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

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I:6 Indexchromosomes (continued)mitotic chromosomes 182, 183F, 184,185F, 187–188, 625, 626F, 631F,632–634, 635Fsegregation errors 662–663chromosome condensation 183-184, 625chromosome painting 179, 180F, 184F,722Fchromosome pairing in meiosis 655,657, 659chromosome segregation 181, 610, 615,619, 629F, 655, 662F, 722Fchromosome structurecompressed state of DNA 183–184in eukaryotes 178–187gene expression and 278nucleosomes in 184–186regulation of 188–192chymotrypsin 125F, 132, 307Fcilia 26–27, 118F, 580, 582, 590–592primary cilia 592stereocilia 13F, 409ciliary dynein 586, 591–592circular DNA 34, 179, 201, 211F, 213,273, 337cisternae (Golgi apparatus) 512F, 513T,518–519citrate synthase 142T, 442Fcitric acid cycleacetyl group oxidation in 438biosynthetic pathways beginningwith 441, 461diagrams 429F, 442F–443Felucidation of 444–445mitochondrial matrix 438oxaloacetate in 110F, 438sequential pathways 444as third stage of catabolism 430Cl – concentrations inside and outsidecells 391Tclam eggs 616clamp loaders 211–212, 213Tclassical genetics approaches 29, 354,564, 674–676clathrin-coated pits/vesicles 512–513,514F, 524–525, 526Fclaudins 704cleavage divisions 611, 615cleavage furrows 636, 637Fclone-by-clone sequencing 348–349cloningcancers as clones 718–719, 722Fmulticellular organisms as clones709see also DNA cloningCML (chronic myeloid leukemia) 148,729CNVs (copy number variations) 679co-immunoprecipitation 563, 730coated vesicles 512–513, 514F, 524–525,526Fcodes and abbreviationsfor amino acids 120F, 245Ffor bases and nucleotides 79F,176genetic code 178, 244–248, 249F“coding problem” 243codonsdefined 244neutral mutations 302start codons 254, 255Fstop codons 245F, 251, 254, 255F,324coenzymes 79F, 148–149coenzyme A see acetyl CoAcohesins 625, 626F, 627, 633, 634F,658F, 660, 661Fcoiled coils 128, 576, 600colchicine 584, 590, 633, 637collagen 48, 135, 136F, 696–698, 699F,700–702, 703Fcolor-blindness 672colorectal cancer 218, 223F, 715, 719F,721F, 726–727, 730–731combinatorial transcription control 279,282–285common ancestors 15, 34–35, 313see also ancestral cellcomparative genomics 312, 349compartments, eukaryotic cells seeorganellescompetitive inhibition 145, 444–445complement system 685complementary base-pairingcodon–anticodon recognition 248F,249defined 176, 177FDNA probes and cloning 184, 335F,340–341, 341, 352Freplication fidelity and 202, 207, 209,244RNA 240, 241F, 260, 291in transcription 229–231, 233see also DNA hybridizationcomplementary DNA (cDNA)cDNA libraries 339, 340FmRNA analysis 351complementation tests 675F, 678concentration gradientscontributing to electrochemicalgradient 393–394inorganic ions 391Na + pump 398–399osmosis 394–395passive transport and 393in velocity sedimentation 165Fcondensation reactionsbiopolymers generally 59disaccharide formation 53driven by ATP hydrolysis 106, 110peptide bond formation as 119Fphosphorylation as 105condensins 187F, 625, 626F, 628Fconditional knockout mice 357conditional mutants 676–678confocal fluorescence microscopy 9F,12F, 17F, 24T, 32Fconformationsmacromolecules 62NADH and NADPH 108conformations, DNAchromosome visibility and 174space-filling model 177Fconformations, proteinchanges driven by ATP hydrolysis602, 603Fchanges in ATP synthase 466changes in gated ion channels 404,408, 414–415Fchanges in transporters and pumps396–397, 398F, 475Fchanges on binding ligands 151–152,554F, 559, 566, 586, 698changes on dimer cleavage 641Fchanges on inhibition 151–152, 621changes on phosphorylation 152–153disulfide bond stabilization 136HPr bacterial protein 124, 125–126F,129hydrophobicity and 121, 122Fconjugate acid–base pairs 470conjugation, bacterial 308Fconnective tissues 692F, 693, 695–698,700, 702, 703F, 723connexons 707consanguineous marriages 668, 681conservative model, DNA replication202–203, 204Fconserved DNA/mechanismscell-cycle control system 30–31, 613evolutionary relationships and309–310, 313–315, 350functionally important regions as310–313, 314in human genome 323conserved orientation in membranes374, 377, 510conserved proteins 31, 131, 186conserved synteny 311constitutive exocytosis pathway 519,522contact-dependent signaling 535–536contractile bundles 27, 592, 593F, 595,601, 605, 705Fcontractile ring 592, 598, 600, 636–638control mechanisms 447COP-coated vesicles 513corn (maize) 307, 308F, 360F, 450F, 667cortisol 270, 282, 536T, 550T, 565, 566Fcoupled reactionsactivated carriers and 101, 106–107energetics of 92, 94F–95Fin glycolysis 434“paddle-wheel” analogy 104photosystems I and II 484coupled transporters 467, 468Fcovalent chemical bonds 43–46disulfide bonds 77F, 136, 139F, 516“high-energy” bonds 67, 95F, 102–103,109F, 111, 112Fpeptide bonds 60, 67F, 70F, 76F, 92,126polar covalent bonds 43F, 45, 47–49single and double bonds 44–45covalent modificationbiotin and 149DNA methylation as 287of histone tails 188–189of proteins 153–154, 258F, 447, 516see also protein kinasescrawling see cell locomotionCre recombinase 357Fcreatine phosphate 102–103Crick, Francis 174–175, 202, 204CRISPR gene editing 358–359, 564cross-linking see disulfide bondscross-pollination 664–665cross-talk 278, 568crossovers (meiosis) 657–660, 661F,662, 671–672, 675F, 679–680gene duplication and 303–304independent segregation and671–672cryoelectron microscopy 11, 160T, 161,169F, 379, 483F, 513Fcrypts, intestinal 713–714, 715F, 727F,728T, 731crystallization see X-ray diffractionCTP (cytidine triphosphate) 151F, 231

