BIOPHYSICS

An Introduction Biophysics An Introduction

by CHRISTIAAN SYBESMA

Kluwer Academic Publishers DORDRECHT / BOSTON / LONDON Library of Congress Cataloging in Publication Data

Sybesma. C. Biophysics. an introduction I by Christiaan Sybesma. p. cm. Rev. ed. of: An i ntroduct i on to b i ophys i cs. 1977.

1. B1ophys1cs. I. Sybesma. C. Introduction to biophysics. II. Title. OH505.S857 1989 574.1·91--dc19 88-30781 CIP

ISBN-13: 978-0-7923-0030-4 e-ISBN-13: 978-94-009-2239-6 DOl: 10.1007/978-94-009-2239-6

Second printing 1995

Published by Kluwer Academic Publishers, P.O. Box 17,3300 AA Dordrecht, The Netherlands

Kluwer Academic Publishers incorporates the publishing programmes of D. Reidel, Martinus Nijhoff, Dr W. Junk and MTP Press.

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In all other countries, sold and distributed by Kluwer Academic Publishers Group, P.O. Box 322, 3300 AH Dordrecht, The Netherlands.

All rights Reserved © 1989 by Kluwer Academic Publishers Softcover reprint of the hardcover I st edition 1989 No part of the material protected by this copyright notice may be reproduced or utilized in any form or by any means, electronic or mechanical induding photocopying, recording or by any information storage and retrieval system, without written permission from the copyright owner. Contents

Preface lX

l. Introduction 1.1 What is biophysics I l.2 The fundamental principles of biology 3

2. Biological structures 7 2.1 The structures of life 7 2.2 The morphology of cells 11 2.3 The biological macromolecules 18 2.4 Membranes 29 2.5 Cell evolution 34

3. Physical principles and methods in biology 37 3.1 The electronic structure of atoms 37 3.2 The structure of molecules and molecular complexes 44 3.3 Absorption and emission spectroscopy 59 3.4 Infrared and Raman spectroscopy 70 3.5 Magnetic resonances 76 3.6 Size and shape of biological macromolecules 85 3.7 X-ray crystal structure analysis 94

4. Structure and function of proteins and nucleic acids 109 4.1 The structure of proteins 109 4.2 Enzymes 112 4.3 Recognition proteins 119 4.4 The genetic systyem 124 4.5 Regulation and control 131 4.6 Recombinant DNA 136

5. Biological energy conversion 143 5.1 The biological energy flow 143 5.2 Adenosine triphosphate in coupled reactions; pyridine nucleotides 146 5.3 Fermentation and glycolysis 151 5.4 The citric acid cycle 153 5.5 Respiration 158

6. Photosynthesis 167 6.1 Photosynthetic structures 167 6.2 Transfer and trapping of excitation energy 170 6.3 Photosynthetic electron transport in higher plants and algae 178 6.4 Photosynthetic electron transport in prokaryotes 183 6.5 Reaction centers 185 6.6 Carbon fixation 190

7. Biological transport processes 195 7.1 Passive and active transport 195 7.2 Osmotic equilibrium 196 7.3 Ionic equilibrium 198 7.4 Flow across membranes 201 7.5 Transport mechanisms 205

8. Membrane-bound energy transduction 213 8.1 The high-energy intermediate 213 8.2 The chemiosmotic model 214 8.3 Proton translocation 218 8.4 pH gradient and membrane potential 220 8.5 The proton-translocating ATPase 225

9. Biophysics of nerves 229 9.1 Nerves 229 9.2 The action potential 230 9.3 Synapses 234 9.4 Information processing in neuronal systems 237

10. Biophysics of contractility 239 10.1 Intracellular motion 239 10.2 Cellular motion 240 10.3 Muscular contraction 242 10.4 The energetics of contraction 251

11. Biophysics of sensory systems 255 ILl The transmission of information 255 11.2 The visual receptor 259 11.3 The otic receptors 270 11.4 The chemical, somatic, and visceral receptors 276

VI 12. Theoretical biology 281 12.1 Physical concepts and biology 281 12.2 Nonequilibrium thermodynamics 282 12.3 Modeling 284 12.4 Cybernetics 285 12.5 Generalizations in biology 288

Appendix I. Some elements of quantum mechanics 291 ALI The principle of quantization and the uncertainty principle 291

Appendix II. Elements of equilibrium thermodynamics 297

All. 1 Definitions 297 AII.2 First and second laws of thermodynamics 298 AII.3 Entropy 301 AII.4 Thermodynamic potentials 303 AILS The chemical and the electrochemical potentials 304 AII.6 The standard free energy of a chemical reaction 307 All. 7 Oxidation-reduction potentials 308

