Biological Thermodynamics

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Biological Thermodynamics

  1. 1. Cambridge University Press 0521791650 - Biological Thermodynamics - Donald T. Haynie Frontmatter More information Biological Thermodynamics Biological Thermodynamics provides an introduction to the study of energy transformation in the biological sciences. Don Haynie uses an informal writing style to discuss this core subject in a way which will appeal to the interests and needs of undergraduate students of biology and biochemistry. The emphasis throughout the text is on understanding basic concepts and developing problem-solving skills, but mathematical difficulty is kept to a minimum. Each chapter comprises numerous examples taken from differ- ent areas of biochemistry, as well as a broad range of exercises and list of references for further study. Topics covered include energy and its trans- formation, the First Law of Thermodynamics, the Second Law of Thermodynamics, Gibbs free energy, statistical thermodynamics, binding equilibria, reaction kinetics, and a survey of the most exciting areas of bio- logical thermodynamics today, particularly the origin of life. Don Haynie has a B.S. in physics (South Florida) and a Ph.D. in biophysics (Biocalorimetry Center, The Johns Hopkins University). Following post- doctoral research in physical biochemistry at the University of Oxford, he took up a lectureship in biochemistry in the Department of Biomolecular Sciences at the University of Manchester Institute of Science and Technology (UMIST), UK. He has taught thermodynamics, to biology, biochemistry, and engineering students at Johns Hopkins and UMIST, and at Louisiana Tech University, where he is now Associate Professor in the Institute for Micromanufacturing. © Cambridge University Press www.cambridge.org
  2. 2. Cambridge University Press 0521791650 - Biological Thermodynamics - Donald T. Haynie Frontmatter More information BiologicalThermodynamics Donald T. Haynie © Cambridge University Press www.cambridge.org
  3. 3. Cambridge University Press 0521791650 - Biological Thermodynamics - Donald T. Haynie Frontmatter More information PUBLISHED BY THE PRESS SYNDIC ATE OF THE UNIVERSIT Y OF C AMBRIDGE The Pitt Building, Trumpington Street, Cambridge, United Kingdom CAMBRIDGE UNIVERSIT Y PRESS The Edinburgh Building, Cambridge CB2 2RU, UK 40 West 20th Street, New York, NY 10011-4211, USA 477 Williamstown Road, Port Melbourne, VIC 3207, Australia Ruiz de Alarcón 13, 28014 Madrid, Spain Dock House, The Waterfront, Cape Town 8001, South Africa http://www.cambridge.org © Cambridge University Press 2001 This book is in copyright. Subject to statutory exception and to the provisions of relevant collective licensing agreements, no reproduction of any part may take place without the written permission of Cambridge University Press. First published 2001 Reprinted 2003 Printed in the United Kingdom at the University Press, Cambridge Typeface Swift 9.5/12.25pt. System QuarkXPress™ [S E ] A catalogue record for this book is available from the British Library ISBN 0 521 79165 0 hardback ISBN 0 521 79549 4 paperback © Cambridge University Press www.cambridge.org
  4. 4. Cambridge University Press 0521791650 - Biological Thermodynamics - Donald T. Haynie Frontmatter More information For my great-grandfather JOSEPH R AFFEL my grandmother HELENE MINDER and my friend BUD HERSC HEL © Cambridge University Press www.cambridge.org
  5. 5. Cambridge University Press 0521791650 - Biological Thermodynamics - Donald T. Haynie Frontmatter More information The trouble with simple things is that one must understand them very well anonymous © Cambridge University Press www.cambridge.org
  6. 6. Cambridge University Press 0521791650 - Biological Thermodynamics - Donald T. Haynie Frontmatter More information Contents Preface page xi Chapter 1 Energy transformation A. Introduction 1 B. Distribution of energy 5 C. System, boundary, and surroundings 8 D. Animal energy consumption 11 E. Carbon, energy, and life 14 F. References and further reading 15 G. Exercises 16 Chapter 2 The First Law of Thermodynamics A. Introduction 21 B. Internal energy 24 C. Work 26 D. The First Law in operation 29 E. Enthalpy 32 F. Standard state 35 G. Some examples from biochemistry 36 H. Heat capacity 40 I. Energy conservation in the living organism 43 J. References and further reading 43 K. Exercises 45 Chapter 3 The Second Law of Thermodynamics A. Introduction 49 B. Entropy 52 C. Heat engines 56 D. Entropy of the universe 59 E. Isothermal systems 60 F. Protein denaturation 62 G. The Third Law and biology 63 H. Irreversibility and life 64 I. References and further reading 67 J. Exercises 69 Chapter 4 Gibbs free energy – theory A. Introduction 73 B. Equilibrium 76 C. Reversible processes 80 D. Phase transitions 82 E. Chemical potential 85 © Cambridge University Press www.cambridge.org
