This page intentionally left blank Biological Thermodynamics Biological Thermodynamics provides an introduction to the study of energy transformation in the biological sciences. Don Haynie uses an informal writingstyletodiscussthiscoresubjectinawaywhichwillappealtothe interestsandneedsofundergraduatestudentsofbiologyandbiochemistry. Theemphasisthroughoutthetextisonunderstandingbasicconceptsand developingproblem-solvingskills,butmathematicaldifficultyiskepttoa minimum.Eachchaptercomprisesnumerousexamplestakenfromdiffer- entareasofbiochemistry,aswellasabroadrangeofexercisesandlistof references for further study. Topics covered include energy and its trans- formation, the First Law of Thermodynamics, the Second Law of Thermodynamics,Gibbsfreeenergy,statisticalthermodynamics,binding equilibria,reactionkinetics,andasurveyofthemostexcitingareasofbio- logicalthermodynamicstoday,particularlytheoriginoflife. DonHayniehasaB.S.inphysics(SouthFlorida)andaPh.D.inbiophysics (Biocalorimetry Center, The Johns Hopkins University). Following post- doctoralresearchinphysicalbiochemistryattheUniversityofOxford,he tookupalectureshipinbiochemistryintheDepartmentofBiomolecular SciencesattheUniversityofManchesterInstituteofScienceandTechnology (UMIST),UK.Hehastaughtthermodynamics,tobiology,biochemistry,and engineeringstudentsatJohnsHopkinsandUMIST,andatLouisianaTech University, where he is now Associate Professor in the Institute for Micromanufacturing. BiologicalThermodynamics Donald T. Haynie           The Pitt Building, Trumpington Street, Cambridge, United Kingdom    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 2004 First published in printed format 2001 ISBN 0-511-03157-2 eBook (Adobe Reader) ISBN 0-521-79165-0 hardback ISBN 0-521-79549-4 paperback First published 2001 Reprinted 2003 Formygreat-grandfather JOSEPH RAFFEL mygrandmother HELENE MINDER andmyfriend BUD HERSCHEL Thetroublewithsimplethingsisthatonemustunderstandthemverywell anonymous Contents Preface pagexi Chapter1 Energytransformation A. Introduction 1 B. Distributionofenergy 5 C. System,boundary,andsurroundings 8 D. Animalenergyconsumption 11 E. Carbon,energy,andlife 14 F. Referencesandfurtherreading 15 G. Exercises 16 Chapter2 TheFirstLawofThermodynamics A. Introduction 21 B. Internalenergy 24 C. Work 26 D. TheFirstLawinoperation 29 E. Enthalpy 32 F. Standardstate 35 G. Someexamplesfrombiochemistry 36 H. Heatcapacity 40 I. Energyconservationinthelivingorganism 43 J. Referencesandfurtherreading 43 K. Exercises 45 Chapter3 TheSecondLawofThermodynamics A. Introduction 49 B. Entropy 52 C. Heatengines 56 D. Entropyoftheuniverse 59 E. Isothermalsystems 60 F. Proteindenaturation 62 G. TheThirdLawandbiology 63 H. Irreversibilityandlife 64 I. Referencesandfurtherreading 67 J. Exercises 69 Chapter4 Gibbsfreeenergy–theory A. Introduction 73 B. Equilibrium 76 C. Reversibleprocesses 80 D. Phasetransitions 82 E. Chemicalpotential 85 viii CONTENTS F. Effectofsolutesonboilingpointsandfreezingpoints 89 G. Ionicsolutions 90 H. Equilibriumconstant 93 I. Standardstateinbiochemistry 96 J. EffectoftemperatureonK 98 eq K. Acidsandbases 100 L. Chemicalcoupling 102 M. Redoxreactions 104 N Referencesandfurtherreading 108 O. Exercises 110 Chapter5 Gibbsfreeenergy–applications A. Introduction 119 B. Photosynthesis,glycolysis,andthecitricacidcycle 119 C. OxidativephosphorylationandATPhydrolysis 123 D. Substratecycling 129 E. Osmosis 130 F. Dialysis 136 G. Donnanequilibrium 139 H. Membranetransport 140 I. Enzyme–substrateinteraction 144 J. Molecularpharmacology 146 K. Hemoglobin 151 L. Enzyme-linkedimmunosorbentassay(ELISA) 154 M. DNA 155 N. Polymerasechainreaction(PCR) 159 O. Freeenergyoftransferofaminoacids 161 P. Proteinsolubility 163 Q. Proteinstability 165 R. Proteindynamics 171 S. Non-equilibriumthermodynamicsandlife 173 T. Referencesandfurtherreading 174 U. Exercises 178 Chapter6 Statisticalthermodynamics A. Introduction 185 B. Diffusion 188 C. Boltzmanndistribution 192 D. Partitionfunction 198 E. Analysisofthermodynamicdata 200 F. Multistateequilibria 204 G. Proteinheatcapacityfunctions 209 H. Cooperativetransitions 210 I. ‘Interaction’freeenergy 212 J. Helix–coiltransitiontheory 214 K. Referencesandfurtherreading 217 L. Exercises 220