IndexI:7cultured cell types 285cultured cells 12F, 32, 33Fcurare 419, 544Tcyanide 468, 475cyanobacteria 314F, 315, 458, 478, 482,489cyclic AMP 79Fadenylyl cyclase and 549binding example 138FCAP activator and 275hormones mediated by 550T, 551Fsignaling pathway effects 549–551cyclic AMP-dependent protein kinase(PKA) 550–551, 552Fcyclic AMP phosphodiesterase 549–550cyclic GMP 555, 557Fcyclin–Cdk complexes 614, 617–618,619F, 620, 623cyclins 31, 614, 615–616G 1cyclin 617, 620G 1/S cyclin 614, 620M cyclin 614–616, 617F, 618–619,625, 633regulation 617–618, 620–621S cyclin 614, 617vertebrate cyclins and Cdks 617Tsee also Cdkscysteine residuesdisulfide bonds 77F, 136, 139F, 516palmitate addition 153cystic fibrosis 517, 672, 682, 685cytochalasin 594cytochromesheme group 474cytochrome b 562131Fcytochrome b 6-f complex 482F, 484,485Fcytochrome c in apoptosis 642cytochrome c oxidase complex 464,474, 475, 484cytochrome c reductase complex 473cytokinesis 636–639contractile ring in 636–638and mitosis as M phase 627, 629Fin plants 638cytosinedeamination 262methylation 287as a pyrimidine base 57, 67Fcytidine triphosphate (CTP) 151Fcytoskeletoncell junctions linked to 691, 693,698–699, 700F, 704–707and cell wall in plants 695enzyme-coupled receptors and 557extracellular matrix coupling698–699functions 22–24, 573mitotic spindle and contractile ring626–627motor proteins and 154–155muscle contraction and 600–606organelle location and movement498types of protein filament 574see also actin filaments;centrosomes; intermediatefilaments; microtubulescytosoldefined 21–22, 496diffusion rates 99as dynamic 23–24intercytosolic communication 707Dion concentrations 391, 399mRNA degradation in 242–243pH control 401DAG (diacylglycerol) 549, 551–553dalton (unit) 41Darwin, Charles 8, 28, 616databasescomparative genomics 35, 341in DNA cloning 361genome sequences 341–342, 350,684genomes and protein structure159–161, 162, 361FddNTPs (dideoxynucleosidetriphosphates) 346, 347Fde-differentiation 269F, 285deafness, inherited 668, 673–674, 680deamination in DNA 215, 216–217F,261–262death receptors 642definitions, genetics 675Fdehydrogenations as oxidations 88Delbrück, Max 202Delta protein 536T, 565G (delta G) see free energy changedenaturation, DNA 341, 342Fdenaturation, protein 123dendrites 3F, 353F, 410–411, 416F,420Fdensity gradient centrifugation 165F,203deoxyribose formation 261depolarizationneurons 411, 414–415, 418plasma membrane 408, 421 422Fdepurination in DNA 215, 216–217Fdesmosomes 575, 577, 579and cell junctions 704–707hemidesmosomes 578F, 704, 707,708Fdetergents 378–379, 385Fdevelopment process see embryonicdevelopmentdiabetes 427, 518, 680, 682–684diacylglycerol (DAG) 549, 551–553Dicer protein 290–291dideoxy sequencing (Sanger) 346, 347F,351FDidinium 26differential centrifugation 165F, 498differentiationde-differentiation 269F, 285in embryonic development 6,282–284induced, in ES cells 716RTK role 559, 560as selective gene expression267–268terminal differentiation 286, 622,644, 712–714diffusioncontrasted with facilitated transport390nitric oxide 554rates in the cytosol 99diffusion coefficients 384Fdigestion, in catabolism 430dihybrid crosses 669, 670Fdihydrofolate reductase 147dihydrolipoyl dehydrogenase/transacetylase 438Fdihydroxyacetone phosphate 436Fdimensions see sizesdiploid cells 652disaccharides 53, 73Fdisease statesatherosclerosis 526caused by mitochondrial dysfunction459caused by viruses 318Tdiabetes 427, 518, 680, 682–684matrix proteases in 697see also cancers; genetic disordersdisease susceptibility/predisposition526, 592, 678–680, 683–686disorder (entropy) 83–84, 94Fdisulfide bonds 77F, 136, 139F, 516DNA3′ and 5′ ends 176, 206chemical differences from RNA 58,229in chloroplasts 19, 458double-helix formation 58, 175–176gene expression and 6, 228genetic information storage 3, 58,174, 193–195isolating and cloning 334–341localization in prokaryotes andeukaryotes 16Fmitochondrial 17, 458packaging into chromosomes179–180, 183–184reading, between species 31see also conserved DNA; DNAstructure; genomes; nucleotides;regulatory DNADNA/RNA hybrid helices 319DNA-binding proteins 118F, 130F, 132,188F, 272single-strand 211DNA cloninggenomic and complementary DNA340, 344Fby PCR 341–345using bacteria 334–341using vectors 337–339, 360–361FDNA damageapoptosis and 621cell-cycle control and 621, 623depurination and deamination 215double-strand breaks 214, 219–222,358, 458F, 658F, 728effects of mutagens 674failure to repair 300–302point mutations 300–301DNA duplication see gene duplicationDNA fingerprinting 343–344, 345FDNA helicases 211, 212F, 213T, 357F,623, 628FDNA hybridization (renaturation)chromosome painting 179Fdetecting nucleotide sequences340–341in dideoxy sequencing 347Fand DNA cloning 340–341by siRNAs 355in situ hybridization 352DNA libraries/genomic libraries 339,348see also genomic librariesDNA ligase 142T, 210, 213T, 218, 220T,337–338, 339F

