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Contents XXIII6CellMembranes 105A signal transduction pathwayinvolves a signal, a receptor, andresponses 1267.2 How Do Signal ReceptorsInitiate a CellularResponse? 1276.1 What Is the Structure of aBiological Membrane? 106Lipids form the hydrophobic coreof the membrane 106Membrane proteins areasymmetrically distributed 107Membranes are constantlychanging 109Plasma membrane carbohydratesare recognition sites 109Receptors that recognize chemicalsignals have specific bindingsites 127Receptors can be classified bylocation and function 128Intracellular receptors are locatedin the cytoplasm or thenucleus 1306.2 How Is the PlasmaMembrane Involved in CellAdhesion andRecognition? 110Cell recognition and adhesioninvolve proteins andcarbohydrates at the cellsurface 111Three types of cell junctionsconnect adjacent cells 111Cell membranes adhere to theextracellular matrix 111Different energy sources distinguishdifferent active transportsystems 1186.5 How Do Large MoleculesEnter and Leave aCell? 1206.3 What Are the PassiveProcesses of MembraneTransport? 113Diffusion is the process of randommovement toward a state ofequilibrium 113Simple diffusion takes placethrough the phospholipidbilayer 114Osmosis is the diffusion of wateracross membranes 114Diffusion may be aided by channelproteins 115Carrier proteins aid diffusion bybinding substances 1176.4 What are the ActiveProcesses of MembraneTransport? 118Active transport is directional7.3 How Is the Response to aSignal Transduced throughthe Cell? 131118Macromolecules and particles enterthe cell by endocytosis 120Receptor-mediated endocytosis ishighly specific 121Exocytosis moves materials out ofthe cell 1227Cell Communicationand Multicellularity1257.1 What Are Signals, and HowDo Cells Respond toThem? 126Cells receive signals from thephysical environment and fromother cells 126A protein kinase cascade amplifiesa response to ligandbinding 131Second messengers can amplifysignals between receptors andtarget molecules 132Signal transduction is highlyregulated 1367.4 How Do Cells Change inResponse to Signals? 137Ion channels open in response tosignals 137Enzyme activities change inresponse to signals 138Signals can initiate DNAtranscription 1397.5 How Do Cells in aMulticellular OrganismCommunicateDirectly? 139Animal cells communicate throughgap junctions 139Plant cells communicate throughplasmodesmata 140Modern organisms provide cluesabout the evolution of cell–cellinteractions andmulticellularity 140PART THREECells and Energy8Energy, Enzymes,and Metabolism1448.1 What Physical PrinciplesUnderlie Biological EnergyTransformations? 145There are two basic types ofenergy 145There are two basic types ofmetabolism 145The first law of thermodynamics:Energy is neither created nordestroyed 146The second law ofthermodynamics: Disorder tendsto increase 146Chemical reactions release orconsume energy 147Chemical equilibrium and freeenergy are related 1488.2 What Is the Role of ATPin BiochemicalEnergetics? 149ATP hydrolysis releasesenergy 149 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufacturedor disseminated in any form without express written permission from the publisher.

