Page numbers followed by “f” indicate figures.

Page numbers followed by “t” indicate tables.

T cells, 1081, 1082, 1083f, 1095, 1104. See also Cytotoxic T cells

activation of, 1122, 1122f

antibody production and, 1128, 1129f

antigen-specific receptors triggering, 1118, 1120

cancer defenses and, 1131

CD4 or CD8 lineage commitment, 1121–1122

cytokine production by, 1123–1124

development of, 1120, 1121f

helper, 1124

MHC molecules interacting with, 1107–1109

T loop, 883

TAFs. See TBP-associated factors

Tail-anchored proteins, 597

Talin, 930f, 963

Tamoxifen, 993f, 1157, 1158

Tandemly repeated arrays, 307–308

Target of rapamycin (TOR), 452

Targeting sequences, 585, 609–610, 609t

on cargo proteins, 641

coat proteins and, 641

TARPs. See Transmembrane AMPA receptor regulatory proteins

Tastes, 1064–1066, 1065f

Tat protein, 377, 377f, 617

TATA box, 371–372, 371f, 413f

TATA box-binding protein (TBP), 374

Tau proteins, 830–831

Taxol, 830

TAZ, 911

TBP. See TATA box-binding protein

TBP-associated factors (TAFs), 374

TCA cycle. See Tricarboxylic acid cycle

T-cell malignancies, 725

T-cell receptors (TCRs)

