Physical Chemistry: Principles and Applications in Biological Sciences 5th Edition

Book Preface

There is a deep sense of pleasure to be experienced when the patterns and symmetry of  nature are revealed. Physical chemistry provides the methods to discover and understand  these patterns. We think that not only is it important to learn and apply physical chemistry  to biological problems, it may even be fun. In this book, we have tried to capture some of the excitement of making new discoveries and finding answers to fundamental questions.

This is not an encyclopedia of physical chemistry. Rather, we have written this text  specifically with the life-science student in mind. We present a streamlined treatment that  covers the core aspects of biophysical chemistry (thermodynamics and kinetics as well as  quantum mechanics, spectroscopy, and X-ray diffraction), which are of great importance  to students of biology and biochemistry. Essentially all applications of the concepts are  systems of interest to life-science students; nearly all the problems apply to life-science examples.

For the fifth edition, we have extensively revised and updated the treatment of  biophysical chemistry, bringing in theoretical approaches earlier and also updating the  text to current IUPAC conventions. We have added a new chapter on electrochemistry and  expanded our treatment of single molecule methods, quantum mechanics, and magnetic resonance.

Chapter 1 introduces representative areas of active current research in biophysical  chemistry and molecular biology: the human genome, the transfer of genetic information  from DNA to RNA to protein, ion channels, and cell-to-cell communication. We encourage  students to read the current literature to see how the vocabulary and concepts of physical  chemistry are used in solving biological problems.

Chapters 2 through 4 cover the laws of thermodynamics and their applications to  chemical reactions and physical processes. Essentially all of the examples and problems  deal with biochemical and biological systems. For example, after defi ning work as a  force multiplied by the distance moved (the displacement), we discuss the experimental  measurement of the work necessary to stretch a single DNA molecule from its randomcoiled form to an extended rod, introducing the intuitive and accessible concept of  molecular force microscopy. We also include a new and more comprehensive treatment  of heat capacities, beginning with the kinetic theory of gases, which is now treated much  earlier in chapter 2 , and moving systematically to a consideration of what affects the heat  capacity of a protein. Molecular interpretations of energies and entropies are emphasized in each of chapters 2 through 4 . We also introduce isothermal titration calorimetry in  chapter 3 . Despite this new content, the length of chapters 2 through 4 as been reduced by over 30 pages, largely by eliminating redundant material.

In chapter 5 , we show how the thermodynamic laws discussed in chapters 2 through 4  can be explained by a statistical treatment of molecular motion and interactions, and apply  these statistical methods to the conformation of proteins and DNA and the binding of  ligands. This section has been combined with the conceptually-related statistical treatment  of Maxwell-Boltzmann gases and appears much earlier. In chapter 6 , we immediately use  these statistical insights to explain physical phenomena such as phase transitions, ligand binding, and surface and membrane effects.

In chapter 7 , we present a new and integrated treatment of electrical and electrontransfer phenomena in biophysics, starting with classical electrochemistry, and considering  how the chemical processes of electron transfer are linked to the physical processes of ion translocation to explain most of biological energy transduction.

Chapters 8 through 10 cover molecular motion and chemical kinetics. Chapter 8 starts  with a discussion of molecular collisions, random walks, and brownian motion. Fluorescence  microscopic tracking of single protein molecules diffusing in membranes is shown to  beautifully corroborate Einstein’s equation relating average distance traveled by a single  molecule to its bulk diffusion coeffi cient. Following this direct experimental demonstration  of thermal motion of a molecule, we consider the bulk transport of molecules by diffusion,  sedimentation, viscous fl ow, and electrophoresis. The next two chapters deal with general  chemical kinetics and enzyme kinetics, including single-molecule enzyme kinetics.

In the 5th edition, we refl ect the rapidly expanding importance of quantum mechanics  and diverse powerful spectroscopies in understanding molecular biological phenomena  by presenting these subjects in four more focused and augmented chapters. Chapter 11 ,  “Molecular Structures and Interactions: Theory,” now focuses solely on the origins and key  introductory results of quantum theory, including a review of the postulates. Chapter 12 ,  “Molecular Structures and Interactions: Biomolecules,” presents molecular orbital theory,  interactions, and an overview of computational methods applied to macromolecules.  Similarly, the treatment of spectroscopy is now more focused in two separate chapters  on optical ( chapter 13 ) and magnetic ( chapter 14 ) methods, respectively. Chapter 13  increases emphasis on absorption and fl uorescence, and includes new material on protein  IR spectroscopy. Chapter 14 introduces the classical framework for NMR in more detail and covers new methods in multidimensional and diffusion NMR.  Chapter 15 discusses X-ray diffraction, electron microscopy, and scanning microscopies  (such as atomic force microscopy), and emphasizes how structures are determined  experimentally. We added a new section on crystal lattices and symmetry, and expanded the discussion of modern methods such as X-ray imaging and free-electron lasers.

A new appendix in the fi fth edition is an accessible, self-contained, and pragmatic  review of the mathematics expectations in this text. We hope the carefully defi ned scope  of the mathematics (a characteristic of previous editions) will be reassuring in preparing  to study this text.

We are gratified by the number of faculty who have elected to use this book over  the many years since it was first published. We are also grateful for the many students  and faculty who have given us their thoughts and impressions. Such feedback has helped  improve the book from edition to edition. We are particularly grateful to those of our  colleagues who commented on the fifth edition:

Noah W. Allen, III—University of North Carolina, Asheville
Jason Benedict— University of Buffalo
Tim Keiderling— University of Illinois, Chicago
Ruth Ann Murphy— University of Mary Hardin Baylor
Tatyana Smirnova— North Carolina State University
Keith J. Stine— University of Missouri-St. Louis
Gianluigi Veglia— University of Minnesota
Jeff Woodford— Missouri Western State University
Danny Yeager— Texas A&M University
Kazushige Yokoyama— State University of New York, Geneseo
We welcome your comments.
Ignacio Tinoco, Jr.
Kenneth Sauer
James C. Wang
Joseph D. Puglisi
David Rovnyak
Gerard Harbison