XXIVContentsATP couples exergonic andendergonic reactions 1508.3 What Are Enzymes? 1519.2 What Are the AerobicPathways of GlucoseCatabolism? 169In glycolysis, glucose is partiallyoxidized and some energy isreleased 169Pyruvate oxidation links glycolysisand the citric acid cycle 170The citric acid cycle completesthe oxidation of glucose toCO2 170Pyruvate oxidation and the citricacid cycle are regulated by theconcentrations of startingmaterials 171To speed up a reaction, an energybarrier must be overcome 151Enzymes bind specific reactants attheir active sites 152Enzymes lower the energy barrierbut do not affectequilibrium 1538.4 How Do EnzymesWork? 154Enzymes can orientsubstrates 154Enzymes can induce strain in thesubstrate 154Enzymes can temporarily addchemical groups tosubstrates 154Molecular structure determinesenzyme function 155Some enzymes require othermolecules in order tofunction 155The substrate concentration affectsthe reaction rate 1568.5 How Are Enzyme ActivitiesRegulated? 156Enzymes can be regulated byinhibitors 157Allosteric enzymes are controlledvia changes in shape 159Allosteric effects regulate manymetabolic pathways 160Many enzymes are regulatedthrough reversiblephosphorylation 161Enzymes are affected by theirenvironment 16199.3 How Does OxidativePhosphorylation FormATP? 171The respiratory chain transferselectrons and protons, andreleases energy 172Proton diffusion is coupled to ATPsynthesis 173Some microorganisms use non-O2electron acceptors 1769.4 How Is Energy Harvestedfrom Glucose in the Absenceof Oxygen? 177Cellular respiration yieldsmuch more energy thanfermentation 178The yield of ATP is reduced by theimpermeability of mitochondriato NADH 1789.5 How Are MetabolicPathways Interrelated andRegulated? 179Cells trap free energy whilemetabolizing glucose 166Redox reactions transfer electronsand energy 167The coenzyme NAD is a keyelectron carrier in redoxreactions 167An overview: Harvesting energyfrom glucose 168Light energy is absorbed bychlorophyll and otherpigments 188Light absorption results inphotochemical change 190Reduction leads to ATP andNADPH formation 191Chemiosmosis is the source ofthe ATP produced inphotophosphorylation 19210.3 How Is Chemical EnergyUsed to SynthesizeCarbohydrates? 193Radioisotope labelingexperiments revealed the stepsof the Calvin cycle 193The Calvin cycle is made up ofthree processes 194Light stimulates the Calvincycle 19610.4 How Have Plants AdaptedPhotosynthesis toEnvironmentalConditions? 197Rubisco catalyzes the reaction ofRuBP with O2 or CO2 197C3 plants undergophotorespiration but C4 plantsdo not 198CAM plants also use PEPcarboxylase 20010.5 How Does PhotosynthesisInteract with OtherPathways? 200Catabolism and anabolism arelinked 179Catabolism and anabolism areintegrated 180Metabolic pathways are regulatedsystems 181Pathways ThatHarvest ChemicalEnergy 1659.1 How Does GlucoseOxidation Release ChemicalEnergy? 16610.2 How Does PhotosynthesisConvert Light Energy intoChemical Energy? 18810Photosynthesis:Energy fromSunlight 18510.1 What Is Photosynthesis186Experiments with isotopesshow that O2 comes from H2Oin oxygenicphotosynthesis 186Photosynthesis involves twopathways 188 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufacturedor disseminated in any form without express written permission from the publisher.

Contents XXVPART FOURGenes and Heredity11The Cell Cycle andCell Division 20511.1 How Do Prokaryotic andEukaryotic CellsDivide? 206Prokaryotes divide by binaryfission 206Eukaryotic cells divide by mitosisor meiosis followed bycytokinesis 207The number, shapes, and sizes ofthe metaphase chromosomesconstitute the karyotype 224Polyploids have more than twocomplete sets of chromosomes22411.6 In a Living Organism,How Do Cells Die? 22511.7 How Does UnregulatedCell Division Lead toCancer? 227Cancer cells differ from normalcells 227Cancer cells lose control over thecell cycle and apoptosis 228Cancer treatments target the cellcycle 22811.2 How Is Eukaryotic CellDivision Controlled? 208Specific internal signals triggerevents in the cell cycle 208Growth factors can stimulate cellsto divide 21111.3 What Happens duringMitosis? 211Prior to mitosis, eukaryotic DNAis packed into very compactchromosomes 211Overview: Mitosis segregatescopies of geneticinformation 212The centrosomes determine theplane of cell division 212The spindle begins to formduring prophase 213Chromosome separation andmovement are highlyorganized 214Cytokinesis is the division of thecytoplasm 21611.4 What Role Does CellDivision Play in a SexualLife Cycle? 217Asexual reproduction by mitosisresults in geneticconstancy 217Sexual reproduction by meiosisresults in geneticdiversity 21811.5 What Happens duringMeiosis? 219Meiotic division reduces thechromosome number 219Chromatid exchanges duringmeiosis I generate geneticdiversity 219During meiosis homologouschromosomes separate byindependent assortment 220Meiotic errors lead to abnormalchromosome structures andnumbers 22212Inheritance, Genes,and Chromosomes23212.3 How Do GenesInteract? 