Essential Cell Biology 5th edition
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Essential Cell Biology 5th edition

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I:2 Indexamino acid sequences/sequencing(continued)similarity across species 31see also polypeptides; proteinsamino acid side chainsbasic and acidic side chains 76F–77Fcharged and polar side chains 120Famino acidsbacterial biosynthesis 150Fd- and l-forms 56ionization 76Fmitochondrial matrix breakdown438precursors of 441as protein constituents 4, 56, 76F–77Fprotein sequencing 159–161in proteins from different species 31radiolabeled 246–247, 520as subunits 51three- and one-letter abbreviations120F, 245FtRNA coupling 249amino group in weak bases 50, 69Faminoacyl-tRNA synthetases 249amoebaeas eukaryotes 16genome size 34, 181and osmotic swelling 395phagocytosis 524, 596as protozoa 27FAMP (adenosine monophosphate) 78F,111, 549see also cyclic AMPAMP-PNP 588amphipathic molecules 54–55, 367,368F, 370–371, 376–378amyloid plaques/fibers/structures 129,130F, 157–158Anabaena cylindrica 15Fanabolic pathways 82activated carriers and 101Fglycolysis and citric acid cycleproducts 441NADPH and 108regulation 447anaerobic respiration 14, 433–434anaphase, meiosis 656F, 659–660, 661Fanaphase, mitosis 627F, 629F, 633–639,656Fsee also APC/Canaphase A/anaphase B 634, 635Fancestral cell 5–6, 457, 459see also common ancestorsanemia 191, 715sickle-cell anemia 160T, 222, 680aneuploidy 663angina 555animalsbasic tissue types 695cell signaling in plants and 567cell structure 8F, 9contractile ring 637–638explanation of differences between323, 326glucose transport 400–401model organisms 29, 32optogenetics in living animals 421, 422Fresting membrane potentials 406separate evolution of multicellularityfrom plants 567, 692anionsconcentration gradients 391solution behavior 47annealing see DNA hybridizationantenna complexes 481, 483Fantibiotic resistancehorizontal gene transfer and 308,338mobile genetic elements and 315,316Fplasmids in 338antibiotics and prokaryotic proteinsynthesis 255–256antibodies 138–139, 140Fin affinity chromatography 159, 166Fbinding sites 138–139, 140Fcancer treatment and checkpointinhibitors 728ER assembly of 517immunoglobulin domains 139Fimmunoprecipitation 141F, 563,730labeling with 141F, 384making and using 140F–141Fmonoclonal antibody preparation141Fraising in laboratory animals 140Fspecificity 138, 140Fstaining and 12Fagainst tumors 728antibody labelingmembrane flow investigation384–385anticancer drugs 148, 562, 584anticodons 248–249antifreeze proteins 117–118Fantigen-binding sites 138–139antimitotic drugs 584antiparallel b-sheets 127F, 129, 131F,139Fantiparallel strands, DNA 175F, 176,177F, 206antiparallel tetramers, intermediatefilaments 576Fantiports 400–401, 467, 468FAPC (adenomatous polyposis coli) gene726–727, 728T, 730–731APC/C (anaphase-promoting complexor cyclosome) 617, 618F, 619, 625,633–635apoptosisavoidance by cancer cells 723Bad protein and 561Caenorhabditis elegans 32extracellular signals and 538F, 642as programmed cell death 640response to DNA damage 621suppression by survival factors643–644UPR and 518aquaporins 394, 404Arabidopsis thalianacellular structure 695Fgene numbers 323, 567genome size 35T, 323as a model plant 28, 567regeneration from a callus 360archaea 14–16, 26F, 314, 463, 466,490–491, 499arginine and nitric oxide 555Armadillo protein 730ARPs (actin-related proteins) 595,598–599arthritis 680, 683, 684, 697asexual reproduction, examples 652asparagine glycosylation 516aspartatebacterial biosynthesis and 150Fprecursors 441aspartate transcarbamoylase 125F, 151Fasters 627F, 630, 632Fatherosclerosis 526atomic number 40atomic weights 41, 43Fatomsdefined and described 40–41visualization 11ATP (adenosine 5′-triphosphate)as an activated carrier 57, 104–106,109TATP/ADP ratio 467–468formation in mitochondria 17generation by oxidativephosphorylation 446, 456as a nucleotide 57, 79Fin photosynthesis 479–480, 482production in the earliest cells 455,488–489protein phosphorylation and152–153rate of ADP conversion 466, 468rate of turnover 422, 468resulting from glucose oxidationprocesses 428, 469Tresulting from glycolysis 423,434–435, 469TATP analogs 588ATP cycle 57F, 104ATP-driven pumps 397, 399, 400F, 488F,526–527ATP synthaseevolution of oxidativephosphorylation 456in Methanococcus jannaschii 491in photosynthesis 478–479, 482,484stage 2 of oxidative phosphorylation456, 461use of electrochemical protongradient 465–466, 477ATP synthesischemiosmotic coupling and476–477electron transport and 446ATPasesATP synthase reversibility 466kinesins and dyenins as 578protein pumps as 397, 399attachment proteins 381auditory hair cells 13F, 408, 409F,419T, 702autism 347, 359, 420, 717autocatalysis 5F, 259–260autocrine signaling 535–536automated genetic screening 676automated genome sequencing346–348autophagy 528Avery, Oswald et al. 194–195Avogadro’s number 41axonsgrowth of 596intermediate filaments in 577signaling function 410–411, 415squid giant axons 411–413, 588terminals 411, 415, 420F, 535, 585transport along 585voltage-gated ion channels 419Taxoplasm 412–413F, 588

