Essential Cell Biology 5th edition
I:8 IndexDNA methylation 287DNA-only transposons 315, 316FDNA polymerasesand cDNA libraries 339, 340Fcompared to RNA polymerases 232DNA polymerases I and III 210PCR use 342proofreading by 207–208, 209Frepair polymerases 210F, 215,217–218, 221reverse transcriptase as 316template-based synthesis by 205–207DNA probes 184, 341, 352FDNA repair 215–223mismatch repair system 218–219DNA replication 200–215avoiding re-replication 623as bidirectional 205cell cycle phases 623conservative, semiconservative, anddispersive models 201, 202–204elucidation 202–204“end replication problem” 213error rates 218, 720leading and lagging strandsdistinguished 207in meiosis 655–656preservation of genome sequences223rates in prokaryotes and eukaryotes200replication machine 200–201, 205,210–211, 218S-Cdks and 623temperature-sensitive mutants 677transcription distinguished from230–231see also replication forks; replicationoriginsDNA sequencing see genome;nucleotide sequencesDNA structure elucidation 174–178DNA topoisomerases 212DNA viruses 319DNP (2,4-dinitrophenol) 476–477docking siteshistone 189phosphorylated tyrosines 558,560–561, 563protein 153dogs, genetic traits 667Fdolichol 75F, 516, 517Fdomainsdefined 130and exon shuffling 306–307illustrated 131Finteraction domains 558–559prokaryotic 15–16and protein families 162dominant alleles 665–666dopamine 707–708double bonds 45in phospholipids 371resonance 66Fdouble helix, in tRNAs 245double-strand breaks 214, 219–222,358, 458F, 658F, 728double-stranded RNA (dsRNA) 318Down syndrome 662driver mutations in cancer seecancer-criticalDrosophila melanogasterArmadillo protein 730effects of mobile genetic elements307Fembryonic development 12F, 710Eve gene 280–281Ey gene/transcription regulator284–286genome size 35, 309, 323mitotic spindles 633Fas model organism 29Notch receptor 565drugsanticancer drugs 148, 562, 584development using human stemcells 717effects on microtubule dynamics 584pharmaceutical proteins 334see also antibiotic resistance; toxinsdsRNA (double-stranded RNA) 290, 354dynamin 512, 514Fdyneins 118F, 586–587, 590–592, 634ciliary dyneins 586, 591–592cytoplasmic dyneins 586–587EE. colichemical complexity 51cytosol 22Fevolutionary ancestors 490gene regulation experiments280–281genome 34–35Lac operon 275–276, 279as model organism 14F, 27–28E site, ribosomes 251, 252F, 253EcoRI enzyme 335–337Feffector proteins 537, 540, 552, 560eggsenucleated 269Fexperiments on enucleated eggs268–269as gametes 652multicellular organisms from709–710oocytes 615, 616Fsize difference from sperm 653Fzygotes as fertilized eggs 652, 663elastase 132elastin 135, 136F, 696electrical signal interconversion withchemical 416–417electrochemical gradientsactive transport 396–397component forces 393–394Na + and K + gradients 394Na + pump and 399oxidative phosphorylation and 456passive transport 396electrochemical H + gradients 402,464–465, 466–467, 482, 491electrochemical Na + gradients 399–400,401F, 402, 403Felectronsactivated carriers of 106–107and chemistry 40–47in oxidation and reduction 87–88see also “high-energy”electron affinities 470–471electron carriers 464, 470–474chlorophyll special pairs and 481cytochrome c oxidase complex474–475in the electron-transport chain 446,456, 471–473FADH 2as 438mobile electron carriers 464,482–484NADH and NADPH as 107plastocyanin as 484plastoquinone and ferredoxin as482electron microscopyand cell structure 9–11light microscopes and 6transmission and scanning electronmicroscopes 10–11electron shells 41–44, 46electron-transport systemsanaerobic respiration 434in chloroplasts/photosynthesis 456Fenergetics 471first appearance 455in mitochondria 430, 432, 439molecular mechanisms 469–475in oxidative phosphorylation 445, 456in photosynthesis 456F, 479, 481respiratory enzyme complexes464–465electronegativity 