Page numbers followed by “f” indicate figures.

Page numbers followed by “t” indicate tables.

I-1

A box, 413

A kinase-associated proteins (AKAPs), 705–706

AAA ATPase family, 608

ABC superfamily proteins, 484f, 485, 492f, 492t

drug and toxin export by, 491–493

phospholipids and, 493–494

ABCB1. See Multidrug-resistance transport protein

ABCB4, 493f, 494

ABL kinase, 1158

ABO blood groups, 290t

ABO blood-group antigens, 289–290, 290f

Ac elements. See Activator (Ac) elements

ACAT. See Acyl:cholesterol acyl transferase

Acceptor stem, 185

Accessory proteins, 805

Acetabularia, 185

Acetate, 293

Acetic acid, 56, 56f

Acetyl CoA, 293, 1053

citric acid cycle and, 533–535, 535f

structure of, 533, 534f

Acetyl groups, 44

Acetylation, 45

Acetylcholine, 676, 715, 1026, 1050, 1052f, 1053, 1055

muscle contraction and, 1057–1058

Acetylcholine receptors (AChR), 1050, 1050f, 1051

muscarinic, 693–694, 694f

nicotinic, 1057, 1058–1059, 1059f

Acetylcholinesterase (AChE), 1050f, 1057

Acetyl-CoA carboxylase, 293

AChE. See Acetylcholinesterase

Acid hydrolases, 17

Acid-base catalysis, 95

Acidic activation domains, 386

Acidic keratins, 863, 864t

Acids, 55, 55f

Acquired immune deficiency syndrome (AIDS), 218, 967, 1152

Acrosome, 977, 978f

ACTH. See Adrenocorticotropic hormone

Actin, 778–779

capping proteins and, 785, 785f

in contractile bundles, 807

critical concentration of, 782

cytoskeleton, 815f

dynamics of, 791–792, 792f

filament assembly mechanisms, 786–792

filament growth, 782–784, 783f

filament turnover regulation, 784f

GTP-binding proteins and organization of, 813–815

intracellular movements and, 789–790, 790f

membranes linked to, 793–796, 794f

myosin steps and, 802–803

myosin V-bound vesicles and, 808–810

in myosins, 796–803

nucleation by Arp2/3 complex, 787–789, 788f

nucleation by formins, 786, 787f

polymerization of, 781–782, 782f, 789–790, 790f

structure organization, 793–796

thymosin-β₄ and, 785

toxins perturbing monomer pool, 791–792, 792f

treadmilling, 783f, 784–785

Actin cross-linking proteins, 793, 794f

Actin structures, 778–781

Actin-activated ADPase activity, 798

Actin-binding proteins, skeletal muscle contraction and, 805–807, 806f

Actin-nucleating proteins, 786

Action potential, 805, 1026, 1027–1028, 1027f

conduction in myelinated axons, 1043, 1043f

generation of, 1035–1037, 1059–1060, 1060f

Na⁺ influx and, 1034–1035

propagation, 1037–1039, 1038f

Activation, 1151, 1151f

of B cells, 1128

feed-forward, 517

by G proteins, 691–693

gene, during cellular differentiation, 395–396

of integrins, 963f

of JAK kinase, 728–730, 729f

of mitotic CDKs, 896–897

of PKA, 701–702, 702f, 703–704

receptor, EGF, and, 736–737, 737f

of receptor proteins, 682

of rhodopsin, 695–696, 696f

of RTKs, 734–735, 734f

separase, by APC/C, 901–902

splicing, 436f

SREBP activation, cholesterol and, 765, 765f

of STAT proteins, 731, 732f

of T cells, 1122, 1122f

of TLRs, 1126f

Activation domain (AD), 382, 386–387, 387f, 403f

Mediator complex and, 396–397, 397f

Activation energy, 60–61, 60f, 90, 90f

Activation loop, 730, 730f, 734–735, 883

Activation-induced deaminase (AID), 1099–1100, 1103, 1137

Activator (Ac) elements, 314

Activator proteins, 354, 359, 364

CAP, 357

histone acetylation directed by, 394–395

Activators, 384f

DNA-binding, 358–359

functional domains, 381–383

splicing, 437–439

TPA, 77–78

Active immunization, 1089

Active site, 91–92, 91f

