CH347 (BYS347)
Biophysical Chemistry - Course Syllabus

Chemistry and Biological Sciences 347
Text: Physical Chemistry by Thomas Engel and Philip Reid, 2nd Ed. (abbreviated ER below)
Course Information: Supplement-1 (pdf).

I. Mathematics and Computers
  • Mathematics, simulations, and data analysis using computers play a central role in much of modern physical chemistry, and therefore they are an essential part of this course.
  • There are a number of powerful software packages available for doing mathematics and data analysis on the computer.
  • In this course we will make extensive use of Mathematica 7.0. Tutorials are provided below. It is essential that you learn how to use this program.
  • All homework assigments must be submitted via email in Mathematica 7.0 notebook format.
  • You can obtain Mathematica as a student at a greatly reduced rate. Licences are available for one semester, a year, or your college career. More information can be found at the Mathematica for Students site.

A. Mathematics Review - self study
  • Basic math, logarithms, algebra, trigonometry
  • Differentiation
  • Integration - definite and indefinite integrals
  • Unit conversion
Supplement-2 : Mathematics Review (pdf)

B. Mathematica Tutorial
  • Supplement-3 (in Notebook format or pdf): Mathematica Tutorial 1. Basics
  • Supplement-4 : Mathematica for Calculations, Simulations and Data Analysis (pdf)
  • Simulating functions
  • Importing and exporting data
  • Plotting
  • Functions - deferred execution and iterations
  • Supplement-5 (nb file and pdf file): Mathematica Tutorial 2. Deferred Execution and Iterative Procedures
  • Curve fitting - linear and nonlinear regression

Homework Problem Set 1: Download pdf file. Due Monday, August 24.
(Important: Do these and all future homework problem sets using Mathematica. Please submit your work as a notebook file (.nb) via email. )


II. Basic Thermodynamics

A. Introduction
  • Definitions  (ER: Chapter 1)
  • State functions and equations of state

Homework Problem Set 2: Download here. Due ~August 29.

Practice Problems: in Mathematca Notebook format (.nb) (Chapter 1: 1.1-1.4) - For self-study.
(on a Mac, control-click on the link; on a PC, download by right clicking on the link, save the link as a .nb file, open in Mathematica)

Supplement-6: Description of Macroscopic Systems (pdf)

Homework Problem Set 3: Chapter 2 (ER): P2.1, 2.2, 2.3, 2.4, 2.6, 2.8, 2.27 (Due ~Sept. 3).

B. Energy and the First Law
  • The basics: Heat, work, and energy (ER: Chapter 2)
  • Enthalpy and Heat capacity
  • Variation of State Functions with temperature (ER: Chapter 3)
  • Gas expansions - isothermal and adiabatic
  • Heat, deltaH, deltaE, and deltaCp as measurable quantities - DSC and ITC and the Kirchhoff Relationship
  • Exact differentials and state functions
  • Molecular interpretation of enthalpy and heat capacity changes
  • Effect of T and P on gases, liquids, and solids
  • Joule-Thomson Effect
  • Thermochemistry - (ER: Chapter 4)
  • Calorimetry - bomb, solution, ITC, DSC

Supplement-7: Modern Calorimetry (pdf)

Homework Problem Set 4: Chapter 3 (ER): P3.1, 3.3, 3.5, 3.9 (Use Mathematica) (Due ~Sept. 8)
(In addition, for P3.1, Prove dz is exact using Euler's criterion. )

Homework Problem Set 5: Chapter 4 (ER): P4.10, 4.15, 4.21, 4.22. (Due ~Sept. 12)

EXAM I: - September 17 - (A practice exam can be downloaded from here in pdf form) -

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C. Entropy and the Second Law
  • Entropy and the condition of spontaneity
  • The second law of thermodynamics - various statements handout
  • 1/T is an integrating factor for dQ
  • General principles and examples of spontaneous processes
  • Combined first and second laws
  • The third law of thermodynamics
  • Calculation of entropy changes

Homework Problem Set 6: Chapter 5 (ER): P5.10, 5.11, 5.16.