244Hybrid vigor results from newgene combinations andinteractions 244The environment affects geneaction 245Most complex phenotypes aredetermined by multiple genesand the environment 24612.1 What Are the MendelianLaws of Inheritance? 233Mendel used the scientificmethod to test hishypotheses 233Mendel’s first experimentsinvolved monohybridcrosses 234Mendel’s first law states that thetwo copies of a genesegregate 236Mendel verified his hypothesesby performing testcrosses 237Mendel’s second law states thatcopies of different genes assortindependently 237Probability can be used to predictinheritance 239Mendel’s laws can be observed inhuman pedigrees 24012.4 What Is the Relationshipbetween Genes andChromosomes? 247Genes on the same chromosomeare linked 247Genes can be exchangedbetween chromatids andmapped 247Linkage is revealed by studies ofthe sex chromosomes 24912.5 What Are the Effects ofGenes Outside theNucleus? 25212.6 How Do ProkaryotesTransmit Genes? 253Bacteria exchange genes byconjugation 253Bacterial conjugation is controlledby plasmids 25412.2 How Do Alleles Interact?241New alleles arise bymutation 241Many genes have multiplealleles 242Dominance is not alwayscomplete 242In codominance, both alleles at alocus are expressed 243Some alleles have multiplephenotypic effects 24313DNA and Its Rolein Heredity 25913.1 What Is the Evidence thatthe Gene Is DNA? 260 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufacturedor disseminated in any form without express written permission from the publisher.DNA from one type of bacteriumgenetically transforms anothertype 260

XXVIContentsViral infection experimentsconfirmed that DNA is thegenetic material 261Eukaryotic cells can also begenetically transformed byDNA 26313.2 What Is the Structure ofDNA? 264Watson and Crick used modelingto deduce the structure ofDNA 264Four key features define DNAstructure 265The double-helical structure ofDNA is essential to itsfunction 26613.3 How Is DNAReplicated? 267Three modes of DNA replicationappeared possible 267An elegant experimentdemonstrated thatDNA replication issemiconservative 268There are two steps inDNA replication 268DNA polymerases addnucleotides to the growingchain 269Many other proteins assist withDNA polymerization 272The two DNA strands growdifferently at the replicationfork 272Telomeres are not fully replicatedand are prone to repair 27513.4 How Are Errors in DNARepaired? 27613.5 How Does the PolymeraseChain Reaction AmplifyDNA? 277The polymerase chain reactionmakes multiple copies of DNAsequences 27714From DNA toProtein: GeneExpression 28114.1 What Is the Evidence thatGenes Code forProteins? 282One gene determines onepolypeptide 28314.2 How Does InformationFlow from Genes toProteins? 284Three types of RNA have roles inthe information flow from DNAto protein 285In some cases, RNA determinesthe sequence of DNA 28514.3 How Is the InformationContent in DNATranscribed to ProduceRNA? 286RNA polymerases share commonfeatures 286Transcription occurs in threesteps 286The information for proteinsynthesis lies in the geneticcode 28814.4 How Is Eukaryotic DNATranscribed and the RNAProcessed? 290Many eukaryotic genes areinterrupted by noncodingsequences 290Eukaryotic gene transcripts areprocessed beforetranslation 29114.5 How Is RNA Translated intoProteins? 293Transfer RNAs carry specificamino acids and bind tospecific codons 293Each tRNA is specifically attachedto an amino acid 294The ribosome is the workbenchfor translation 294Translation takes place in threesteps 295Polysome formation increases therate of protein synthesis 29715Gene Mutationand MolecularMedicine 30415.1 What Are Mutations? 305Mutations have differentphenotypic effects 305Point mutations are changes insingle nucleotides 306Chromosomal mutations areextensive changes in thegenetic material 307Retroviruses and transposons cancause loss of functionmutations or duplications 308Mutations can be spontaneous orinduced 308Mutagens can be natural orartificial 310Some base pairs are morevulnerable than others tomutation 310Mutations have both benefits andcosts 31015.2 What Kinds of MutationsLead to Genetic Diseases?311Genetic mutations may makeproteins dysfunctional 311Disease-causing mutations mayinvolve any number of basepairs 312Expanding triplet repeatsdemonstrate the fragility ofsome human genes 313Cancer often involves somaticmutations 31414.6 What Happens toPolypeptides afterTranslation? 298Signal sequences in proteinsdirect them to their cellulardestinations 298Many proteins are modified aftertranslation 300Observations in humans led tothe proposal that genesdetermine enzymes 282Experiments on bread moldestablished that genesdetermine enzymes 282 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufacturedor disseminated in any form without express written permission from the publisher.

