Molecules and Life: An Introduction to Molecular Biology PDF
Preview Molecules and Life: An Introduction to Molecular Biology
MOLECULES AND LIFE An Introduction to Molecular Biology MOLECULES AND LIFE An Introduction to Molecular Biology Mikhail V. Vol'kenshtein Institute of Molecular Biology Academy of Sciences of the USSR, Moscow Translated from the Russian by Serge N. Timasheff Graduate Department of Biochemistry Brandeis University Waltham, Massachusetts <±'PLENUM PRESS· NEW YORK-LONDON The Russian text, originally published by Nauka Press in Moscow in 1965, has been extensively revised by the author for this edition. The present translation is published under an agreement with Mezhdunarodnaya Kniga, the Soviet book export agency. MuxaU.1 BAa{}UJlUp08U~ BOAhl<eHmmetht MOJleKY JIbI 11 )IU13Hb MOLEKULY I ZHIZN' MOLECULES AND LIFE library of Congress Catalog Card Number 66-22787 ISBN-13: 978-1-4684-1727-2 e-ISBN-13: 978-1-4684-1725-8 001: 10.1007/978-1-4684-1725-8 © 1970 Plenum Press, New York Softcover reprint of the hardcover 1s t edition 1970 A Division of Plenum Publishing Corporation 227 West 17th Street, New York, N.Y. 10011 United Kingdom edition published by Plenum Press, London A Division of Plenum Publishing Corporation, ltd. Donington House, 30 Norfolk Street, London W.C.2, England All rights reserved No part of this publication may be reproduced in any form without written permission from the publisher This book is dedicated to S. I. Alenikova-Vol'kenshtein PREFACE TO THE TRANSLATION The Russian edition of this book was published in the Fall of 1965; the manuscript had been finished a year earlier. Since then, many changes ha ve taken place in molecular biology. No other field of science is currently undergoing as rapid a development. As a result, this book has been extensively revised for the translation, and much new material has been introduced. And yet, even this version will to some extent be obsolete at the time the translation appears in print. This, of course, cannot be helped. I believe, however, that the basic concepts of molecular biophysics which are the subject of this book will remain significant for a considerable length of time. M. V. Vol'kenshtein vii Nature is not what you believe~- It is neither a mold nor a spiritless face. It has a soul, it has freedom, It has love, it has a tongue. F. I. TYUTCHEV Nature is not a temple, but a workshop, in which man is the laborer. I. s. TURGENEV PREFACE TO THE RUSSIAN EDITION Nature has been described as a "work of beauty and love" by the Russian poet Tyutchev, and as a "workshop" by Turgenev. Are these two descrip tions mutually contradictory? Must we wonder at the beauty and charm of living nature, at the soft aroma of a rose, at the flight of a butterfly, at the thoughts of man, or are these amazing phenomena the rightful subjects of a scholarly examination? Nature is a magnificent workshop in which the development of matter under strict laws has led to the creation of living organisms, of highly complicated systems, characterized by an amazing structural and functional coordination. The culmination of this development on earth is the human mind, which at present can not only understand the laws of life, but can actively interfere with the surrounding nature and modify it to man's benefit. This is the aim of material science. True science, however, cannot exist without an esthetic appreciation of the objects examined. That very soul and freedom of nature, of which the Russian poet sings, from a scientist's point of view are expressions ofthe laws of biology, physics, and chemistry. This does not, however, render them any less attractive and interesting. This book has for its purpose the introduction to molecular bio physics. Molecular biophysics is, on one hand, a part of molecular physics and, on the other hand, a part of molecular biology, a new realm of science, developed during the last decades. The joint efforts of biologists, physicists, and chemists have made it possible to unravel the essence of a number of the basic phenomena of life, starting from the structure and properties of molecules which form organisms, and principally of proteins and nucleic ix x PREFACE TO THE RUSSIAN EDITION acids. The achievements of molecular biology testify to the success of material science in a realm which, until recently, appeared totally enig matic and mysterious. Further scientific developments should bring to mankind vast developments both in theoretical knowledge and in practical applications, namely, in agriculture, medicine, and technology. The purpose of this book is to explain molecular biophysics to all who might wish to learn about it, to biologists, to physicists, to chemists. This book contains descriptive sections, as well as sections devoted to rigorous mathematical treatment ofa number of problems, some of which have been studied by the author and his collaborators. These sections may be omitted during a first reading. Each chapter has a selected bibliography. This book is far from an exhaustive treatise on molecular biophysics. It deals principally with questions related to the structures and functions of proteins and nucleic acids. M. V. Vol'kenshtein Leningrad, September, 1964 CONTENTS Chapter 1 Physics and Biology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Physics and Life. