Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

I:50 Index
and riboswitches 415
and RNA processing 315–316
transcription factors see transcription
regulators
transcription initiation
chromatin modification using 387–388
in eukaryotes 310–313, 387
and termination 306–309
transcription initiation complexes 311
transcription rate constants 513
transcription regulators (transcription
factors)
ability to read DNA sequences
374–375
activating differentiation 1170–1171
in bacteria 380–383
chromatin immunoprecipitation and
505
in chromatin modification 196–197,
199–201, 206
combinatorial gene control 396, 397F,
399, 520–521
controlled activation 395, 396F
cooperative binding 378–380, 517F
dimerization 375–378
in eukaryotes 384–392
extracellular signaling 867–880
Hox modulated 1163
ligand-modulated 874–876, 877F
maintaining embryonic stem cells
1254–1255
master transcription regulators
398–399, 1171
neurons expressing 1200F
p53 protein as 1116
as proteins 30
role and mode of operation 373–380,
389–390
sequential expression 1179
in specialized cells 399–400
as switches 384–392, 402–403
in the syncytial blastoderm 1157
see also latent transcription regulators;
transcription activators;
transcription repressors
transcription repressors (repressor
proteins)
activators and 381–383, 394
binding site occupancy 514
co-repressors 385, 386F, 392, 394,
395F
combinatorial controls 394–395
DNA inversion and 294F
DNA methylation and 405
fusion with bacterial Cas9 497
negative feedback 402, 515
switch to activators 868, 871
tryptophan repressor 376, 380–383,
392
transcription units 306
transcriptional activators, regulators,
repressors see transcription
activators etc.
transcriptional synergy 388–389
transcytosis 732, 737, 738F, 749F
transdifferentiation 1258–1259
transducin (G t ) 845, 846T, 848
transduction and horizontal gene transfer
1268
transesterifications in RNA splicing 318,
321
transfer RNAs (tRNAs)
function 7, 305, 334
initiator tRNA 347–348
and the nucleolus 330
ribosomal binding sites 347
structure 335F
unusual bases 335F, 337F
transferrin 427, 553F
transferrin receptor 734–735
transformation, horizontal gene transfer
by 1268
transformed phenotypes 1098, 1106
transforming growth factor-β see TGFβ
transgenic organisms 495–497, 500, 506,
543, 1221F
transgenic plants 507–508
transit amplifying cells 1121–1122, 1219,
1220F, 1223, 1225, 1226F
transition-metal ions 764–766
transition states, enzyme stabilization of
141–146
translation
accuracy and free energy 345–346
co-translational protein folding
353–354, 355F
conserved gene families 20, 21T
control with 3ʹ and 5ʹ UTRs 422–423
control with IRES 425–426
converting RNA into proteins 6–7,
315F, 333–362
initiation and termination 347–349
messenger RNA in 343–344
quality control 351–353
ribosome profiling technique 505–506
speed of 346
stepwise 343–344F
translation initiation mechanisms 425F,
1288
translation recoding 350
translational control, gene expression
372, 373F
translational repressors 623
translesion polymerases 273, 274F
translocation steps, ribosomal 342
translocations 487
translocator proteins 1270–1271F
the translocon 677
transmembrane proteins
adhesion proteins 1037
association with the lipid bilayer 577F
ATG9 as 726
β-barrels in 579–581, 659, 662–663
cadherins and integrins as 1037
death receptors as 1024
enzyme-coupled receptors as 849
ER capture 672
fates of endocytosed 738F
hydrophobicity 577, 579F, 593
integration process 678
IRE1 as a transmembrane protein
kinase 687
most receptors as 816
Notch as 720
PERK as a transmembrane protein
kinase 688
single-pass and multipass 578–579
SRP receptor as 674
see also multipass; single-pass
transmission electron microscopy (TEM)
305F, 554, 555–556F, 558, 1210F
transmitter-gated ion channels 614,
627–632, 636
A-to-I editing 418
acetylcholine receptors as 630–631
allostery in 618, 825
ion-channel-coupled receptors 817F,
818, 843
types in neurons 631, 636
transport ATPases (ATP-driven pumps)
601–602, 606–607
transport proteins, inner mitochondrial
membrane 779–780
transport vesicles 644–648, 650, 656F,
670, 691
coated vesicles 697
formation 701
scope 695
see also vesicular transport
transporters (protein) 599
in epithelial cells 605
in plants 883
regulation of cytosolic pH 604–605
transposable elements (transposons)
conservative site-specific
recombination and 293
DNA-only transposons 288–290
double-stranded RNA in 421
eukaryotic genomes 28
and genome changes 217–218, 222
nonretroviral retrotransposons 291
retroviral-like transposons 291
RNA interference and 429, 432–433
three classes 288T, 292
virulence genes 1268
transposition 287–292
trastuzumab 1137
treadmilling, actin filaments 901,
903–904, 953–954
tree of life see phylogenetic trees
triacylglycerols 78, 81, 83F, 98–99
tricarboxylic acid cycle see citric acid
cycle
tricellulin 1049
trichothiodystrophy 497F
trigger mechanism of invasion 1281,
1282F, 1285F
triskelions, clathrin 698, 699F
Trithorax group proteins 1164
Triton X−100 583, 584F
TrkA kinase 853–854, 1209
tropoelastin 1065
tropomodulin 905, 909, 919, 920F
tropomyosin 416, 592F, 905, 907–910,
920F, 921, 922F, 923
α-tropomyosin gene 319F
troponins 921–923
trypanosomes 689, 805, 1290
Trypanosoma brucei 1266, 1290
Trypanosoma cruzi 1283–1284, 1290
trypsin 119, 132T, 440, 456–457, 942F
tryptophan, structure 113
tryptophan repressor 376, 380–383, 392
TSH (thyroid-stimulating hormone) 835T
tube and vesicle formation 1192
tube worms 12F
tubules
branching tubular structures 1190
vesicle budding events 705
see also microtubules
tubulin subunits 893–894, 904T, 927,
928–929, 934–935
α-tubulin 925, 926
β-tubulin 926F, 927