  7. 7. Cambridge University Press 0521791650 - Biological Thermodynamics - Donald T. Haynie Frontmatter More information viii CONTENTS F. Effect of solutes on boiling points and freezing points 89 G. Ionic solutions 90 H. Equilibrium constant 93 I. Standard state in biochemistry 96 J. Effect of temperature on Keq 98 K. Acids and bases 100 L. Chemical coupling 102 M. Redox reactions 104 N References and further reading 108 O. Exercises 110 Chapter 5 Gibbs free energy – applications A. Introduction 119 B. Photosynthesis, glycolysis, and the citric acid cycle 119 C. Oxidative phosphorylation and ATP hydrolysis 123 D. Substrate cycling 129 E. Osmosis 130 F. Dialysis 136 G. Donnan equilibrium 139 H. Membrane transport 140 I. Enzyme–substrate interaction 144 J. Molecular pharmacology 146 K. Hemoglobin 151 L. Enzyme-linked immunosorbent assay (ELISA) 154 M. DNA 155 N. Polymerase chain reaction (PCR) 159 O. Free energy of transfer of amino acids 161 P. Protein solubility 163 Q. Protein stability 165 R. Protein dynamics 171 S. Non-equilibrium thermodynamics and life 173 T. References and further reading 174 U. Exercises 178 Chapter 6 Statistical thermodynamics A. Introduction 185 B. Diffusion 188 C. Boltzmann distribution 192 D. Partition function 198 E. Analysis of thermodynamic data 200 F. Multistate equilibria 204 G. Protein heat capacity functions 209 H. Cooperative transitions 210 I. ‘Interaction’ free energy 212 J. Helix–coil transition theory 214 K. References and further reading 217 L. Exercises 220 © Cambridge University Press www.cambridge.org
  8. 8. Cambridge University Press 0521791650 - Biological Thermodynamics - Donald T. Haynie Frontmatter More information CONTENTS ix Chapter 7 Binding equilibria A. Introduction 223 B. Single-site model 225 C. Multiple independent sites 226 D. Oxygen transport 231 E. Scatchard plots and Hill plots 235 F. Allosteric regulation 240 G. Proton binding 242 H. References and further reading 245 I. Exercises 247 Chapter 8 Reaction kinetics A. Introduction 251 B. Rate of reaction 254 C. Rate constant and order of reaction 255 D First-order and second-order reactions 257 E. Temperature effects 259 F. Collision theory 261 G. Transition state theory 262 H. Electron transfer kinetics 265 I. Enzyme kinetics 267 J. Inhibition 271 K. Reaction mechanism of lysozyme 273 L. Hydrogen exchange 275 M. Protein folding and pathological misfolding 278 N. Polymerization 281 O. Muscle contraction and molecular motors 284 P. References and further reading 286 Q. Exercises 288 Chapter 9 The frontier of biological thermodynamics A. Introduction 293 B. What is energy? 293 C. The laws of thermodynamics and our universe 296 D. Thermodynamics of small systems (e.g. molecular motors) 297 E. Formation of the first biological macromolecules 298 F. Bacteria 303 G. Energy, information, and life 304 H. Biology and complexity 314 I. The Second Law and evolution 319 J. References and further reading 323 K. Exercises 327 Appendix A. General references 331 Appendix B. Biocalorimetry 335 Appendix C. Useful tables 341 © Cambridge University Press www.cambridge.org
  9. 9. Cambridge University Press 0521791650 - Biological Thermodynamics - Donald T. Haynie Frontmatter More information x CONTENTS Appendix D. BASIC program for computing the intrinsic rate of amide hydrogen exchange from the backbone of a polypeptide 347 Glossary 363 Index of names 373 Subject index 375 © Cambridge University Press www.cambridge.org
