Contentsin Brie - libcatalog.embl.de
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[ xiv] Pre fac e r-. 1A Genetic Foundations 27 Genetic Continuity Is Ves ted in Single DNA Molecules 27 The Struc tu re of DNA Allows for Its Replication and Repair with Near-Perfect.Fidelity 28 The Linear Sequ ence in DNA Encodes Proteins with Three-Dimensional Structures 29 1.1 Cellular Foundations 2 Cells Are t he Structural and Functional Units of All Living Organisms 3 Cellular Dimens ions Are Limited by Diffusion There Are Three Distinct Domains of Life 4 Escherichia coli Is the Most-Studied Bacterium 5 Eukaryotic Cells Have a Variety of Membra nous Organelles, Which Can Be Isolated for Study 7 The Cytoplasm Is Organized by the Cytoskeleton and Is Highly Dynamic 8 Cells Build Supramolecular Structures n In Vitro Studies May Overlook Important Interactions among Molecu les 10 1 1 The Foundations ofB iochemi stry 1.2 Chemical Foundations 11 Biomolecules Are Compounds of Carh on with a Variety of Fun ctional Groups 11 Cells Contain a Universal Set of Small Molecules 13 Box 1-1 Molecular Weight, Molecular Mas s,and T heir Correct Units 14 Macromolecules Are the Major Constituen ts of Cells 14 Three-Dimensional Structure Is Described by Configuration and Conformation 15 Box 1-2 louis Pasteur and Optical Activity: In V ino , Veritas 17 Int eractions between Biorno leculos Are Stereospecific 18 1.3 Physical Foundations 19 Living Organisms Exist in a Dynamic Steady State, Never at Equilibrium with Their Surroundings 20 Organisms T ran sform Energy and Matter from Their Surroundings 20 Box 1-3 Entropy: The Ad vantagesofBe ing Di sorganized 21 The Flow of Electrons Provides Energy for Organisms 22 Creating and Maintaining Order Requires Work and Energy 22 Energy Coupling Links Reactions in Biology 22 [{ I' ll and .1Go Are Measures of a Reaction's Tendency to Proceed Spontaneously 24 Enzymes Promote Sequences of Chemical Reac tions 25 Metabolism Is Regulated to Achieve Balance and Economy 26 Preface v iii The Foundations of Biochemistry I STRUCTURE AND CATALYSIS 41 2 Water 43 3 Amino Aclds, Peptides, an d Prote ins 71 4T he Ihree-Dimens ional Struct u re of Proteins 113 5 Protein Function 153 6 Enzymes 1B3 7 Carbohydrates and Glycobio logy 235 B Nucleotides a nd Nucle ic Aclds 271 9 DNA-Based Info rmation Techno log ies 303 10 Lipids 343 11 Biological Membranes and Transport 371 12 Biosigna ling 417 II BIOENERGETICS AND METABOLISM 48S 13 Bioenergetics a nd B iochemical Reaction Types 489 14 Glycolysis, G l uconeogenes is,and the Pentose Phosphate Pathway 527 15 Princlples of Metabolic Regula tion 569 16 The Citric Acid Cycle 6 15 17 FattyAcld Cata bolism 647 18 Amino Acld Ox idatio n and the Productio n of Urea 673 19 Oxidat ive Phosp ho ry lation an d Photo p hosphory lat ion 707 20 Ca rbo hyd rate Biosynthesis in Pl ants an d Bacteria 773 21 Lipid Biosynt hesis 8 05 22 Bi osyn thesis of Ami no Aclds, N ucl eotldes,and Relate d Mo lecules 85 1 23 Hormona l Regulation and Integ rat io n of Mam malia n Metabolism 901 III INFORMATION PATHWAYS 945 24 Genes an dC hromosomes 947 25 DNA Metabo lism 975 26 RNA Metabolism 1021 27 Protein Meta bo lism 1 065 28 Reg u lation of Gene Exp ress io n 1115 Conte nts in B rie Appendix ACommon Abbreviationsin the Biochemical Res earch Literature A-I Appendix BAbbreviatedSolutions to ProblemsAS-I Glossary G- I Credits C- I IndexI -I Scott C. Mohr, Boston U niversity Kimberly Mowry, Brown University Leisha Mullins, Texas A&MUniversity Sewite Negash, California State University, Long Beach Allen W.Nicholson, Temple Univers