45–46, 88Felectrophoresis see gel electrophoresiselectrostatic attraction 48, 62, 71Fhistones and DNA 186and protein conformation 121elements (chemical)defined 40in living organisms 41–42periodic table 43reactivity 15, 42, 46, 54Embden–Meyerhof pathway 432Fembryonic developmentapoptosis in 640asymmetric cell division 637differentiated cell types in 6differentiation in 6, 282–284epithelial sheets in 705, 706Fmodel organisms 32, 710transcription regulators in 280–281zebrafish 32, 710embryonic stem cells (ES cells) 283,285–286, 355–356, 715–718“end replication problem” 213endocrine cells/signaling 534endocytosisbalanced by exocytosis 21endocytic pathways 523–528and lysosomes 511phagocytosis and pinocytosis523–526, 528F, 592receptor-mediated 525–526endomembrane system 499, 500F, 501,507, 511, 512F, 519, 522endoplasmic reticulum (ER)cell division and 639ER retention signals 517, 519extent 498, 507Finternal ER signal sequences 510,511Fphospholipid synthesis at 373positioning 587possible origins 499ribosome attachment 507rough and smooth 20F, 497, 507sarcoplasmic reticulum 400F, 403T,604–605as source of proteins and lipids 506
IndexI:9endosomes 497–500, 507, 511–513,522–523, 525–528early and late 526endosymbiosis 26endothelial cells 386F, 536T, 555,710–711energetically favorable reactionscarbon fixation 486DNA double helix formation 176formation of activated carriers 101,104formation of lipid bilayers 370free-energy change and 91protein conformations and 122energetically unfavorable reactionsADP phosphorylation 106free-energy changes 92gluconeogenesis 448–449membrane fusion as 515energyfrom chemical bonds in food 427from fermentation 455glucose as predominant source 427from glycolysis 430–431membrane-based mechanisms456–457storage in electrochemical gradients399transcription 231use by living cells 82–88see also free energyenergy carriers 57energy conversion in cells 84–85energy sourcesevolution of energy-generatingsystems 488–491small molecules as 51, 54, 427enhancers (gene activation) 276, 278entropy (disorder) 83–84environmental factorsand cancer 719–720, 721and human disease 680, 682–686microenvironment modification 723sexual reproduction benefits 654enzymesclassification 142Tcoenzymes 79F, 148–149effectiveness of catalysis by 81–82,89–90energetics of catalysis by 88–100feedback inhibition 149–150mechanisms of catalysis by 139,142–143, 146–147performance 144as proteins 59regulation of catalytic effects150–151ribozymes 109, 252–253, 259–260,261Tribulose bisphosphate carboxylase59, 118F, 168F, 485–486selectivity/specificity 142see also substrate bindingenzyme-coupled receptors 543, 545,557–569enzyme–substrate complexesformation and stabilization 142F,143, 146, 147Flysozyme 146–147Fenzyme inhibitioncompetitive and feedback inhibition145, 150by drugs 147–148epidemiology of cancers 719–720epidermis see skinepidermolysis bullosa simplex 577, 579epigenetic changes 724epigenetic inheritance 287, 724epinephrine 450, 536T, 550–551, 555GPCR binding 545Fepithelial cellsapical, basal, and lateral surfaces382, 401cilia 590formation of cups, tubes, andvesicles 705, 706Fglucose transport 400–401keratin filaments 575Fsheets of, as polarized 702–703stratified epithelia 702, 713, 714Fuse of symports 400–401equilibrium constant, K 95F–97equilibrium density centrifugation 203equilibrium reactions 92, 93F, 94F, 100equilibrium sedimentation 165FER see endoplasmic reticulumerror ratesDNA replication 218, 720meiosis 662–663transcription 232Escherichia coli see E. coliestradiol 536T, 565, 566Fethylenebond geometry 45as a plant hormone 567, 568Fethylene glycol poisoning 145euchromatin 190eukaryoteschromosome structure in 178–187eukaryotic cell 16–27genome size 34–35membrane-enclosed organelles496–500origins 24, 26–27prokaryotes distinguished from 11transcription initiation in 233Eve (even-skipped) gene 280–281evolutionancestral cell 5–6ancestral genes 33–35atmospheric oxygen and 439, 455,490Fof brains 326of cancer cells 721–723as complementary to cell theory 8conserved mechanisms 309–310,313–315, 350of energy-generating systems 488–491of oxidative phosphorylation 456of prokaryotes 14reconstructing the process 309–315of RNA before DNA 109, 259separate, of plants and animals 567,692see also conserved DNAexocytosisbalanced by endocytosis 21, 523constitutive exocytosis pathway 519,522regulated exocytosis pathway 522secretory pathways 515in vesicular transport 511exon shuffling 298, 299F, 306–307exons (expressed sequences)introns and 239mobile genetic elements and 317Fexpression vectors 361extracellular matrixfibrous proteins in 32, 135, 696light microscopy 8, 25F, 692Fin plants and animals 692–701protein cross-linking 136space-filling gels 577, 595see also basal lamina; cell wallsextracellular signal moleculesactin filaments and 598binding 537Fcontact-dependent cell signaling535–536hormones as 536local mediators 535–536, 545, 550T,555, 557mitogens as 620, 643plasma membrane crossing 565–567range 534–536role in cell signaling 534see also neurotransmittersextracellular signalsapoptosis induction 538, 642and cancer 645necessary for survival 642–643speed of response 538–539stem cell populations and 714–715Wnt pathway 714–715, 726, 730–731extreme environments 16Ey gene/transcription regulator284–286eye cup/optic cup 705, 706F, 717–718FFactor VIII gene 239F, 317FADH 2(flavin adenine dinucleotide,reduced form) 108, 109T, 438, 439F,440–443F, 445F, 446, 462, 463–464F,473energy yield 468–469familial hypertrophic cardiomyopathy605Fas receptor/ligand 642fat droplets, chloroplasts 450, 487fat droplets, cytoplasmic 54, 75F,450–451Ffatsas an energy source 438breakdown and utilization 428brown fat cells 476–477storage 450fatty acidsacetyl CoA from 438, 439Fbiosynthesis 108as lipids 55, 74F–75Fsaturated and unsaturated 54,74Fas subunits 51feedback inhibition 145, 150, 274feedback loops 4, 5Ffeedback regulationcell-cycle control system 612intracellular signaling pathways 540,541Fmetabolic enzymes 447–448in signaling pathways 540, 541F, 556fermentation 433–435, 455ferredoxins 482, 483–485F, 489Ffertilizationdiploid genomes from 663egg development following 709–710
- Page 799 and 800: Answers A:311 2 3 4OUTSIDEFigure A1
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Index
I:9
endosomes 497–500, 507, 511–513,
522–523, 525–528
early and late 526
endosymbiosis 26
endothelial cells 386F, 536T, 555,
710–711
energetically favorable reactions
carbon fixation 486
DNA double helix formation 176
formation of activated carriers 101,
104
formation of lipid bilayers 370
free-energy change and 91
protein conformations and 122
energetically unfavorable reactions
ADP phosphorylation 106
free-energy changes 92
gluconeogenesis 448–449
membrane fusion as 515
energy
from chemical bonds in food 427
from fermentation 455
glucose as predominant source 427
from glycolysis 430–431
membrane-based mechanisms
456–457
storage in electrochemical gradients
399
transcription 231
use by living cells 82–88
see also free energy
energy carriers 57
energy conversion in cells 84–85
energy sources
evolution of energy-generating
systems 488–491
small molecules as 51, 54, 427
enhancers (gene activation) 276, 278
entropy (disorder) 83–84
environmental factors
and cancer 719–720, 721
and human disease 680, 682–686
microenvironment modification 723
sexual reproduction benefits 654
enzymes
classification 142T
coenzymes 79F, 148–149
effectiveness of catalysis by 81–82,
89–90
energetics of catalysis by 88–100
feedback inhibition 149–150
mechanisms of catalysis by 139,
142–143, 146–147
performance 144
as proteins 59
regulation of catalytic effects
150–151
ribozymes 109, 252–253, 259–260,
261T
ribulose bisphosphate carboxylase
