LEHNINGERPRINCIPLESOFBIOCHEMISTRYFIFTHEDITIONDavid L.NelsonProfessorof BiochemistryUniversity of Wisconsin-MadisonMichael M.CoxProfessor of BiochemistryUniversity of Wisconsin-MadisonW.H.FREEMANAND COMPANYNewYork
HNI PRINCIPLES OF BIOCHEMISTRY FIFTH EDITION David L. N e lso n Professor of Bio chemistry Uniu er sity of Wi s c onsin-M adi s on Michael M. Cox Profes sor of Bi,o chemistry Uni,uersity of Wi,sconsin-Madi,son l= W.H. FREEMAN AND COMPANY New York
About theAuthorsDavid L.Nelson,born in Fairmont,Minnesota, received hisBSinChemistry andBiology fron St.OlafCollege in1964 and earned hisPhD in Biochemistry atStanford Medical School under Arthur Kornberg.HewasapostdoctoralfellowattheHarvardMedicalSchoolwith Eugene P. Kennedy, who was one of AlbertLehninger's first graduate students.Nelson joined thefaculty of the University of Wisconsin-Madison in 1971and becameafull professor ofbiochemistryin1982.Heis the Director of the Center for Biology Education atthe Universityof Wisconsin-MadisonNelson's research has focused on the signal trans-ductions that regulate ciliary motion and exocytosis inthe protozoan Paramecium.The enzymes of signaltransductions,including avarietyofproteinkinases,areprimary targets of study.His researchgroup has usedenzyme purification,immunological techniques,elec-tron microscopy, genetics, molecular biology,and elec-David L.Nelson and Michael M.Coxtrophysiology to study these processes.Dave Nelson has a distinguished record as a lecturerand research supervisor.For 36 years he has taught anintensive surveyof biochemistryfor advancedbiochem-tions.At Stanford, hebegan work on theenzymes in-istry undergraduates in the life sciences. He has alsovolved in genetic recombination.The work focused par-taught a survey of biochemistry for nursing studentsticularly ontheRecA protein,designingpurification andand graduate courses on membrane structure and func-assay methods that are still in use, and lluminating thetion and on molecular neurobiology.Hehas sponsoredprocess of DNAbranchmigration.Exploration of the en-numerous PhD, MS, and undergraduate honors theses,zymes of genetic recombination has remained the cen-and has received awards for his outstanding teaching,tral theme of his research.including the Dreyfus Teacher-Scholar Award, theMike Cox has coordinated a large and active re-AtwoodDistinguishedProfessorship,and theUnterkoflersearch team at Wisconsin,investigating the enzymologyExcellence in Teaching Award from the University oftopology, and energetics of genetic recombination. AWisconsin System.In1991-1992hewasavisitingprofes-primary focus has been the mechanism of RecAsor of chemistry and biology at Spelman College.Hisprotein-mediatedDNAstrand exchange,theroleof ATPsecond love is history,and in his dotage he has begun toin the RecA system, and the regulation of recombina-teach the history of biochemistry to undergraduates andtional DNA repair. Part of the research program nowto collectantiquescientific instruments.focuses on organisrns that exhibit an especially robustcapacity for DNA repair, such as Deinococcus radiodu-Michael M.Cox was born in Wilmington,Delawarerans,andtheapplicationsof thoserepairsvstemstoIn hisfirstbiochemistry course,Lehninger'sBiochembiotechnology.Forthepast24years hehastaught (withistry was amajor influenceinrefocusinghis fascinationDave Nelson)the survey of biochemistry to undergradu-withbiology and inspiringhim to pursue a career inbio-ates and has lectured ingraduate courses on DNA struc-chemistry. After graduating from the University ofture and topology,protein-DNA interactions, and theDelaware in1974,Cox went to Brandeis University to dobiochemistryofrecombination.Amorerecentprojecthis doctoral work with William P.Jencks, and then tohas been the organization of a new course on profes-Stanford in 1979 for postdoctoral studywith I.Robertsionalresponsibilityforfirst-veargraduatestudents.HeLehman. He moved to the University of Wisconsin-has received awards for both his teaching and hisMadison in1983,and becamea full professor ofresearch,including theDreyfusTeacher-ScholarAwardbiochemistry in 1992.and the1989 Eli Lilly Award inBiological Chemistry.HisCox's doctoral research was on general acid andhobbies includegardening,wine collecting,and assistingbase catalysis as a model for enzyme-catalyzed reac-in the design of laboratory buildings