  10. 10. Cambridge University Press 0521791650 - Biological Thermodynamics - Donald T. Haynie Frontmatter More information Preface Interest in the biological sciences has never been greater. At the dawn of twenty-first century, biology and biochemistry are captivat- ing the minds of young people in the way that physics did 40–50 years ago. There has been a massive shift in public opinion and in the allocation of resources for university-based research. Break- throughs in genetics, cell biology, and medicine are transforming the way we live, from improving the quality of produce to eradicat- ing disease; they are also stimulating pointed thinking about the origin and meaning of life. Growing awareness of the geometry of life, on length scales extending from an individual organism to a structural element of an individual macromolecule, has led to a reassessment of the principles of design in all the engineering disci- plines, including computation. And a few decades after the first determination at atomic resolution of the structures of double- stranded DNA and proteins, it is becoming increasingly apparent that both thermodynamic and structural information are needed to gain a deep sense of the functional properties of biological macro- molecules. This book is about the thermodynamics of living organisms. It was written primarily for undergraduate university students of the biologi- cal, biochemical and medical sciences. It could also serve as an introduc- tory text for undergraduate students of chemistry or physics who are interested in biology, and for graduate students of biology or biochem- istry who did their first degree in a different subject. The style and depth of presentation reflect my experience learning thermodynamics as an undergraduate student, doing graduate-level research on protein thermodynamics at the Biocalorimetry Center at Johns Hopkins University, teaching thermodynamics to biochemistry undergraduates in the Department of Biomolecular Sciences at the University of Manchester Institute of Science and Technology and to pre-meds at Johns Hopkins, and discussing thermodynamic properties of proteins with colleagues in Oxford Centre for Molecular Sciences. My sense is that an integrated approach to teaching this subject, where the principles of physical chemistry are presented not as a stand- © Cambridge University Press www.cambridge.org
  11. 11. Cambridge University Press 0521791650 - Biological Thermodynamics - Donald T. Haynie Frontmatter More information xii PREFACE alone course but as an aspect of biology, has both strengths and weak- nesses. On the one hand, most biological science students prefer to encounter physical chemistry in the context of learning about living organisms, not in lectures designed for physical chemists. On the other hand, applications-only courses tend to obscure fundamental concepts. The treatment of thermodynamics one finds in general biochemistry textbooks can compound the difficulties, as the subject is usually treated separately, in a single chapter, with applications being touched on only here and there in the remainder of the text. Moreover, most general biochemistry texts are written by scientists who have little or no special training in thermodynamics, making a coherent and integrated presentation of the subject that much more difficult. A result of this is that many students of the biological sciences complete their undergrad- uate study with either a shallow or fragmented knowledge of thermody- namics, arguably the most basic area of all the sciences and engineering. Indeed, many scientists would say that the Second Law of Thermodynamics is the most general idea in science and that energy is its most important concept. It is not difficult to find compelling statements in support of this view. According to Albert Einstein, for example, ‘Classical thermody- namics . . . is the only physical theory of universal content concerning which I am convinced that, within the framework of applicability of its basic concepts, will never be overthrown.’ Einstein, a German– American physicist, lived from 1879 to 1955. He was awarded the Nobel Prize in Physics in 1921 and described as ‘Man of the Century’ by Time magazine in late 1999. Sir Arthur S. Eddington (1882–1944), the eminent British astronomer and physicist, has said, ‘If your theory is found to be against the second law of Thermodynamics I can give you no hope; there is nothing for it but to collapse in deepest humiliation.’ Sir Charles P. Snow, another British physicist, likened lack of knowledge of the Second Law of Thermodynamics to ignorance of Shakespeare, to under- score the importance of thermodynamics to basic awareness of the character of the physical world. Finally, M. V. Volkenstein, member of the Institute of Molecular Biology and the Academy of Sciences of the USSR, has written, ‘A physical consideration of any kind of system, including a living one, starts with its phenomenological, thermody- namic description. Further study adds a molecular content to such a description.’ The composition and style of this book reflect my own approach to teaching thermodynamics. Much of the presentation is informal and qualitative. This is because knowing high-powered mathematics is often quite different from knowing what one would like to use mathe- matics to describe. At the same time, however, a firm grasp of thermo- dynamics and how it can be used can really only be acquired through quantitative problem solving. The text therefore does not avoid expressing ideas in the form of equations where it seems fitting. Each chapter is imbued with l’esprit de géométrie as well as with l’esprit de finesse. In general, the mathematical difficulty of the material increases from beginning to end. Worked examples are provided to © Cambridge University Press www.cambridge.org
  12. 12. Cambridge University Press 0521791650 - Biological Thermodynamics - Donald T. Haynie Frontmatter More information PREFACE xiii illustrate how to use and appreciate the mathematics, and a long list of references and suggestions for further reading are given at the end of each chapter. In addition, each chapter is accompanied by a broad set of study questions. These fall into several categories: brief calculation, extended calculation, multiple choice, analysis of experimental data, short answer, and ‘essay.’ A few of the end-of-chapter questions are open-ended, and it would be difficult to say that a ‘correct’ answer could be given to them. This will, I hope, be seen as more of a strength of the text than a weakness. For the nature of the biological sciences is such that some very ‘important’ aspects of research are only poorly defined or understood. Moreover, every path to a discovery of lasting significance has had its fair share of woolly thinking to cut through. Password-protected access to solutions to problems is available on line at http://chem.nich.edu/homework Several themes run throughout the book, helping to link the various chapters into a unified whole. Among these are the central role of ATP and glucose in life processes, the proteins lysozyme and hemoglobin, the relationship between energy and biological information, and the human dimension of science. The thermodynamics of protein folding/unfolding is used to illustrate a number of points because it is well known to me and because it is of more general significance than some people might think. After all, about 50% of the dry mass of the human body is protein, no cell could function without it, and a logical next step to knowing the amino acid sequence encoded by a gene is pre- dicting the three-dimensional structure of the corresponding func- tional protein. We also draw attention to how thermodynamics has developed over the past several hundred years from contributions from researchers of many different countries and backgrounds. The principal aim of this text is to help students of the biological sci- ences gain a clearer understanding of the basic principles of energy transformation as they apply to living organisms. Like a physiologically meaningful assembly of biological macromolecules, the organization of the text is hierarchical. For students with little or no preparation in thermodynamics, the first four chapters are essential and may in some cases suffice for undergraduate course content. Chapter 1 is introduc- tory. Certain topics of considerable complexity are dealt with only in broad outline here; further details are provided at appropriate points in later chapters. This follows the basic plan of the book, which highlights the unity and primacy of thermodynamic concepts in biological systems and processes and not simply the consistency of specific biolog- ical processes with the laws of thermodynamics. The second and third chapters discuss the First and Second Laws of Thermodynamics, respec- tively. This context provides a natural introduction to two important thermodynamic state functions, enthalpy and entropy. Chapter 4 dis- cusses how these functions are combined in the Gibbs free energy, a sort of hybrid of the First and Second Laws and the main thermodynamic potential function of interest to biological scientists. Chapter 4 also elaborates several basic areas of physical chemistry relevant to biology. In Chapter 5, the concepts developed in Chapter 4 are applied to a wide © Cambridge University Press www.cambridge.org
