Lehninger, principles of biochemistry 5th ed d nelson, m cox (w h freeman, 2008) 1

HNI PRINCIPLESOF BIOCHEMISTRY FIFTH EDITION David L Ne lson Professorof Bio chemistry Uniuersity of Wisconsin-Madison Michael M Cox Professor of Bi,ochemistry Uni,uersity of Wi,sconsin-Madi,son l= ANDCOMPANY W.H.FREEMAN N e wY o r k Publisher: SARATENNEY fuecutiveEditor: KATHERINE AHR Senior DevelopmentalEditor: RANDIROSSIGNOL CLARE Associate Dhectotof Marketing: DEBBIE MarketingDirector: JOHNBRITCH SHRINER SeniorMedioEditor: PATRICK McCAFFREY ManagingEditor: PHILIP GELLER ProjectEditor: ELIZABETH PhotoEditor: BIANCA MOSCATELLI PhotoResearcher: DENABFTZ TextandCoverDesigner: VICKITOMASELLI PageMakeup: MARSHA COHEN IIIustrotion Coodinator: SUSANTIMMINS NETWORK GRAPHICS lllustrations: H.ADAMSTEINBERG; MolecularGraphics: H.ADAMSTEINBERG; JEAN-YVES SGRO ROHLOFF Ptoduction Coordinotor: PAULW Composition: APTARA,INC Manufocturing: RRDONNELLEY On the cover: RNA polymeraseII from yeast, bound to DNA and in the act of transcribing it into RNA Imagecreatedby H Adam Steinbergusing PDB ID 1I6Has modi.fledby Seth Darst Library of CongressControl Number: 2007941224 ISBN-13:978-0-7167-7108-1 ISBN-I0: 0-7167-7r08-X @2008by W H Freemanand Company All rights reserved Printed in the United States of America First printing W H Freeman and Company 41 MadisonAvenue New York,NY 10010 Houndmills,BasingstokeRG216XS,England www.whfreeman.com To Our Teachers PauLR Burton Albert Fi,ntuolt Wi,LLi,am P Jencks Eugene P Kennedy Homer Knoss ArtLtur Kornberg L RobertLeltman EarL K, I{elson Dauid E, Sh,eppard Harold B Wti,te DaVid L NelSOn,bornin Fairmont, Minnesora, received his BS in Chemistry and Biology from St Olaf College in 1964 and earned his PhD in Biochemistry at Stanford Medical School under Arthur Kornberg He was a postdoctoral felLowat the Harvard Medical School with Eugene P Kennedy, who was one of Albert Lehninger's first graduate students Nelson joined the faculty of the University of Wisconsin-Madison h 1971 and became a full professor of blochemrstry in 1982 He is the Director of the Center for Biology Education at the University of Wisconsin-Madison Nelson's research has focused on the signal transductions that regulate ciliary motion and exocytosis in the protozoan Parameci,um The enzymes of signal transductions, including a variety ofprotein kinases, are primary targets of study His research group has used enzyme purification, immunological techniques, electron microscopy, genetics, molecuiar biology, and electrophysiologyto study these processes Dave Nelson has a distinguished record as a lecturer and research superuisor For 36 years he has taught an intensive survey of brochemistry for advanced biochemistry undergraduates in the life sciences He has also taught a survey of biochemistry for nursing students, and graduate courses on membrane structure and function and on molecular neurobiology He has sponsored numerous PhD, MS, and undergraduate honors theses, and has received awards for his outstanding teaching, including the Dreyfus Teacher-Scholar Award, the Atwood Distinguished Professorship, and the Unterkofler Excellence in Teaching Award from the University of Wisconsin System.In 1991-1992he was a visiting professor of chemistry and biology at Spelman College His second love is history and in his dotage he has begun to teach the history of biochemistry to r-mdergraduatesand to collect antique scientific instruments MiChagl M COXwasbornin Wlmington, I)elaware In his first biochemistry course,Lehninger's Biochem'istry was a major influence in refocusing his fascination with biology and inspiring him to pursue a career in biochemistry After graduating from the University of Delaware inl974, Cox went to Brandeis University to his doctoral work with MIIiam P Jencks, and then to Stanford in 1979 for postdoctoral study with I Robert Lehman He moved to the University of WisconsinMadison in 1983, and became a full professor of biochemistry in 1992 Cox's doctoral research was on general acid and base catalysis as