Index 313

VB Preface

Today, courses on biophysics are taught in almost all universities in the world, often in separate biophysics departments or divisions. This reflects the enormous growth of the field, even though the problem of its formal definition remains unsettled. In spite of this lack of definition, biophysics, which can be considered as an amalgamation of the biological and the physical sciences, is recognized as a major scientific activity that has led to spectacular developments in biology. It has increased our knowledge of biological systems to such an extent that even industrial and commercial interests are now beginning to put their stamps on biological research. A major part of these developments took place during the last two decades. Therefore, an introductory textbook on biophysics that was published a dozen years ago (c. Sybesma, An Introduction to Biophysics, Academic Press, 1977) no longer could fulfil " ... the need for a comprehensive but elementary textbook ... -" (R. Cammack, Nature 272 (1978), 96). However, because of the increased proliferation of biophysics into higher education, the need for introductory course texts on biophysics is stronger than ever. This fact, together with valuable comments of many readers, have encouraged me to revise the original book. The basic conception of this new textbook is the same as that of the original book: biophysics is considered as an approach to biology from the conceptual viewpoint of the physical scientist. It is an integrating scientific activity, rather than just an application of physics or physical chemistry to biology. Like in the original book, the major emphasis is on fundamental biological problems and not so much on problems related to medical physics or biotechnology, although, obviously, reference to the latter sometimes could not be avoided. This new version has twelve chapters. After an introductory chapter, in which the relation between the physical sciences and biology is discussed and an approach to biology based on the concepts of the physical sciences is developed, the universal aspects of the structures of life, the cell and its components, are described in Chapter 2. In this chapter, new insights about cell structure, including those on cytoskeleton, are described and the discussion about membranes is substantially extended. Chapter 3 brings together a description of the physical aspects of (bio )molecular structure and of physical methods used in biophysical (biochemical) research. The reason for treating these two topics together in one chapter is that, after all, the physics of molecular structure lies at the basis of many methods of biophysical measurement. Discussions of techniques now widely in use, such as Raman spectroscopy, chromatography, gel electrophoresis, and magnetic resonance spectroscopy, have been included, as well as a somewhat enlarged and more thorough section on X-ray diffraction analysis. Chapter 4 then discusses molecular and su• permolecular structure and function of proteins and nucleic acids; it contains also a short description of recombinant DNA technology. Chapters 5 to 8 describe the energy converting apparatus and membrane transport. A chapter on the biophysics of nerves (Chapter 9) then precedes discussions of contraction (Chapter 10) and of sensory systems (Chapter 11). In the latter chapter a description of the latest developments in our knowledge about signal trans• mission is included. The final chapter deals with theoretical biology, an area of biology that emerged much as a result of the physical sciences-approach to biology. Its impact on biology may be considerable, not only because it improves our understanding of existing problems but also because it often leads to and determines the direction of experimental biophysical research. An attempt is made to keep the subject matter of the book strictly on an introductory level without sacrificing too much of the rigor in the treatment. The book is aimed at undergraduate or first year graduate students with a major in physics and/or chemistry, who wish to get acquainted with biophysics in order to be able to determine which area of the field they want to explore in depth. Some knowledge of elementary calculus, quantum mechanics, thermodynamics and some physical chemistry is assumed. If such a background is lacking, readers may find some help in the two appendices on the concepts of quantum mechanics and (equilibrium) thermodynamics. I already referred to the many comments I received on the previous book, comments which were an important factor in my decision to rewrite it. A number of these comments included valuable suggestions for which I am particularly grateful. To mention all those who were instrumental in the preparation of this text by name would be impossible. I feel, however, that special thanks are due to Mrs. Saskia Vandenbranden-Laame, who pains• takingly took care of the wide diversity of illustrations, and to Mrs. Martine De Valck-Van de Perre, who did so much to put the many versions of the text on floppy. A final word to my readers: my intention in writing this book was to convey the notion that scientific activity, nowadays, can only be successful if it transgresses the boundaries between the disciplines which in the past were so rigidly distinct. For, indeed, biophysics is a scientific activity that does not just overlap with several of the classic disciplines but that integrates them into a science that surpasses those disciplines. If I have conveyed such a notion, I may also have given a deeper meaning to K.S. Cole's somewhat ironic, but good-natured, definition of biophysics: "Biophysics includes everything that is interesting and excludes everything that is not".

C.S. Brussels, May 1989

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