Index

I:7

cultured cell types 285

cultured cells 12F, 32, 33F

curare 419, 544T

cyanide 468, 475

cyanobacteria 314F, 315, 458, 478, 482,

489

cyclic AMP 79F

adenylyl cyclase and 549

binding example 138F

CAP activator and 275

hormones mediated by 550T, 551F

signaling pathway effects 549–551

cyclic AMP-dependent protein kinase

(PKA) 550–551, 552F

cyclic AMP phosphodiesterase 549–550

cyclic GMP 555, 557F

cyclin–Cdk complexes 614, 617–618,

619F, 620, 623

cyclins 31, 614, 615–616

G 1

cyclin 617, 620

G 1

/S cyclin 614, 620

M cyclin 614–616, 617F, 618–619,

625, 633

regulation 617–618, 620–621

S cyclin 614, 617

vertebrate cyclins and Cdks 617T

see also Cdks

cysteine residues

disulfide bonds 77F, 136, 139F, 516

palmitate addition 153

cystic fibrosis 517, 672, 682, 685

cytochalasin 594

cytochromes

heme group 474

cytochrome b 562

131F

cytochrome b 6

-f complex 482F, 484,

485F

cytochrome c in apoptosis 642

cytochrome c oxidase complex 464,

474, 475, 484

cytochrome c reductase complex 473

cytokinesis 636–639

contractile ring in 636–638

and mitosis as M phase 627, 629F

in plants 638

cytosine

deamination 262

methylation 287

as a pyrimidine base 57, 67F

cytidine triphosphate (CTP) 151F

cytoskeleton

cell junctions linked to 691, 693,

698–699, 700F, 704–707

and cell wall in plants 695

enzyme-coupled receptors and 557

extracellular matrix coupling

698–699

functions 22–24, 573

mitotic spindle and contractile ring

626–627

motor proteins and 154–155

muscle contraction and 600–606

organelle location and movement

498

types of protein filament 574

see also actin filaments;

