Syllabus Introductory Biophysics

Description/Objectives
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.

Requirements
The course is intended as a bridge to Biophysics for students trained in either Life or Physical Sciences, and will assume no more than the common denominator in typical undergraduate preparations for majors in these areas. Students should have at least one undergraduate course in Physics or Physical Chemistry and one in Biology or Biochemistry. Discussion will assume mathematical literacy at the level of Calculus II. If uncertain, please contact the course directors.

Instructors
The course will be team-taught by faculty from Portland State University and Oregon Health & Science University.

Topics (see Schedule for details)

 * 1) Macromolecular Structure
 * 2) Primary Through Quaternary Structure
 * 3) Covalent stereochemistry & Force fields
 * 4) Non-bonded interactions & Force fields
 * 5) Thermodynamics & Kinetics
 * 6) * Illustrated with applications to Membrane Transport.
 * 7) Energy, Entropy, Free energy
 * 8) Activation energy & transition states
 * 9) Hydrophobic effect
 * 10) Statistical mechanics
 * 11) Equilibria
 * 12) Reactions
 * 13) Binding
 * 14) Conformation
 * 15) Calorimetry
 * 16) Membrane proteins, ion channels & pumps
 * 17) Transport & Diffusion
 * 18) Action potentials / measurement / synapses
 * 19) Crystallographic theory
 * 20) X-ray Diffraction
 * 21) Phasing methods - MIR & MAD
 * 22) Maps, Models & Refinement
 * 23) Quality assessment & Biochemical interpretation
 * 24) Spectroscopy - Visible & UV
 * 25) Quantum mechanical foundation
 * 26) Absorption
 * 27) Polarization - CD
 * 28) Fluorescence
 * 29) Fluorescence anisotropy
 * 30) FRET
 * 31) Introduction to Magnetic Resonance
 * 32) Spin interactions & relaxation
 * 33) Magnetic Resonance Imaging
 * 34) Biomolecular Structure (Introduction)

Schedule

Recommended Text
Principles of Physical Biochemistry (2nd Ed.) by van Holde, K.E., Johnson, C. & Ho, P.S. (2006) Prentice Hall, ISBN-10: 0130464279 / ISBN-13:  9780130464279

Web resources

 * Chapter-articles published by the Biophysics Society.

Lecture notes
In-class presentations will be posted at the discretion of the instructor following class with links from Schedule.

Evaluation
There will be one mid-term and a final examination contributing ~40% & 60% respectively to the overall assessment.