DNA transcription, 177

serine proteases and, 92–96, 94f

Active transport, 476, 477t

Acute inflammatory demyelinating polyneuropathy, 1045

Acylation, 288

Acyl:cholesterol acyl transferase (ACAT), 764

AD. See Activation domain

ADAM 10, 761–762, 762f

ADAMs, 763, 960

ADAMTSs, 960

Adapter protein complexes (AP complexes), 641, 651–652

Adapter proteins, 741–742, 793–796, 924

Adaptive immune system, 1079, 1080, 1080f, 1087f, 1088–1089

Ig production of B cells in, 1101–1102

lymph nodes initiating, 1083f

ADCC. See Antibody-dependent cell-mediated cytotoxicity

Adenine, 45, 46f

post-transcription modifications of, 447

Adenoma, 1146, 1155

Adenosine, 701

Adenosine diphosphate (ADP), 6, 6f, 514

mitochondria and, 18

mitochondrial oxidation rate and, 558

Adenosine monophosphate (AMP/cAMP), 517, 679, 699, 699f

anchoring proteins localizing effects of, 705–706

I-2

cellular responses to rise in, 703–704, 704f

glycogen metabolism regulation by, 703f

PKA activation by, 701–702, 702f, 703–704

signal amplification and, 704

signal suppression, 706–707

Adenosine triphosphate (ATP), 6, 6f, 513, 514

axonal transport and, 834, 835

chloroplasts and, 18

generation of, 62–63

glycolysis regulation and demand for, 516–518

glycolytic pathway and, 516, 517f

hydrolysis of, 61–62, 61f

kinesin-1 cycle, 836–837, 837f

mitochondria and, 18

mitochondrial protein import and, 613

myosin movement and, 800, 801f

in photosynthesis, 563

post-translational translocation and, 591–592

proton-motive force and, 551–559

synthesis of, 515f, 516, 551–559, 551f, 552f, 563

Adenovirus, 431–432, 967

Adenylyl cyclase, 692, 699f, 700f

G_αs binding to, 701, 701f

GPCRs activating or inhibiting, 699–707

stimulation and inhibition by receptor-ligand complexes, 699–701, 700f

Adherens belt, 778

Adherens junctions, 796, 933, 935f

Adhesion molecules. See also Cell-adhesion molecules

evolution of, 928–929

JAMs, 940, 940f, 965

NCAM, 965, 1072

plant, 971–972, 971f

Adhesion receptors, 923, 925

Adhesive interactions, 922f, 961–967

leukocyte movement and, 966–967, 966f

Adipocytes, differentiation of, 770, 771f

Adipose cells

abnormal metabolism in, 770

adenylyl cyclase and, 700f

in obesity, 770

ADP. See Adenosine diphosphate

ADPKD. See Autosomal dominant polycystic kidney disease

Adrenocorticotropic hormone (ACTH), 655, 700–701

AE1 antiporter, 506–507

Aequorea victoria, 146

Aerobic glycolysis, 1138, 1138f

Aerobic metabolism, 519f

Aerobic oxidation, 513, 514f, 515, 533, 534f

Aerobic reactions, 63

Aerobic respiration, 513, 515

Afferent neurons, 1028

Affinity, 89, 681–682

signal sensitivity and, 683

Affinity chromatography, 111, 683–684

Aflatoxin, 1145

Agarose gels, 246

Aggrecan, 956, 957f

AGO2 protein, 450–451

Agonists, 683

Agrin, 1050f, 1051

AID. See Activation-induced deaminase

AIDS. See Acquired immune deficiency syndrome

AIRE, 1120

AKAPs. See A kinase-associated proteins

Akt, 750

Alanine, 43

Alb1 gene, 396

Alcoholic fermentation, 519f

Aldehyde, 47

Algae, 4f, 22. See also Chlamydomonas reinhardtii

Alleles, 224

autosomal dominant, 255

dominant, 224–225

dominant-negative, 262–264, 265f

recessive, 224–225, 255

Allelic exclusion, 1100

Allogenic tissue transplantation, 1120

Allosteric regulation, 100–101, 518f

Allostery, 100

All-trans-retinal, 1046, 1046f

Alpha carbon atom (C_α), 42

Alpha helix, 70–71, 71f

α-actinin, 793, 794f

α₁-adrenergic receptor, 692

α₁-antitrypsin, 607

α₂-adrenergic receptor, 692