ity Hiroshi Nikaido, University oj California, Berkeley James Ntambi, University oj Wisconsin-1Vfadison Timothy F. Os borne, University of California, Iruine Jose R. I'erez-Casttneira, Univ ersi ty oj Seville, Sp ain Ter ry Platt, Univ er sity qf Rochester We ndy Pogozelski, State Unioersitu oj New York at Geneseo Jon athan Poppe r, Univ ersi ty oj Wisconsin-Madison Thom as Poulos, University oj California, Irvine Jack Preiss, Micniaan State Univers ity Anna Radominsk a-Pandya, University oj Arkansas Ron Raines, University QfWisconsin-Madison Tom A. Rapoport, Harvard Medical School Jas on J. Reddick, University oj North Carolina, Greensboro Mary Roberts, Boston College Ingrid K. Ruf Univ er sity oj Calif ornia, Irvine Aboozar Soleirnan t, Tehran U niv ersi ty, Ir an Mark Spaller, Wayne State Unio ersuu Step hen Spiro, University of Tex as at Dallas Narasimha Sreerama, Colorado State University Jon D. Stewar t, University oj Florida Koni Stone, California State Unioersuu, Stanislaus Jon H. St ult zfus, Michigan State University Jeremy Thorner, University of California, Berkeley Dean R. Tolan, Boston University Sandr a 1. Turchi, Millersville University Manuel Varela, Eastern New Mexico University Bob Warburt on , Shepherd University Tracy Ware, Salem Stale College Susan Weintra ub, University oj T e:ras, Health Science Center Michael Yaffe, Massacnusetts Institute of Techn ology We lac k th e s pace here to acknowledge all the other individuals wh ose s pecial efforts went into this book. We offer instead our sincere t hanks -and th e finished book that they helped guide to comp let ion. We, of co urse ,a ssume full resp onsibility for errors at fact or emphasis. We want especially to thank our students at the- University of Wisconsin-Madison for their numerous com- ments and suggestions. If something in the book does not work, tliey are never shy about letting us know it. We are grateful to the stu dents and staff of our research groups and of the Center for Biology Education, who helped us balance the competing demands on our time; to our colleagues in the Department of Biochemistry at t. he University of Wisconsin-Madison, who helped us with advice and criticism; and tothe many students and teachers who have written to suggest ways of improving the book. We hope our readers will continue to provide input for future editions. Finally, we ex press our deepest ap preciation to our wives, Brook and Beth, and our families, who sho wed extraordinary patience with, and supp ort for, our book writing. David L. Nelson Michael Ivl. Cox Madison, Wisconsin J anuary 2008 colleague. We feel very fortunate to have such gifted part- ners as Brook, Shelley,Adam, and Jean-Yves on our team. We are also deeply indebted to Brian White of the Uni- versity of Massa chusetts-Boston, who wrote the new data analysis problems at the end of each chapter. Many colleagues played a spec ial role through their inte rest in the pr oject and their timely input. Prominent among these are Laurens And erson of the University of Wisconsin- Madison; Jeffrey D. Esko of the University of California, San Diego; Jack Kirsch and his students at the University of California, Berkeley; and Dana Aswad, Shiou-Chuan (Sheryl) Tsai, Michael G. Cumsky, and the ir colleag ues (listed below) at the University of California, Irvine . Many others he lped us shape this fif th edition with their comments, suggestions,and criticisms. To all of them, we are deeply grateful: Richard M. Amasino, University of Wisconsin-Madison Louise E. Anderson, University oj Illinois at Chicago Cheryl