Outline of Topics – Chemistry
and Biological Sciences 347
(EC: Eisenberg
and Crother’s text)
I. Mathematics Review
Basic math, logarithms, algebra, trigonometry
Differentiation
Integration - definite and indefinite integrals
Unit conversion
-
Supplement 2: Mathematics Review (pdf document download from here).
-
Homework Problem Set 1: (download here) Due Friday 25 Aug 2006
There are a number of powerful software packages available for doing mathematics and data analysis on the computer.
We will use Igor Pro 5 and a free copy will be supplied to you by the instructor.
You may also want to take a look at Mathematica. Some simple examples of how Mathematica can be used are found here.
You can obtain Mathematica as a student at a greatly reduced rate. Licences arealso available for one semester or a year.
II. Computers in Simulations and Analysis
Simulating functions
Importing and exporting data
Plotting
Curve fitting - linear and nonlinear regression
-
Supplement 3: Computers in Simulations and Analysis (pdf document download from here).
-
Homework Problem Set 2: (download here) Due Wednesday, 30Aug 2006
Units Handout (pdf document). Go to NIST web site on SI units.
III. Basic Themodynamics
Definitions (EC: Chapter 1)
State functions and equations of state
Homework Problem Set 3:
Energy and the First Law of Thermodynamics
(EC: Chapter 2)
The basics: Heat, work, and energy
Heat, deltaH, deltaE, and deltaCp as measurable
quantities - DSC and ITC
and the Kirchhoff Relationship
Molecular interpretation of enthalpy and heat capacity
changes
Thermochemistry
Homework Problem Set 4:
Gas expansions - isothermal and adiabatic problems.
Homework Problem Set 5:
Additional practice with problem solving can be obtained by working the problems found in many physical chemistry texts which often include answers at the end of the book. (e.g. Physical Chemistry by Atkins and Physical Chemistry by Laidler and Meiser)
EXAM I - (Sample Exam here) -
Entropy and the Second Law of Thermodynamics
(EC: Chapter 3)
Entropy and the condition of spontaneity
The second law of thermodynamics
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
Free Energy and spontaneity (EC: Chapter 4)
Helmholtz
Gibbs
Gibbs-Helmholtz Equation
Modified Gibbs-Helmholtz Equation
Protein stability curves - Schellman
Practical aspects - Handout
on Equilibria and Temperature here
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 - computer analysis
Current applications of calorimetry in biochemistry
Differential scanning calorimetry (DSC) -
Sturtevant, Privalov and Freire
Protein folding - computer simulations
Homework Problem Set 7
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).
IV. Intermolecular and Intramolecular Forces
Electrostatics
Dipole-dipole interactions
Bond stretching and rotation
van der Waals interactions
Hydrogen Bonds
Hydrophobic "interactions"
EXAM II - (Practice Questions here) -
V. Binding
- (Binding handout here)
Binding - a central problem in biochemistry
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 - Basics handout
here and Fitting with Excel handout here.
A handout on nonlinear fitting with Mathematica will be distributed in class.
Coordinate transformations
Why not use a Scatchard plot?
Homework Problem
Set 8:
Multiple equilibria - molecular partition functions
Independent site binding
Linked functions -
Allosterism - Wyman and Gill
Homework Problem
Set 9:
Practical aspects
Methods of evaluating binding constants by non-linear
regression
Isothermal titration calorimetry (ITC)
- Handout here
Binding heats
EXAM
III:
VI. Solution Thermodynamics (EC: Chapter 7)
Solution concentrations
Partial molal and partial molar quantities
Gibbs-Duhem Equation
Ideal solutions and Raoult's Law
Henry's Law
Fugacity and Real Gases
Activity and Real Solutions
Activity and chemical potentials
Activity coefficients and choice of standard states
Colligative properties
Membrane equilibria and osmotic pressure
Equilibrium sedimentation
EXAM
IV:
VII. Electrolyte Solutions (EC: Chapter 8)
Coulomb's Law and Electrostatic Forces
Electrolytes and Water
Thermodynamics of Ion Solvation
Conductivity of Aqueous Solutions
Ion Mobilities
Chemical Potential of Electrolytes
Debye-Hückel Theory
Salting-in and Salting-out
The Hoffmeister Effect - Baldwin
Chaotropes and Kosmotropes - Kim Collins
VIII. Water and Macromolecules
Osmolytes and proteins - Bolen
Solvent exclusion - Timasheff
Water as a ligand - Parsegian, Record
IX. Electrostatics in Proteins and Nucleic Acids
Definition of the potential
Gauss's Law
Poisson's Equation
Dielectric constants and their significance
Current problems in macromolecule electrostatics - Tanford, Kirkwood, Honig, Garcia-Moreno, Record
Protein electrostatics
Protein-DNA binding and the polyelectrolyte effect
FINAL:
url: http://chemistry.uah.edu/shriver.htm
The University of Alabama
in Huntsville, Huntsville, AL 35899
site updated: 15 August 2006 (jws)