genes, 1116–1118, 1117f

signal transduction from, 1119f

structure of, 1115–1116, 1116f

variable residues of, 1118

T-cells, formation of, 728

TCF. See Ternary complex factor

TCRs. See T-cell receptors

TdT. See Terminal deoxynucleotidyltransferase

TE. See Trophectoderm

Telomerase, 347–349, 348f, 1140

Telomere terminal transferase. See Telomerase

Telomeres, 345, 347–349, 391, 392f

Telophase, 851, 859, 876

nuclear envelope reassembly in, 903, 903f

TEM. See Transmission electron microscope

Tem1, 910

Temperate phages, 216

Temperature-sensitive mutation, 21, 228, 229f, 878, 881, 905

Template DNA strands

duplex DNA unwound for, 199

transcription of, 176–179

Terminal deoxynucleotidyltransferase (TdT), 1116–1117

Termination, 353

Ternary complex, 646f

Ternary complex factor (TCF), 745

Tertiary structure, 72

RNA, 175, 175f

Tetrahymena, 345, 347, 348f, 394, 526

Tetrahymena thermophila, 466

Tetramers, 861

TFIIA, 374

TFIIB, 374, 376

TFIIB recognition element (BRE), 376

TFIID, 333, 373–376, 394

TFIIE, 374

TFIIF, 374

TFIIH, 374, 375

TFIIIB, 413

TFIIIC, 413

TfR. See Transferrin receptor

T-G mismatches, 205, 205f

TGF-α. See Transforming growth factor α

TGF-β. See Transforming growth factor β

TGF-β receptor proteins, 722–724

Smad transcription factors and, 724

TGF-β binding and signal transduction, 722–724, 723f

TGF-β/Smad signaling pathway, 723, 723f

Thalassemia, 444

Thermal energy, 57

Thermoacidophiles, 10

Thermogenesis, 559

Thermogenin, 559

Thermosynechococcus elongatus, 570

Thermus aquaticus, 241, 589

Thermus thermophilus, ribosome of, 189f, 190f

Thick filaments, 804

Thick-filament regulation, 808

Thin filaments, 804

Thin-filament regulation, 806, 806f

Thiol groups, 603

Thioredoxin, 574

3T3 cells, 1140, 1140f

3′ cleavage and polyadenylation, 419, 430–432, 431f

3′ poly(A) tail, 430

3-D adhesions, 961, 962f

Three-Na⁺/one-Ca²⁺ antiporter, 504–505

Threonine, 44

Threshold potential, 1059, 1060f

Thrombopoietin, 727

Thrombospondin (TSP), 1049

Thylakoids, 18, 560, 617, 618f

Thymine, 45, 46f

Thymine-thymine dimers, 206, 206f, 375–376

Thymocytes, 1111

Thymosin-β₄, 785

Thymus, 1111, 1121–1122

Tight junctions, 508, 932, 932f, 939–942, 939f, 940f, 941f

Tim proteins, 611

Time-lapse microscopy, 142

+TIPs, 831–832, 832f

TIRF microscopy. See Total internal reflection fluorescence microscopy

Tissue, classical cadherins and differentiation of, 936

Tissue culture cells, 880

Tissue grafts, 1104–1105

Tissue plasminogen activator (TPA), 77–78

Tissues, 921

allogenic transplantation of, 1120

basal lamina and, 945–947, 946f

cancer cells escaping, 1140

I-34

evolution of, 928–929

organization into organs, 24, 25f

plant, 968–972

Titration curves, 56f

TLRs. See Toll-like receptors

TM. See Tropomyosin

TN. See Troponin

TNFα. See Tumor necrosis factor alpha

Tobacco smoke, 1144, 1144f, 1157

Tolerance, 1080

Toll-like receptors (TLRs), 758, 760, 1084, 1122, 1125–1127

activation of, 1126f

diversity of, 1126

engagement of, 1127–1128

signaling cascade, 1127

structure of, 1125–1126

Tom proteins, 610

TOP mRNAs, 453

Topogenic sequences, 593, 599

Topoisomerase I, 174, 174f

Topoisomerase II, 174

Topological domains, 78

within chromosome territories, 336–339

Topology

deduction of, 599–600

of membrane proteins, 593–594, 594f

TOR. See Target of rapamycin

TOR pathway, 452–454

Torsional stress, 174, 174f

Total internal reflection fluorescence microscopy (TIRF microscopy), 150–151, 151f

Totipotent cells, 976

Touch-receptor complex, 1062, 1062f

TPA. See Tissue plasminogen activator

Tra protein, 436, 436f

TRADD, 1021–1022

Trans fats, 50

Transcellular pathway, 941, 941f

Transcellular transport, 508–510

Transcription, 8, 81, 169f

activated, 356, 357–358

alternative splicing and, 435

chromatin-mediated repression of, 390

chromatin-remodeling complexes and, 395

divergent, 372–373

DNA methylation repressing, 404–405

epigenetic regulation of, 404–411

eukaryote regulatory elements and, 364, 365f, 366–367

MAP kinase regulating, 745–746, 745f

molecular mechanisms of repression and activation, 390–397

pervasive, 432–433

of protein-coding genes, 176–182

regulation of, 339, 354

repressed, 356, 357–358

stages of, 176–178, 178f

of template DNA strands, 176–179

termination of, 402

Transcription bubble, 177

Transcription elongation factors, 369

Transcription factors, 9, 9f, 168, 333, 339. See also specific transcription factors

