Physics
303/607
Biology 303/607
Class times: MWF
10-10:50 AM
Instructors:
(1) Professor Jed Macosko, Phone: 758-4981, Office: 302 Olin, e-mail:macoskojc@wfu.edu, http://www.wfu.edu/~macoskojc/
(2) Professor Daniel Kim-Shapiro, Phone: 758-4993, Office: 208 Olin, e-mail:shapiro@wfu.edu, http://www.wfu.edu/~shapiro/
Office hours: Mondays and Wednesdays 2-4 pm, or by appointment.
Texts: Principles of Physical Biochemistry, 2nd Edition, by K.E. van Holde, W. C. Johnson, and P.S. Ho; Neurodynamix,by W.O. Friesen and J.A. Friesen. Additional reading will be assigned in the form of journal articles and handouts
Supplementary texts: 1. Biophysical Chemistry Part II, Techniques for the study of biological structure and function, by Charles Cantor and Paul Schimmel (1980). 2. Biochemistry by Lupert Stryer (1988).
Grading:
Undergraduate Students
2 hour exams.............................................................40%
Project..................................................................10%
Final Exam................................................................30 %
Problem Sets............................................................20%
Graduate Students
2 hour exams.............................................................30%
Project..................................................................10%
Presentation of Journal Article......................................10%
Final Exam................................................................30 %
Problem Sets............................................................20%
Emphasis in grading will be placed on how each problem is solved. All work showing how the solution was obtained must be shown. An answer with the correct answer but poor method is inferior to one with the wrong answer but good method.
Problem sets will generally be assigned on a
weekly basis and the students will have one week to complete them. Students may
help each other on problem sets but each student must write their own solution
to each problem. The project that all
students do will be a 5-10 page paper focusing on a particular topic in
biophysics. The project could be a service learning project (see instructors
for more information on that).
Graduate students will present one of the journal articles that are part of the reading assignments.
Exam
Schedule
Hour Exams: February 26,
April 21; Final Exam: April 30
(2 PM)
Click here to look at the x-ray scattering from linear arrays of atoms onto a cylindical screen. (This was developed by Ching-Wan Yip and Yue Ling Wong).
X-Ray Diffraction sites: An Introduction to the Scope, Potential and Applications of X-ray Analysis , Elementary X-Ray Diffraction for Biologists.
Other sites: ExPASy Molecular Biology Server: The ExPASy (Expert Protein Analysis System) You will probably want to download Swiss-PdbViewer - it is really cool. Go through Swiss Model under Tools and Software Packages.
Biophysics
Syllabus
Date |
Topic |
Lecture notes |
HW |
Reading |
Jan. 13 & 15 |
Introduction-1: Structures biological macromolecules, mainly proteins, DNA and RNA | van Holde, Ch. 1 |
||
Jan. 20 & 22 |
Introduction-2: Molecular interactions in biological macromolecules | HW-2, see lecture notes | van Holde Ch. 3.1 - 3.3 |
Part I Biophysical Methods
HW 1: (book, see lecture notes)
1. Overview, 2. Detailed lecture
Bragg's law, von Laue conditions, reciprocal space, Fourier Transforms, electron density r(r) & Structure factor F(hkl), phase problem, Patterson maps, fiber (DNA) diffraction , History of Watson, Crick, Franklin & Wilkin's discoveries (two movies)
Reading: van Holde chapter 6, and the following papers:
April 25, 1953 papers: Watson and Crick Paper 1, Wilkins paper, Franklin paper 1,
Later 1953 papers: Watson Crick Paper 2, Franklin paper 2
HW 3: (see lecture notes)
Sedimenation, mass spectrometry, Gel electrophoresis (Fick's Law), Light Scattering (Classical, Dynamic, Polarized)
DNA Topology (Length, Twist, and Writhe), Chromosome Structure
Reading: van Holde, chapters 5 and 7, Shapiro et al: Polarized Light Scattering
Additional Papers:
Wang et al: Helical repeat in DNA solution
Dorigo et al: Nucleosome Arrays Reveal theTwo-Start Organization of the Chromatin Fiber
Mohd et al: Perspective chromatin
Francis et al: Chromatin Compaction by a Polycomb Group Protein Complex (with perspective above)
HW 6 (separation) Maple program for gel-1, Maple program for gel-2 and Explanation for maple program for gel-2
UV, VIS spectroscopy, linear and circular dichroism
Protein primary, secondary, tertiary, quaternary structure
Reading: van Holde chapters 8-10
Addtional papers:
Hofrichter et al: Nanosecond absorption spectroscopy of hemoglobin: Elementary processes in kinetic cooperativity
Goldbeck et al: Multiple pathways on a protein-folding energy landscape: Kinetic evidence
Monod Wyman and Changeux On the Nature of Allosteric Transitions:A Plausible Model
Fluorescence (phenomenon), Fluorescence microscopy, native fluorophores in proteins, solvent effects, Quantum yield, fluorescence decay, FRET (resonance energy transfer), linear polarization of fluorescence and emissin anisotropy, Perrin plots.
Reading: van Holde, Chapter 11
Papers:
Ha et al (1): Single molecule FRET (early, basic, using SNOM) (also single molecule)
Ha et al (2): Single molecule FRET (RNA conformation) (also single molecule)
Raney et al: Detecting helicase by fluorescence
HW 7: van Holde 11.2 to 11.7
Single molecule vs. bulk experiments, Atomic Force Microscopy (imaging and manipulating), laser tweezers, single molecule fluorescence
Reading: Handout
Papers:
Liphardt et al: Single molecule RNA folding (laser trap)
Davenport et al: Observing a single RNA polymerase transribing (laser tweezer and pipette)
Schwesinger et al: AFM Force spectroscopy, relation between force and off rate
Guthold et al: AFM observing a single RNA molecule transcribing
Lu et al: Single molecule enzyme dynamics (single molecule fluorescence)
Bokinsky et al: Single molecule FRET of RNA unfolding
Tskhovrebeva et al Single molecule Titin stretching with laser tweezer
HW 8: (see lecture notes).
Electron Paramagnetic Resonance, Hemoglobin cooperativity Studies using EPR and time-resolved absorption spectroscopy
Reading: Handout
Paper:
Yonetani et al: NO hemoglobin
Part II
Membrane Biophysics
Description of membranes, Diffusion, Facilitated transport, Nernst Equation, Donnan Equilibrium
Reading: van Holde chapters 13-14
Neurons, Action Potential, Propagation of action potential, measurements in membrane biophysics, Synaptic transmission
Reading: Frisens Sections 1 and 2