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Physical Chemistry for the Life Sciences
Fall Semester 2008

Professor Peter Qin
LJS 251
Tel: : (213) 821-2461
pzq@usc.edu
 

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Course Schedule

Topics

Summary Note

Week 1

Aug. 25 - Aug. 29
(ch. 1)

  • Introduction to Biophysical Chemistry

Thermodynamics

  • Heat, Energy, and Work
  • First Law of Thermodynamics

L1

 

L2

Week 2

Sept.3 - Sept. 5
(ch. 1 & 2)

  • Enthalpy of reaction, Enthalpy of Formation
  • Entropy and the Second Law of Thermodynamics

Week 3

Sept. 8 - 12

(ch. 2)

  • Entropy Measurements
  • Entropy and hydrophobic interactions
  • Third Law of Thermodynamics

Week 4

Sept. 15 - 19

(ch. 2)

  • Entropy of Substances and Chemical Reactions
  • Spontaneity and Gibbs Free Energy
  • Calculating DGorxn and temperature dependence
  • Protein-substrate binding

Week 5

Sept. 22 - 26

(selective topics from ch. 3 & 4)

  • Thermodynamics of hydrogen-bonding and hydrophobic interaction
  • Application: DNA base recognition and replication fidelity
  • Application: DNA duplex stability and melting

Week 6

Sept. 29 – Oct. 3

(ch. 4)

  • Chemical Potential and Chemical Equilibrium Solutions and Non-ideality
  • Standard States in Solution

Exam 1, Wednesday, Oct. 1; in class

Week 7

Oct. 6 - 10

(ch. 4,5)

  • Acid Base Equilibria
  • Temperature Dependence of Equilibrium Constant
  • Redox Reactions

Week 8

Oct. 13 - 17

(ch. 5,6)

  • Nernst Equation

Application: Biological Electron Transfer

Chemical Kinetics

  • Reaction Rates

Week 9

Oct. 20 - 24

(ch. 6)

  • Rate Laws

Week 10

Oct. 27 - 31

(ch. 7)

  • Temperature Dependence and Transition State Theory
  • Reaction mechanisms

Week 11

Nov. 3 - 7

(ch. 8)

  • Kinetics and Mechanisms of Enzymatic Reactions
  • Michaelis-Menten Equation and relationship to energetics of catalysis

Exam 2, Wednesday Nov. 5; in class

LAB: Visualizing Enzyme Kinetics

Week 12

Nov. 10 - 14

(ch. 8)

      Class Presentation:  Enzyme Lab

      Structure and Spectroscopy

  • Absorption

Week 13

Nov. 17 - 21

(ch. 13)

  • Beers law, bio-chromophores
  • Emission

Week 14

Nov. 24 - 26

(ch. 13)

  • Fluorescence Spectroscopy and FRET

Week 15

Dec. 1 - Dec. 5

  • Bio-macro molecular structure: X-ray crystallography, NMR and EPR

Dec. 8 - 10

Study Week; Final Reviews

Dec. 15

Final Exam, 8:00 – 10:00 am

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