59, 118F, 168F, 485–486
selectivity/specificity 142
see also substrate binding
enzyme-coupled receptors 543, 545,
557–569
enzyme–substrate complexes
formation and stabilization 142F,
143, 146, 147F
lysozyme 146–147F
enzyme inhibition
competitive and feedback inhibition
145, 150
by drugs 147–148
epidemiology of cancers 719–720
epidermis see skin
epidermolysis bullosa simplex 577, 579
epigenetic changes 724
epigenetic inheritance 287, 724
epinephrine 450, 536T, 550–551, 555
GPCR binding 545F
epithelial cells
apical, basal, and lateral surfaces
382, 401
cilia 590
formation of cups, tubes, and
vesicles 705, 706F
glucose transport 400–401
keratin filaments 575F
sheets of, as polarized 702–703
stratified epithelia 702, 713, 714F
use of symports 400–401
equilibrium constant, K 95F–97
equilibrium density centrifugation 203
equilibrium reactions 92, 93F, 94F, 100
equilibrium sedimentation 165F
ER see endoplasmic reticulum
error rates
DNA replication 218, 720
meiosis 662–663
transcription 232
Escherichia coli see E. coli
estradiol 536T, 565, 566F
ethylene
bond geometry 45
as a plant hormone 567, 568F
ethylene glycol poisoning 145
euchromatin 190
eukaryotes
chromosome structure in 178–187
eukaryotic cell 16–27
genome size 34–35
membrane-enclosed organelles
496–500
origins 24, 26–27
prokaryotes distinguished from 11
transcription initiation in 233
Eve (even-skipped) gene 280–281
evolution
ancestral cell 5–6
ancestral genes 33–35
atmospheric oxygen and 439, 455,
490F
of brains 326
of cancer cells 721–723
as complementary to cell theory 8
conserved mechanisms 309–310,
313–315, 350
of energy-generating systems 488–491
of oxidative phosphorylation 456
of prokaryotes 14
reconstructing the process 309–315
of RNA before DNA 109, 259
separate, of plants and animals 567,
692
see also conserved DNA
exocytosis
balanced by endocytosis 21, 523
constitutive exocytosis pathway 519,
522
regulated exocytosis pathway 522
secretory pathways 515
in vesicular transport 511
exon shuffling 298, 299F, 306–307
exons (expressed sequences)
introns and 239
mobile genetic elements and 317F
expression vectors 361
extracellular matrix
fibrous proteins in 32, 135, 696
light microscopy 8, 25F, 692F
in plants and animals 692–701
protein cross-linking 136
space-filling gels 577, 595
see also basal lamina; cell walls
extracellular signal molecules
actin filaments and 598
binding 537F
contact-dependent cell signaling
535–536
hormones as 536
local mediators 535–536, 545, 550T,
555, 557
mitogens as 620, 643
plasma membrane crossing 565–567
range 534–536
role in cell signaling 534
see also neurotransmitters
extracellular signals
apoptosis induction 538, 642
and cancer 645
necessary for survival 642–643
speed of response 538–539
stem cell populations and 714–715
Wnt pathway 714–715, 726, 730–731
extreme environments 16
Ey gene/transcription regulator
284–286
eye cup/optic cup 705, 706F, 717–718
F
Factor VIII gene 239F, 317
FADH 2
(flavin adenine dinucleotide,
reduced form) 108, 109T, 438, 439F,
440–443F, 445F, 446, 462, 463–464F,
473
energy yield 468–469
familial hypertrophic cardiomyopathy
605
Fas receptor/ligand 642
fat droplets, chloroplasts 450, 487
fat droplets, cytoplasmic 54, 75F,
450–451F
fats
as an energy source 438
breakdown and utilization 428
brown fat cells 476–477
storage 450
fatty acids
acetyl CoA from 438, 439F
biosynthesis 108
as lipids 55, 74F–75F
saturated and unsaturated 54,
74F
as subunits 51
feedback inhibition 145, 150, 274
feedback loops 4, 5F
feedback regulation
cell-cycle control system 612
intracellular signaling pathways 540,
541F
metabolic enzymes 447–448
in signaling pathways 540, 541F, 556
fermentation 433–435, 455
ferredoxins 482, 483–485F, 489F
fertilization
diploid genomes from 663
egg development following 709–710
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