(On this Page: 1. Schedule of Lectures, 2. Supplementary Textbooks, 3. Papers)
(i) Attend (>90%)
(ii) Participate (ask questions, volunteer information, participate in discussions and presentations)
(iii) Complete Assignments (in-class & take-home problem sets, origin-based problem sets, final problem set)
Num |
Date |
Day |
Topic |
Reading |
Homework |
|---|---|---|---|---|---|
1 |
1/26 |
Thu |
Course Introduction, Random Walk |
Cooper Ch.1, all. P2: Knight et al. (2010) |
|
2 |
1/31 |
Tue |
Random Walk/Diffusion, EPR 1 | Cooper Ch.2, p. 69-75. EPR Review (Wiki Site) P3: Columbus & Hubbell (2002) |
|
3 |
2/2 |
Thu |
EPR 2 (L03_EPR1) | ||
4 |
2/7 |
Tue |
EPR 3 & Diffusion 2 |
||
5 |
2/9 |
Thu |
Relaxation and Correlation Times |
||
6 |
2/14 |
Tue |
no class | Cooper Ch. 8, P4: Hendrickson (1991)
|
|
7 |
2/16 |
Thu |
Dynamic Light Scattering (L05_DLS) | Cooper Ch. 4 |
|
8 |
2/21 |
Tue |
Analytical Ultracentrifugation, Sedimentation Velocity |
Cooper Ch. 4 |
|
9 |
2/23 |
Thu |
Analytical Ultracentrifugation, Sedimentation Equilibrium (L07_AUC) | Cooper Ch. 4 |
|
10 |
2/28 |
Tue |
Thermodynamics, Review of Thermodynamic Functions: Energy, Enthalpy, Entropy, Heat Capacity (Protein Stability Handout) |
Cooper Ch. 5 |
|
11 |
3/1 |
Thu |
no class, Study Protein Stability Handout | Cooper Ch. 5
|
|
12 |
3/6 |
Tue |
Protein Stability (L08_ProStab), Protein Folding (L09_ProtFold) | Cooper Ch. 5 |
|
13 |
3/8 |
Thu |
Heat Capacity Changes in Biochem Reactions (L10_dCp) |
Cooper Ch. 5 |
|
14 |
3/13 |
Tue |
no class, Read about Ligand Binding in Cooper |
Cooper Ch. 5 |
|
15 |
3/15 |
Thu |
Ligand Binding (L11&12_LigBind, L11a_FluorAnis) |
Cooper Ch. 5
|
|
16 |
3/27 |
Tue |
No Class, project meetings with groups |
||
17 |
3/29 |
Thu |
Cooperativity (L11&12_LigBind) (L13_Mar_29_12) |
Cooper Ch. 5 |
|
18 |
4/3 |
Tue |
No Class, Cooperativity (L14_Binding_Polynomials.pdf) |
Cooper Ch. 5 |
|
19 |
4/5 |
Thu |
Kinetics (L15_Kinetics.pdf) |
Cooper Ch. 6 |
|
20 |
4/10 |
Tue |
Single Molecule Spectroscopy, Prof. Mike Barnes (L16_SingMolSpec.pdf) |
||
21 |
4/12 |
Thu |
Single Molecule Spectroscopy, Prof. Mike Barnes |
||
4/17 |
Tue |
No Class, Monday class schedule followed (Patriots Day) |
|||
22 |
4/19 |
Thu |
Fluorescence Resonance Energy Transfer (L17_FRET.pdf) | ||
23 |
4/24 |
Tue |
Presentation (Huang, Lee, Li, Yang) |
||
24 |
4/26 |
Thu |
Presentations (Dagbay, Martin, Muneeruddin, Serrano) (Eron, Hangasky, Jeskey) |
||
25 |
5/1 |
Tue |
Presentation (Cui, Haglin, Zhao) |
*EC/Optional. You may do one or both of the EC/optional homework sets. The first one will be extra credit, that is the score will be added to the overall homework score. The grade on the second EC/optional homework set will substitute for a poorer score recceived on any of the required problem sets 1 to 6. (No substitutes are being given for required problem set 7). A required problem set must have been turned in and graded to be replaced by the second EC/optional set. Also, you can designate either 8 or 9 as the 'EC' set. Make sure the problem sets you turn in are marked 'EC' or 'Substitute'. (NO LATE SETS ACCEPTED.)