a model for enz;,,rne-catalyzedreacvl David [ Nelson andMichael M.Cox tions At Stanford,he beganwork on the enzymesinvolvedin geneticrecombination.The work focusedparticularly on the RecAprotein, designingpuriflcation and assaymethodsthat are still in use, and illuminating the processof DNAbranchmigration.Explorationof the en4,.rnesof genetic recombinationhas remained the central themeof his research Mike Cox has coordinateda large and active researchteam at Wisconsin,investigatingthe enzymology, topology,and energeticsof genetic recombination.A primary focus has been the mechanism of RecA protein-mediatedDNA strand exchange,the role of ATP in the RecA system,and the regulationof recombinational DNA repair Part of the researchprogram now focuseson organismsthat exhibit an especiallyrobust capacityfor DNA repair, such asDei,nococcusrad'i,odurans, and the applicationsof those repair systemsto biotechnology.For the past24 yearshe has taught (with DaveNelson)the suwey of biochemistryto undergraduatesand haslectured in graduatecourseson DNA structure and topology,protein-DNAinteractions,and the biochemistryof recombination.A more recent project has been the organizationof a new courseon professionalresponsibilityfor fi.rst-yeargraduatestudents.He has received awards for both his teaching and his research,including the Dreyfus Teacher-ScholarAward and the 1989EIi Lilly Award in BiologicalChemistry His hobbiesinclude gardening,wine collecting,and assisting in the designof laboratorybuildings I n this twenty-flrst century a typical scienceeducation I often leavesthe philosophicalunderpinningsof scienceunstated,or relies on oversimplifieddefinitions.As you contemplatea careerin science,it may be usefulto consideronce againthe terms science, scientist, and scientifie method Science is both a way of thinking about the natural world and the sum of the information and theory that result from such thinking.The power and successof scienceflow directlyfrom its relianceon ideasthat can be tested: information on natural phenomenathat can be observed,measured,and reproducedand theoriesthat havepredictivevalue.The progressof sciencerestson a foundationalassumptionthat is often unstatedbut crucial to the enterprise:that the lawsgoverningforcesand phenomenaexisting in the universe are not subject to change.The NobellaureateJacquesMonodreferredto this underlyingassumptionasthe "postulateof objectivity." The natural world can therefore be understoodby applying a processof inquiry-the scientific method Sciencecould not succeedin a universe that played tricks on us Other than the postulateof objectivity,science makesno inviolate assumptionsabout the natural world.A usefiilscientiflcideais onethat (1) hasbeenor can be reproduciblysubstantiatedand (2) can be used to accuratelypredict new phenomena Scientrflcideastake many forms.The terms that scientists use to describetheseforms havemeaningsquite differentfrom thoseappliedby nonscientists Ahypothesesis an idea or assumptionthat providesa reasonable and testableexplanationfor one or more observations, but it may lack extensiveexperimentalsubstantiation.A sci,enti,fi,ctheorA is much more than a hunch It is an idea that has been substantiatedto some extent and provides an explanationfor a body of experimentalobservations.A theory can be tested and built upon and is thus a basisfor further advanceand innovation.When a scientiflctheory has been repeatedlytested and validatedon manyfronts,it canbe acceptedas a fact In one importantsense,what constitutesscienceor a scientiflc idea is defined by whether or not it is published in the scientiflc literature after peer review by other working scientists.About 16,000peer-reviewed scientific journals worldwide publish some 1.4 million articles eachyear, a continuing rich harvest of information that is the birthright of every human being Scientists are indiredualswho rigorouslyapply the scientific method to understand the natural world Merely having an advanceddegreein a scientiflc discipline doesnot makeone a scientist,nor