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Molecular Physics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Molecular Biophysics ..... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Thermodynamics and Biology. . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 Information Theory. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Chapter 2 Cells, Viruses, and Heredity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 The Living Cell. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 Cell Division. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 Viruses and Bacteriophages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 Basic Laws of Genetics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 Mutations and Mutability. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 Genetics of Bacteria and Phages . . . . . . . . . . . . . . . . . . . . . . . . . . 66 Chapter 3 Biological Molecules. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 Amino Acids and Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 Asymmetry of Biological Molecules ....................... 87 Primary Structure of Proteins ............................ 94 Nucleic Acids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 Some Biochemical Processes in the Cell. . . . . . . . . . . . . . . . . . . . 109 Chapter 4 Physics of Macromolecules. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123 Physical Properties of Macromolecules .................... 123 Rotational-Isomeric Theory of Macromolecules. . . . . . . . . . . . . 132 Macromolecules-Cooperative Systems. . . . . . . . . . . . . . . . . . . . 138 xi xii CONTENTS Crystalline Polymers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145 Methods for Studying Macromolecules in Solution. . . . . . . . . . 152 Polyelectrolytes ........................................ 159 Chapter 5 The Physics of Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165 Secondary Structure of Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . 165 Tertiary and Supramolecular Structures of Proteins. . . . . . . . . . 176 Interactions Which Determine the Three-Dimensional Structure of Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185 Conformational Transitions of Proteins. . . . . . . . . . . . . . . . . . . . 193 Theory of Helix-Coil Transitions. . . . . . . . . . . . . . . . . . . . . . . . . . 199 Optical Properties of Proteins and Polypeptides. . . . . . . . . . . . . 207 Optical Activity of Polypeptide Chains. . . . . . . . . . . . . . . . . . . . . 218 Anomalous Dispersion of Magneto-Optical Rotation.. . . . . . . . 228 Chapter 6 The Physics of Nucleic Acids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233 Biological Role of Nucleic Acids. . . . . . . . . . . . . . . . . . . . . . . . . . 233 Secondary Structure of DNA, RNA, and Polynucleotides . . . . . 239 Denaturation of DNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254 Renaturation of DNA and Forces Which Stabilize the Double Helix.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265 DNA Reduplication. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273 Statistical Physics and Kinetics of DNA Reduplication. . . . . . . 286 Chapter 7 Protein Synthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301 Problems of the Genetic Code . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301 Matrix Synthesis of Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309 The Genetic Code ...................................... 322 Point Mutations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 336 Problems of Regulation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 344 Chapter 8 Biological Specificity and Structure of Molecules. . . . . . . . . . . . . . 357 Immunity.. . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . .. . . . . . . . . . . . 357 Antibodies and Antigens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367 Enzyme Reactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 377 Nature of Enzymatic Action. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 386 Allostery and Oxygenation of Hemoglobin.... . . . . . . . . . . . . . . 397 Nucleoproteins and Synapsis of Chromosomes. . . . . . . . . . . . . . 407 Chapter 9 Mechanochemical Processes............................... 417 The Nature of Mechanochemical Processes. . . . . . . . . . . . . . . . . 417 Muscle Action. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 425 CONTENTS xiii Molecular Theories of Muscle Action. . . . . . . . . . . . . . . . . . . . . . 435 Motion of Cells and Mitosis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451 Chapter 10 Problems of Molecular Biophysics. . . . . . . . . . . . . . . . . . . . . . . . . . . 459 Macromolecules and Biology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 459 Molecular Biophysics and Quantum Mechanics. . . . . . . . . . . . . 464 Chapter 11 Conclusion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471 References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 475 Index. . . . . .. . . .. . . .. . .. . . . . . . .. . . . . . . . . . . .. . . . . .. . . .. .. . 505
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