DaVid L. NelSOn, born in 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 felLow at 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 electrophysiology to 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 1991-1992 he 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-mdergraduates and to collect antique scientific instruments. MiChagl M. COX was born in 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 do 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-catalyzed reactions. At Stanford, he began work on the enzymes involved in genetic recombination. The work focused particularly on the RecA protein, designing puriflcation and assay methods that are still in use, and illuminating the process of DNA branch migration. Exploration of the en- 4,.rnes of genetic recombination has remained the central theme of his research. Mike Cox has coordinated a large and active research team at Wisconsin, investigating the enzymology, topology, and energetics of genetic recombination. A primary focus has been the mechanism of RecA protein-mediated DNA strand exchange, the role of ATP in the RecA system, and the regulation of recombinational DNA repair. Part of the research program now focuses on organisms that exhibit an especially robust capacity for DNA repair, such as Dei,nococcus rad'i,odurans, and the applications of those repair systems to biotechnology. For the past 24 years he has taught (with Dave Nelson) the suwey of biochemistry to undergraduates and has lectured in graduate courses on DNA structure and topology, protein-DNA interactions, and the biochemistry of recombination. A more recent project has been the organization of a new course on professional responsibility for fi.rst-year graduate students. He has received awards for both his teaching and his research, including the Dreyfus Teacher-Scholar Award and the 1989 EIi Lilly Award in Biological Chemistry His hobbies include gardening, wine collecting, and assisting in the design of laboratory buildings. v l David [.Nelson and Michael M. Cox
A NoteontheNatureof Sciencenthistwenty-firstcentury,atypical scienceeducationreproducible observations,and the scientistmust reportoften leaves the philosophical underpinnings of sci-these observations with completehonesty.ence unstated, or relies on oversimplified definitions.AsThe scientifie method is actually a collection ofyou contemplatea career in science,it maybe useful topaths,all ofwhich maylead to scientific discovery.In theconsider once again the terins science, scientist, andhypothesis and experiment path,a scientist poses a hy-scientific methodpothesis, then subjects it to experimental test. Many ofScience isboth a way of thinking about the naturaltheprocesses thatbiochemistswork with everydaywereworld and thesumof theinformation and theorythatre-discoveredinthismanner.TheDNAstructureelucidatedsult fron such thinking.The power and success of sci-byJamesWatsonandFrancis Crick ledto thehypothesisenceflowdirectlyfrom itsrelianceon ideas thatcanbethat base pairing is the basis for information transfer intested: information on natural phenomena that can bepolynucleotide synthesis.This hypothesis helped inspireobserved,measured, and reproduced and theories thatthediscovery of DNAand RNApolymerases.have predictive value.The progress of science rests on aWatson and Crick produced their DNA structurefoundational assumption that is often unstated but cru-through a process of model building and calcula-cial to the enterprise:that the laws governing forces andtion, No actual experiments were involved, althoughphenomena existing in the universe are not subject tothe model building and calculations used data colchange.The Nobel laureate Jacques Monod referred tolected by other scientists.Many adventurous scientiststhis underlying assumption as the“postulate of objectivhaveappliedtheprocess ofecplorationandobserva-ity."The natural world can therefore be understood bytion as a path to discovery. Historical voyages of dis-applying a process of inquiry-the scientific methodcovery (Charles Darwin's 1831 voyage on H.M.SScience could not succeed in a universe that playedBeagleamongthem)helped tomaptheplanet, catalogtricks onus.Other than thepostulateof objectivity,sciits living occupants, and change the way we view theence makes no inviolate assumptions about thenaturalworld.Modern scientists followa sirnilarpath whenworld.A useful scientific idea is one that (D) has been orthey explore the ocean depths or launch probes tocan be reproducibly substantiated and (2) can be usedotherplanets.Ananalog of hypothesis and experimenttoaccuratelypredictnewphenormena.is hypothesis and deduction. Crick reasoned thatScientific ideas take manyforms. The terms that sci-there must be