(Physics 422/V3800/738)

Thus Aug 30-Thurs Dec 13, 2011
Tues-Thurs 5:00 to 6:15
Class in Marshak 418 **

Marilyn Gunner
J-301 (office)

2013 syllabus [new for 2013-updated]

Section 1: Proteins & Motifs Homework I
Section 2 : Forces & Folding Homework II (still under construction)
Transmembrane electron & proton transfer proteins
Reading III
Class talks and papers Nov 29, Dec 3, 6, 11

Useful web sites

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. The grade will be on class participation + the paper + your talk. How to write your paper. You may enjoy this online debate on are research papers a waste of time?
In addition, there will be homework to be handed in most weeks. 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.


Molecular visualization: PYMOL or VMD From the Schulten lab a U of Ill.
When you get your protein please look for it here: membrane proteins of known structure (from Steve White (if you can't find it let me know)
I'd like to have you play with this: FOLDITat home - A computer game that lets you fold proteins
Please look at Useful web sites frequently. Things that did not seem important at first will become useful as the class progresses.

1-: Class outline; basic definitions; Mitochondria and electron transfers.
Before doing anything Please send me an email so I have youre email address.
Major and year:
Number of years of Biology, Chemistry and Physics you have taken
Are you doing independent research - If yes who is your mentor.
Do you have specific areas of interest that might relate to this class?
Do you have a specific protein that you are interested in?

class 1 ppt (2013)

2-: Lecture: Mitochondria, biological energy, electron tunneling overview; proton transfers; cofactors
class 2 ppt (2013)

Lecture: Amino acid properties; peptide bonds
class 3 ppt (2013)

Lecture: Protein Motifs;
class 4 ppt (2013)

5-: Lecture: Protein folds and families
5. Long one slide/pageview (2011)

6-: Membranes and the difference between membrane and soluable proteins.
lecture (2013)
Rocking motion to allow substrates cross the membrane. paper

Thermodyanmics #1Lecture #2 and 3

pKa lecture here.


How to write your paper.


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

Last revised September 30, 2013

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