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Biophysical chemistry / Dagmar Klostermeier, Markus G. Rudolph. -- Boca Raton : CRC Press, Taylor & Francis Group, [2017]. – (58.171/K66) |
Contents
Preface
Acknowledgments
Authors
PART I
Thermodynamics
Chapter 1. Systems and their Surroundings
Questions
Chapter 2. State Functions and the Laws of Thermodynamics
2.1 General Considerations: State Variables and
State Functions
2.2 The Internal Energy U and the First Law of
Thermodynamics
2.3 The Enthalpy H
2.4 The Entropy S and the Second Law of
Thermodynamics
2.5 The
Free Energy G: Combining System and Surroundings
2.6 The Chemical Potential μ
Questions
References
Chapter 3. Energetics and Chemical Equilibria
3.1 The Free Energy Change and
the Equilibrium Constant
3.2 Binding and Dissociation
Equilibria and Affinity
3.3 Protolysis Equilibria: The
Dissociation of Acids and Bases in Water
3.4 Thermodynamic Cycles, Linked
Functions and Apparent Equilibrium Constants
Questions
References
Chapter 4. Thermodynamics of Transport Processes
4.1 Diffusion
4.2 The Chemiosmotic Hypothesis
4.3 Active and Passive Transport
4.4 Directed Movement by the
Brownian Ratchet
Questions
References
Chapter 5.
Electrochemistry
5.1 Redox Reactions and
Electrochemical Cells
5.2 Types of Half-Cells
5.3 Standard Electrode Potentials
5.4 The Nernst Equation
5.5 Measuring pH values
5.6 Redox Reactions in Biology
5.7 The Electrochemical Potential
and Membrane Potentials
5.8
Electrophysiology: Patch-Clamp Methods to Measure Ion Flux through Ion
Channels
Questions
References
PART II
Kinetics
Chapter 6.
Reaction Velocities and Rate Laws
Questions
Chapter 7.
Integrated Rate Laws for Uni-and Bimolecular Reactions
Questions
Chapter 8.
Reaction Types
8.1 Reversible Reactions
8.2 Parallel Reactions
8.3 Consecutive Reactions
Questions
Reference
Chapter 9.
Rate-Limiting Steps
Questions
References
Chapter 10. Binding Reactions: One-Step and
Two-Step Binding
Questions
References
Chapter 11. Steady-State (Enzyme) Kinetics
11.1 Rapid Equilibrium
(Michaelis-Menten Formalism)
11.2 Steady-State Approximation
(Briggs-Haldane Formalism)
11.3 pH Dependence
11.4
Two or More Non-Interacting Active Sites
11.5 Two or More Interacting
Active Sites: Cooperativity and the Hill Equation
11.6 Inhibition of Enzyme
Activity
Questions
References
Chapter 12. Complex Reaction Schemes and
their Analysis
12.1 Binding of Two Substrates
12.2 Ping-Pong Mechanism
12.3 Net Rate Constants and
Transit Times
Questions
References
Chapter 13. Temperature Dependence of Rate
Constants
13.1 The Arrhenius Equation
13.2 Transition State Theory
13.3 Collision Theory
13.4 Kinetic and Thermodynamic
Control of Reactions
Questions
Chapter 14. Principles of Catalysis
14.1 Enzyme Catalysis
14.2 Acid-Base Catalysis
14.3 Electrostatic and Covalent
Catalysis
14.4 Intramolecular Catalysis and
Effective Concentrations
Questions
References
PART III
Molecular Structure and Stability
Chapter 15. Molecular Structure and
Interactions
15.1 Configuration and
Conformation
15.2 Covalent Interactions
15.3 Non-Covalent Interactions
Questions
References
Chapter 16. Proteins
16.1 Amino Acids and the Peptide
Bond
16.2 Protein Structure
16.3 Folding and Stability
Question
References
Online Resources
Chapter 17. Nucleic Acids
17.1 Nucleobases, Nucleosides and
Nucleotides
17.2 Ribose and Nucleobase
Conformations
17.3 Primary Structure of Nucleic
Acids
17.4 Base Pairing and Stacking
17.5 DNA Structures and
Conformations
17.6 RNA Structure
Questions
References
Online Resources
Chapter 18. Computational Biology
18.1 Sequence Analysis
18.2 Molecular Modeling
Questions
References
Online resources
PART IV
Methods
Chapter 19. Optical Spectroscopy
19.1 Interaction of Light and
Matter
19.2 Absorption
19.3 Linear and Circular
Dichroism
19.4 Infrared Spectroscopy
19.5 Fluorescence
Questions
References
Chapter 20. Magnetic Resonance
20.1 Nuclear Magnetic Resonance
20.2 Electron Paramagnetic
Resonance
Questions
References
Chapter 21. Solution Scattering
21.1 Light Scattering
21.2 Small Angle Scattering
Questions
References
Chapter 22. X-ray Crystallography
22.1 Generation of X-rays
22.2 Phase Problem and
Requirement for Crystals
22.3 Crystallization of
Macromolecules
22.4 Symmetry and Space Groups
22.5 X-ray Diffraction from
Crystals
22.6 Diffraction Data Collection
and Analysis
22.7 Phasing Methods
22.8 Electron Density and Model
Building
22.9 Model Refinement and
Validation
Questions
References
Online Resources
Chapter 23. Imaging and Microscopy
23.1 Fluorescence Microscopy
23.2 Electron Microscopy
Questions
References
Chapter 24. Force Measurements
24.1 Force Spectroscopy by AFM
24.2 Optical Tweezers
24.3 Magnetic Tweezers
Questions
References
Chapter 25. Transient Kinetic Methods
25.1 Stopped Flow
25.2 Quench Flow
25.3 Laser Flash Photolysis
25.4 Relaxation Kinetics:
Pressure- and Temperature-Jump
Questions
References
Chapter 26. Molecular Mass, Size, and Shape
26.1 Mass Spectrometry
26.2
Analytical Ultracentrifugation
26.3 Surface Plasmon Resonance
Questions
References
Online resources
Chapter 27. Calorimetry
27.1 Isothermal Titration
Calorimetry
27.2 Differential Scanning
Calorimetry
Questions
References
Appendix
Chapter 28. Prefixes, Units, Constants
28.1 Prefixes
28.2 SI (Systeme international)
or Base Units
28.3
Derived Units Used in this Book
28.4 Natural Constants Used in
This Book
Chapter 29. Mathematical Concepts Used in
This Book
29.1 Sums and Products
29.2 Quadratic Equation
29.3 Binomial Coefficients
29.4 Trigonometry
29.5 Logarithms and Exponentials
29.6 Differentiation and
Integration
29.7 Partial fractions
29.8 I'Hopital's rule
29.9 Vectors
29.10 Complex Numbers
29.11 Basic Elements of Statistics
29.12 Error Propagation
29.13 Series Expansion
29.14 Fourier Transformation
29.15 Convolution
Index