α-like globins, 306, 307

α-SNAP, 644

αβ-tubulin, 822–824, 827

Alport’s syndrome, 950

Alprenolol, 683, 683f

ALS. See Amyotrophic lateral sclerosis

Alternative pathway, 1085, 1085f

Alternative polyadenylation, 450

Alternative RNA splicing, 181–182, 182f

mRNA, 417, 438

neurological disorders linked to, 438, 438t–439t

Alternative splicing, 304

in pre-mRNA processing regulation, 435

Alternatively spliced mRNAs, 417, 438

Alu elements, 320–321

ALV. See Avian leukosis virus

Alzheimer’s disease, 87, 88f, 763, 764f, 984

Amanita phalloides, 792

Amino acids, 7, 42–45

codons to, 184, 184f

DNA information converted to, 9f

essential, 44

import against high concentration gradients, 503–504

linear arrangement of, 69–70

protein folding and sequence of, 81–82

proteins composed from, 42–45, 43f

side chains, 42–45, 45f

symporters, 504, 505f

transport across epithelia, 508–509, 508f

tRNA activation of, 188

Aminoacyl-tRNA, 185, 186f, 191

Aminoacyl-tRNA synthetases, 185, 188

Aminoglycoside antibiotics, 527

Amoeba dubia, 309

Amoebidium parasiticum, 526

AMP kinase (AMPK), 453f, 454

AMPA receptors, 1073–1074, 1074f

Amphipathic, 32, 75

Amphipathic molecules, 273

Amphiphilic, 32

Amphitelic attachment, 898, 899f

Amplification, 679, 1151

of extracellular signaling, 679

in rhodopsin signal transduction pathway, 696–697

by signal transduction pathways, 679–680

AMPPNP, 835

Amyloid fibrils, 87, 88f

Amyloid plaques, 87, 763

Amyloid precursor protein (APP), 763, 764f

Amyloids, 87, 88f

Amyotrophic lateral sclerosis (ALS), 984–986

Anaerobic metabolism, 519f

Anaerobic respiration, 515

Anaphase, 851, 857f, 859, 876

Anaphase A, 857–858, 857f

Anaphase B, 857f, 858

Anaphase II, 913

Anaphase-promoting complex (APC/C), 886, 901f

separase activation by, 901–902

Anchoring junctions, 932, 932f

Anchoring proteins, 705–706

Androstenone, 1067

Anemia, 795

sickle-cell, 225

Aneuploid organisms, 225

Aneuploidy, 850, 909, 916, 1137

Anfinsen, Christian, 82

Angiogenesis, 1141

Angiotensin, 808

Animal cloning, 983

Anion antiporter, 506–507

Aniridia, 364

Ankyrin, 794, 795

Annular phospholipids, 287, 287f

Antagonistic interactions, 1004

Antagonists, 683

Antenna complex, 563

Anterograde transport vesicles, 632

Antibiotics

resistance to, 322–323

ribosomes and, 190

Antibodies, 89, 1081, 1088–1089, 1088f. See also Immunoglobulins

antigen-specific, 1091

in immunoelectron microscopy, 159, 159f

monoclonal, 135–136, 136f, 144, 684, 1080, 1094

for oncoproteins, 1158

organelle-specific, 162–164, 164f

phosphorylated peptide-specific, 684

polyclonal, 144

I-3

production of, 1128, 1129f

Antibody assays, 111–112

Antibody-affinity chromatography, 110f, 111. See also Immunoprecipitation

Antibody-dependent cell-mediated cytotoxicity (ADCC), 1094

Anticodon, 183

in nonstandard base pairing, 186, 187f, 188

Antidepressant drugs, 1057

Antidiuretic hormone, 483

Antigen processing and presentation, 1109–1115

Antigen-presenting cells (APCs), 1084, 1127–1128

professional, 1105–1106

Antigens, 1081, 1083f, 1089

ABO blood group, 289–290, 290f

in antibody production process, 1128

large T-antigens, 199, 200f

MHCs binding, 1107–1109, 1108f

PCNA, 200

SC40 large T-antigen, 624

Sialyl Lewis-x, 966

Antigen-specific antibodies, 1091

Antigen-specific receptors, 1118, 1120

Anti-growth factors, 881

Anti-mitogens, 889

Antiporters, 476, 502–507, 558, 1052–1054, 1053f

Antisera, 1089