an adaptor molecule that facilitatedentistsusetodescribetheseforms havemeanings quitetranslation oftheinformationin messenger RNAintodifferentfromthoseappliedbynonscientists.Ahypoth-protein.This adaptor hypothesis led to the discovery ofesis is an idea orassumption that providesareasonabletransferRNAbyMahlon Hoagland andPaul Zamecnikandtestableexplanationforoneormoreobservations,Notallpaths todiscovery involveplanning.Serendip-but itmaylackextensive experimental substantiation.Aity often plays a role.The discovery of penicillin byscientific theoryis much more than a hunch.Itis anAlexander Fleming in1928,and ofRNAcatalysts byidea that has been substantiated to some extent andThomasCechin theearly1980s,werebothchancediscov-providesan explanationforabodyof experimental oberies,albeitby scientistswell prepared toexploit them.servations. A theory can be tested and built upon and isInspirationcan alsolead to importantadvances.Thepoly-thus a basis for further advance and innovation. When amerasechainreaction(PCR),nowacentralpartofbiotech-scientific theory has been repeatedly tested and vali-nology, was developed by Kary Mullis after a flash ofdated on many fronts,it can be accepted as a fact.inspiration duringaroadtripin northernCalifornia in1983.In one important sense,what constitutes scienceorThese rnany paths to scientific discovery can seema scientific idea is defined by whether or not it is pub-quite different, but they have sone important thingslished in the scientific literature after peer review byin common.They are focused on the natural world.other working scientists.About 16,000 peer-reviewedThey rely on reproducibleobservationand/or experi-scientific journals worldwidepublish some 1.4millionment.All oftheideas,insights,andexperimentalfactsarticles each year,a continuing rich harvest of informa-that arise from these endeavors can be tested andtion that is the birthright of every human being.reproduced by scientists anywhere in the world. All canSeientists are individuals who rigorously apply thebeusedbyother scientists tobuild newhypotheses andscientific method to understand the natural worldmake new discoveries.All lead to information that isMerely having an advanced degree in a scientific disciproperly included in the realn of science.Understand-pline does not make one a scientist, nor does the lack ofing our universe requires hard work. At the same time,such a degree prevent one from making important sci-no hunan endeavoris more exciting and potentially re-entific contributions.Ascientistmust be willing to chal-warding than trying,and occasionallysucceeding,tounlenge any idea when new findings demand it.The ideasderstand somepart of thenatural world.that a scientist accepts must be based on measurable,vii
I n this twenty-flrst century a typical science education I often leaves the philosophical underpinnings of science unstated, or relies on oversimplified definitions. As you contemplate a career in science, it may be useful to consider once again the 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 success of science flow directly from its reliance on ideas that can be tested: information on natural phenomena that can be observed, measured, and reproduced and theories that have predictive value. The progress of science rests on a foundational assumption that is often unstated but crucial to the enterprise: that the laws governing forces and phenomena existing in the universe are not subject to change. The Nobel laureate Jacques Monod referred to this underlying assumption as the "postulate of objectivity." The natural world can therefore be understood by applying a process of inquiry-the scientific method. Science could not succeed in a universe that played tricks on us. Other than the postulate of objectivity, science makes no inviolate assumptions about the natural world. A usefiil scientiflc idea is one that (1) has been or can be reproducibly substantiated and (2) can be used to accurately predict new phenomena. Scientrflc ideas take many forms. The terms that scientists use to describe these forms have meanings quite different from those applied by nonscientists. Ahypotheses is an idea or assumption that provides a reasonable and testable explanation for one or more observations, but it may lack extensive experimental substantiation. A sci,enti,fi,c theorA is much more than a hunch. It is an idea that has been substantiated to some extent and provides an explanation for a body of experimental observations. A theory can be tested and built upon and is thus a