THIS WEB SITE IS UNDER CONSTRUCTION FOR 2009
Ciurrent Syllabus
Section 1 Sep 1- Sept 17: Proteins
& Motifs Homework I
Section 2 Sept 22-Oct 29: Forces & Folding
Homework II
Section 3 Nov 3-Dec 1: Transmembrane
electron & proton transfer proteins Reading
III
Class talks and papers Dec 3, 8, 10.
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-Tues Sept 1: Class
outline; basic definitions; Mitochondria and electron transfers.
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-Thurs Sept 3: Lecture: Mitochondria, biological energy, electron tunneling
overview; proton transfers; cofactors
Homework & Reading-2.
3-Tues, Sept 8: Lecture: Amino acid properties; peptide bonds
Homework & Reading-3.
(hand in Homework-1Introduction
and Our Proteins)
4-Thurs Sept 10: Lecture: Protein Motifs; 1°,2°,3° structures;
visualization
Homework & Reading-4
5-Tues Sept 15: Lecture: Protein folds and families
Homework & Reading-5.
(hand in Homework amino acids (lec 3))
6-Thurs Sept 17: Matching primary sequences
Homework & Reading 6.
Web site with a good overview of forces
7-Tues Sept 22: Thermodynamics
I
Reading & homework-8 (hand
in Homework motifs and folds (lec 4&5)
8-Thurs Sept 24: 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
Tues Sept 29 - Monday schedule - no class
9-Thurs Oct 1:2nd class for talks
10-Tues Oct 6 Thermodynamics II (hand in Homework
lecture primary sequences)
Reading
& homework-8 Thermo I & II have same homework )
11-Thurs Oct 8 : Hydrogen bonds; Lennard Jones Interactions
& Molecular Volume & Packing
Reading & homework-11 (hand in Homework Thermodynamics)
12-Tues Oct 13: Solvation of ions..
Reading & homework-12
13-Thurs Oct 15 + 1: Hydrophobicity
Reading & homework-13.
(hand in Homework 10,11 (hydrogen bonds & solvation)
14-Tues Oct 20: pKs and stat. mech
Reading & homework-14.
15-Thurs Oct 22: Electrochemistry and pKs-Thermodynamic boxes
Reading & homework-15.
16-Tues Oct 27: Guest Lec Dr. Ghose - How we determine protein structures
15-Thurs Oct 29:Sums of small forces
Reading & homework-16. (Hand in homework 12 (hydrophobicity)
17-Tues Nov 3/Thurs Nov 5: 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 13,14,15: pKs, electroch chem, small forces)
18-Tues Nov 10 Electron transfer I: electrons
Reading & homework-18 .
19-Thurs Nov 12: .Electron Transfer II: nuclei
Reading & homework-19
20-Tues Nov 17: :Electron transfer chains
Reading & homework-20
21-22 Thurs Nov 19, Tues Nov 24: Photosynthetic proteins; Pure Proton pumps: bacteriorhodopsin; ATPase: protons and motors; Succinate DH and others; Electrons in all directions: Bc1
& oxidase
Reading & homework-21 (hand in homework 18, 19: electron tunneling)
Thurs Nov 26 - Thanksgiving
25-Tues Dec 1: Class reports I
If your talk is on Dec 10 your paper is due today
26-Thurs Dec 3: Class reports II
If your talk is on Dec 8 your paper is due today
27- Tues Dec 8: Class reports III
If your talk is on Dec 1 your paper is due today
28- Thurs Dec 10: Class reports IV
If your talk is on Dec 3 your paper is due today
Tues Dec 17: Corrected Paper Due
Suggested books (see me)
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