(Physics 422/V3800/738)

Thus Aug 27-Thurs Dec 10, 2015
Tues-Thurs 5:00 to 6:15
Class in Marshak 418 **

Marilyn Gunner
CDI-306 (office)

syllabus 2016 (updated 9/6/16)

Section 1: Proteins & Motifs Homework I
Section 2 : Forces & Folding Homework II (still under construction)

Useful web sites

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.

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 and ion transfer proteins. These allow us to study protein function combining biochemistry, structural biology, physics, and engineering principles. We will study bioenergetic proteins that store energy to make ATP. Some initial references here


Your grade will be 5% homework; 15% attendance: 20% presentations: 60% paper
You will do 2 short presentations and one longer presentation on your protein.

You must finish the homeworks. The last homework is due Nov 19. If you don't get the homework done you will fail. If it is consistently late I will take points off.

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.You may enjoy this online debate on are research papers a waste of time?

Class talks and papers due Dec 1, 3, 8 and 10
After I get your paper I will meet with each of you individually and discuss how to improve your paper. I will expect an appendix based on our discussion by Dec 22, 2014.

Please bring to class all handouts for the section on which we are working.

Molecular visualization:Chimera PYMOL or VMD. I will expect you to download and learn to use a program to visualize proteins. There are several good programs (see Useful web sites for several). I will give you guidance for Chimera and PYMOL.Chimera is a good tool and easy to learn.

When you get your protein please look for it here: membrane proteins of known structure (from Steve White (if you can't find you protein on that list let me know)

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.

Homework is pass/fail. If you do not get at least 70% your should resubmit the problems you got wrong. Do not give me raw print-outs or a huge amount of numbers. For example I dont want a list of every homologous protein. Rather tell me how many their are. Do they fall into interesting classes-how many from bacteria or higher animals? Are they from different organs? Are there lots of mutants? If you are lost for how to organize your findings ask each other or ask me in person or by email.

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?

Lecture notes class 1
before class 2
--download a molecular modeling program I will use Chimera but PYMOL or VMD are also fine. Try to look at yeast cytochrome c (2ycc.pdb) if you can.
--Look at Oxidative Phosphorylation at the fin de siecle (I handed this out as well). Come prepared to class having written down 5 questions you have about this paper. I will collect these questions and use them for our discussion.
--I will assign proteins from the classes of intramembrane electron and proton transfer proteins; ion channels and pumps; and molecular motors.
-- You should look at the paper by Gadsby for an introduction to ion channels and pumps; and to reviews on molecular motors and on myosin. An online textbook for nerve transmission.
--Look at the links to homework 1

2-: Lecture: Mitochondria, biological energy, electron tunneling overview; proton transfers; cofactors
lec 2 2016

Lecture: Amino acid properties; peptide bonds; secondary structure
Lec 3 2016

4-:Lecture: Protein folds and families

lecture notes: class 4

5-: Membranes and the difference between membrane and soluable proteins.
lecture notes: class 5

Papers of interes
Membrane and proteins. paper
Inserting proteins into membranes. paper
Rocking motion to allow substrates cross the membrane. paper

6- Thermodynamics 1Handout
Powerpoint 2015
2016 thermo-1 thermo-2

7-Thermodynamics 2nd lecture

Your presentation #1 Sept 20; Use this template. template 2

8- pK lecture notes

Suggested books (see me)
Cell Biology will be more of an over view
Biochemistry will have more specific info on proteins

I will be taking information from these books
Creighton: Proteins
Darby and Creighton: Protein Structure
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


Last revised September 14, 2016

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