basis for further advance and innovation. When a scientiflc theory has been repeatedly tested and validated on many fronts, it can be accepted as a fact. In one important sense, what constitutes science or a scientiflc idea is defined by whether or not it is published in the scientiflc literature after peer review by other working scientists. About 16,000 peer-reviewed scientific journals worldwide publish some 1.4 million articles each year, a continuing rich harvest of information that is the birthright of every human being. Scientists are indireduals who rigorously apply the scientific method to understand the natural world. Merely having an advanced degree in a scientiflc discipline does not make one a scientist, nor does the lack of such a degree prevent one from making important scientific contributions. A scientist must be willing to challenge any idea when new findings demand it. The ideas that a scientist accepts must be based on measurable, reproducible observations, and the scientist must report these observations with complete honesty. The scientific method is actually a collection of paths, all of wtuch may lead to scientific discovery. In the hypothesi,s and erperiment path, a scientist poses a hypothesis, then subjects it to experimental test. Many of the processes that biochemists work with every day were discovered in this manner. The DNA structure elucidated by James Watson and Francis Crick led to the hypothesis that base pairjrg is the basis for information transfer in po\mucleotide sS,nthesis. This hlpothesis helped inspire the discovery of DNA and RNA pol5.'rnerases. Watson and Crick produced their DNA structure through a process of model bui,ldi,ng and calculat'ion. No actual experiments were involved, although the model building and calculations used data collected by other scientists. Many adventurous scientists have applied the process oferp\oration and obseruat'ion as a path to discovery. Historical voyages of discovery (Charles Darwin's 1831 voyage on H.M.S. Beagle among them) helped to map the planet, catalog its living occupants, and change the way we view the world. Modern scientists follow a similar path when they explore the ocean depths or launch probes to other planets. An analog of hypothesis and experiment is hypothesi,s and deduct'ion. Crick reasoned that there must be an adaptor molecule that facilitated translation of the information in messenger RNA into protein. This adaptor hypothesis led to the discovery of transfer RNA by Mahlon Hoagland and Paul Zamecnik. Not all paths to discovery involve planrung. Serendipi,tg often plays a role. The discovery of penicilJin by Alexander Fleming in 1928, and of RNA catalysts by Thomas Cech in the early 1980s, were both chance discoveries, albeit by scientists well prepared to exploit them. Irnpi,rati,on can also lead to important advances. The polymerase chain reaction (PCR), now a central part of biotechnology, was developed by Kary Mullis afler a flash of inspration dudng a road trip in northern Califomia in 1983. These many paths to scientiflc discovery can seem quite different, but they have some important things in common. They are focused on the natural world. They rely on reproducCble obseruat'ion anilor erperiment. Nl of the ideas, insights, and experimental facts that arise from these endeavors can be tested and reproduced by scientists an5,where in the world. All can be used by other scientists to build new hypotheses and make new discoveries. All lead to information that is properly included in the realm of science. Understanding our universe requires hard work. At the same time, no human endeavor is more exciting and potentially rewarding than trying, and occasionally succeeding, to understand some part of the natural world. vtl
Prefacehefirstedition ofPrinciplesof Biochemistry,writtenWeareat the threshold of a newmolecular physiolIbyAlbert Lehningertwenty-fiveyears ago,has servedasogy in which processes such as membrane excitationthe starting point and the model for ourfour subsequentsecretion,hormone action,vision,gustation,olfaction,editions.Over that quarter-century, the world ofbiochem-respiration,muscle contraction.and cell movements willistryhas changedenormously.Twenty-fiveyears ago,notabe explicable in molecular terms and will become acces-single genome had been sequenced, not a single membranesibletogeneticdissectionandpharmacological manipu-proteinhadbeen solved by crystallography,andnotasin-lation.Knowledge of the molecular structures of thegleknockout mouse existed.Ribozymeshad