Bailey, Univ ersity oj Nebraska, Lincoln Kenneth Balazovich, University oj Michigan Thomas O. Baldwin, Unive rsity oj A rizon a Vahe Bandarian, University of Arizona Eugene Barber, University oj Rochester Sebasti an Y . Bednarek, Univ ersity oj Wisconsin-Madison. Ramachandra Bhat, Lincoln University J ames Blankenship, Corne tt University Sandra J. Bonetti , Colorado State University, Pueblo Barbara Bowman, University oj California, Berkeley Scott D. Briggs , Purdue Unive rsity Jeff Brodsky, University oj Pitt sburgh Ben Cald well, Missouri Western State University David Camerini, Univ er sity of California, Irvine Guillaume Chanfreau , U niversity oj California, Los Angeles Melan ie Coccal University oj California) Irvine Je ffrey Cohlberg, Calif ornia State University, Long Beach Kim D. Collins, University of Maryl and Charles T. Dameron, Duquesne University Ric hard S. Eise nstein, University oj Wisconsin-Madison Gerald W. Feigenso n, Cornell Univers ity Robert H. Fillingame, University of Wisconsin-Madison Brian Fox, Unio ersuu Of Wisconsin-Madison Gerald D. Frenkel, Rutgers University Perry Frey, University oj Wisconsin-Madison David E. Grah am , Uruoersitu of Texas- Austin William J. Gr imes, Univers ity O f Arizona Martyn Gunn, Texas A&M Univ ersity Olivia Hanson, University oj Central Oklahoma Amy Hark, Muhlenbe rg College Shaun V. Hernandez, University OfWisconsin-Madison Peter Hinkle, Cornell Univ er sity P. Shing Ho, Oreg on Stat e Unive rsily Charles G. Hoogstraten, Afichigan State Univers ity Gerwald Jogl. Brown Univers ity Sir Hans Kornberg, Boston University Bob Landick, U niversity oj Wisconsin-Madison Patrick D. Larkin, Texas A&M Unioersuu, Corpus Christi Ryan P. Liegel, Univ ers ity of Wisconsin-Madison Maria Linder, California State University, Fullerton Andy C. Lawang. Texas A&MUniversity John M akemson, Florid a Int ernational University JohnC. Matthews, Uniuereitu ojMt, ,,iBsi ppi , School ojPharmacu Benjamin J. McFarland, Seattl e Pacific Uniuersiu) Anant Menon, W eill Cornell Med ical College Sabeeha Mercha nt , Unioersiiu oj Calif ornia, Los Angeles
Transcript of Contentsin Brie - libcatalog.embl.de
[ xiv] Preface
r-.
1A Genetic Foundations 27Gene tic Continu ity Is Ves ted in Single
DNA Molecules 27The St ruc tu re of DNA Allows for Its Replication
and Repair wit h Near-Pe rfect. Fidelity 28The Line ar Sequence in DNA Encodes Proteins with
Three-Dimensional Structu re s 29
1.1 Cellular Foundations 2Cells Are the Structural and Functional
Units of All Living Organisms 3Cellular Dimens ions Are Limited by Diffusion ~3
There Are Three Dist inct Domains of Life 4Escherichia coli Is the Most -St udied Bacterium 5Eukaryotic Cells Have a Variet y of Membra nous
Organel les , Which Can Be Isolated for Study 7The Cytoplasm Is Organized by th e Cytoskeleton
and Is Highly Dynamic 8Cells Build Supramolecular St ruct ures nIn Vitro Studies May Overlook Important
Interactions among Molecu les 10
11 The Foundations ofBiochemistry
1.2Chemical Foundations 11Biomolecules Are Compounds of Carh on with
a Varie ty of Functional Groups 11Cells Contain a Universal Set of Small Molecules 13
Box 1-1 Molecular Weight,Molecular Mass,andTheir Correct Units 14Macromolecules Are the Major
Const ituen ts of Cells 14Three-Dimensiona l Stru cture Is Described
by Configuration and Conformation 15
Box 1-2 louis Pasteur and Optical Activity:In Vino, Veritas 17In teractions between Biorno lecu los
Are Stereospecific 18
1.3 Physical Foundations 19Living Organisms Exist in a Dynam ic
Steady Stat e, Never a t Equilibrium withTheir Surroundings 20
