Page numbers followed by “f” indicate figures.

Page numbers followed by “t” indicate tables.

S. cerevisiae. See Saccharomyces cerevisiae

S. mediterranea. See Schmidtea mediterranea

S (synthesis) phase, 19, 875

CDK and entry into, 888

loss of regulation of, 1164–1165

onset of, 890–891, 891f

S phase CDK inhibitor, 890–891, 891f

S phase CDKs, 882, 883, 897

S phase cyclins, 884, 890f

S. pombe. See Schizosaccharomyces pombe

S4 helices, 1039–1040, 1042

SA sequence. See Signal-anchor sequence

Saccharomyces cerevisiae, 19, 20f, 21, 21f, 22, 124, 224, 877, 877f

cell cycle commitment, 888

centromeres of, 346–347, 346f

DNA replication initiation in, 890

mating pathways, 746, 747f

mRNA localization in, 457, 459, 459f, 460f

myosin V cargo movement in, 809f

ribosome components, 189t

ribosome structure, 190f

RNA polymerases, 368, 368f

segregation in breeding, 227, 228f

temperature-sensitive mutation in, 228, 905

S-adenosylmethionine, 421

SAGA complex, 394

SALL1 gene, 366, 366f

Salmeterol, 687t

Saltatory conduction, 1043

Salty taste, 1066

SAM complex, 616

Sar1 protein, 639, 640, 640f, 646f

Sarcomas, 1136, 1166

Sarcomeres, 804, 804f

Sarcoplasmic reticulum (SR), 486, 487f, 805, 806f

Ca²⁺ regulation by, 805, 806f

Satellite DNA, 310–311

Saturated fatty acids, 48, 50, 293

SC. See Synaptonemal complex

SCA. See Stigma/stylar cysteine-rich adhesin

Scaffold proteins, 67, 746–748, 747f, 805

Scanning electron microscope (SEM), 157, 157f, 161, 161f

SCAP. See SREBP cleavage-activating protein

Scatter factor, 816

Scavenger receptors, 1084

SCF. See Stem cell factor

Schizosaccharomyces pombe, 877, 878f

centromeres of, 346–347

growth cycle of, 905

mitotic CDKs in, 896

Schleiden, Matthias, 129

Schmidtea mediterranea, 20f, 27–28, 753, 754f

Schwann, Theodore, 129

Schwann cells, 1030, 1044, 1044f, 1045–1046, 1045f

SCID. See Severe combined immunodeficiency

SCNT. See Somatic-cell nuclear transfer

Scribble complex, 1007, 1010

Scurvy, 952

SC-β cells, 986

SDS. See Sodium dodecylsulfate

SDS-PAGE. See SDS-polyacrylamide gel electrophoresis

SDS-polyacrylamide gel electrophoresis (SDS-PAGE), 107–108, 108f, 115

sec mutants. See Secretion mutants

Sec61 complex, 590, 591f

Sec61α, 590, 590f

Sec63 complex, 591

Seckel syndrome, 906

Second messengers, 678–679, 942

glycogenolysis regulation with, 714

from PLC, 709–710, 710f, 712

Secondary active transport, 476

Secondary cell walls, 969

Secondary lymphoid organs, 1082

Secondary structure

protein, 70–71, 71f, 72f

RNA, 175, 175f

Secreted Ig, 1101–1102, 1102f

Secretion mutants (sec mutants), 636, 637f

I-31

Secretogranin II, 655

Secretory pathway, 584–585, 631, 633f

assaying protein transport through, 634–635, 635f

early stages of, 645–650

ER and, 645–648

Golgi complex in, 632, 633f

later stages of, 650–658

rough endoplasmic reticulum in, 632

study techniques for, 634–638

Secretory proteins, 585

ER targeting by, 586–588, 587f

synthesis of, 587, 588–589, 589f

Secretory vesicles, 13f

Securin, 901–902, 901f, 913

Sediment, 106

Segmental duplication, 307

Segregation of mutations, 225, 227, 227f, 228f

Selectins, 966

Selection medium, 135

Selective serotonin reuptake inhibitors (SSRIs), 1057

Selectivity filter, 497–500, 499f

Self-splicing

