| |
| |
Preface | |
| |
| |
| |
Basic thermodynamic and biochemical concepts | |
| |
| |
| |
Fundamental thermodynamic concepts | |
| |
| |
States of matter | |
| |
| |
Pressure | |
| |
| |
Temperature | |
| |
| |
Volume, mass, and number | |
| |
| |
| |
Properties of gasesThe ideal gas lawsGas Mixtures | |
| |
| |
| |
Kinetic energy of gases | |
| |
| |
| |
Real GasesLiquifying gases for low temperature spectroscopy | |
| |
| |
| |
Molecular Basis for Life | |
| |
| |
Cell Membranes | |
| |
| |
Amino acids | |
| |
| |
Classification of amino acids by their side chains | |
| |
| |
DNA and RNA | |
| |
| |
| |
First law of thermodynamics | |
| |
| |
Systems | |
| |
| |
State Functions | |
| |
| |
First law of thermodynamics | |
| |
| |
| |
Research Direction: Drug design IWork | |
| |
| |
Specific heat | |
| |
| |
Internal energy for an ideal gas | |
| |
| |
Enthalpy | |
| |
| |
Dependence of specific heat on enthalpy | |
| |
| |
Derivative box: State Functions described using partial derivatives | |
| |
| |
Enthalpy changes of biochemical reactions | |
| |
| |
| |
Research Direction: Global climate change | |
| |
| |
| |
Second law of thermodynamicsEntropy | |
| |
| |
Entropy changes for reversible and irreversible processes | |
| |
| |
The second law of thermodynamics | |
| |
| |
Interpretation of entropy | |
| |
| |
Third law of thermodynamics | |
| |
| |
Gibbs energy | |
| |
| |
Relationship between the Gibbs free energy and the equilibrium constant | |
| |
| |
| |
Research Direction: Drug design IIGibbs free energy for an ideal gas | |
| |
| |
Using the Gibbs free energy | |
| |
| |
Carnot cycle and hybrid cars | |
| |
| |
Derivative box: Entropy as a state function | |
| |
| |
| |
Research Direction: Nitrogen fixation | |
| |
| |
| |
Phase diagrams, mixtures and chemical potential | |
| |
| |
Substances may exist in different phases | |
| |
| |
Phase diagrams and transitions | |
| |
| |
Chemical potential | |
| |
| |
Properties of lipids described using the chemical potential | |
| |
| |
| |
Research Direction: lipid rafts | |
| |
| |
Determination of micelle formation using surface tension | |
| |
| |
Mixtures Raoult's law Osmosis | |
| |
| |
| |
Research Direction: Protein crystallization | |
| |
| |
| |
Equilibria and reactions involving protons | |
| |
| |
Gibbs free energy minimum | |
| |
| |
Derivative box: Relationship between the Gibbs energy and equilibrium constant | |
| |
| |
Response of the equilibrium constant to condition changes | |
| |
| |
Acid-base equilibria | |
| |
| |
Protonation states of amino acid residues | |
| |
| |
BuffersBuffering in the cardiovascular system | |
| |
| |
| |
Research Direction: Proton coupled electron transfer and pathways | |
| |
| |
| |
Oxidation/reduction reactions and bioenergetics | |
| |
| |
Oxidation/reduction reactionsElectrochemical cells | |
| |
| |
The Nernst Equation: Midpoint potentials | |
| |
| |
Gibbs energy of formation and activity | |
| |
| |
Ionic strength | |
| |
| |
Adenosine triphosphate, ATP Chemiosmotic hypothesis | |
| |
| |
| |
Research Direction: Respiratory chain | |
| |
| |
| |
Research Direction: ATP synthase | |
| |
| |
| |
Kinetics and enzymesThe rate of a chemical reaction | |
| |
| |
Parallel first-order reactions | |
| |
| |
Sequential first order reactions | |
| |
| |
Second-order reactions | |
| |
| |
The order of a reaction | |
| |
| |
Reactions that approach equilibrium | |
| |
| |
Activation energy | |
| |
| |
| |
Research Direction: Electron transfer I: Energetics | |
| |
| |
Derivative box Derivation of Marcus relationship | |
| |
| |
Enzymes | |
| |
| |
Enzymes lower the activation energy | |
| |
| |
Enzyme mechanisms | |
| |
| |
| |
Research Directions: Dynamics in enzyme mechanism | |
| |
| |
Michaelis-Menten mechanism | |
| |
| |
Lineweaver-Burk equation | |
| |
| |
Enzyme activity | |
| |
| |
| |
Research direction: The RNA world | |
| |
| |
| |
The Boltzmann distribution and statistical thermodynamics | |
| |
| |
ProbabilityBoltzmann distribution | |
| |
| |
Partition function | |
| |
| |
Statistical thermodynamics | |
| |
| |
| |
Research Direction: Protein folding and prionsPrions | |
| |
| |
| |
Quantum theory: Introduction and principles | |
| |
| |
Classical concepts | |
| |
| |
Experimental failures of classical physics | |
| |
| |
Blackbody radiationPhotoelectric effectAtomic spectra | |
| |
| |
Principles of quantum theory | |
| |
| |
Wave Particle Duality Schrodinger's Equation | |
| |
| |
Born Interpretation | |
| |
| |
General approach for solving Schrodinger's equation | |
| |
| |
Interpretation of quantum mechanics | |
| |
| |
Heisenberg Uncertainty Principle | |
| |
| |
A quantum mechanical world | |
| |
| |
| |
Research Direction: Schrodinger's cat | |
| |
| |
| |
Particle in box and tunneling | |
| |
| |
One-dimensional particle in the box | |
| |
| |
Properties of the solutions | |
| |
| |
Energy and wave function Symmetry | |
| |
| |
Wavelength | |
| |
| |
Probability | |
| |
| |
Average or expectation value | |
| |
| |
Transitions | |
| |
| |
| |
Research Direction: Carotenoids Two-dimensional particle in a box Tunneling | |
| |
| |
| |
Research Direction: Probing biological membranes | |
| |
| |
| |
Research Direction: Electron transfer II: Distance dependence | |
| |
| |
| |
Vibrational motion and infrared spectroscopy | |
| |
| |
Simple Harmonic Oscillator: Classical theory | |
| |
| |
Potential energy for the simple harmonic oscillator | |
| |
| |
Simple Ha | |