Organisms Transform Energy and Matterfrom Their Surroundings 20
Box 1-3 Entropy:The AdvantagesofBeing Disorganized 21The Flow of Electrons Provides Energy
for Organisms 22Creating and Maintaining Order Requires Work
and Energy 22Energy Coupling Links Reactions in Biology 22[{I' ll and .1GoAre Measures of a Reac tion's
Ten dency to Proceed Spontaneously 24Enzymes Promote Sequences of Chemical Reac tions 25Metabolism Is Regulated to Achieve Balance
and Econo my 26
Preface viii
The Foundations of Biochemistry
I STRUCTURE AND CATALYSIS 412 Water 433 Amino Aclds, Peptides, andProteins 71
4 The Ihree-Dimensional Structure of Proteins 1135 Protein Function 1536 Enzymes 1B37 Carbohydrates and Glycobiology 235B Nucleotides and Nucleic Aclds 2719 DNA-Based Information Technologies 30310 Lipids 34311 Biological Membranesand Transport 37112 Biosignaling 417
II BIOENERGETICS AND METABOLISM 48S13 Bioenergetics and Biochemical Reaction Types 48914Glycolysis, Gluconeogenesis,and the Pentose
PhosphatePathway 52715 Princlples of Metabolic Regulation 56916 The Citric Acid Cycle 61517 FattyAcldCatabolism 64718 Amino Acld Oxidationand the Productionof Urea 67319 Oxidative Phosphorylation andPhotophosphorylation 70720 Ca rbohydrate Biosynthesis in PlantsandBacteria 77321 Lipid Biosynthesis 80522 Biosynthesis of Amino Aclds, Nucleotldes,and
RelatedMolecules 85123 HormonalRegulation and Integrationof
MammalianMetabolism 901
III INFORMATION PATHWAYS 94524 Genes andChromosomes 94725 DNA Metabolism 97526 RNA Metabolism 102127 Protein Metabolism 106528 Regulation of Gene Exp ression 1115
Contentsin Brie
Appendix ACommon Abbreviationsin theBiochemical
Research Literature A- I
Appendix BAbbreviatedSolutions to ProblemsAS- IGlossary G- I
Credits C- I
IndexI-I
Scott C. Mohr, Boston UniversityKimberly Mowry, Brown UniversityLeisha Mullins, Texas A&M Univ ersitySewite Negash, California State University, Long BeachAllen W. Nicholson, Temple Univ ersityHiroshi Nikaido , University oj California, BerkeleyJames Ntambi, Universi ty oj Wisconsin-1VfadisonTimothy F. Osborne , University ofCalifornia, IruineJose R. I'erez-Casttneira, Univ ersi ty oj Seville, SpainTer ry Platt, Univ ersity qfRochesterWendy Pogoze lski, State Unioersi tu oj New York at GeneseoJonathan Popper, Univ ersi ty oj Wisconsin-MadisonThom as Poulos, University ojCaliforn ia, IrvineJack Preiss , Micniaan State UniversityAnna Radominska-Pandya, Univ ersity oj ArkansasRon Raines, Univ ersity QfWisconsin-MadisonTom A. Rapoport, Harvard Medi cal SchoolJason J. Reddick, University ojNor th Carolina, GreensboroMary Roberts , Boston CollegeIngrid K. Ruf Univ ersity oj California, IrvineAboozar Soleirnan t, Tehran Universi ty, IranMark Spaller , Wayne State UnioersuuStephen Spiro, Universi ty of Tex as at DallasNarasimha Sreerama, Colorado Stat e UniversityJon D. Stewart, Univ ersity oj FloridaKoni Stone, California State Unioersuu, StanislausJon H. Stultzfus, Michigan State Un iversityJeremy Thorn er, Unive rsity of California, BerkeleyDean R. Tolan, Boston Univ ersitySandr a 1. Turchi , Millersville Univ ersityManuel Varela, Eastern New Mexico UniversityBob Warburt on , Shepherd Un iversi tyTracy Ware, Salem Stale CollegeSusan Weintra ub, University oj Te:ras, Health Science CenterMichael Yaffe, Massacnusetts Ins titute of Technology
We lac k th e space here to acknowledge all the othe rindividuals whose special effort s went int o this book.We offer inst ead our sincere thanks-and th e finishedbook that they help ed guide to completion. We, ofcourse, assume full resp onsibility for errors at fact oremphasis.