doesthe lack of such a degreeprevent one from making important scientific contributions.A scientistmust be willing to challenge any idea when new findings demandit The ideas that a scientistacceptsmust be basedon measurable, reproducibleobservations, and the scientistmust report with completehonesty theseobservations The scientific method is actually a collection of paths,all of wtuch may lead to scientificdiscovery.In the hypothesi,sand erperiment path,a scientistposesa hypothesis,then subjectsit to experimentaltest Many of the processesthat biochemistswork with everyday were discoveredin this manner.The DNA structure elucidated by JamesWatsonand FrancisCrick led to the hypothesis that basepairjrg is the basisfor information transfer in po\mucleotide sS,nthesis This hlpothesis helpedinspire the discoveryof DNA and RNA pol5.'rnerases Watsonand Crick produced their DNA structure through a process of model bui,ldi,ng and calculat'ion No actual experimentswere involved, although the model building and calculations used data collectedby other scientists.Many adventurousscientists haveappliedthe processoferp\oration and obseruat'ion as a path to discovery.Historicalvoyagesof discovery (Charles Darwin's 1831 voyage on H.M.S Beagleamongthem) helpedto map the planet,catalog its living occupants,and changethe way we view the world Modern scientists follow a similar path when they explore the ocean depths or launch probes to other planets.An analogof hypothesisand experiment is hypothesi,sand deduct'ion Crick reasoned that there must be an adaptor molecule that facilitated translationof the information in messengerRNA into protein.This adaptorhypothesisled to the discoveryof transfer RNA by MahlonHoaglandand Paul Zamecnik Not all paths to discoveryinvolve planrung.Serendipi,tg often plays a role The discovery of penicilJin by Alexander Fleming in 1928, and of RNA catalysts by ThomasCechin the early 1980s,wereboth chancediscoveries,albeit by scientistswell preparedto exploit them Irnpi,rati,on canalsoleadto important advances.The polymerasechainreaction(PCR),now a centralpart of biotechnology, was developedby Kary Mullis afler a flash of inspration dudng a road trip in northern Califomiain 1983 Thesemany paths to scientiflc discoverycan seem quite different, but they have some important things in common They are focused on the natural world They rely on reproducCbleobseruat'ion anilor erperiment Nl of the ideas,insights, and experimentalfacts that arise from these endeavorscan be tested and reproducedby scientistsan5,wherein the world All can be usedby other scientiststo build new hypothesesand make new discoveries.All lead to information that is properlyincludedin the realm of science.Understanding our universerequires hard work At the sametime, no human endeavoris more exciting and potentially rewarding than trying, and occasionallysucceeding,to understandsomepart of the natural world vtl first edition of Pnnctples oJBi,ochenuistry, v'ritten Albert Lehningertwenty-flveyearsago,hasservedas the starting point and the model for our four subsequent editions.Overthat quarter-centurythe world of biochemistry haschangedenormously yearsago,not a TWenty-flve singlegenomehadbeensequenced, not a singlemembrane proternhad beensolvedby crystallography, and not a sinjust beendishnockout mouse existed RibozJrmes had $e covered, PCR technology introduced, and archaea recognizedasmembersof a kingdomseparatefrom bacteria Now,newgenomicsequences areannouncedweekly, new protern structures even more frequently, and researchershave engineeredthousandsof djfferent lcrockout mice, with enormouspromise for advancesin basic biochemistryphysiology,and medicine.This ffih edition containsthe photographsof 31 Nobellaureateswho have receivedtheirprizesfor Chemistryor for Physiologror Medicine sincethat first edition of Prhrciples of Binchemistry One major challengeof each edition has been to reflect the torrent of new information without making the book overwhelmingfor students having their first encounterwith