justbeen dis-highly organized membrane complexes of oxidativecovered,PCR technology introduced,and archaeaphosphorylation and photophosphorylation,for exam-recognized asmembersofakingdomseparatefrombac-ple, will certainly bring deepened insight into thoseteria.Now, new genomic sequences are announced weekly,processes, so central to life. (These developments makenew protein structures even more frequently,and re-us wish we were young again, just beginning our careerssearchers have engineered thousands of differentknock-inbiochemical researchand teaching.Our book isnotout mice,with enormous promise for advancesin basicthe only thing that has acquired a touch of silver overbiochemistry, physiology, and medicine. This fifth editionthe years!)contains the photographs of 31 Nobel laureateswhohaveIn the past two decades, we havestrivenalways toreceivedtheirprizesforChemistryorforPhysiologyorMed-maintain the qualities that made the original Lehningericinesincethatfirstedition of Principlesof Biochemistry.texta classic-clearwriting,careful explanations of diffi-One major challenge of each edition has been to re-cult concepts,and communicating to studentsthewaysflect thetorrent ofnewinformationwithoutmakingthein which biochemistry is understood and practiced today.book overwhelming for students having theirfirst en-We have written together for twenty years and taught to-counter with biochemistry.This has required much care-gether for almost twenty-five.Our thousands of studentsful sifting aimed at emphasizing principles while stillat the University of Wisconsin-Madison over those yearsconveying the excitement of current research and itshavebeenan endless sourceofideas abouthowtoprespromisefor the future.The cover of this newedition ex-entbiochemistrymoreclearly:theyhaveenlightenedandemplifies this excitement and promise:in thex-ray struc-inspired us.We hope that this twenty-fifth anniversaryture of RNA polymerase, we see DNA, RNA, and proteinedition will enlighten and inspire current students of bio-in theirinformationalroles,inatomicdimensions,caughtchemistry everywhere,and perhapslead some ofthem toin the central act of information transfer.lovebiochemistryas wedo.Major Recent Advances in BiochemistryEvery chapter has been thoroughly revised and up-by plants,and ofbirdfeatherpigments deriveddated to include the most important advances in bio-fromcolored lipidsinplantfoods (Chapter10)chemistry including:Expanded andupdated section on lipidraftsandcaveolae to include newmaterial onmembraneConcepts of proteomes and proteomics,curvatureand theproteinsthatinfluenceit.andintroduced earlier in thebook (Chapter1)introducingamphitropicproteinsand annularNew discussion of amyloid diseases inthelipids (Chapter11)contextofproteinfolding (Chapter 4)Newsection on theemerging role of ribuloseNewsectiononpharmaceuticalsdevelopedfrom5-phosphate as a central regulator of glycolysisan understanding of enzymemechanism,usingandgluconeogenesis (Chapter15)penicillin and HIVprotease inhibitors as examplesNewBox16-1,MoonlightingEnzymes:Proteins(Chapter6)with More Than One Job New discussion of sugar analogs as drugs thatNew section on therole of transcription factorstarget viral neuraminidase (Chapter7)(PPARs)inregulationof lipidcatabolismNew material on green fluorescent protein(Chapter17)(Chapter9)Revised and updated section on fatty acidNew section on lipidomics (Chapter 10)synthase,including newstructural informationNewdescriptions of volatile lipids used as signalsonFASI(Chapter21)vili
first edition of Pnnctples oJ Bi,ochenuistry, v'ritten Albert Lehninger twenty-flve years ago, has served as the starting point and the model for our four subsequent editions. Over that quarter-century the world of biochemistry has changed enormously. TWenty-flve years ago, not a single genome had been sequenced, not a single membrane protern had been solved by crystallography, and not a sin- $e hnockout mouse existed. RibozJrmes had just been discovered, PCR technology introduced, and archaea recognized as members of a kingdom separate from bacteria Now, new genomic sequences are announced weekly, new protern structures even more frequently, and researchers have engineered thousands of djfferent lcrockout mice, with enormous promise for advances in basic biochemistry physiology, and medicine. This ffih edition contains the photographs of 31 Nobel laureates who have received theirprizes for Chemistry or for Physiologr or Medicine since that first edition of Prhrciples of Binchemistry. One major challenge of each edition