Principles and Problems in Physical Chemistry for Biochemists

by Price, Nicholas C.; Dwek, Raymond A.; Wormald, Mark; Ratcliffe, R. G.

• ISBN13: 9780198792819
• ISBN10: 0198792816
• Edition: 3rd
• Format: Paperback
• Copyright: 2002-01-10
• Publisher: Oxford University Press

Summary

What use is physical chemistry to the student of biochemistry and biology? This central question is answered in this book mainly through the use of worked examples and problems. The book starts by introducing the laws of thermodynamics, and then uses these laws to derive the equations relevantto the student in dealing with chemical equilibria (including the binding of small molecules to proteins), properties of solutions, acids and bases, and oxidation-reduction processes. The student is thus shown how a knowledge of thermodynamic qualities makes it possible to predict whether, and how,a reaction will proceed.Thermodynamics, however, gives no information about how fast a reaction will happen. The study of the rates at which processes occur (kinetics) forms the second main theme of the book. This section poses and answers questions such as 'how is the rate of a reaction affected by temperature, pH, ionicstrength, and the nature of the reactants? These same ideas are then shown to be useful in the study of enzyme-catalysed reactions.

Author Biography

Nicholas Price is Professor of Protein Science in the Division of Biochemistry and Molecular Biology, University of Glasgow Raymond Dwek, FRS, is Head of the Department of Biochemistry and Director of the Glycobiology Institute, University of Oxford and a Professorial Fellow of Exeter College, Oxford George Ratcliffe is Professor of Plant Sciences in the Department of Plant Sciences, University of Oxford and a Fellow of New College, Oxford Mark Wormald is a University Research Lecturer in the Glycobiology Institute, Department of Biochemistry, University of Oxford and a Fellow of Corpus Christi College, Oxford

