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Dept. Biochemistry & Molecular Biology
Portland Biophysics Society

Chapman Teaching


BCMB 630: Introductory Biophysics

Biophysics involves the application of physical techniques to achieve an understanding of life processes at a molecular level. Physical techniques are central to the measurement of the atomic structure, dynamics and interactions of molecules that are a core foundation of modern molecular biology, while physical theory governs the predicted behavior of biomolecules and helps us achieve a mechanistic understanding of how they work. Thus, biophysics is a central science in the fundamentals of normal physiology, molecular pathology, and in the development of pharmaceutical remedies for a wide range of diseases.

This is the first of two lecture courses that will prepare graduate and advanced undergraduates for research and professional work in Molecular Biophysics. It will cover macromolecular structure and underlying atomic interactions, and the thermodynamics and kinetics through which function is understood, using membrane proteins as an example. It will then introduce three of the experimental technologies used to elucidate structure and dynamics: Crystallography, Spectroscopy and Magnetic Resonance.

At the conclusion of this course, students will have the theoretical foundation to understand the properties of macromolecular functions, and understand the principles by which their actions are simulated. Students will be able to critically assess primary literature written for a general scientific audience in the area of macromolecular structure & function, understanding the experimental basis in crystallography, NMR and spectroscopy. Students will also be prepared for the Advanced Biophysics course which would be the entry point into practical application of biophysical techniques.

Course directors: Michael S. Chapman (OHSU) & David Peyton (PSU); Winter semesters, even years.

Course materials: available from Sakai (registered students). Past syllabus & schedule (w/o links to materials).


BCMB 631: Advanced Biophysics

Biophysics involves the application of physical techniques to achieve an understanding of life processes at a molecular level. Physical techniques are central to the measurement of the atomic structure, dynamics and interactions of molecules that are a core foundation of modern molecular biology, while physical theory governs the predicted behavior of biomolecules and helps us achieve a mechanistic understanding of how they work. Thus, biophysics is a central science in the fundamentals of normal physiology, molecular pathology, and in the development of pharmaceutical remedies for a wide range of diseases.

This is the second of two primarily lecture courses that will prepare graduate and advanced undergraduates for research and technical work in Molecular Biophysics. It will cover the practical aspects of the elucidation of macromolecular structure and dynamics by NMR spectroscopy and x-ray crystallography, and the characterization of macromolecular interactions by electron microscopy, mass spectrometry and fluorescence methods. It will examine computational methods for interpreting structure, predicting properties and simulating mechanisms of action.

At the conclusion of this course, students will have a working understanding of the primary experimental and computational methods by which the structure, dynamics and interactions of biomolecules are elucidated and their actions simulated. Students will be able to critically assess primary research literature written for a general scientific audience that uses any of the common physical approaches to understand macromolecular systems. Students will understand the nature of advances that can be made with the principal techniques and their limitations. They will also be prepared for mentored practical research investigations that use the primary methods.

Course directors: Michael S. Chapman (OHSU) & David Peyton (PSU); Spring semesters, even years.

Course materials: available from Sakai (registered students). Past syllabus & schedule (w/o links to materials).


CONJ 668: Molecular Biophysics & Experimental Bioinformatics

Introduction to Macromolecular X-ray crystallography (2 lectures): X-ray Crystallography

MGEN 624 Gene and Cell Therapy

Structural biology of AAV vector delivery (lecture): coming soon.

MSCI 612 Cell Structure & Function

Small group facilitator; Medical School year 1; Course site for registered students: Sakai.

Topics: Hypercholesterolemia; Gaucher’s Disease; Enzymes in Medicine.

Lewis & Clark College: HHMI Workshop

Macromolecular Crystallography - October / November 2009

Week

Topics

Practicals

1

Introduction (PowerPoint) (PDF handout);

Crystallization (PowerPoint) (PDF handout)

Lysozyme crystallization lab (PDF)

2

Diffraction theory & Data collection (PowerPoint) (PDF handout)

 

3

The Phase Problem (PowerPoint) (PDF handout)

 

4

Modeling, Refinement, Accuracy & Validation (PowerPoint) (PDF handout)

Building with computer graphics (Modeling_tutorial.htm)