Supplementary Textbooks in Biophysics and Biophysical Chemistry |
Comment |
|---|---|
| Author(s), Title, Edition, Year, Publisher, ISBN | |
| Comprehensive Textbooks | |
| Charles R Cantor, & Paul RSchimmel, Biophysical Chemistry Parts I, II & III, 1st Edition, 1980, W. H. Freeman & MacMillon Higher Ed. ISBN-10: 0-7167-1188-5 (Pt. I), 0-7167-1190-7 (Pt. II) & 0-7167-1192-3 (v. III) | The classic, authoriative 3-part set that treats the subject thoroughly. Available new from Macmillon Higher Ed. and used from Amazon.com. ~$110 per volume. |
| Philip Nelson, Biological Physics, Updated Edition, 2008, W. H. Freeman, ISBN-10: 0-7167-9897-2. | The diffrences between biophysical chemistry and biological physics become apparent with treatment from a physicist. A useful viewpoint. ~$50 |
| Kensel E van Holde, W. Curtis Johnson & P. Shing Ho,Principles of Physical Biochemistry, 2nd Edition, 2005, Pearson, ISBN-10: 0-1304-6427-9 | A modern alternative to Cantor & Schimmel in a single book. Treatment is at a high level and assumes a background in physical chemistry and mathematics. ~$100 |
| Companion Books | |
| Howard C. Berg, Random Walks in Biology, Expanded Edition, 1993, Princeton University Press, ISBN-10: 0-6910-0064-6 | An inspiring readable book focused on the treatment of diffusion, random walks, hydrodyamics, the Boltzmann and probability distributions. Mathematics is at a simple, understandable level. ~$30 |
| David S. Goodsell, The Machinery of Life, 2nd Edition, 2009, Springer, ISBN-10: 0-3878-4924-9. | Not a biophysics book, but rather (cartoon-like) space-filling representations proteins and subcellular structures in the context of the cell. Accompanied by nonmathematical description of the functional properties. ~$16 |
| Kensel E van Holde, Physical Biochemistry, 2nd Edition, 1985, Prentice-Hall, ISBN-10: 0-1304-6427-9 | A concise book, but covers a lot. Out of print, used copies can are affordable ~$20, but goes on up to $900 |
| Ken Dill & Sarina Bromberg,Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience, 2nd Edition, 2010, Taylor & Francis, ISBN-10: 0-8153-4430-8 | A thorough treatment of the statistical thermodynamics of complex systems -- biological macromolecules. ~$75 |
| Monographs | |
| Thomas Heimburg, Thermal Biophysics of Membranes, 1st Edition, 2007, Wiley-VCH, ISBN-10: 3-5274-0471-1 | Specialized treatment of the biophysics of cell membranes, mainly thermodynamic properties and classical surface physics (no spectroscopy). Relatively modern but poorly referenced with respect to the original literature. ~$165 |
| Greg Ralston, Introduction to Analytical Ultracentrifugation. Beckman Corp. | Booklet on the use of AUC to determine hydrodynamic properties and molecular weights of macromolecules. |
| Jeffries Wyman and Stanley J. Gill, 1990, Binding and Linkage: Functional Chemistry of Biological Macromolecules, University Science Books, ISBN-10: 0-935702-56-3. | Thorough treatment of allosteric interactions, thermodynamic linkage, ligand binding measurements and cooperativity. ~$90 |
Num.