IndexI:3BB lymphocytes/B cells 140F, 141F,268Bacillus subtilis 303backbone models, protein structure124, 126F, 132F“backstitching” maneuver 207–208BACs (bacterial artificial chromosomes)348–349bacteriaCas9 defense mechanism 358cell walls and lysozyme 136chemical composition 51, 52Tcircular DNA in 179conjugation in 308FDNA cloning in 334–341in genetic engineering 106habitats 14–15membrane fluidity 372origins of chloroplasts as 15, 18–19,457–458, 490, 499origins of mitochondria as 14, 17–18,457, 490, 499, 500Fas prokaryotes 11, 15replication rate 14restriction nucleases and 335shapes and sizes 14start codons 254sugar digestion regulators 275–276surface-to-volume ratios 499thermophilic 342Ftoxins and G proteins 547–548transcription initiation in 233,235transcription regulators 271–275translation accompanyingtranscription 255see also E. colibacterial flagella 467bacteriorhodopsin 118F, 160T, 379–380,397, 402, 403T, 477, 545Bad protein 561“bait” proteins 563, 730Bak protein 642, 643Fball-and-stick models 44F, 52F, 56–57F,107F, 109FBarr bodies 191Fbarrier DNA sequences 190–191basal bodies 580F, 582, 590basal lamina 383F, 578F, 702–703,704–707, 713, 719F, 722base-pairing 58, 176, 179F, 216, 217F,230, 241, 289enabling DNA replication200–201hydrogen bonds, A-T and C-G177F, 201tRNA with rRNA 251wobble base-pairing 248see also complementary base-pairingbases (in solution)basic side-chain amino acids 76Fhydroxyl ion formation 50, 69Fproton acceptance by 50bases (nucleotide)abbreviations 79F, 176in DNA and RNA 57, 175, 209external features 234, 272as purines and pyrimidines 57, 78Funusual, in tRNA 248Fsee also adenine; cytosine; guanine;thymine; uracilbasic side-chain amino acids 76FBax protein 642, 643FBcl2 family proteins 642, 644Beggiatoa 15Fbehavioral effects of mutations 676bg complex, G protein 546, 547F, 548,553Fb barrels 376F, 378b cells, pancreatic 267–268, 523F,536Tb-galactosidase 281F, 353Fb sheets 126, 127F, 129–130, 131F, 139F,157, 158F, 160Tmembrane proteins 378bi-orientation 632Bicoid gene 281Fbindingextracellular signal molecules 537Fas a protein function 137–138binding energies 97–98binding sites 137–138cooperative binding 305F, 400multiple binding sites 151multiple polypeptide chains132–133oxygen 474transporters 392, 396, 400see also active sites; substratebindingbinding strength, noncovalentinteractions 97biosynthesisactivated carriers and 101–112pathways beginning with glycolysisor the citric acid cycle 441see also anabolic pathways; catabolicpathwaysbiotechnology industry 161bioterrorism 343biotin as an activated carrier 109, 110F,149birth defects 681bisphosphoglycerate 434–435, 437F1,3-bisphosphoglycerate 434, 435F,437F, 476, 486Fbivalents 657–659, 661, 670blastocysts 716blebs 640blindness 361, 681, 685blood cellslubrication 383types 714, 715Fblood groups 54, 73Fblood platelets 699blood samples 341, 344F, 714body plan formation 280body size, determination of 639bond angles 44bond energiesin activated carriers 86, 101, 427,466Fconversion 84–85covalent bonds 44, 46“high-energy” bonds 95F, 428bond lengths 44, 48T, 68Fbond strengths 45–46, 48T, 67Fbone 693, 695–697, 698F, 700, 711bone marrow 710, 712, 714–715Boveri, Theodor 24Tbrainnerve cell receptors 421transmitter-gated ion channels419brainsCaM-kinase effects 554energy consumption 416gene expression 551, 552Fregulatory DNA and evolution 326Brca1 and Brca2 proteins 728brewer’s yeast see Saccharomycescerevisiaebrown fat cells 476–477brush-border cells/absorptive cells 523,703–704, 712–714budding yeasts 2, 16, 17F, 28see also Saccharomyces cerevisiaebuffers 50bypass reactions 448CC. elegans see CaenorhabditisC-termini, polypeptides 56, 120Ca 2+ ionsCa 2+ channel abnormalities 717concentrations inside and outsidecells 391T, 399fertilization and egg development553, 663inositol trisphosphate effects552–553intracellular messenger role 545,553ion-channel-coupled receptors544required by cadherins 705sequestration in smooth ER 497triggering muscle contraction 553,604–605voltage-gated Ca 2+ channels 416,417F, 604FCa 2+ pumps 118F, 399, 400F, 403T,554, 605cadherins 705, 706–707F, 711, 723, 725Caenorhabditis eleganscentrosome 582Fgenome 35T, 309, 676–677introducing dsRNA 355as model organism 29, 32social behavior 676caffeine 549calcium ions see Ca 2+calcium phosphate in bone 696F,700calico cats 191, 192Fcallus formation 359–360calluses 359–360calmodulin 125F, 554calories, conversion with joules 45,94FCalvin cycle 486zCaM-kinases (Ca 2+ /calmodulindependentprotein kinases) 554cancer cellscharacteristics 718–719, 722–723competitive advantage 721–723favoring glycolysis 723invasiveness 718–719matrix proteases in 697mismatch repair and 218–219and somatic mutations 223and telomere shortening 215, 723unrestrained proliferation 718–719cancer-critical/driver mutations/genes720–721, 723–727, 728T, 730–731