biochemistry.This hasrequiredmuch careful sifting aimed at emphasizingprinciples while still conveyingthe excitementof current researchand its promisefor the future The cover of this new edition exempli-fles this excitementand promise:in the x-ray structure of RNA polymerase,we seeDNA, RNA, and protein in their informationalroles,in atomrcdimensions,caught in the central act of in-formationtransfer We are at the threshold of a new molecularphysiology in which processessuch as membrane excitation, secretion,hormoneaction,vision, gustation,olfaction, respiration,musclecontraction,and cell movementswill be explicablein molecularterms and will becomeaccessible to genetic dissectionand pharmacologicalmanipulation Knowledgeof the molecular structures of the highly organizedmembrane complexes of oxidative phosphorylation and photophosphorylation,for example, will certainly bring deepenedinsight into those processes, so centralto life (Thesedevelopments make us wish we were young again,just beginningour careers in biochemicalresearchand teaching Our book is not the only thing that has acquired a touch of silver over the years!) In the past two decades,we have striven alwaysto maintain the qualitiesthat made the original Lehninger text a classic-clear wdting, careftrlexplanationsof difflcult concepts,and communicatingto studentsthe ways in which biochemistryis understoodand practicedtoday Wehavewritten togetherfor twenty yearsand taught together for almosttwenty-flve.Our thousandsof students at the Universityof Wisconsin-Madison over thoseyears havebeen an endlesssourceof ideasabout how to present biochemistrymore clearly;they haveenlightenedand rnspired us We hope that this twenty-flfth aruLiversary edition will erLlightenand inspire current studentsof biochemistryeverywhere,and perhapsleadsomeof them to Iovebiochemistryaswe Major Recent Advances in Biochemistry Every chapter has been thoroughly revised and updated to include the most important advancesin biochemistryincluding: r Conceptsof proteomes and proteomics, introducedearlierin the book (Chapter1) r New discussionof amyloid diseasesin the context of protein folding (Chapter 4) r New section on pharmaceuticals developedfrom an understandingof enzymemechanism,using penicillinand HIV proteaseinlLibitorsas examples (Chapter6) r New discussionof sugar analogs as drugs that target viral neuraminidase(Chapter 7) r New material on green fluorescent protein (Chapter9) r New sectionon lipidomics (Chapter10) r w descriptionsof volatile lipids used as signals vi by plants, and of bird feather pigmentsderived from coloredlipids in plant foods (Chapter10) Expandedand updated sectionon lipid rafrts and caveolae to rncludenew material on membrane curvature and the proteins that influenceit, and introducng amphitropic proteins and anmrlar Iipids (Chapter11) New sectionon the emergingrole of ribulose 5-phosphate as a central regulator of $ycolysis (Chapter 15) andgluconeogenesis New Box 16-1, MoonlightingErzymes:Proteins with More Than One Job New sectionon the role of transcriptionfactors (PPARs) in regulationof lipid catabolism (Chapter17) Revisedand updated sectionon fatty acid synthase, including new structural information on FASI (Chapter21) Preface tx Updatedcoverageof the nitrogen cycle, including new Box 22-1, UnusualLife Stylesof the Obscure but Abundant, discussinganammox bacteria (Chapter22New Box 24-2, Epigenetics,Nucleosome Structure,and Histone Variantsdescribingthe role of histone modification and FIGURE 21-3 Thestructure typeI systems offattyacidsynthase nucleosome deposition in the transmissionof New information on the roles of RNA epigeneticinformation in heredity in protein biosynthesis New information on the initiation of replication (Chapter 27) and the dymamicsat the replicationfork, New sectionon riboswitches introducing AAA+ ATPases and their functions (Chapter28) in replication and other aspectsof DNA metabolism(Chapter25) New Box 28-1, Of Fins,Whgs, Beaks,and Things, New sectionon the expandedunderstandingof the roles of RNA