has been to reflect the torrent of new information without making the book overwhelming for students having their first encounter with biochemistry. This has required much careful sifting aimed at emphasizing principles while still conveying the excitement of current research and its promise for the future. The cover of this new edition exempli-fles this excitement and promise: in the x-ray structure of RNA polymerase, we see DNA, RNA, and protein in their informational roles, in atomrc dimensions, caught in the central act of in-formation transfer. Major Recent Advances in Biochemistry Every chapter has been thoroughly revised and updated to include the most important advances in biochemistry including: r Concepts of proteomes and proteomics, introduced earlier in the book (Chapter 1) r New discussion of amyloid diseases in the context of protein folding (Chapter 4) r New section on pharmaceuticals developed from an understanding of enzyme mechanism, using penicillin and HIV protease inlLibitors as examples (Chapter 6) r New discussion of sugar analogs as drugs that target viral neuraminidase (Chapter 7) r New material on green fluorescent protein (Chapter 9) r New section on lipidomics (Chapter 10) r w descriptions of volatile lipids used as signals vi We are at the threshold of a new molecular physiology in which processes such as membrane excitation, secretion, hormone action, vision, gustation, olfaction, respiration, muscle contraction, and cell movements will be explicable in molecular terms and will become accessible to genetic dissection and pharmacological manipulation. Knowledge of the molecular structures of the highly organized membrane complexes of oxidative phosphorylation and photophosphorylation, for example, will certainly bring deepened insight into those processes, so central to life. (These developments make us wish we were young again, just beginning our careers in biochemical research and 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 always to maintain the qualities that made the original Lehninger text a classic-clear wdting, careftrl explanations of difflcult concepts, and communicating to students the ways in which biochemistry is understood and practiced today. We have written together for twenty years and taught together for almost twenty-flve. Our thousands of students at the University of Wisconsin-Madison over those years have been an endless source of ideas about how to present biochemistry more clearly; they have enlightened and rnspired us. We hope that this twenty-flfth aruLiversary edition will erLlighten and inspire current students of biochemistry everywhere, and perhaps lead some of them to Iove biochemistry as we do. by plants, and of bird feather pigments derived from colored lipids in plant foods (Chapter 10) Expanded and updated section on lipid rafrts and caveolae to rnclude new material on membrane curvature and the proteins that influence it, and introducng amphitropic proteins and anmrlar Iipids (Chapter 11) New section on the emerging role of ribulose 5-phosphate as a central regulator of $ycolysis and gluconeogenesis (Chapter 15) New Box 16-1, Moonlighting Erzymes: Proteins with More Than One Job New section on the role of transcription factors (PPARs) in regulation of lipid catabolism (Chapter 17) Revised and updated section on fatty acid synthase, including new structural information on FAS I (Chapter 21)
PrefaceUpdated coverage of(a)(b)the nitrogen cycle,KRincluding newBoxDH22-1, Unusual LifeMATStyles of the Obscurebut Abundant,discussing anammoxDHWheebacteria (Chapter 22)KR-New Box 24-2,Epigenetics,NucleosomeMATKSStructure,and HistoneVariants describing theKSMATDHERKRACPErole of histonemodification andFIGURE 21-3 The structure offatty acid synthase type Isystems.nucleosome depositioninthetransmissionofNew information on theroles of RNAepigeneticinformationin heredityin protein biosynthesisNewinformationontheinitiationof replication(Chapter 27)and thedynamicsat thereplicationfork,Newsectiononriboswitches-introducingAAA+ATPases and theirfunctions(Chapter 28)inreplicationand otheraspectsofDNAmetabolism (Chapter 25)New Box 28-1, Of Fins, Wings,Beaks,and ThingsNewsection ontheexpandedunderstandingofdescribingtheconnections betweenevolutionBtheroles of RNAin cells (Chapter 26)anddevelopmentBiochemical Methods(b)(a)Gene fortarget proteinGlutathioneGla-Op-G!An appreciation of biochemistry oftenGemefarCST(GSH)requires an understanding of how bio-chemical information is obtained. SomeGenefor fasion proteitGlutathioe-S-ranferase(GST)of