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Physical Chemistry for the Biological Sciences provides an introduction to physical chemistry that is directed toward applications to the biological sciences. Advanced mathematics is not required and can be used for either a one semester or two semester course, and as a reference volume by students and faculty in the biological sciences.
THERMODYNAMICS
1. Heat, Work and Energy
Introduction
Temperature
Heat
Work
Definitions of Energy
Enthalpy
Standard States
Calorimetry
Reaction Enthalpies
Temperature Dependence of Enthalpies
References
Problems
2. Entropy and Gibbs Energy
Introduction
Statement of the Second Law
Calculation of the Entropy
Third Law of Thermodynamics
Molecular Interpretation of Entropy
Gibbs Energy
Chemical Equilibria
Pressure and Temperature Dependence of the Gibbs Energy
Phase Changes
Additions to the Gibbs Energy
References
Problems
3. Applications of Thermodynamics to Biological Systems
Biochemical Reactions
Metabolic Cycles
Direct Synthesis of ATP
Establishment of Membrane Ion Gradients by Chemical Reactions
Protein Structure
Protein Folding
Nucleic Acid Structures
DNA Melting
RNA
References
Problems
4. Thermodynamics Revisited
Introduction
Mathematical Tools
Maxwell Relations
Chemical Potential
Partial Molar Quantities
Osmotic Pressure
Chemical Equilibria
Ionic Solutions
References
Problems
CHEMICAL KINETICS
5. Principles of Chemical Kinetics
Introduction
Reaction Rates
Determination of Rate Laws
Radioactive Decay
Reaction Mechanisms
Temperature Dependence of Rate Constants
Relationship between Thermodynamics and Kinetics
Reaction Rates Near Equilibrium
Single Molecule Kinetics
References
Problems
6. Applications of Kinetics to Biological Systems
Introduction
Enzyme Catalysis: The Michaelis-Menten Mechanism
a-Chymotrypsin
Protein Tyrosine Phosphatase
Ribozymes
DNA Melting and Renaturation
References
Problems
QUANTUM MECHANICS
7. Fundamentals of Quantum Mechanics
Introduction
Schrödinger Equation
Particle in a Box
Vibrational Motions
Tunneling
Rotational Motions
Basics of Spectroscopy
References
Problems
8. Electronic Structure of Atoms and Molecules
Introduction
Hydrogenic Atoms
Many-Electron Atoms
Born-Oppenheimer Approximation
Molecular Orbital Theory
Hartree-Fock Theory and Beyond
Density Functional Theory
Quantum Chemistry of Biological Systems
References
Problems
SPECTROSCOPY
9. X-ray Crystallography
Introduction
Scattering of X-rays by a Crystal
Structure Determination
Neutron Diffraction
Nucleic Acid Structure
Protein Structure
Enzyme Catalysis
References
Problems
10. Electronic Structure
Introduction
Absorption Spectra
Ultraviolet Spectra of Proteins
Nucleic Acid Spectra
Prosthetic Groups
Difference Spectroscopy
X-ray Absorption Spectroscopy
Fluorescence and Phosphorescence
RecBCD: Helicase Activity Monitored by Fluorescence
Fluorescence Energy Transfer: A Molecular Ruler
Application of Energy Transfer to Biological Systems
Dihydrofolate Reductase
References
Problems
11. Circular Dichroism, Optical Rotary Dispersion, and Fluorescence Polarization
Introduction
Optical Rotary Dispersion
Circular Dichroism
Optical Rotary Dispersion and Circular Dichroism of Proteins
Optical Rotary Dispersion and Circular Dichroism of Nucleic Acids
Small Molecule Binding to DNA
Protein Folding
Interaction of DNA with Zinc Finger Proteins
Fluorescence Polarization
Integration of HIV Genome into Host Genome
α-ketoglutarate Dehyrogenase
References
Problems
12. Vibrations in Macromolecules
Introduction
Infrared Spectroscopy
Raman Spectroscopy
Structure Determination with Vibrational Spectroscopy
Resonance Raman Spectroscopy