introns, 429–430, 430f, 466, 466f

protein, 105

RNA, 175

SEM. See Scanning electron microscope

Senses, 1061

Sensory neurons, 1016, 1017f, 1026, 1028, 1071

Separase, 901f

APC/C activating, 901–902

cohesin cleavage and, 901, 901f

Septation initiation network, 910

Sequence drift, 306

Sequence homology, 600

Sequence motif, 76

Sequence-reading helix, 384

Sequence-specific DNA affinity chromatography, 381

Serine, 44, 184

Serine proteases, 92–96, 94f

Serotonin, 1026, 1052f, 1057

Sertraline, 1057

Serum, 1088, 1088f

Serum response element (SRE), 745

Serum response factor (SRF), 745

Serum starvation, 881

SET domain, 407, 408f

Severe combined immunodeficiency (SCID), 728

Sex-lethal gene, 435–436

SH2 domain, 730, 731, 731f

SH3 domains, 742, 742f

shaker mutation, 1039, 1042, 1042f

Sheet-forming and anchoring collagens, 951

Shh. See Sonic Hedgehog

Shigella species, 790

shiverer mutation, 1045

Shmoos, 1003, 1004f

Shoot apical meristem, 997, 998–999, 998f, 999f

Short interfering RNAs (siRNAs), 419, 420t, 445

Short interspersed elements (SINEs), 318–319, 320–321

Short tandem repeats (STRs), 256

shRNA. See Small hairpin RNA

Sialyl Lewis-x antigen, 966

Sic1, 890–891, 891f

Sickle-cell disease, 225, 995

Side chains

amino acid, 42–45, 43f, 45f

oligosaccharide, 602–603

Side-binding proteins, 830–831

Sigma factors. See σ (sigma) factors

σ⁵⁴-RNA polymerase, alternative, 359–360

σ (sigma) factors, 357, 359t

alternative, 359

Signal amplification

in cAMP-PKA pathway, 704

in rhodopsin signal transduction pathway, 696–697

Signal peptidase, 591

Signal peptides, 585

Signal recognition particle (SRP), 195, 367, 588–589, 588f, 589f

Signal sequences, 585

Signal transduction, 674, 675–680

Signal transduction pathways, 674, 680f

adipocyte differentiation and, 770, 771f

amplification by, 679–680

types of, 719–720, 720f

Signal transduction proteins, 685f

studying, 681–686

Signal-anchor sequence (SA sequence), 594–597, 598f

Signaling cascade, 904

Signaling molecules, 674, 675–676

near-maximal cellular response to, 682, 682f

Signaling pathways

in apoptosis regulation, 1019f

cancer and aberrations in, 1161–1163

growth factor, 905

Hh, 754–757, 756f, 758f

insulin and, 766–770, 768f, 771f

integration of responses to multiple, 766–770, 768f, 771f

integrin adhesion receptors and, 929f

JAK/STAT, 726–733

kinases in, 676–677

mitochondrial membrane permeability and, 1019f

Notch, 607

ordering of, 231, 231f

phosphatases in, 676–677

phosphoinositide, 748–751

protein cleavage-controlled, 761–766

repurposing in evolution, 911

ubiquitinylation controlling, 751–760

Signaling proteins, 68, 674, 674f

Signal-transducing proteins, 1160

SILAC. See Stable isotope labeling with amino acids in cell culture

Silencer sequences, 391

Silent mutations, 204, 225

Silver staining, 112

SIM. See Structured illumination microscopy

Simple diffusion, 474–475, 477t

Simple-sequence DNA, 310–311

SINEs. See Short interspersed elements

Single-nucleotide polymorphisms (SNPs), 256, 256f

Single-pass membrane proteins, 593, 594–597

Single-pass transmembrane proteins, 285–286, 285f

Single-stranded DNA, 906

SIR proteins, 391, 392f, 393

siRNA knockdown, 451

siRNAs. See Short interfering RNAs; Small inhibitory RNAs; Small interfering RNAs

