thurs Nov 30: Electrons in all directions: Bc1
& oxidase
Reading & homework-25
26-Tues Dec 5: Class reports I
27- Thurs Dec 7: Class reports II
If your talk is on the 12 your paper is due today
28- Tues Dec 12: Class reports III
If your talk is on the 5th or 7th your paper is due today
Tues Dec 9: Corrected Paper Due
On reserve
Creighton: Proteins
Darby and Creighton: Protein Structure (the library has this under Narby)
Introduction to Protein Science. Brandon and Tooze
An introduction to hydrogen bonding: George Jeffrey
The hydrophobic effect: Tanford
Atoms and Molecules: Karplus and Porter
Nicholls: Bioenergetics
Also get a Biochemistry and/or Cell Biology Text
Cell Biology will be more of an over view
Biochemistry will have more specific info on proteins
several are on reserve in library or borrow one from a friend