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? copernic- ium ? 6d107s2 About the cover image: the chemical connection The cover shows a cheetah (Acinonyx jubatus), which can run at speeds of up to 110 kilometres per hour. Such energy-consuming processes are ultimately powered by the high-energy molecule, adenosine triphosphate (ATP). During acceleration, the cheetah uses ATP at a rate of around 55 g per second. This corresponds to a rate of consumption around 40 times greater than your current rate of consumption of ATP as you sit reading this (which is a rate of around just 1.4 g per second). The design of limbs is different in cheetahs as compared with humans; these differences give the cheetah the ability to run using significantly less energy than humans. Indeed, as an approximation, the ATP consumed when a human sprinter runs 100 m would be enough to power a cheetah for a far greater distance – somewhere between 500 m to 1 km. The efficient anatomical design of the cheetah leg is reflected in interesting ways: the special prosthetic lower legs used by the South African amputee athlete Oscar Pistorius are known as ‘cheetahs’. We learn more about the concept of energy, and the energy of biochemical processes in Chapter 13. We encounter ATP, a critically important molecule in biological systems, many times throughout this book, beginning with the opening paragraphs of Chapter 1. Chemistry for the Biosciences The essential concepts SECOND EDITION Jonathan Crowe Oxford, UK Tony Bradshaw Oxford Brookes University, Oxford, UK 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 © Jonathan Crowe and Tony Bradshaw, 2010 The moral rights of the authors have been asserted Database right Oxford University Press (maker) First published 2006 Second edition 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 MPS Limited, A Macmillan Company Printed in Italy on acid-free paper by L.E.G.O. S.p.A. ISBN 978–0–19–957087–4 10 9 8 7 6 5 4 3 2 1 JWC: For Mum, Nick, and Christina, and the latest generation: Aimee, Samuel, Jacques, Kenai, and Sebastian. TKB: For Mum, and the family who were always there; and for my newly discovered American family. Physical quantities commonly used in chemistry Physical quantity Symbol SI unit Amount of substance, chemical amount n mol Atomic mass amu (atomic mass unit) Molar mass M kg mol21 Molecular weight M r Atomic weight A r Concentration of B [B] mol L21 Wavelength l metre, m Base SI units Physical quantity Symbol SI unit Length l metre, m Mass m kilogram, kg Time t seconds, s Thermodynamic temperature T kelvin, K Other physical quantities Physical quantity SI unit Area m2 Volume m3 Force newton, N Energy joule, J Pressure pascal, Pa Prefixes to form the names and symbols of the decimal multiples and submultiples of SI units Multiple Prefix Symbol 10215 femto f 10212 pico p 1029 nano n 1026 micro m 1023 milli m 1022 centi c ↑ Getting smaller 1021 deci d ↓ Getting larger 10 deca da 102 hecto h 103 kilo k 106 mega M 109 giga G Contents at a glance Periodic table of the elements i Acknowledgements xix Welcome to the book xx 1 Introduction: why biologists need chemistry 1 2 Atoms: the foundations of life 10 3 Compounds and chemical bonding: bringing atoms together 38 4 Molecular interactions: holding it all together 82 5 Organic compounds 1: the framework of life 120 6 Organic compounds 2: adding function to the framework of life 151 7 Biological macromolecules: providing life’s infrastructure 185 8 Molecular shape and structure 1: from atoms to small molecules 218 9 Molecular shape and structure 2: the shape of large molecules 247 10 Isomerism: generating chemical variety 278 11 Chemical analysis 1: how do we know what is there? 319 12 Chemical analysis 2: how do we know how much is there? 373 13 Energy: what makes reactions go? 410 14 Kinetics: what affects the speed of a reaction? 459 15 Equilibria: how far do reactions go? 498 16 Acids, bases, and the aqueous environment: the medium of life 538 17 Chemical reactions 1: bringing molecules to life 583 18 Chemical reactions 2: reaction mechanisms driving the chemistry of life 609 Epilogue 657 Bibliography 658 Answers to self-check questions 660 Index 665 This page intentionally left blank Contents Periodic table of the elements i Acknowledgements xix Welcome to the book xx 1 Introduction: why biologists need chemistry 1 1.1 Science: revealing our world 2 I’m a biologist: what has chemistry to do with me? 3 1.2 The essential concepts 4 1.3 The language of chemistry 7 Units: making sense of numbers 8 Symbols 9 2 Atoms: the foundations of life 10 2.1 The chemical elements 10 2.2 Atomic composition 12 Protons, electrons, and electrical charge 13 Identifying the composition of an atom: atomic number and mass number 14 The formation of ions 15 Isotopes: varying the number of neutrons 17 Relative abundances and atomic weight 18 Protons and chemical identity 21 2.3 Atomic structure 22 Atomic orbitals 22 2.4 The energy of atoms 24 Orbitals and energy levels 24 Filling up orbitals–the building-up principle 25 The filling of subshells 27 Moving between orbitals: electron excitation 29 Energy levels and quantization 32 2.5 Valence shells and valence electrons 33 Valence electrons and the underlying logic of the periodic table 35 The variety of life: not so varied after all? 36