sis oncogene, 1159

Sister chromatids, 15f, 851, 875, 893, 894f, 895

co-orientation of, 913

resolution of, 899

Sister kinetochores, co-orientation of, 917

60S subunit, 192f

Skeletal muscle, 804f

accessory proteins, 805

contraction of, 803–804, 805f

regulation of contraction of, 805–807, 806f

Ski, 725–726, 726f

Skin, structural integrity of, 864–865

Skin cancer, 744

SKL sequence, 619–621

SLE. See Systemic lupus erythematosus

Sleeping sickness, 1082

Sliding clamp, 200

Sliding-filament assay, 798, 798f

Sliding-filament contraction model, 803–805, 805f

Slow-acting retroviruses, 1152

SM. See Sphingomyelins

SM proteins, synaptic vesicle fusion and, 1055

SMAC/DIABLO family, 1018

Smad3/Smad4 complex, 724–725, 725f

Smads, 722–726

loss of TGF-β and, 1162

negative feedback loops regulating, 725–726, 726f

transcription factors, 724

Small hairpin RNA (shRNA), 266, 1158

Small inhibitory RNAs (siRNAs), 264–265

Small interfering RNAs (siRNAs), 367, 368, 448f

Small nuclear ribonucleoprotein particles (snRNPs), 424

in spliceosome, 426–427

splicing, 426

Small nuclear RNAs (snRNAs), 308, 321, 367, 420t

pre-mRNA splicing with, 424, 425f, 426

Small nucleolar RNAs (snoRNAs), 308, 420t

pre-rRNA processing and, 462–465, 464f

Small rRNA, 190

I-32

Small subunit processome, 464

Small-molecule proteasome inhibitors, 99

Smallpox, 1079, 1130

SMC. See Structural maintenance of chromosome proteins

smewdi-1 gene, 988

Smooth endoplasmic reticulum, 13f, 16

Smooth muscle

contraction regulation in, 808

vascular, 714–716, 715f

SNAP-25, 643, 643f, 644, 1055

SNARE proteins, 643f. See also t-SNAREs; v-SNAREs

dissociation of, 644

synaptic vesicle fusion and, 1055

vesicle fusion and, 642–644, 643f

SnoN, 725–726

snoRNAs. See Small nucleolar RNAs

SNPs. See Single-nucleotide polymorphisms

snRNAs. See Small nuclear RNAs

snRNPs. See Small nuclear ribonucleoprotein particles

SOCS proteins, 733, 770, 1124

SOD. See Superoxide dismutase

SOD1, 984, 986

Sodium chloride (NaCl), 36, 37f

Sodium deoxycholate, 291, 291f

Sodium dodecylsulfate (SDS), 108, 291, 291f

Solitary genes, 303

Somatic cell recombination, 261–262

Somatic cells, 977

iPS cells from, 983–986

Somatic gene rearrangement, 1095, 1096f

Somatic hypermutation, 1099–1100

Somatic mutations, 1153, 1153f

Somatic recombination, 1095

Somatic-cell nuclear transfer (SCNT), 983, 984f

Sonic Hedgehog (Shh), 755, 1162

Sorting signals, 641

cytoplasmic, 642t

diacidic, 646, 646f

endocytosis targeting, 660–661

KDEL, 647

KKXX, 647

luminal, 641, 642t

NPXY, 661

transport vesicles and, 642t

YXXΦ, 651

Sos protein, 741–742, 741f, 743f

Sound, perception of, 437–438, 437f

Sour taste, 1066

Southern, Edwin Mellor, 246

Southern blotting, 246–247

Specific activity, 114

Specificity, 89, 681–682, 1080, 1088

Spectrin, 793, 794f, 795

Sperm, 975, 977, 978f

Sphingolipids, 277f

clustering with proteins, 282–283

synthesis and intracellular movement, 293–297

Sphingomyelins (SM), 277f, 278, 279, 295

Sphingosine, 295

Spinal muscular atrophy, 428

Spindle assembly checkpoint pathway, 856–857, 908–909, 908f

Spindle midzone, 903

Spindle pole bodies, 897

Spindle poles, 825, 857f, 876

Spindle position checkpoint, 860

Spindle position checkpoint pathway, 909–911, 909f

Spinning disk confocal microscope, 147, 148–149, 149f

Splice sites, 303, 423

globin-gene, 444

Spliceosomes, 426–428, 426f, 427f, 443, 466f

Splicing activation, 436f

Splicing activators, 437–439

Splicing factors, 427, 468f

Splicing repressors, 437–439

Sporogenous tissue, 968

Sporozoites, 23f

Spot desmosomes, 933

SR. See Sarcoplasmic reticulum

SR proteins, 428–429, 429f

mRNP export directionality and, 441–442, 442f

mRNP exporter and, 441

Src gene, 730

SRE. See Serum response element

SRE-binding proteins (SREBPs), 763–766, 765f

SREBP cleavage-activating protein (SCAP), 765–766, 765f

SREBs. See SRE-binding proteins

SREs. See Sterol regulatory elements

SRF. See Serum response factor

SRP. See Signal recognition particle

SSRIs. See Selective serotonin reuptake inhibitors

STA sequence. See Stop-transfer anchor sequence

Stabilizing proteins, 805

Stable isotope labeling with amino acids in cell culture (SILAC), 118

Stable transfection, 252

Stahl, Franklin William, 197

Starch, 47, 560

structure of, 560f

START, 888–889

Start (initiation) codons, 184, 190–191

STAT pathway, 1124

STAT proteins, activation of, 731, 732f

STAT transcription factors, 731

Statins, 296

Steady state, 52–53, 53f

STED microscopy. See Stimulated emission depletion microscopy

Stem cell, mesenchymal, 770

Stem cell factor (SCF), 886, 996, 997f

Stem cells, 27, 976. See also Embryonic stem cell; Induced pluripotent stem cells

