Chem. 87901 Molecular Biophysics

Professor: María Luisa Tasayco (J1304, J1305, J1336)
Lectures: Tuesdays from 10:00 am to 1:00 pm, in Room 8405

Fall 2005

1. Protein Unfolding and Degradation Machines Information about AAA+ enzymes like ClpX and associated-proteins can be found at the web pages of Bob Sauer and Tania A. Baker.
2. Molecular motors Information about Kinesin and Myosin Motor Proteins can be found at the web page of Ron A. Milligan.

Objectives

The main objective of this course is to teach graduate students how to design independent research projects in biophysics and structural biology. The theme of the Fall, 2005 class is "The Assembly and Function of Molecular Machines"

Format of the course

• Several proteins will be selected as the target systems.
• Each of the students will be assigned a protein; this protein will be his/her system of study during the entire semester.
• Each class will be dedicated to addressing a particular aspect of biophysics and structural biology of proteins in general and of each of the proteins selected for the course. These aspects include: protein function in the living cell; protein isolation; biochemical and biophysical methods used for activity measurements; protein structure.
• A few class sessions will be devoted to each of the topics (see syllabus for details). The course will include introductory lectures by instructors and seminars by speakers. Each student will give a (10 or 20 min.) Powerpoint presentation on the current topic, but in the context of the protein he/she has been assigned to study. The student will submit a one- to two-page written report summarizing the presentation.
• The last class sessions will consist of seminars given by each of the students, summarizing current knowledge on the protein and proposing experiments to address unanswered research questions. These seminars and the associated final papers may serve as the basis for your Second Level Proposal in the Ph.D. Programs in Chemistry or Biochemistry; consult your mentor for administrative details. During the semester, each of the students will give four presentations.

Grading

• Final seminar
• Final paper
• Individual presentations during each of the class sessions
• Intermediate reports on the individual topics (see calendar and assignments for details)
• Report on the literature search
• Participation in class discussions on systems other than his/her own protein

Final paper

Practical aspects of the course will involve training in:

• scientific presentations
• grant proposal writing
• literature and database searching
• macromolecular visualization software

References

• Introduction to Protein Structure (2 edition), Carl-Ivar Branden & John Tooze, Garland Publishing, 1999
• Molecular Aspects of Cell Biology, Reginald H. Garnett & Charles M. Grisham, Saunders College, 1995

Syllabus