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Biophysical Chemistry Syllabus
Fall, 2009
A) Introduction to Biopolymer Processes (e.g. Folding, Assembly, Binding,
Dissolving) and the Applications of Chemical Thermodynamics and Chemical
Kinetics to Study these Processes (1-2 lectures: see Overview, Introduction, Ch. 1)
B) Fundamentals of Chemical Thermodynamics of Systems and Processes (~12
lectures)
1) Preliminaries: Math of State Functions, Exact, Inexact Differentials, Partial
Derivatives (Ch. 1 Appendix); Work, Heat; Reversible, Irreversible Processes (see Ch.
2).
2) First Law: Energy, Enthalpy, Heat Capacity of Systems; Changes in these Functions
in Processes (see Ch. 2).
3) Second Law; Physical and Mathematical Properties of Entropy (see Ch. 3).
4) Free Energy and Work: Criteria for a Spontaneous Process and for Equilibrium at
Constant T and P; Summary of State Functions; Maxwell Relations
5) Calculations of Entropy, Free Energy Changes for Simple Processes (see Ch. 4,5)
6) Mixing as a Spontaneous Thermodynamic Process; Ideal Gas Mixtures.
7) Extensive, Intensive Quantities; Molar and Partial Molar Quantities; MultiComponent Systems, Mixtures; Characterizing Contributions of Different Components
to the Thermodynamic Properties of a Mixture (see Ch. 5, 6).
8) Chemical Potential (Partial Molar Gibbs Free Energy).
9) Applications of Chemical Potential to Analyze Fundamental Processes: Reaction and
Chemical Equilibrium in a Gas-Phase Molecular Mixture; Phase Change and Phase
Equilibrium in a Pure System where Molecular Mixing is Not Involved (see Ch. 7)
C) Thermodynamics of Solutions (~5 lectures; see Ch. 8)
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1) Ideal Solutions (Ideal Liquid Mixtures), Mole Fraction Concentration Scale;
Nonideal Solutions, Activity Coefficients.
2) “Ideal Dilute” Solutions; Thermodynamic Characterization of SoluteSolvent Interactions and Solute-Solute Interactions.
3) Solvent, Solute Chemical Potentials; Molar and Molal Concentration Scales.
4) Electrolyte Solutions (Dissociation; Hydration of Ions; Coulombic ion-ion Interactions).
(After 4 problem sets, Exam 1 covers this material: Thursday, October 8, 7:15
PM)
D) Biochemical Processes and Equilibria in Solution (~10 lectures; Ch 9-12)
1) Processes and Equilibria Involving Solvent in Solution (Colligative Properties): Osmotic
Pressure, Living Cells as Osmotic Systems (see Ch. 9).
2) Processes and Equilibria Involving Solutes in Solution:
Chemical Reactions and Noncovalent Interactions (see Ch. 10);
Transfer of Solutes Between Environments (see Ch. 11).
3) The Hydrophobic Effect: Thermodynamics of Exposing Nonpolar (Hydrocarbon) Molecular
Surface to Water (see Ch. 11)
Thermodynamics of Forming Ions from Uncharged Solutes in Water (see Ch. 11).
4) Macromolecular Recognition, Self-assembly and Other Noncovalent Biopolymer
Processes in Water: Micelle Formation, Nucleic Acid Helix Formation and Folding,
Protein Folding, Protein-Ligand and Protein-Protein Interactions; Roles of the Hydrophobic
Effect, Base Stacking and other Noncovalent Interactions (Ch. 12)
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E) Ligand Binding to Biopolymers; Regulatory Roles of [Ligand]
(~10 lectures ; see Ch. 13)
1) Noncooperative and Cooperative Binding Isotherms for Ligand-Biopolymer
Interactions
2) Thermodynamic Characterization of Ligand Binding: Equilibrium Dialysis,
Spectroscopic and Calorimetric Methods
3) Analysis of Ligand Binding and Ligand Effects using Binding Polynomials.
4) [Ligand] as a Regulator of Processes and Equilibria of Biopolymers.
5) Applications: O2 Binding to Mb and Hb, Lac Repressor-lac Operator Interactions
(Two classic examples of binding interactions which are regulated by other (allosteric,
competitive) binding interactions)
(After 4 problem sets, Exam 2 covers this material: Thursday, November 12, 7:15
PM)
F)
Solute-Biopolymer and Salt-Polyelectrolyte Interactions; Solute and Salt Effects
on Biopolymer Processes (~4 lectures; see Ch. 14,15)
1) Survey of Large Solute and Salt Effects on Protein and Nucleic Acid Processes
2) Thermodynamic Description of Solute-Biopolymer and Salt-Polyelectrolyte Interactions
using Chemical Potential Derivatives (23 = d2/dm3). Interpretation of Signs, Magnitudes
of 23 of Solutes, Ions in terms of the Partitioning of the Solute or Ion between the
Biopolymer Surface and the Bulk Solution, as well as Long Range Coulombic Interactions
of Salt Ions with Biopolymer Charges, Short Range Hofmeister Interactions of Salt Ions
with Biopolymer Surfaces.
G) Chemical Kinetics and Mechanisms of Biopolymer Processes
(~16 lectures; Ch 16-19)
1) Rate Laws, Rate Equations for Elementary Reactions (First Order, Second Order;
Irreversible, Reversible; Relaxation Analysis (see Ch. 16).
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2) Diffusion-Collision Step in Second Order Reactions in Solution (Diffusion Limit, Facilitated
Diffusion) (see Ch. 17).
3) Chemical Limitations to Reaction Rates: Enthalpic and Entropic Activation Barriers;
Intermediates (see Ch. 17)
4) Mechanisms and their Analysis using Steady State or Rapid Equilibrium
Approximations (see Ch. 18).
5) Kinetics and Mechanisms of Enzyme-Catalyzed Reactions: Biophysical Basis of Catalysis,
Catalytic Antibodies, Cooperative Enzymes, Regulation of Catalytic Activity by Ligand
Concentration (see Ch.19).
6) Examples: Kinetics and Mechanisms of Protein Folding, Nucleic Acid Helix Formation, and
Protein-Nucleic Acid Interactions (RNA Polymerase-Promoter, Lac Repressor-lac Operator).
After 3-4 problem sets, Exam 3 covers this material in the Final Exam time slot
(Tuesday, December 22, 2:45–4:45 PM).