I:2 Index

amino acid sequences/sequencing

(continued)

similarity across species 31

see also polypeptides; proteins

amino acid side chains

basic and acidic side chains 76F–77F

charged and polar side chains 120F

amino acids

bacterial biosynthesis 150F

d- and l-forms 56

ionization 76F

mitochondrial matrix breakdown

438

precursors of 441

as protein constituents 4, 56, 76F–77F

protein sequencing 159–161

in proteins from different species 31

radiolabeled 246–247, 520

as subunits 51

three- and one-letter abbreviations

120F, 245F

tRNA coupling 249

amino group in weak bases 50, 69F

aminoacyl-tRNA synthetases 249

amoebae

as eukaryotes 16

genome size 34, 181

and osmotic swelling 395

phagocytosis 524, 596

as protozoa 27F

AMP (adenosine monophosphate) 78F,

111, 549

see also cyclic AMP

AMP-PNP 588

amphipathic molecules 54–55, 367,

368F, 370–371, 376–378

amyloid plaques/fibers/structures 129,

130F, 157–158

Anabaena cylindrica 15F

anabolic pathways 82

activated carriers and 101F

glycolysis and citric acid cycle

products 441

NADPH and 108

regulation 447

anaerobic respiration 14, 433–434

anaphase, meiosis 656F, 659–660, 661F

anaphase, mitosis 627F, 629F, 633–639,

656F

see also APC/C

anaphase A/anaphase B 634, 635F

ancestral cell 5–6, 457, 459

see also common ancestors

anemia 191, 715

sickle-cell anemia 160T, 222, 680

aneuploidy 663

angina 555

animals

basic tissue types 695

cell signaling in plants and 567

cell structure 8F, 9

contractile ring 637–638

explanation of differences between

323, 326

glucose transport 400–401

model organisms 29, 32

optogenetics in living animals 421, 422F

resting membrane potentials 406

separate evolution of multicellularity

from plants 567, 692

anions

concentration gradients 391

solution behavior 47

annealing see DNA hybridization

antenna complexes 481, 483F

antibiotic resistance

horizontal gene transfer and 308,

338

mobile genetic elements and 315,

316F

plasmids in 338

antibiotics and prokaryotic protein

synthesis 255–256

antibodies 138–139, 140F

in affinity chromatography 159, 166F

binding sites 138–139, 140F

cancer treatment and checkpoint

inhibitors 728

ER assembly of 517

immunoglobulin domains 139F

immunoprecipitation 141F, 563,

730

labeling with 141F, 384

making and using 140F–141F

monoclonal antibody preparation

141F

raising in laboratory animals 140F

specificity 138, 140F

staining and 12F

against tumors 728

antibody labeling

membrane flow investigation

384–385

anticancer drugs 148, 562, 584

anticodons 248–249

antifreeze proteins 117–118F

antigen-binding sites 138–139

antimitotic drugs 584

antiparallel b-sheets 127F, 129, 131F,

139F