cancer and, 1160–1161

ES cell pluripotency and, 982, 982f

in eukaryotes, 364

gene induction by, 721f

general, 373–376

HOXD13 encoding, 354

interactions, 387–388, 388f, 389f

iPC cells and, 983

master, 25–27, 27f, 721, 721f, 725f

master transcriptional regulators, 770

mutations in genes encoding, 355f

nuclear-receptor superfamily, 400, 401f

oncogenes and, 1160–1161

Pol II, 373–376

regulation of activity of, 398–403

Smad, 724

transcription-control elements as binding sites for, 380

Wnt signaling releasing, 752–753, 753f

Transcription initiation complex, 78–79, 78f

Transcription unit, 303–305, 305f

microsatellites in, 310

pre-rRNA, 462, 462f

Transcriptional control, eukaryotic, 356f

Transcriptional elongation, regulation of, 361–362, 362f

Transcriptional machine, 78–79, 78f

Transcriptional profiling, 122

Transcription-control elements, 379–380, 379f

Transcription-control regions, 354, 378, 378f

Transcription-coupled repair, 207

Transcytosis, 658, 1008, 1090, 1091, 1092f

Transducin, 694, 698, 698f

Transesterification reactions, 423, 425f, 466

Transfection, 251, 382f

stable, 252

transient, 251–252

Transfer RNA (tRNA), 168, 169f

amino acid activation, 188

folded structure and decoding functions of, 185–186, 186f

mRNA decoding, 183–188

nonsense mutations and, 196–197

processing of, 461–469

protein synthesis role, 183, 183f

structure of, 187f

tandemly repeated genes for, 308

wobble position, 186, 187f

Transferrin receptor (TfR), 456, 456f

Transferrin receptor complex, 663–664, 664f

Transformation, 236

oncogenic, 1140

Transformed cells, 132

Transformer gene, 436

Transforming growth factor α (TGF-α), 1141

Transforming growth factor β (TGF-β), 722, 990

binding and signal transduction, 722–724, 723f

cancer and, 722, 725

gene expression and, 1162, 1162f

loss of signaling, 1162

negative feedback loops regulating, 725–726, 726f

synthesis and protein storage, 722

Transgenes, 263

Transgenic mice, 263, 264f

trans-Golgi, 632, 649

M6P receptors and, 653–654

protein aggregation in, 655

protein sorting and, 657–658, 658f

proteolytic processing and, 656–657

vesicle-mediated protein transport from, 651–652, 651f

Transient amplifying cells, 988

Transient transfection, 251–252

Transition state, 60

Transition-state intermediate, 60

Translation, 8, 81, 168, 169f, 176

error rates, 188

GTPase superfamily role in, 195–196

initiation in eukaryotes, 191, 192f, 193

miRNA repression of, 447–450

mRNA structure and efficiency of, 195, 196f

polysomes and, 195

ribosome recycling and, 195

termination of, 194f, 195

Translocation, 193, 194, 343f

cell-body, 812

cell-free, 612

chromosomal, 1151

cotranslational, 588–589, 589f

post-translational, 591–592, 592f

proton, 556

termination of, 194f

Translocation channel, 585

Translocon, 589–591, 590f

mitochondrial protein import and, 610–612, 611f

Transmembrane ADAMs, 761

Transmembrane AMPA receptor regulatory proteins (TARPs), 1074

Transmembrane channels, 556

Transmembrane collagens, 951

Transmembrane electric gradient, 495–497, 496f

Transmembrane proteins, 285–287, 285f, 286f, 289–290

Transmembrane transport, 474–477

Transmissible spongiform encephalopathy, 87

Transmission electron microscope (TEM), 157, 157f, 167f

Transport proteins

in epithelia, 508–509, 508f

MDR1/ABCB1, 491, 492f

membrane, 68, 271, 474–477, 475f, 476f, 487

in plant vacuoles, 507

study approaches, 480

Transport vesicles, 632

budding, 665

in Golgi complex, 649f

lysosomes and, 665

retrograde, 632

sorting signals and, 642t

I-35

Transporters, 475f, 476

Transposable (mobile) DNA elements, 312–323

Transposase, 314, 315f, 322f

Transposition, 312–313, 318f

exon shuffling by, 322f

Trans-splicing, 428

Transverse tubules, 805

TRE, 401f, 402

Treadmilling, actin, 783f, 784–785

Treg cells, 1131

Triacylglycerols, 49, 536–537

Tricarboxylic acid cycle (TCA cycle), 533, 1137–1138. See also Citric acid cycle

Tricellulin, 940

Trichomonas vaginalis, 22

Tricyclic antidepressants, 1057

Triglycerides, 49, 50, 536–537

Trimeric G protein, 454

Triplet codes, 183

Triskelions, 651

tri-SNRP complex, 426, 426f

Trisomies, 916

Trisomy 21, 342, 916

Trithorax proteins, 406–407, 408f, 409

Triton X-100, 291, 291f, 292

TrkA, 1016–1017, 1017f, 1019f

TrkC, 1016–1017, 1017f

Trks, 1016

tRNA. See Transfer RNA

tRNA_i^Met, 190–191, 192f

Trophectoderm (TE), 979, 980f

Trophic factors, 1011, 1015, 1016, 1018–1019, 1019f

Tropoelastin, 960

Tropomodulin, 785, 785f

Tropomyosin (TM), 806, 806f, 807

Troponin (TN), 806–807

TRPV1, 1062, 1063f

True-breeding strains, 227

Trypanosoma brucei, 22, 526

Trypsin, 607

Tryptophan, 43, 44, 179, 180f, 184, 1052f

t-SNAREs, 638, 639f, 642–644, 643f, 1055

TSP. See Thrombospondin

tTA, 1148

Tuberculosis, 1130

Tubulin proteins, 325, 325f, 822

dimers of, in microtubule walls, 822–824, 824f

drugs affecting, 829–830

microtubule modifications and classes of, 842–844, 843f

polymerization of, 829–830

Tumor microenvironment, 1141

Tumor necrosis factor alpha (TNFα), 681, 758, 763, 770, 1011, 1021–1022

Tumorigenesis, 1136

Tumors. See also specific cancers and tumors

angiogenesis in, 1141

blood supply, 1137

cell differences, 1136–1143, 1136f

epigenetic changes and, 1155

as heterogeneous organs, 1140–1141

invasive, 1141–1143, 1142f

malignant, 1141

miRNA and, 1155–1156

protein composition, 1137–1139

Tumor-suppressor genes, 1135, 1150t, 1164–1165

apoptosis regulation genes as, 1163

inherited mutations in, 1153–1155, 1154f

loss-of-function mutations, 1152–1153

mutations in, 1162

Tunicamycin, 602

Tunneling nanotubes, 970–971, 971f

Turgor pressure, 481, 956

Turnover number, 92

Two-component regulatory systems, 360–361, 361f

Two-dimensional gel electrophoresis, 108–109, 109f

2,4-dinitrophenol (DNP), 559

2-hydroxyglutarate, 1139, 1139f

Two-Na⁺/one-glucose symporter, 503–504, 504f

Two-photon excitation microscopy, 149–150, 150f

Ty transposition, 318f

Type 1 diabetes mellitus, 769, 986

Type 2 diabetes mellitus, 504, 769, 770, 986

Type I collagen, 952–953

Type I transmembrane proteins, 594–595, 595f

Type II collagen, 952–953

Type II transmembrane proteins, 595–597, 596f

Type III transmembrane proteins, 595–597, 596f

Type IV collagen, 945, 948–950, 949f

Type IV transmembrane proteins, 597–598

Tyrosine, 43, 467