Contents XXVIIMost diseases are caused bymultiple genes andenvironment 31415.3 How Are MutationsDetected and Analyzed?315Restriction enzymes cleave DNAat specific sequences 315Gel electrophoresis separatesDNA fragments 316DNA fingerprinting combinesPCR with restriction analysisand electrophoresis 317Reverse genetics can be used toidentify mutations that lead todisease 318Genetic markers can be used tofind disease-causinggenes 318The DNA barcode project aims toidentify all organisms onEarth 31915.4 How Is Genetic ScreeningUsed to DetectDiseases? 320Screening for disease phenotypesinvolves analysis of proteinsand other chemicals 320DNA testing is the most accurateway to detect abnormalgenes 320Allele-specific oligonucleotidehybridization can detectmutations 32115.5 How Are Genetic DiseasesTreated? 322Genetic diseases can be treatedby modifying thephenotype 322Gene therapy offers the hope ofspecific treatments 32316Regulation of GeneExpression 32816.1 How Is Gene ExpressionRegulated inProkaryotes? 329Regulating gene transcriptionconserves energy 329Operons are units oftranscriptional regulation inprokaryotes 330Operator–repressor interactionscontrol transcription in the lacand trp operons 330Protein synthesis can becontrolled by increasingpromoter efficiency 332RNA polymerases can be directedto particular classes ofpromoters 33216.2 How Is Eukaryotic GeneTranscription Regulated?333General transcription factors actat eukaryotic promoters 333Specific proteins can recognizeand bind to DNA sequencesand regulate transcription335Specific protein–DNA interactionsunderlie binding 335The expression of transcriptionfactors underlies celldifferentiation 336The expression of sets of genescan be coordinately regulatedby transcription factors 336Many bacteriophages undergo alytic cycle 339Some bacteriophages can undergoa lysogenic cycle 340Eukaryotic viruses can havecomplex life cycles 341HIV gene regulation occurs at thelevel of transcriptionelongation 34116.4 How Do EpigeneticChanges Regulate GeneExpression? 343DNA methylation occurs atpromoters and silencestranscription 343Histone protein modifications affecttranscription 344Epigenetic changes can be inducedby the environment 344DNA methylation can result ingenomic imprinting 344Global chromosome changesinvolve DNA methylation 34516.5 How Is Eukaryotic GeneExpression Regulated afterTranscription? 34616.3 How Do Viruses RegulateTheir GeneExpression? 339PART FIVEGenomes17Genomes 35217.1 How Are GenomesSequenced? 353New methods have beendeveloped to rapidly sequenceDNA 353Genome sequences yield severalkinds of information 35517.2 What Have We Learnedfrom SequencingProkaryotic Genomes? 356Prokaryotic genomes arecompact 356The sequencing of prokaryoticand viral genomes has manypotential benefits 357Metagenomics allows us todescribe new organisms andecosystems 357Some sequences of DNA canmove about the genome 358 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufacturedor disseminated in any form without express written permission from the publisher.Different mRNAs can be madefrom the same gene byalternative splicing 346Small RNAs are importantregulators of geneexpression 347Translation of mRNA can beregulated by proteins andriboswitches 348

XXVIIIContentsWill defining the genes requiredfor cellular life lead to artificiallife? 35918.4 What Other Tools Are Usedto Study DNAFunction? 380Genes can be expressed indifferent biologicalsystems 380DNA mutations can be created inthe laboratory 381Genes can be inactivated byhomologousrecombination 381Complementary RNA can preventthe expression of specificgenes 382DNA microarrays reveal RNAexpression patterns 38217.3 What Have We Learnedfrom SequencingEukaryotic Genomes? 361Model organisms reveal manycharacteristics of eukaryoticgenomes 361Eukaryotes have genefamilies 363Eukaryotic genomes containmany repetitivesequences 36417.4 What Are theCharacteristics of theHuman Genome? 