antiparallel strands, DNA 175F, 176,

177F, 206

antiparallel tetramers, intermediate

filaments 576F

antiports 400–401, 467, 468F

APC (adenomatous polyposis coli) gene

726–727, 728T, 730–731

APC/C (anaphase-promoting complex

or cyclosome) 617, 618F, 619, 625,

633–635

apoptosis

avoidance by cancer cells 723

Bad protein and 561

Caenorhabditis elegans 32

extracellular signals and 538F, 642

as programmed cell death 640

response to DNA damage 621

suppression by survival factors

643–644

UPR and 518

aquaporins 394, 404

Arabidopsis thaliana

cellular structure 695F

gene numbers 323, 567

genome size 35T, 323

as a model plant 28, 567

regeneration from a callus 360

archaea 14–16, 26F, 314, 463, 466,

490–491, 499

arginine and nitric oxide 555

Armadillo protein 730

ARPs (actin-related proteins) 595,

598–599

arthritis 680, 683, 684, 697

asexual reproduction, examples 652

asparagine glycosylation 516

aspartate

bacterial biosynthesis and 150F

precursors 441

aspartate transcarbamoylase 125F, 151F

asters 627F, 630, 632F

atherosclerosis 526

atomic number 40

atomic weights 41, 43F

atoms

defined and described 40–41

visualization 11

ATP (adenosine 5′-triphosphate)

as an activated carrier 57, 104–106,

109T

ATP/ADP ratio 467–468

formation in mitochondria 17

generation by oxidative

phosphorylation 446, 456

as a nucleotide 57, 79F

in photosynthesis 479–480, 482

production in the earliest cells 455,

488–489

protein phosphorylation and

152–153

rate of ADP conversion 466, 468

rate of turnover 422, 468

resulting from glucose oxidation

processes 428, 469T

resulting from glycolysis 423,

434–435, 469T

ATP analogs 588

ATP cycle 57F, 104

ATP-driven pumps 397, 399, 400F, 488F,

526–527

ATP synthase

evolution of oxidative

phosphorylation 456

in Methanococcus jannaschii 491

in photosynthesis 478–479, 482,

484

stage 2 of oxidative phosphorylation

456, 461

use of electrochemical proton

gradient 465–466, 477

ATP synthesis

chemiosmotic coupling and

476–477

electron transport and 446

ATPases

ATP synthase reversibility 466

kinesins and dyenins as 578

protein pumps as 397, 399

attachment proteins 381

auditory hair cells 13F, 408, 409F,

419T, 702

autism 347, 359, 420, 717

autocatalysis 5F, 259–260

autocrine signaling 535–536

automated genetic screening 676

automated genome sequencing

346–348

autophagy 528

Avery, Oswald et al. 194–195

Avogadro’s number 41

axons

growth of 596

intermediate filaments in 577

signaling function 410–411, 415

squid giant axons 411–413, 588

terminals 411, 415, 420F, 535, 585

transport along 585

voltage-gated ion channels 419T

axoplasm 412–413F, 588

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