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Department of Chemistry & Biochemistry |
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University of Maryland Baltimore County |
This is a survey course covering an assortment of physical principles and
techniques commonly used in biochemical research.
Prerequisites are Biochem. 437 and Physical Chem 301 or 303 or equivalents.
Text:
Required: Principles of Physical Biochemistry'' by van Holde,
Johnson and Ho. (1998) Prentice-Hall
Recommended: These books will be on reserve in the library.
``The Physical Chemistry of Biopolymer Solutions''
by R.F. Steiner and L. Garone. (1991).
Recommended:
"Biophysical Chemistry" by Cantor and Shimmel. Publ. Freeman. (1980)
Instructor: C. Allen Bush - Room 204e Chemistry-Physics ext. 5-2506
course web site at http://www.gl.umbc.edu/ ~ bush/course/ch442/ch442.html
Course outline
- 1. Introduction - Review of topics in Chem 437 to be used in
Physical Biochemistry. Structure
of proteins and nucleic acids. Water and hydrophobic
effects. Chirality and symmetry. (van Holde, Ch. 1).
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2. Basic thermodynamics from Chem. 301,
D G, solution equilibrium, chemical potential
non-ideality, osmotic pressure, statistical thermodynamics. (van Holde
Ch. 2)
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3. Equilibrium - multiple ion binding sites on a protein, Scatchard eq.,
electrostatic interaction, cooperative binding, allosteric effect
(van Holde, Ch 15, Steiner and Garone Ch. 2)
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4. Transport - Diffusion of molecules in solution, frictional effect and
molecular size, Fick's law, sedimentation, centrifugation, electrophoresis,
viscosity, gel filtration, averages of molecular weight, density gradient
centrifugation, associating proteins (van Holde, Ch. 5;
Steiner & Garone, ch 3; C & S, ch 10, 11,12)
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5. Light scattering - Rayleigh scatter, scattering from macromolecules in
solution, size and shape of molecules, radius of gyration, inelastic light
scattering, Raman scattering (van Holde, Ch. 7, S & G, ch 4)
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6. Light absorption - excited states, electronic spectra, uv vis,
hypochromism of peptides and DNA, vibrational spectra, IR absorption.
(van Holde, Ch. 8, 9; S & G, ch 5; C & S, ch 7).
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7. Circular dichroism and optical rotatory dispersion - chromophore
interaction, dependence on peptide and protein conformation,
polynucleotides, polysaccharides. (van Holde, Ch. 10;
S & G, ch 6; C & S, ch 8).
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8. Fluorescence spectroscopy - Fluorophores, polarization of fluorescence,
fluorescence decay and molecular rotation, energy transfer
(van Holde, Ch. 11; S & G, ch 5; C & S, ch 8)
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9. Calorimetry -Instrumentation, isothermal titration calorimetry and
thermodynamics of ligand binding. Differential scanning calorimetry
and mechanism of protein folding.
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10. Structure of biopolymers, secondary and tertiary structure of peptides,
proteins, polynucleotides and polysaccharides,
Structure determination by NMR spectroscopy.
spectrum assignment, T1 and
T2 relaxation, nuclear Overhauser effect, coupling constants
(van Holde, Ch. 12; C & S, ch 9)
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11. X-ray crystallography- fiber diffraction, 3-d crystallography,
phase determination, direct methods, heavy atom isomorphous replacement,
anomalous scattering,
molecular replacement, homology modeling. (C & S, ch 13).
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On 7 Jan 2003, 13:58.