366The human genome sequenceheld some surprises 366Comparative genomics revealsthe evolution of the humangenome 366Human genomics has potentialbenefits in medicine 36718.5 What Is Biotechnology?383Expression vectors can turn cellsinto protein factories 384Medically useful proteins can bemade usingbiotechnology 384DNA manipulation is changingagriculture 386There is public concern aboutbiotechnology 388The proteome is more complexthan the genome 369Metabolomics is the study ofchemical phenotype 3701818.1 What Is RecombinantDNA? 37418.2 How Are New GenesInserted into Cells? 375Genes can be inserted intoprokaryotic or eukaryoticcells 376A variety of methods are used toinsert recombinant DNA intohost cells 376Reporter genes help select oridentify host cells containingrecombinant DNA 37718.3 What Sources of DNA AreUsed in Cloning? 379Libraries provide collections ofDNA fragments 379cDNA is made from mRNAtranscripts 379Synthetic DNA can be made byPCR or by organic chemistry38019.4 How Does GeneExpression DeterminePattern Formation? 399Multiple proteins interact todetermine developmentalprogrammed cell death 399Plants have organ identitygenes 400Morphogen gradients providepositional information 401A cascade of transcription factorsestablishes body segmentationin the fruit fly 40119.5 Is Cell DifferentiationReversible? 405Plant cells can be totipotent 405Nuclear transfer allows thecloning of animals 406Multipotent stem cellsdifferentiate in response toenvironmental signals 408Pluripotent stem cells can beobtained in two ways 40818.6 How Is BiotechnologyChanging Medicine andAgriculture? 38417.5 What Do the NewDisciplines of Proteomicsand MetabolomicsReveal? 369Recombinant DNAand Biotechnology373Differential gene transcription is ahallmark of celldifferentiation 39819Differential GeneExpression inDevelopment 39219.1 What Are the Processes ofDevelopment? 393Development involves distinct butoverlapping processes 393Cell fates become progressivelymore restricted duringdevelopment 39420Genes,Development, andEvolution 41220.1 How Can Small GeneticChanges Result in LargeChanges in Phenotype?413Developmental genes in distantlyrelated organisms aresimilar 41319.2 How Is Cell FateDetermined? 395Cytoplasmic segregation candetermine polarity and cell fate395Inducers passing from one cell toanother can determine cellfates 39519.3 What Is the Role of GeneExpression inDevelopment? 397Cell fate determination involvessignal transduction pathwaysthat lead to differential geneexpression 397 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufacturedor disseminated in any form without express written permission from the publisher.

Contents XXIX20.2 How Can Mutations withLarge Effects Change OnlyOne Part of the Body? 415Genetic switches govern how thegenetic toolkit is used 415Modularity allows for differencesin the patterns of geneexpression 41620.3 How Can DevelopmentalChanges Result inDifferences amongSpecies? 418Differences in Hox geneexpression patterns result inmajor differences in bodyplans 418Mutations in developmentalgenes can produce majormorphological changes 41820.4 How Can the EnvironmentModulate Development?420Dietary information can be apredictor of futureconditions 421A variety of environmental signalsinfluence development 42120.5 How Do DevelopmentalGenes ConstrainEvolution? 423Evolution usually proceeds bychanging what’s alreadythere 423Conserved developmental genescan lead to parallelevolution 423Temperature can determinesex 420PART SIXThe Patterns and Processes of Evolution21Mechanisms ofEvolution 42721.1 What Is the Relationshipbetween Fact and Theoryin Evolution? 428Darwin and Wallace introduced theidea of evolution by naturalselection 428Evolutionary theory has continuedto develop over the pastcentu

The Science of Life and Its Chemical Basis Studying Life 1 1.1 What Is Biology? 2 Life arose from non-life via chemical evolution 3 Cellular structure evolved in the common ancestor of life 3 Photosynthesis allows some organisms to capture energy from the sun 4 Biological information is