Structure of Enzyme-Substrate Complexes
Conclusion
References
Problems
13. Principles of Nuclear Magnetic Resonance and Electron Spin Resonance
Introduction
NMR Spectrometers
Chemical Shifts
Spin-spin Splitting
Relaxation Times
Multi-dimensional NMR
Magnetic Resonance Imaging
Electron Spin Resonance
References
Problems
14. Applications of Magnetic Resonance in Biology
Introduction
Regulation of DNA Transcription
Protein-DNA Interactions
Dynamics of Protein Folding
RNA Folding
Lactose Permease
Proteasome Structure and Function
Conclusion
References
STATISTICAL MECHANICS
15. Fundamentals of Statistical Mechanics
Introduction
Kinetic Model of Gases
Boltzmann Distribution
Molecular Partition Function
Ensembles
Statistical Entropy
Helix-Coil Transition
References
Problems
16. Molecular Simulations
Introduction
Potential Energy Surfaces
Molecular Mechanics and Docking
Large-Scale Simulations
Molecular Dynamics
Monte Carlo
Hybrid Quantum/Classical Methods
Helmholtz and Gibbs Energy Calculations
Simulations of Enzyme Reactions
References
Problems
SPECIAL TOPICS
17. Ligand Binding to Macromolecules
Introduction
Binding of Small Molecules to Multiple Identical Binding Sites
Macroscopic and Microscopic Equilibrium Constants
Statistical Effects in Ligand Binding to Macromolecules
Experimental Determination of Ligand Binding Isotherms
Binding of Cro Repressor Protein to DNA
Cooperativity in Ligand Binding
Models for Cooperativity
Kinetic Studies of Cooperative Binding
References
Problems
18. Hydrodynamics
Introduction
Frictional Coefficient
Diffusion
Centrifugation
Velocity Sedimentation
Equilibrium Centrifugation
Preparative Centrifugation
Density Centrifugation
Viscosity
Electrophoresis
Peptide Induced Conformational Change of a Major Histocompatibility Complex Protein
Ultracentrifuge Analysis of Protein-DNA Interactions
References
Problems
19. Mass Spectrometry
Introduction
Mass Analysis
Tandem Mass Spectrometry
Ion Detectors
Ionization of the Sample
Sample Preparation/Analysis
Proteins and Peptides
Protein Folding
Other Biomolecules
References
Problems
APPENDICES
Appendix 1. Useful constants and conversion factors
Appendix 2. Structures of the common amino acids at neutral pH
Appendix 3. Common nucleic acid components
Appendix 4. Standard Gibbs energies and enthalpies of formation at 298 K, 1 atmosphere, pH 7, and 0.25 M ionic strength
Appendix 5. Standard Gibbs energy and enthalpy changes for biochemical reactions at 298 K, 1 atmosphere, pH 7.0, pMg 3.0, and 0.25 M ionic strength
Appendix 6. Introduction to Electrochemistry
Gordon G. Hammes, PhD, is the Distinguished Service Professor of Biochemistry Emeritus at Duke University. He is a member of the National Academy of Sciences and the American Academy of Arts and Sciences, and has received several national awards, including the American Chemical Society Award in Biological Chemistry and the American Society for Biochemistry and Molecular Biology William C. Rose Award. Dr. Hammes was Editor of the journal Biochemistry from 1992-2003.
Sharon Hammes-Schiffer, PhD, is the Swanlund Professor of Chemistry at the University of Illinois at Urbana-Champaign. She is a fellow of the American Physical Society, the American Chemical Society, the Biophysical Society, and the American Association for the Advancement of Science. She is a member of the American Academy of Arts and Sciences, the National Academy of Sciences, and the International Academy of Quantum Molecular Science. Dr. Hammes-Schiffer has served as the Deputy Editor of The Journal of Physical Chemistry B and is currently the Editor-in-Chief of Chemical Reviews.
