Biophysical Chemistry > Biochemistry

2008년 6월 출시예정 This text presents physical chemistry through the use of biological and biochemical topics, examples and applications to biochemistry. It lays out the necessary calculus in a step by step fashion for students who are less mathematically inclined, leading them through fundamental concepts, such as a quantum mechanical description of the hydrogen atom rather than simply stating outcomes. Techniques are presented with an emphasis on learning by analyzing real data. * Presents physical chemistry through the use of biological and biochemical topics, examples and applications to biochemistry * Lays out the necessary calculus in a step by step fashion for students who are less mathematically inclined * Presents techniques with an emphasis on learning by analyzing real data * Features qualitative and quantitative problems at the end of each chapter * All art available for download online and on CD-ROM

차 례 Preface 0. Basic thermodynamic and biochemical concepts 0.1 Fundamental thermodynamic concepts States of matter Pressure Temperature Volume, mass, and number 0.2 Properties of gases The ideal gas laws Gas Mixtures 0.3 Kinetic energy of gases 0.4 Real Gases Liquifying gases for low temperature spectroscopy 0.5 Molecular Basis for Life Cell Membranes Amino acids Classification of amino acids by their side chains DNA and RNA 1. First law of thermodynamics Systems State Functions First law of thermodynamics 1.1 Research Direction: Drug design I Work 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 1.2 Research Direction: Global climate change 2. Second law of thermodynamics Entropy 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 2.1 Research Direction: Drug design II Gibbs free energy for an ideal gas Using the Gibbs free energy Carnot cycle and hybrid cars Derivative box: Entropy as a state function 2.2 Research Direction: Nitrogen fixation 3. 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 3.1 Research Direction: lipid rafts Determination of micelle formation using surface tension Mixtures Raoult's law Osmosis 3.2 Research Direction: Protein crystallization 4. 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 Buffers Buffering in the cardiovascular system 4.1 Research Direction: Proton coupled electron transfer and pathways 5. Oxidation/reduction reactions and bioenergetics Oxidation/reduction reactions Electrochemical cells The Nernst Equation: Midpoint potentials Gibbs energy of formation and activity Ionic strength Adenosine triphosphate,ATP Chemiosmotic hypothesis 5.1 Research Direction: Respiratory chain 5.2 Research Direction: ATP synthase 6. Kinetics and enzymes The 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 6.1 Research Direction: Electron transfer I: Energetics Derivative box Derivation of Marcus relationship Enzymes Enzymes lower the activation energy Enzyme mechanisms 6.2 Research Directions: Dynamics in enzyme mechanism Michaelis-Menten mechanism Lineweaver-Burk equation Enzyme activity 6.3 Research direction: The RNA world 7. The Boltzmann distribution and statistical thermodynamics Probability Boltzmann distribution Partition function Statistical thermodynamics 7.1 Research Direction: Protein folding and prions Prions 8. Quantum theory: Introduction and principles Classical concepts Experimental failures of classical physics Blackbody radiation Photoelectric effect Atomic 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 8.1 Research Direction: Schrodinger's cat 9. Particle in box and tunneling One-dimensional particle in the box Properties of the solutions Energy and wavefunction Symmetry Wavelength Probability Average or expectation value Transitions 9.1 Research Direction: Carotenoids Two-dimensional particle in a box Tunneling 9.2 Research Direction: Probing biological membranes 9.3 Research Direction: Electron transfer II: Distance dependence 10. Vibrational motion and infrared spectroscopy Simple Harmonic Oscillator: Classical theory Potential energy for the simple harmonic oscillator Simple Harmonic Oscillator: Quantum theory Derivative box: Solving Schrodinger's equation for the simple harmonic oscillator Properties of the wavefunctions Energy and wavefunction Forbidden region Transitions Vibrational Spectra 10.1Research Direction: Hydrogenase 11. Atomic structure: Hydrogen atom and Multi-electron atoms Schrodinger's equation for the hydrogen atom Derivative box: Solving Schrodinger's equation for the hydrogen Separation of variables Angular Solution Radial solution Properties of the general solution Angular Momentum Orbitals s-orbitals p-orbitals d-orbitals Transitions 11.1 Research Direction: Hydrogen economy Spin Derivative box:Relativistic equations Many electron atoms Empirical constants Self-consistent field theory (Hartree-Fock) Helium atom Spin-orbital coupling Periodic table 12. Chemical bonds and protein interactions Schrodingers' equation for the hydrogen molecule Valence bonds Huckel model Interactions in proteins Peptide bonds Steric effects Hydrogen bonds Electrostatic interactions Hydrophobic effects Secondary structure Determination of secondary structure using circular dichroism 12.1 Research Direction: Modeling protein structures 13. Electronic Transitions and optical spectroscopy The nature of light The Beer-Lambert law Measuring absorption Transitions Derivation box: Relationship between the Einstein coefficient Lasers Selection Rules Franck Condon Principle The Relationship Between Emission and Absorption Spectra The yield of fluorescence Fluorescence Resonance Energy Transfer: FRET Measuring fluorescence Phosphorescence 13.1 Research Direction: Probing Energy transfer using 2D optical spectroscopy 13.2 Research Direction: Single molecule spectroscopy Holliday junctions 14. X-ray diffraction and EXAFS Diffraction theory Bragg's Law Bravais lattices Protein crystals Diffraction from Crystals Derivative box: Phases of complex numbers Phase determination Molecular Replacement Isomorphous Replacement Anomalous Dispersion Model Building Experimental measurement of X-ray diffraction Examples of protein structures 14.1 Research Direction: Nitrogenase EXAFS 15. Magnetic resonance Nuclear magnetic resonance Chemical shifts Spin-spin interactions Pulse techniques Two dimensional NMR:Nuclear Overhauser effect NMR spectra of amino acids 15.1 Research Direction: Development of new NMR techniques 15.2 Research Direction: Spinal Muscular Atrophy Magnetic Resonance Imaging (MRI) Electron Spin Resonance Hyperfine structure Spin probes ENDOR 15.3 Research Direction: heme proteins 15.4 Research Direction: ribonucleotide reductase 16. Signal transduction Biochemical pathway for visual response Spectroscopic studies of rhodopsin Bacteriorhodopsin Structural studies Comparison of rhodopsins from different organisms Rhodopsin proteins in visual response 17. Membrane potentials, transporters, and channels Membrane potentials Energetics of transport across membranes Transporters Ion channels 18. Molecular imaging Green fluorescent protein,GFP Mechanism of chromophore formation FRET: fluorescence resonance energy transfer Imaging of GFP in cells Imaging in organisms Radioactive decay Positron emission tomography Parkinson's disease 19. Photosynthesis Energy transfer and light-harvesting complexes Electron transfer, bacterial reaction centers, and photosystem I Water oxidation

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