THIS WEB SITE IS UNDER CONSTRUCTION FOR 2005
Section 1 Jan 28 - Feb 13: Proteins
& Motifs Homework I
Section 2 Feb18-Feb27: Forces & Folding
Homework II
Section 3 Apr 1-May 8: Biological molecular
motors Reading III
Books on reserve
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 motor proteins. These allow us to study protein function combining biochemistry, structural biology, physics, and engineering principles. We will study motor proteins that use chemical energy of ATP to generate mition. To see where we are going look at the movies showing myosin and tubulin moving down a filament.
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. 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.
Please bring
Petsco & Ringe to Class each day during section 1 Jan 28 - Feb 13
Please bring to class all handouts for the section on which we are working.
Schedule
1-Mon Jan 31: Class
outline; basic definitions; Start genetic code
Homework.
2-Wed Feb 2: Lecture: Amino acids, Nucleic Acids, The genetic
code; protein synthesis
Homework.
3-Mon Feb 7: Lecture: Amino acid properties; peptide bonds
Homework.
(hand in Homework lecture 1,2)
4-Wed Feb 9: Lecture: Protein Motifs; 1°,2°,3° structures;
visualization
Homework
5-Mon Feb 14: Lecture: Protein folds and families
Homework. (hand
in Homework lecture 3,4)
6-Wed Feb 16: Matching primary sequences
Homework.
Mon Feb. 21 - No class
7-Wed Feb 23: Structure and sequences of motor and
scaffold proteins.
Homework.
Web site with a good overview of forces
8-Mon Feb 28: Thermodynamics
I
reading & homework (hand
in Homework lecture 5,6,7)
9-Wed Mar 2: Thermodynamics II
10-Mon Mar 7: Hydrogen bonds; Lennard Jones Interactions
& Molecular Volume & Packing
. reading & homework
(hand in Homework lecture 8-9 Thermodynamics)
11-Wed Mar 9: Solvation of ions.
Thermodynamic homework due today. There will be a review after class Mar 4
if needed.
reading & homework
12-Mon Mar 14: Hydrophobicity
reading & homework. Solvation
energy and Hbd homework due. (hand in
Homework lecture 10,11)
13-Wed Mar 16: Sums of small forces
reading & homework.
. .
14-Mon Mar 21: Protein structure determination.
15-Wed Mar 23: pKs and stat. mech
reading & homework.
(hand in Homework lecture 12,13)
Mon Mar. 28 - No class
16-Wed Mar 30: Reactions and catalysis (hand in Homework lecture
14,15)
17-Mon Apr 4 Summary forces; Connection to motor proteins (hand in Homework lecture 15,16)
18-Wed April 6: .Work on a molecular level
19-Mon April 11: .Methods to look at molecular motors
20-Wed April 13: ATPase reactions & biological energy & regulation of protein function
21-Mon April 18: Guest Lecture: Dr. Lazaridis. Calculation
of protein structure and function
themis@sci.ccny.cuny.edu
22-Wed April 20:
April 25, 27 Break
23-Mon May 2: Scaffold proteins: Actin & Tubulin
24-Wed May 4: ATPase & rotors
25-Mon May 9: Motors
26-Wed May 11: Class reports
27- Mon May 15: Class reports
28- Wed May 18: Class reports
Wed May 18 Final 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