centrosomes; intermediate

filaments; microtubules

cytosol

defined 21–22, 496

diffusion rates 99

as dynamic 23–24

intercytosolic communication 707

D

ion concentrations 391, 399

mRNA degradation in 242–243

pH control 401

DAG (diacylglycerol) 549, 551–553

dalton (unit) 41

Darwin, Charles 8, 28, 616

databases

comparative genomics 35, 341

in DNA cloning 361

genome sequences 341–342, 350,

684

genomes and protein structure

159–161, 162, 361F

ddNTPs (dideoxynucleoside

triphosphates) 346, 347F

de-differentiation 269F, 285

deafness, inherited 668, 673–674, 680

deamination in DNA 215, 216–217F,

261–262

death receptors 642

definitions, genetics 675F

dehydrogenations as oxidations 88

Delbrück, Max 202

Delta protein 536T, 565

G (delta G) see free energy change

denaturation, DNA 341, 342F

denaturation, protein 123

dendrites 3F, 353F, 410–411, 416F,

420F

density gradient centrifugation 165F,

203

deoxyribose formation 261

depolarization

neurons 411, 414–415, 418

plasma membrane 408, 421 422F

depurination in DNA 215, 216–217F

desmosomes 575, 577, 579

and cell junctions 704–707

hemidesmosomes 578F, 704, 707,

708F

detergents 378–379, 385F

development process see embryonic

development

diabetes 427, 518, 680, 682–684

diacylglycerol (DAG) 549, 551–553

Dicer protein 290–291

dideoxy sequencing (Sanger) 346, 347F,

351F

Didinium 26

differential centrifugation 165F, 498

differentiation

de-differentiation 269F, 285

in embryonic development 6,

282–284

induced, in ES cells 716

RTK role 559, 560

as selective gene expression

267–268

terminal differentiation 286, 622,

644, 712–714

diffusion

contrasted with facilitated transport

390

nitric oxide 554

rates in the cytosol 99

diffusion coefficients 384F

digestion, in catabolism 430

dihybrid crosses 669, 670F

dihydrofolate reductase 147

dihydrolipoyl dehydrogenase/

transacetylase 438F

dihydroxyacetone phosphate 436F

dimensions see sizes

diploid cells 652

disaccharides 53, 73F

disease states

atherosclerosis 526

caused by mitochondrial dysfunction

459

caused by viruses 318T

diabetes 427, 518, 680, 682–684

matrix proteases in 697

see also cancers; genetic disorders

disease susceptibility/predisposition

526, 592, 678–680, 683–686

disorder (entropy) 83–84, 94F

disulfide bonds 77F, 136, 139F, 516

DNA

3′ and 5′ ends 176, 206

chemical differences from RNA 58,

229

in chloroplasts 19, 458

double-helix formation 58, 175–176

gene expression and 6, 228

genetic information storage 3, 58,

174, 193–195

isolating and cloning 334–341

localization in prokaryotes and

eukaryotes 16F

mitochondrial 17, 458

packaging into chromosomes

179–180, 183–184

reading, between species 31

see also conserved DNA; DNA

structure; genomes; nucleotides;

regulatory DNA

DNA/RNA hybrid helices 319

DNA-binding proteins 118F, 130F, 132,

188F, 272

single-strand 211

DNA cloning

genomic and complementary DNA

340, 344F

by PCR 341–345

using bacteria 334–341

using vectors 337–339, 360–361F

DNA damage

apoptosis and 621

cell-cycle control and 621, 623

depurination and deamination 215

double-strand breaks 214, 219–222,

358, 458F, 658F, 728

effects of mutagens 674

failure to repair 300–302

point mutations 300–301

DNA duplication see gene duplication

DNA fingerprinting 343–344, 345F

DNA helicases 211, 212F, 213T, 357F,

623, 628F

DNA hybridization (renaturation)

chromosome painting 179F

detecting nucleotide sequences

340–341

in dideoxy sequencing 347F

and DNA cloning 340–341

by siRNAs 355

in situ hybridization 352

DNA libraries/genomic libraries 339,

348

see also genomic libraries

DNA ligase 142T, 210, 213T, 218, 220T,

337–338, 339F

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