in cells (Chapter 26) describingthe cormectionsbetweenevolution and development Biochemical Methods An appreciation of biochemistry often requires an understanding of how biochemical information is obtained Some of the new methodsor updatesdescribed in this editionare: r Circulardicluoism (Chapter4) r Measurementof glycated hemoglobinas an indicator of averagebloodglucoseconcentration, over days,in personswith diabetes (Chapter7) r Useof MALDI-MSin determinationof oligosaccharide structure (Chapter7) r ForensicDNA analysis,a majorupdate coveringmodernSTRanalysis(Chapter 9) r More on microarrays(Chapter9) r Use of tags for protein analysisand purification (Chapter9) r r PET combinedwith CT scansto pinpoint cancer (Chapter14) Glutathione (GSH) G€ne for tusion prctein flcuflt9-12 The useof taggedproteinsin protein purification The use of a CST tag is illustrated(a) Clu(CST)is a smallenzyme(depicted tathione-s-transferase (a Slutahereby the purpleicon)that bindsglutathione at materesidue to whicha Cys-Clydipeptideis attached the carboxylcarbonof theClu sidechain,hencetheabbreviationCSH) (b) The CST tag is fusedto the catr boxyl terminus of the target protein by Senetic engineeringThe taggedprotein is expressedin host cells,and is presentin the crudeextractwhen the cells are lysed The extract is subjectedto chromatography on a column containinga mediumwith immobilized SlutathioneThe CsT{aggedproteinbinds to the 8lutathione,retardinBits migrationthroughthe column, while the other proteinswash through rapidly The elutedfrom the column taggedproteinis subsequently or elevatedsaltconcentration with a solutioncontaining free glutathione I v Express tu8ion Foteh h a cell Add gotein EIub fusion plobin IIGURE 9-12 Chromatinimmunoprecipitationand ChlP-chip experiments(Chapter24) r Developmentof bacterial strainswith altered ge netic codes,for site-specific insertion of novel amino acids into proteins (Chapter 27) x Preface Medically Relevant Examples This icon is used throughoutthe book to denote materialof specialmedicalinterest.As teachers, our goal is for students to learn biochemistryand to understand its relevance to a healthier life and a healthier planet We have included many new examples that relatebiochemistryto medicineand to health issuesin general.Someof the medicalapplicationsnew to this edition are: r r r r r The role of polyunsaturatedfatty acidsand trans fatty acidsin cardiovascular disease(Chapter10) G protein-coupledreceptors(GCPRs)and the range of diseasesfor which drugs targeted to GPCRsare beingusedor developed(Chapter12) G proterns,the regulationof GTPaseactivity, and the medicalconsequences of defectiveG protein function(Chapter12),includingnew Box 12-2, G Proteins:Binary Switchesin Health and Disease Box 12-5,Developmentof ProteinKinaseInhibitors for CancerTleatment Box 14-1,HtghRateof Glycolysisin Tlmors Suggests Targetsfor Chemotherapyand FacrlitatesDiagnosis r Box 15-3, GeneticMutationsThat Leadto Rare Formsof Diabetes r Mutationsin citric acid cycle enzyrnesthat lead to cancer(Chapter16) r Perniciousanemiaand associatedproblemsin strict vegetarians(Chapter 18) r Updatedinformationon cyclooxygenase hhibitors (pain relieversVioxx, Celebrex,Bextra) (Chapter21) r HMG-CoAreductase(Chapter21) and Box 21-3, The Lipid Hypothesisand the Developmentof Statins r Box 24-1, CuringDiseaseby Inhibiting Topoisomerases, describingthe use of topoisomeraseinhibitors in the treatment of bacterial rnfectionsand cancer,including material on ciprofloxacin (the antibiotic effective for anthrax) Special Theme: Understanding Metabolism through 0besity andDiabetes Obesity and its medical consequences-cardiovascular diseaseand diabetes-are fast becomingepidemic in the industrializedworld, and we include new material on the biochemicalconnectionsbetween obesity and health throughout this edition Our focus on diabetes provides an integrating theme throughout the chapterson metabolismand its control, and this will, we hope, inspire some students to find solutions for this disease.Some of the