D. Free Energy and Spontaneity (ER: Chap 6)
  • Helmholtz
  • Gibbs

F. Free Energy and Maximal Work (Derivation pdf)
  • Gibbs-Helmholtz Equation
  • Modified Gibbs-Helmholtz Equation
  • Protein stability curves - Schellman

Supplement 8 - Equilibria and Temperature (pdf)

G. Free Energy, Entropy, Enthalpy and Equilibria
  • Interpretation of deltaS
  • Entropy and protein folding
  • Entropy and the hydrophobic effect
  • Enthalpy, equilibrium constants, temperature
  • van't Hoff data analysis
  • van't Hoff analysis vs. calorimetry
  • Cooperativity and protein folding ( deltaH cal vs. deltaH vh )
  • Phase transitions
  • computer simulations
  • What is the value in measuring deltaH and deltaCp?
  • Heats of ionization and buffering
  • Current applications of calorimetry in biochemistry
  • Differential scanning calorimetry (DSC)
  • Chemical denaturation - m values
  • Linear extrapolation method
  • Effect of pH on protein stability - linkage (Wyman)
  • Protein Folding - site-directed mutagenesis and thermodynamics

Homework Problem Set 7: Download problem set from here. Due ~Oct 8.

Additional Readings
  • "Forces contributing to the conformatinal stability of proteins" by Pace et al. FASEB J. 10, 75-83 (1996)
  • "Protein structure, stability and solubility in water and other solvents" by Pace et al. Philos. Trans. Royal Soc. London B Biol. Sci. 359, 1225-34 (2004).


III. Intermolecular and Intramolecular Forces
  • Electrostatics
  • Dipole-dipole interactions
  • Bond stretching and rotation
  • van der Waals interactions
  • Hydrogen Bonds
  • Hydrophobic "interactions"

EXAM II: - (Practice Questions - pdf )

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IV. Binding - A Central Theme in Biochemistry

A. Basics - Single Site Binding

Supplement 9: Binding
  • pH - review
  • Binding isotherms - Computer simlulations and fitting of data -
  • Binding - an all-or-nothing process?
  • Direct and Indirect methods -.
  • Nonlinear regression and fitting of binding data
  • Methods of analysis
  • Coordinate transformations
  • Why not use a Scatchard plot?

Homework Problem Set 8 : Due ~October 22.

Homework Problem Set 9: Due ~October 27.

B. Multiple Site Binding
  • Multiple equilibria - molecular partition functions
  • Independent site binding
  • Linked functions
  • Allosterism - Wyman and Gill

Homework Problem Set 10 : Due ~October 31.

C. Practical Aspects
  • Methods of evaluating binding constants by non-linear regression
  • Isothermal titration calorimetry (ITC)
  • Binding heats

EXAM III

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V. Real Gases (ER: Topics from Chap 7)
  • Equations of State
  • Compression Factor
  • Fugacity


VI. Phases and Phase Transitions (ER: Topics from Chap 8)
  • Temperature dependence of chemical potential
  • P-T and P-V diagrams
  • PVT Diagrams
  • Clapeyron equation
  • Vapor pressure dependence on P
  • Surface tension
  • Supercritical fluids

Homework Problem Set 11: Problems P7.1, P7.2, P8.6, and P8.30 (E&R). Due ~Nov 14.


VII. Solution Thermodynamics (ER: Topics from Chap 9)
  • Defining the ideal solution
  • Chemical potential in vapor and solution
  • Binary solutions
  • Gibbs-Duhem equation
  • Colligative properties
  • Freezing point depression and boiling point elevation
  • Osmotic pressure
  • Activity and chemical potentials
  • Activity coefficients and choice of standard states
  • Henry's and Raoult's Laws
  • Experimental measurement of activity coefficients
  • Equilibrium constants and activities
  • Vapor pressure osmometry - Vapro osmometry

Homework Problem Set 12: Download from here. Due ~Nov 17.

VIII. Electrolyte Solutions (ER: Topics from Chap 10)
  • Coulomb's Law and Electrostatic Forces
  • Electrolytes and Water
  • Chemical Potential of Electrolytes
  • Debye-Hückel Theory
  • Salting-in and Salting-out
  • The Hofmeister Series

IX. Electrochemical Equilibria (ER: Topics from Chap 11)
  • Electrochemical cells
  • Electromotive force and standard electrode potentials
  • The Glass Electrode (see also a paper by Kohler et al. to see the level of our current understanding)
  • Ionic effects and membrane equilibria - the Donnan effect (lecture taken from Eisenberg and Crothers Biophysical Chemistry text, p. 389)

EXAM IV: ~Nov 24

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FINAL: ~Dec 1

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