|
Paper (Author(s). year. Title. Journal Vol.:inclusive pages.) |
| Aurelia R. Honerkamp-Smith, Sarah L. Veatch & Sarah L. Keller. 2009. An introduction to critical points for biophysicists; observations of compositional heterogeneity in lipid membranes. Biochim. Biophys. Acta 1788:53–63. |
|
Jefferson D. Knight, Michael G. Lerner, Joan G. Marcano-Velazquez, Richard W. Pasto & Joseph J. Falke. 2010. Single Molecule Diffusion of Membrane-Bound Proteins: Window into Lipid Contacts and Bilayer Dynamics. Biohys. J. 99:2879–2887. Movies in Supporting Information: PH_monomer, PH_dimer, PH_trimer |
|
| Linda Columbus & Wayne L. Hubbell. 2002. A new spin on protein dynamics. Trends in Bioch. Sci. 27:288-295. | |
| Wayne A. Hendrickson. 1991. Determination of macromolecular structure from anomalous diffraction of synchrotron radiation. Science 254:51-58. | |
| Dennis E. Koppel. 1972. Analysis of macromolecular polydispersity in intensity correlation spectroscopy: The method of cumulants. J. Chem. Phys. 57:4814-4820. | |
| J. N. Onuchic, P. G. Wolynes, Z. Luthey-Schulten & N. D. Socci. 1995. Toward an outline of the topography of a realistic protein folding funnel. Proc. Natl. Acad. Sci. USA 92:3626-3630. |
|
| Peter G. Wolynes, Jose N. Onuchic & D. Thirumalai. 1995. Navigating the folding routes. Science 267:1619-1620. | |
| Martin Karplus. 2011. Behind the folding funnel diagram. Nat. Chem. Biol. 7:401-404. | |
| Benjamin Schuler & William A Eaton. 2008. Protein folding studied by single-molecule FRET. Curr. Opin. Struct. Biol. 18:16-26. | |
| Everett A. Lipman, Benjamin Schuler, Olgica Bakajin & William A. Eaton 2003. Single-molecule measurement of protein folding kinetics. Science 301:1223-1235. |
|
| Ruth E. Silversmith. 2005. High mobility of carboxyl-terminal region of bacterial chemotaxis phosphatase CheZ is diminished upon binding divalent cation or CheY-P substrate. Biochemistry 44:7768-7776. |
|
| Julian M. Sturtevant. 1977. Heat capacity and entropy changes in processes involving proteins. Proc. Natl. Acad. Sci. USA 74:2236-2240. | |
| John F. Brandts, Cui Q. Hu, Lung-Nan Lin & Maria T. Mas. 1989. A simple model for proteins with interacting domains. Applications to scanning calorimetry data. Biochemistry 28:8588-8596. |
|
| Jacques Monod, Jeffries Wyman & Jean-Pierre Changeu. 1965. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12:88-118. | |
| Daniel E. Koshland,Jr.,G. Nemethy & D. Filmer. 1966. Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 12:365-385. | |
| H. Peter Lu, Luying Xun & X. Sunney Xie. 1998. Single-Molecule Enzymatic Dynamics. Science 248:1877-1881. | |
| Suliana Manley, Jennifer M. Gillette, George H. Patterson, Hari Shroff, Harald F. Hess, Eric Betzig & Jennifer Lippincott-Schwartz. 2008. High-density mapping of single-molecule trajectories with photoactivated localization microscopy. Nat. Methods 5:155-157. | |
| Gene-Wei Li & X. Sunney Xie. 2011. Central dogma at the single-molecule level in living cells. Nature 475:308-314. |
|
| Andrew F. Kolodziej, Thomas Tan & Daniel E. Koshland, Jr. 1996. Producing positive, negative, and no cooperativity by mutations at a single residue located at the subunit interface in the aspartate receptor of Salmonella typhimurium. Biochemistry 35:14782-14792. |
|
| Lubert Stryer & Richard P. Haugland. 1967. Energy transfer: A Spectroscopic Ruler. Proc. Natl. Acad.Sci. USA 58:719-726. | |
| Benjamin Schuler, Everett A. Lipman, Peter J. Steinbach, Michael Kumke & William A. Eaton. 2005. Polyproline and the ‘‘spectroscopic ruler’’ revisited with single-molecule fluorescence. Proc. Natl. Acad.Sci. USA 102:2754–2759. | |
| Robert B. Best, Kusai A. Merchant, Irina V. Gopich, Benjamin Schuler, Ad Bax & William A. Eaton. 2007. Effect of flexibility and cis residues in single-molecule FRET studies of polyproline. Proc. Natl. Acad.Sci. USA 104:18964–18969. | |
| Asif Iqbal, Sinan Arslan, Burak Okumus, Timothy J. Wilson, Gerard Giraud, David G. Norman, Taekjip Ha & David M. J. Lilley. 2008. Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids. Proc. Natl. Acad.Sci. USA 105:11176–11181. |