Antitermination factors, 377, 377f

Antithrombin III, 955, 955f

AP complexes. See Adapter protein complexes

AP1, 388

Apaf-1, 1020f

APC/C. See Anaphase-promoting complex

APCs. See Antigen-presenting cells

Apical Par complex, 1007

Apical surface, 24, 508, 657, 658f, 931

aPKC, 1007

Aplysia californica, 1070, 1072f

APOB gene, 439, 440f

Apoptosis, 731, 751, 906, 1011

Ca²⁺ in, 1022

caspases in, 1015

evolutionarily conserved pathways in, 1013–1015, 1014f

genes regulating, 1163

mitochondria and, 1017, 1018

neurons and, 1015–1017

phagocytosis in, 1012, 1012f

programmed cell death through, 1012–1013, 1012f

regulation genes for, as tumor-suppressor genes, 1163

regulation in vertebrates, 1020–1021

signaling pathways in regulation of, 1019f

Apoptosome, 1018, 1020f

Apotransferrin, 663, 664f

APP. See Amyloid precursor protein

Aquaporins, 286–287, 481–483, 482f

Arabidopsis thaliana, 20f, 525, 561

meristems of, 998, 998f, 999f

Archaeans, 4f, 10

ARF protein, 639, 640

Arginine, 43, 184

Argonaute protein, 448

Arp2/3 complex, 786, 787–789, 788f, 789f, 790f, 791f

Arrestin, 697–698, 698f

ARSs. See Autonomously replicating sequences

Ascorbic acid, 951–952

Asialoglycoprotein receptor, 600, 600f

Asparagine, 44

Aspartate, 44, 488f

in Ca²⁺ ATPase, 487f

in P-class pumps, 488

Aspartic acid, 43

Assays, 111–114, 113f. See also specific assays

Asters, 850, 853

Asthma, 683

Astral microtubules, 851

Astrocytes, 985–986, 1030–1031, 1031f, 1032, 1044

gap junctions connecting, 1060

synapses and, 1049f

Asymmetric carbon atom, 34

Asymmetric cell division, 27, 903, 975, 976f, 1002f

Ataxia telangiectasia, 906

ATF6, 607

Atherosclerosis, 40, 296, 439–440, 1022

ATM, 906, 908

Atoms

bonding properties in biomolecules, 34t

electron structure of, 33–34

ATP. See Adenosine triphosphate

ATP synthase, 534f, 551, 551f, 553–554, 553f, 557f

protons passing through, 555–556

ATP/ADP antiporters, 558

ATP/ADP transport system, 556, 558, 558f

ATPase, 486

AAA family, 608

actin-activated activity of, 798

Ca²⁺, 486–489, 487f, 488f, 489f

H⁺/K⁺, 509

Na⁺K⁺, 489, 489f, 490f

ATPase fold, 779

ATP-powered pumps, 475f, 476, 483–494

classes of, 484–485, 484f

ATR, 906

Atractylis gummifera, 558

Atractyloside, 558

Attenuation, 361, 1130

AUG codon, 184, 190

and translation initiation, 191, 193

Augmin complex, 826, 858

AU-rich elements, 447

Aurora B, 899

Aurora kinase, 897

Autocrine signaling, 675f, 676, 763

Autoimmune diseases, 986, 1141. See also specific diseases

desmoglein and, 938

TNFα and, 681

Autoimmunity, 1079

Autonomously replicating sequences (ARSs), 345

Autophagic pathway, 667–669, 669f

Autophagic vesicle, 667

Autophagosome, 453, 667

growth and completion, 668

nucleation of, 668

targeting and fusion, 669

Autophagy, 16, 452, 529, 667

Autoproteolytic cleavage, 1014

Autoradiography, 114–116, 634, 684

Autosomal dominant alleles, 255

Autosomal dominant polycystic kidney disease (ADPKD), 849

Autosomal recessive disorders, 255f, 621

Autosomal recessive mutations, 621

Autosomes, 341

Auxins, 969

Avian leukosis virus (ALV), 1152

Avidity, 1090, 1120

Axon termini, 1027

neurotransmitter and synaptic vesicle cycling in, 1053f

synaptic vesicles in, 1049f

Axonal transport, 833–834, 834f, 835

Axonemal dynein, 844, 846f

Axoneme, 844

Axons, 1016, 1027

anterograde transport down, 835

growth cones of, 868, 868f

information moving along, 1027–1028

myelinated, 1043, 1043f

neurofilaments in, 864