Introducing Biological Energetics: How Energy and Information Control the Living World PDF
Preview Introducing Biological Energetics: How Energy and Information Control the Living World
Introducing Biological Energetics This page intentionally left blank Introducing Biological Energetics How energy and information control the living world ‘Energy is the queen of the world, and entropy is her shadow’ German physical chemist W. Ostwald (1853–1932) ‘Information flow, not energy per se, is the prime mover of life’ US cell biologist Werner R. Lowenstein NORMAN W. H. CHEETHAM Adjunct Professor University of the Sunshine Coast, Queensland, Australia 1 3 Great Clarendon Street, Oxford OX2 6DP Oxford University Press is a department of the University of Oxford. It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide in Oxford New York Auckland Cape Town Dar es Salaam Hong Kong Karachi Kuala Lumpur Madrid Melbourne Mexico City Nairobi New Delhi Shanghai Taipei Toronto With offices in Argentina Austria Brazil Chile Czech Republic France Greece Guatemala Hungary Italy Japan Poland Portugal Singapore South Korea Switzerland Thailand Turkey Ukraine Vietnam Oxford is a registered trade mark of Oxford University Press in the UK and in certain other countries Published in the United States by Oxford University Press Inc., New York q Norman W. H. Cheetham 2010 The moral rights of the author have been asserted Database right Oxford University Press (maker) First published 2010 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, without the prior permission in writing of Oxford University Press, or as expressly permitted by law, or under terms agreed with the appropriate reprographics rights organization. Enquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above You must not circulate this book in any other binding or cover and you must impose the same condition on any acquirer British Library Cataloguing in Publication Data Data available Library of Congress Cataloging in Publication Data Data available Typeset by SPI Publisher Services, Pondicherry, India Printed in Great Britain on acid-free paper by CPI Antony Rowe, Chippenham, Wiltshire ISBN 978–0–19–957593–0 (Pbk) 978–0–19–959371–2 (Hbk) 1 3 5 7 9 10 8 6 4 2 To Yuki, for her love, patience, and sense of humour This page intentionally left blank Preface There are many ways to look at the complex phenomenon we call life. The more viewpoints we take, the greater the probability we are likely to ‘understand’ it— whatever that means. The same is true of any challenging topic, for example genetics. No one can appreciate its full implications from a single lecture course, a single text, or a single approach. Above all I have tried to make this book accessible. I hope anyone who reads any of it will read all of it. Look on it perhaps as a friendly textbook. To this end I have kept the story as brief as possible without compromising the discussion to the extent of triviality. I have tried to ensure that no specialist scientific terms or concepts have been introduced without at least some explanation, and have tried to minimize the formal side of each science, while retaining much of its rigour. This approach holds inherent dangers. Readers with expertise in a par- ticular area could be affronted that a pet theme has been omitted or dismissed in a few sentences. The more pedantic readership might deplore a perceived lack of depth or background, or the order of presentation. In anticipation of such responses I say, Introducing Biological Energetics is selective rather than defini- tive, in that I could not possibly cover the range of topics chosen in any great depth. Why choose to look at life through the window of energy? The answer prob- ably lies in my background as a professional scientist and teacher. As a student of chemistry, I was interested in things at the molecular level. Given this interest, it was not much of a step to wondering about what actually drives the chemical reactions I studied. Formally, the answer lies largely in the subject of thermo- dynamics. The science of thermodynamics was born during the development of steam engines and has been called ‘the child of the age of steam’. It began as a narrow, very applied area, and even now is sometimes mistakenly thought to be largely about steam engines. My serious introduction to this rather daunting area of physical chemistry was not spectacular. One day at university, I was preparing for a laboratory class. I said to my lecturer in physical chemistry: ‘I didn’t realize there was any thermodynamics involved in the stretching of rubber’. He looked down his long nose and said quietly, as was his way, ‘There’s thermodynamics in everything’. I almost burst out laughing, he was so serious. Of course he was right, but I didn’t really appreciate this until the relevance struck home when I began to study biochemistry. The ways in which organisms manage to access their chem- ical and physical needs for survival are wonderful to contemplate. The pathways involved in extracting energy from a complex foodstuff, directly from sunlight, or from ‘raw’ chemicals in deep-ocean vents, all obey the laws of physics and chemistry. What makes the study so fascinating is that all these processes are viii Preface carried out under the constraints imposed by being part of something alive. This usually means that chemical reactions need to take place in the presence of an excess of water under quite mild conditions of temperature, pressure, and pH. Most living organisms can’t cope with the high temperatures, strong acids, oxidizing agents, and exotic solvents often used by organic chemists. The fact that these constraints have been overcome by natural selection over 3.5 billion years of evolutionary time makes life all the more intriguing. If they hadn’t been overcome, none of us would be here. Contents Introduction 1 1. The Flow of Energy in Living Systems 3 References 10 2. Origins: The Early Earth 11 General references 29 References 29 3. Force and Energy Explored 31 3.1 Gravitational force 36 3.2 The electromagnetic force 40 3.3 The strong nuclear force 43 3.4 The weak nuclear force 43 References 47 4. Which Way? An Introduction to Thermodynamics 48 General references 72 References 72 5. The Building Blocks 73 General references 108 References 108 6. How Fast, How Far? Chemical Kinetics and Equilibrium 109 General references 138 References 138 7. The Strange Story of Water and Oil 139 General references 161 References 161 8. Size Matters: Proteins and Enzymes 162 8.1 Principles of protein structure 162 8.2 Some very special molecules: enzymes 178 8.3 Regulation of enzyme activity 189 8.4 Coenzymes, vitamins, and enzyme classification 192 References 199 9. Molecular Genetics—the Chemical Basis of Heredity 200 General references 222 10. Electron Gymnastics: Energy Revisited 223 10.1 How many ATP molecules are produced when electrons traverse the entire ETC? 233 10.2 What about the rotary engine? 234 References 249
The list of books you might like