the newmethods or updates describedFiGURE9-12 The use of tagged proteins in protein purifi-in this edition are:cation.Theuse ofa GST tag is ilustrated, (a) Glutathione-S-transferase (GST) is a small enzyme (depictedhere by the purple icon) that binds glutathione (a gluta-Circular dichroism (Chapter4)materesiduetowhichaCys-Glydipeptideisatached atProre codl extthe carboxyl carbon of the Clu side chain, hence the ab-MeasurementofglycatedatftheBretetemtbreviation GSH). (b)The GST tag is fused to thecar.hemoglobin as an indicatorofboxyl terminus of the target protein by geneticaveragebloodglucoseconcentration,engineering,The tagged protein is expressed in hostcells, and is present in the crude extract when the cellsover days,inpersons with diabetesare lysed.Theextract is subjected to chromatographyAdd proteinmediu(Chapter7)on a column containing a medium with immobilizedto columnGSTtglutathione.The GST-tagged protein binds to the gluUseof MALDI-MS in determination oftathione, retarding its migration through the columnoligosaccharidestructure(Chapter7)whie the other proteins wash through rapidly.Thetagged protein is subsequentiy eluted from the columnForensicDNA analysis,amajor updatewithasolutioncontainingelevated saltconcentrationofree glutathione.covering modern STR analysis (Chapter9)More onmicroarrays (Chapter9)Use of tags for protein analysis andpurification (Chapter9)Elute fusion proteinPETcombinedwith新FIGURE9-12CT scans to pinpoint cancer(Chapter 14)Development of bacterial strainswith alteredge图netic codes, for site-specific insertion of novelChromatin immunoprecipitation and ChiP-chipamino acids intoproteins (Chapter27)experiments (Chapter24)
Updated coverage of the nitrogen cycle, including new Box 22-1, Unusual Life Styles of the Obscure but Abundant, discussing anammox bacteria (Chapter22- New Box 24-2, Epigenetics, Nucleosome Structure, and Histone Variants describing the role of histone modification and nucleosome deposition in the transmission of epigenetic information in heredity New information on the initiation of replication and the dymamics at the replication fork, introducing AAA+ ATPases and their functions in replication and other aspects of DNA metabolism (Chapter 25) New section on the expanded understanding of the roles of RNA in cells (Chapter 26) Biochemical Methods An appreciation of biochemistry often requires an understanding of how biochemical information is obtained. Some of the new methods or updates described in this edition are: r Circular dicluoism (Chapter 4) r Measurement of glycated hemoglobin as an indicator of average blood glucose concentration, over days, in persons with diabetes (Chapter 7) r Use of MALDI-MS in determination of oligosaccharide structure (Chapter 7) r Forensic DNA analysis, a major update covering modern STR analysis (Chapter 9) r More on microarrays (Chapter 9) r Use of tags for protein analysis and purification (Chapter 9) r PET combined with CT scans to pinpoint cancer (Chapter 14) r Chromatin immunoprecipitation and ChlP-chip experiments (Chapter 24) Preface FIGURE 21-3 The structure offatty acid synthase type I systems. New information on the roles of RNA in protein biosynthesis (Chapter 27) New section on riboswitches (Chapter 28) New Box 28-1, Of Fins, Whgs, Beaks, and Things, describing the cormections between evolution and development tx r Development of bacterial strains with altered ge netic codes, for site-specific insertion of novel amino acids into proteins (Chapter 27) Glutathione (GSH) G€ne for tusion prctein I v Express tu8ion Foteh h a cell flcuflt 9-12 The use of tagged proteins in protein purification. The use of a CST tag is illustrated (a) Clutathione-s-transferase (CST) is a small enzyme (depicted here by the purple icon) that binds glutathione (a Slutamate residue to which a Cys-Cly dipeptide is attached at the carboxyl carbon of the Clu side chain, hence the abbreviation CSH) (b) The CST tag is fused to the catr boxyl terminus of the target protein by Senetic engineering The tagged protein is expressed in host cells, and is present in the crude extract when the cells are lysed The extract is subjected to chromatography on a column containing a medium with immobilized Slutathione The CsT{agged protein binds to the 8lutathione, retardinB its migration through the column, while the other proteins wash through rapidly The tagged protein is subsequently eluted from the column with a solution containing elevated salt concentration or free glutathione Add gotein EIub fusion plobin IIGURE 9-12