sectionsand boxes that highlight the interplay of metabolism, obesity, and diabetesare: @ Fatty acid oxidatioD Stawation response Fat synthesie and storage and storage Adipokineproduction Fatty acid oxidati Themogenesis r Untreated DiabetesProducesLife-ThreatenineAci dosis(Chapter2) r Box 7-1 , Blood GlucoseMeasurementsin the Diagnosisand T?eatmentof Diabetes,introducing hemoglobinglycation and AGEsand their role in the pathologyof advanceddiabetes Box 11-2,DefectiveGlucoseand WaterT?ansport in TWoFormsof Diabetes FIGURE 23-42 r AdiposeTissueGeneratesGlycerol3-phosphate (Chapter21) by Glyceroneogenesis r GlucoseUptakeIs Deficientin T}pe DiabetesMel Iitus (Chapter14) r DiabetesMellitus Arises from Defectsin Insulin Productionor Action (Chapter23) r KetoneBodiesAre Overproducedin Diabetesand during Starvation (Chapter 17) r r SomeMutationsin MitochondrialGenomesCause Disease(Chapter19) DiabetesCan Resultfrom Defectsin the Mitochon dria ofPancreaticB Cells(Chapter19) Section23.4,Obesityand the Regulationof Body Mass,discussesthe role of adiponectinand insulin sensitivity and tlpe diabetes r Section23.5,Obesity,the MetabolicS;'ndrome,and T\pe Diabetes,includesa discussionof managing type diabeteswith exercise,diet, and medication r r Advances in Teaching Biochemistry 1l-3 WORKED EXAMPII f Revisingtlus textbookis neverjust an updatingexercise.At Ieastasmuch time is spent reexamininghow the core topics of biochemrstryare presented.We haverevisedeachchapterwith an eyeto helpingstudentslearn and masterthe fundamentalsof biochemistry.Studentsencounteringbiochemistryfor the first trmeoften havedifflcultywith two key aspectsof the course:approachingquantitative problemsand drawingon what they learnedin orgarucchemistryto help them understandbiochemistry.Those samestudents must also learn a complex language,with conventionsthat are often unstated.Wehavemadesome major changesin the book to help studentscope with all these challenges: new problem-solvingtools, a focus on organic chemistry foundations, and highlightedkey conventions EnergeticsofPumping bYSYnPort lglumseli, = mtio that can be ': lglucosejour plasma membrme Na*-glucose symachieved by the porter of an epithelial cell, when [Na-]6 is 12 mM, -50 mV [Nat]."1 is 145 ro, the membrme potential is 'C (inside negative), and the temperature is 37 Cahulal,e lhe maimm Soltrtion: Using Equation 11-4 (p 396), we can calcuNa+ late the energy inherent in an electrochemical gradient-that is, the cost of moving one Na- ion up gradientl this AG ' _ R?lnry+ + zr a,r, tNal," We then substitute standardvaluesfor-&, ?, and J, and the given valuesfor [Na-] (expressedas molar concentrations), +l for Z (because Na+ has a positive charge), md 050 V for a,y' Note that the membrane potential is -50 mV (inside negative),so the chmge in potential when m ion moves from inside to outside is 50 mV N e wPr o b l e m-5 o lTvionogl s 45 x 10-' 1.2xto + 1(96,500 JV.mol)(0 050V) AGt : (8 315J/mol K)(3to rcm r New in-text Worked Examples help studentsimprove their quantitativeproblem-solvingskills, taking them through someof the most difficult equations = 112 kJ/mol This AGr is the potential energyper mole of Na- in the Na* $adient that is available to pmp glucose Given that two Na- ions passdom their electrochemicalgradient md into the cell for each glucose canied in by slmport, the energyavailableto pmp mol of Llucose is2 x II2 kJ/mol = 22 kJ/mol We can now calculate the concentrationratio of Elucosethat cm be achieved by this pmp (from Equation l1-3, p 396): r More than 100 new end-of-chapter problems give students further opportunity to practice what they have learned r New Data Analysis Problems (one at the end of eachchapter), tributed by BrianWhite of the Universityof Massachusetts-Boston, en couragestudentsto slmthesizewhat they have learnedand apply their knowledgeto the interpretationof datafrom the literature _ [glucose]r lG, = ft?ln:iLgrucoselour Remnuing, then substitutingthe valuesof AGt,,&,and ?, gives 22.4kJ/mol [g]ucosel* AG, = - o ot 'n n,r E:rs llorot' t