  13. 13. Cambridge University Press 0521791650 - Biological Thermodynamics - Donald T. Haynie Frontmatter More information xiv PREFACE range of topics in biology and biochemistry, an aim being to give stu- dents a good understanding of the physics behind the biochemical tech- niques they might use in an undergraduate laboratory. Chapters 4 and 5 are intended to allow maximum flexibility in course design, student ability, and instructor preferences. Chapters 6 and 7 focus on the molec- ular interpretation of thermodynamic quantities. Specifically, Chapter 6 introduces and discusses the statistical nature of thermodynamic quantities. In the next chapter these ideas are extended in a broad treat- ment of macromolecular binding, a very common and extremely important class of biochemical phenomenon. Chapter 8, on reaction kinetics, is included in this book for two main reasons: the equilibrium state can be defined as the one in which the forward and reverse rates of reaction are equal, and the rate of reaction, be it of the folding of a protein or the catalysis of a biochemical reaction, is determined by the free energy of the transition state. In this way inclusion of a chapter on reaction kinetics gives a more complete understanding of biological thermodynamics. Finally, Chapter 9 touches on a number of topics at the forefront of biochemical research where thermodynamic concepts are of considerable importance. A note about units. Both joules and calories are used throughout this book. Unlike monetary exchange rates and shares on the stock exchange, the values of which fluctuate constantly, the conversion factor between joules and calories is constant. Moreover, though joules are now more common than calories, one still finds both types of unit in the contemporary literature, and calories predominate in older pub- lications. Furthermore, the instrument one uses to make direct heat measurements is a called a calorimeter not a joulimeter! In view of this it seems fitting that today’s student should be familiar with both types of unit. Three books played a significant role in the preparation of the text: Introduction to Biomolecular Energetics by I. M. Klotz, Foundations of Bioenergetics by H. J. Morowitz, and Energy and Life by J. Wrigglesworth. My interest in biophysics was sparked by the work of Ephraim Katchalsky (not least by his reflections on art and science!) and Max Delbrück, which was brought to my attention by my good friend Bud Herschel. I can only hope that my predecessors will deem my approach to the subject a helpful contribution to thermodynamics education in the bio- logical sciences. The support of several other friends and colleagues proved invalu- able to the project. Joe Marsh provided access to historical materials, lent volumes from his personal library, and encouraged the work from an early stage. Paul C. W. Davies offered me useful tips on science writing. Helpful information was provided by a number of persons of goodwill: Rufus Lumry, Richard Cone, Bertrand Garcia-Moreno Esteva, Alan Eddy, Klaus Bock, Mohan Chellani, Bob Ford, Andy Slade, and Ian Sherman. Van Bloch was an invaluable source of encouragement and good suggestions on writing, presenting, and publishing. I thank Chris Dobson. Norman Duffy, Mike Rao, Alan Cooper, Bertrand Garcia- Moreno Esteva, John Ladbury, Alison Roger, Terry Brown, and several © Cambridge University Press www.cambridge.org
  14. 14. Cambridge University Press 0521791650 - Biological Thermodynamics - Donald T. Haynie Frontmatter More information PREFACE xv anonymous reviewers read parts of the text and provided valuable com- ments. I wish to thank Katrina Halliday, Ward Cooper, Beverley Lawrence and Sue Tuck at Cambridge University Press for the energy and enthusiasm they brought to this project. I am pleased to acknowl- edge Tariq, Khalida, and Sarah Khan for hospitality and kindness during the late stages of manuscript preparation. I am especially grateful to Kathryn, Kathleen, and Bob Doran for constant encouragement and good-heartedness. Every attempt has been made to produce a spotless textbook. I alone am responsible for any infelicities that may have escaped the watchful eyes of our red pens. D. T. H. 15th August 2000 Oxford, England References Eddington, A. S. (1930). The Nature of the Physical World, p. 74. New York: MacMillan. The Editor (2000). Resolutions to enhance confident creativity. Nature, 403, 1. Klein, M. J. (1967). Thermodynamics in Einstein’s Universe. Science, 157, 509. Volkenstein, M. V. (1977). Molecular Biophysics. New York: Academic. © Cambridge University Press www.cambridge.org

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