cancer, 1140–1141

differentiation of, 988, 989f

germ-line, 990

hematopoietic, 994–995, 995f, 996f, 997f

intestinal, 991–992, 991f, 992f, 993f, 994

Lgr5-expressing, 992

meristems and, 996–999, 998f, 999f

multicellular organism niches and, 987–999

multipotent, 977, 987

multipotent somatic, 988

neural, 1031–1033, 1032f

Par proteins and, 1008, 1010, 1010f

pluripotent, 988

Stem-cell niche, 989

Stereoisomers, 34, 34f

Steroid receptor superfamily, 386

Sterol regulatory elements (SREs), 764, 766

Sterols, 277f, 278

Sterol-sensing domain, 296, 765

Stigmasterol, 277f, 278

Stigma/stylar cysteine-rich adhesin (SCA), 971

STIM proteins, 713

Stimulated emission depletion microscopy (STED microscopy), 153, 154f

Stimulatory G protein, 692

STING protein, 1085

Stomach, acidification of contents, 509–510, 509f

Stop (termination) codons, 184, 195

Stop-transfer anchor sequence (STA sequence), 594–597, 598f

Stored sequences, 324–325, 324f

Store-operated channels, 713

Strabismus gene, 1008, 1009f

Strand invasion, 209

Streptomyces coelicolor, 359

Stress fibers, 778

Stromal cells, 963, 996, 997f, 1123, 1131

Stromal proteins, 617

Strong promoters, 358

STRs. See Short tandem repeats

Structural domain, 77

Structural maintenance of chromosome proteins (SMC), 336, 336f

Structural motifs, 75–76, 76f, 325

Structural nucleoporins, 622, 623f

Structural proteins, 67

Structured illumination microscopy (SIM), 153, 154f

Sturtevant, Alfred, 232, 233

Subcellular details, imaging, 142–143, 143f

Submitochondrial compartments, protein targeting to, 613–616, 614f

Substrate binding, 93–94, 93f

Substrate-binding site, 91

Substrate-level phosphorylation, 516

Substrates, 90

Subventricular zone (SVZ), 1032, 1032f

Succinate dehydrogenase, 534

Succinate-CoQ reductase, 542, 544

Sucrose, 48f, 560

synthesis of, 573–574, 575f

Sugars, 7, 560

Sulfhydryl group, 44, 603

Supercomplexes, 546–547, 548f

Superoxide dismutase (SOD), 548f, 549

Super-resolution microscopy, 130, 153, 154f, 155

I-33

Suppressor mutations, 231, 232f

SURF complex, 458f

Surveillance mechanisms

in cell cycle regulation, 904–911

checkpoint pathways, 856–857, 874, 876, 904, 905, 908–911, 908f, 909f, 1149

mRNA, 456–457, 458f

SV40 DNA virus, 199, 200f, 201f, 431

NLS discovery and, 624

SV40 large T-antigen, 624

SVZ. See Subventricular zone

Sweet taste, 1066

SWI/SNF chromatin-remodeling complex, 395

Switch proteins, 101

GTPase, 639–641

Symmetric cell division, 975, 976f

Symplekin, 430

Symporters, 476, 502–507

two-Na⁺/one-glucose, 503–504, 504f

Synapses, 25, 1016, 1029f

astrocytes and, 1049f

chemical, 1060

communication at, 1048–1060

electrical, 1060

elimination of, 1051–1052

excitatory, 1026, 1048

formation of, 1048–1052

glial cells and formation of, 1049

information flows in, 1028

inhibitory, 1026

memory formation and, 1070–1071

mRNA localization in, 459–460, 460f

neuromodulatory inputs, 1026

neurotransmitter transport to, 1052–1054

Synapsins, 1054, 1072

Synapsis, 226f

Synaptic plasticity, 1070, 1072–1074, 1072f, 1073f

Synaptic vesicles, 1028, 1049f

cycling of, 1053f

neurotransmitter transport into, 1052–1054

in presynaptic terminal, 1054

recycling, 1056–1057

regulation of fusion on, 1055–1056

Synaptonemal complex (SC), 912

Synaptotagmin, 1056, 1056f

Syncytial divisions, 880

Syntaxin, 643, 644

Syntelic attachment, 898, 899f

Synteny, 25, 26f, 342

Synthetic lethal mutations, 231–232, 232f, 1158

Synthetic lethality, 231–232

Systemic lupus erythematosus (SLE), 425f