Table of Contents

Notes to the reader	xv
Symbols	xvii
Introduction
The consequences of physics and chemistry for life	3	(8)
The constraints imposed on a biological system by its environment
The constraints imposed on a biological system by physics and chemistry
Physical chemistry and `Biochemists'
Scope of this book
THE ENERGETICS OF CHEMICAL REACTIONS
Basic thermodynamics	11	(23)
What is thermodynamics? Basic definitions
Statement of the first law of thermodynamics
Work and heat and internal energy
Work energy in chemical systems
The concept of enthalpy
Standard states
Enthalpy as a state function
The first law and direction of a reaction
Available energy, work and change
Statement of the second law of thermodynamics
The concept of entropy
Alternative expression of the second law of thermodynamics
The concept of free energy
Free energy and equilibrium
Thermodynamics applied to real systems
Molecular basis of enthalpy and entropy
Further reading
Problems
Chemical potential and multiple component systems	34	(20)
The concept of chemical potential
Chemical potential and change
Spontaneous reactions and equilibria
Variation of chemical potential with concentration
Dependence of ΔG on concentration
Mass action ratios and equilibrium constants
Alternative view of equilibrium constants
Variation of equilibrium constant with temperature
Dependence of enthalpy and entropy on temperature
Measurement of the thermodynamic quantities of reactions
Further reading
Problems
Binding of ligands to macromolecules	54	(20)
Ligand binding to a single site on a protein
Simultaneous binding of different ligands to a protein
A single ligand binding to multiple sites on a protein
The binding of multivalent ligands to multivalent proteins
Further reading
Problems
Acids, bases and pH regulation	74	(23)
The ionic dissociation of water
The Arrhenius definition of acids and bases
The concept of pH
Conjugate acids and bases
Quantifying acid and base strengths
Relative and absolute acid and base strengths
Variation of pKa with environment
The neutralisation of acids and bases
pH in biological systems
Buffer solutions
Quantifying buffer strengths
Regulation of pH by ion transport
Measurement of pH
Further reading
Problems
Oxidation--reduction reactions and electrochemistry	97	(25)
Oxidation--reduction reactions
Electrochemical cells
The thermodynamics of reversible cells
Cells and half-cells
Cell and half-cell nomenclature
Types of half-cells
Electrode potentials
The Nernst equation
Potentiometric titrations
Concentration cells
Effect of temperature on cell e.m.f
values
Calculation of thermodynamic quantities from electrochemical data
The effect of non-ideality
Coupled oxidation--reduction processes
Determination of pH
Further reading
Problems
Chemical potentials and the properties of solutions	122	(24)
Colligative properties
Osmosis
Osmotic pressure
Water potentials
Chemical potential of the solute
Determination of pH using permeable weak acids and bases
Equilibration of mobile solutes in the presence of charged macromolecules: the Donnan effect
Charged solutes and electric fields
Membrane potentials
Electrochemical gradients for ions
Electrochemical gradients as energy stores
Oxidative phosphorylation and photophosphorylation
Stoichiometry of proton pumping and ATP synthesis
Further reading
Problems
Ideal and non-ideal solutions	146	(25)
Ideal gases
Thermodynamics of ideal gases
Ideal solutions
Thermodynamics of ideal solutions
Dilute solutions
Non-ideal solutions
Thermodynamics of non-ideal solutions: effective concentrations and activity coefficients
Non-ideality in aqueous ionic solutions
Debye--Huckel theory
Comparison of the Debye--Huckel theory with experiment
Concentrated ionic solutions
Solutions of uncharged solutes
Properties of non-ideal solutions
Further reading
Problems
THE RATES OF CHEMICAL REACTIONS
Basic chemical kinetics and single-step reactions	171	(26)
Kinetics and thermodynamics
Energy profiles
Empirical observations
Reaction rate theories
Order and molecularity
Reaction half-times
Experimental determination of reaction orders and rate constants
Effect of temperature on the rate of a reaction
Effect of ionic strength on the rate of a reaction
Effect of isotopic substitution on the rate of a reaction
Further reading
Problems
Applications of chemical kinetics to multistep reactions	197	(16)
Parallel reactions
Reversible reactions
Consecutive reactions
The rate-determining step in consecutive reactions
The steady-state approximation in consecutive reactions
Effect of pH on the rate of a reaction
Further reading
Problems
Catalysis and enzyme kinetics	213	(24)
Catalysis of chemical reactions
Enzymes
Use of binding energy in catalysing single-substrate reactions
Kinetics of single-substrate enzyme reactions
Discussion of the Michaelis--Menten equation
Enzyme activities
Analysis of kinetic data
Complications to the basic rate equation
Effect of temperature on enzyme-catalysed reactions
Effect of pH on enzyme-catalysed reactions
Further reading
Problems
Multisubstrate enzyme kinetics and enzyme inhibition	237	(20)
Use of binding energy in catalysing multisubstrate reactions
Kinetics and mechanisms of two-substrate enzyme reactions
Enzyme inhibition
Mechanistic implications of inhibitor kinetics
Rate equations for inhibition of single-substrate enzyme reactions
Further reading
Problems
Coupled reactions and biochemical pathways	257	(18)
Sequential coupling of chemical reactions
Parallel coupling of chemical reactions
Coupled reactions and biochemical pathways
Kinetic control of biochemical pathways
The need for a systems-based analysis of kinetic control
Metabolic control analysis
Control coefficients
Elasticities
Further reading
Problems
ATOMIC AND MOLECULAR STRUCTURE
Quantum mechanics: particles, waves and the quantisation of energy	275	(16)
The classical picture of matter and energy
Breakdown of the classical picture
The wave--particle duality and wave-packets
Consequences of the wave-packet nature of matter
Localising waves in space gives quantisation of energy
Quantisation of energy in molecules
Occupancy of energy levels
Further reading
Problems
Electrons in atoms	291	(13)
Classical picture of an atom
Wave-theory model of an atom
Allowed electron orbitals and quantum numbers
Electron spin
Pauli exclusion principle
Electron energies
Electronic configurations of atoms and ions
Atomic and ionic properties
Further reading
Problems
Bonding in molecules	304	(21)
Definition of bonding
Types of molecular bonding
Electrons in molecules
d orbitals in transition metal complexes
d-orbital ground-state electronic configurations
Valence electron bonding in molecules
Properties of molecular bonds
Bonding in heteronuclear molecules
Bonding in multi-atom molecules
Further reading
Problems
Interaction of molecules with electromagnetic radiation	325	(15)
Nature of electromagnetic radiation
Absorption of electromagnetic radiation by matter
Fate of excited atoms or molecules
Basics of spectroscopy
Interpreting spectra
Further reading
Problems.
Non-covalent interactions and macromolecular structure	340	(57)
Non-covalent interactions between atoms
Calculating the energies of molecules
The role of solvent interactions: the hydrophobic effect
Thermodynamic stability of structured macromolecules
Cooperativity of macromolecular folding and unfolding
Further reading
Problems
APPENDICES
Appendix 1. Note on units and constants	361	(2)
Appendix 2. Mathematical tools needed for this text	363	(4)
Appendix 3. Answers to problems	367	(30)
Index	397