We want especially to thank our students at theUniversity of Wisconsin- Madison for their numerous comments and suggestions. If something in the book does notwork, tliey are never shy about letting us know it. We aregrateful to the students and staff of our research groups andof the Center for Biology Education, who helped us balancethe competing demands on our time; to our colleagues inthe Department of Biochemistry at t.he University ofWisconsin-Madison, who helped us with advice and criticism;and to the many students and teachers who have writt en tosuggest ways of improving the book. We hope our readerswill continue to provide input for future editions.
Finally, we express our deep est appreciation to ourwives , Brook and Bet h, and our families, who showedex traordinary patience with, and support for , our bookwriting.
David L. NelsonMichael Ivl. Cox
Madison , WisconsinJanuary 2008
colleague. We feel very fortunate to have such gifted partners as Brook, Shelley,Adam, and Jean-Yves on our team.
We are also deeply indebted to Brian White of the University of Massachusetts- Bosto n, who wrote th e newdata analysis problems at the end of each chapter.
Many colleagues played a special role through theirinte rest in the project and their timely input. Prominentamong these are Laurens Anderson of the Universityof Wisconsin- Madison; Jeffrey D. Esko of the University ofCalifornia, San Diego; Jack Kirsch and his st udents atthe University of California, Berkeley; and Dana Aswad,Shiou-Chuan (Sheryl) Tsai, Michael G. Cumsky, andtheir colleagues (list ed below) at the University ofCalifornia, Irvine . Many others helped us shape th is fifthedition with their comments, suggestions , and criticisms.To all of them, we are deep ly gra teful:
Richard M. Amasino, University of Wisconsin -MadisonLouise E. Anderson , Universi ty oj Illinois at ChicagoCheryl Bailey, Univ ersity ojNebraska, LincolnKenneth Balazovich, University ojMichiganThomas O. Baldwin, Unive rsity oj Arizon aVah e Bandarian, Univ ersity ofArizonaEugene Barber, University oj RochesterSebastian Y. Bedn arek, Univ ersity oj Wisconsin- Madison.Ramachandra Bhat , Lincoln UniversityJames Blankenship, Corne tt Univ ersitySandra J. Bonetti, Colorado State University, PuebloBarbara Bowman , Univ ersity oj California, BerkeleyScott D. Briggs , Purdue Unive rsityJeff Brodsky, University ojPittsburghBen Caldwell, Missouri Western State UniversityDavid Camerini, Univ ersity ofCalifornia, IrvineGuillaume Chanfreau , University oj California, Los AngelesMelanie Coccal Univ ersity ojCalifornia) IrvineJe ffrey Cohlberg, California State University, Long BeachKim D. Collins, Univ ersity ofMarylandCharles T. Dameron, Duquesne UniversityRichard S. Eisenstein , Un iversit y oj Wisconsin-MadisonGerald W. Feigenso n, Cornell UniversityRobert H. Fillingame , University of Wisconsin-MadisonBrian Fox, Unioersuu Of Wisconsin-MadisonGerald D. Frenkel, Rutgers UniversityPerry Frey, Univ ersity oj Wisconsin- MadisonDavid E. Grah am , Uruoersitu of Texas-AustinWilliam J . Grimes , University Of ArizonaMartyn Gunn, Texas A&M UniversityOlivia Hanson, University oj Central OklahomaAmy Hark,Muhlenberg CollegeShaun V. Hernandez, University OfWisconsin-MadisonPeter Hinkle , Cornell Univ ersityP. Shing Ho, Oregon Stat e UniversilyCharles G. Hoogstrat en, Afichigan State Univers ityGerwald Jogl. Brown UniversitySir Hans Kornberg, Boston Univ ersityBob Landick, University oj Wiscons in- MadisonPa trick D. Larkin, Texas A&M Un ioersuu, Corpus ChristiRyan P. Liegel, Univ ersity of Wiscons in- MadisonMaria Linder, California State Universit y, FullertonAndy C. Lawang. Texas A&M UniversityJohn Makemson, Florid a International Univ ersityJohnC. Matthews, Uniuereitu ojMt,,,iBsippi, SchoolojPharmacuBenjamin J . McFarland, Seattl e Pacific Uniuersiu)Anant Menon, Weill Cornell Medical CollegeSabeeha Merchant, Unioersi iu oj California, Los Angeles
