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:44 Index
RNA cleavage 417–418
RNA editing 418–419, 806
RNA folding 302, 303F, 335F, 363
RNA genes
in the human genome 185
for rRNA 327, 330
in S. cerevisiae 305
RNA helicases 1300
RNA interference (RNAi)
as an experimental tool 433
as a defense mechanism 431–432
and heterochromatin formation
432–433
limitations 501
small ncRNAs and 429–431
testing gene function 499–501
RNA ligases 688
RNA localization 421–422
RNA polymerase holoenzyme 306
RNA polymerase I 327
RNA polymerase II
as an “RNA factory” 317F
gene control regions and 384–386
general transcription factors and
309–312, 384–385
modifying proteins 312–313
similarity with bacterial polymerase
309, 310F
snoRNAs and 328–329
RNA polymerase III 328
RNA polymerases 303–305
DNA polymerases compared 304–305
in eukaryotes 309T
paused polymerases 388
RNA-dependent 431
RNA primers 245, 247, 249, 253
RNA processing
in chloroplasts 806
control of gene expression 372, 373F
RNA-req method 371F
RNA sequencing (RNA-seq)
alternative splicing and 482
deep RNA sequencing 477
mRNA analysis 503–504
RNA splicing
and chromatin structure 323
consensus nucleotide sequence for
319
coordination with transcription 322
“cryptic” splice sites/signals 321,
322F, 323, 324F
errors and disease 323–325
as a function of snRNAs 305T
intron sequence removal by 315–316,
317–318, 320F, 336
regulation 416
spliceosome role 319–320
see also alternative splicing
RNA transport and localization 372, 373F
RNA tumor viruses 1105
“RNA world” 69, 362–366, 415
RNAs
antisense 423F, 435
categories and proportions of 305T,
306
conformations 5F
distinctions from DNA 4–5, 302, 366
double-stranded, as viral
characteristic 1304
rearrangements in the spliceosome
321
regulation of transport from the
nucleus 419–421
self-replicating potential 364, 365F
as single-stranded 302, 363
size of molecule 303
in telomerase 263T, 429, 435
in transcription and translation 4–5
see also long noncoding; messenger;
ribosomal; small noncoding;
snRNAs; transfer
RNPs (ribonucleoproteins) see hnRNPs;
mRNPs; snRNPs
Robo1, Robo2 and Robo3 receptors
1203F, 1204
robustness, in biological networks 520,
822
Rock kinase 958F, 997, 998F
rod photoreceptors 844–846, 848, 943
ROS (reactive oxygen species) 808
see also superoxides
rosettes, cellulose synthase 1085–1086
rotary catalysis, ATP synthases 776–778
rough ER, protein glycosylation 683–684
roundworms see Caenorhabditis elegans
Rous sarcoma virus 1105, 1265
RRE (Rev responsive element) 420
RTK/Ras/PI3K pathway 1113
RTKs see receptor tyrosine kinases
Rubisco see ribulose bisphosphate
carboxylase
ruffles, in macropinocytosis 732, 733F,
1280–1281, 1282F
ruthenium red dye 582, 583F
ryanodine receptors 838–840
S
S. cerevisiae see Saccharomyces
S-Cdks 974, 979, 1014
S-cyclins 969, 971, 993, 1013–1014
S4 helix 622
S phase, cell cycle
centrosome duplication 984–985
DNA replication in 258–260, 963,
964F, 974–977
visualization 966
“S” values (sedimentation coefficients)
rRNA 309T, 328
ultracentrifugation 446, 455
Saccharomyces cerevisiae 21T, 31F
cell cycle in 966
centromeres 203
DNA replication in 253–254, 259
gene density 182F
genes essential to growth 499
genes for voltage-gated ion channels
627
intercellular communication 813
kinesins 936
mitochondrial inheritance 807
as model organism 29T, 966
mutant libraries 498
myosin V in 925
RNA coding genes 305
RNA rearrangements at the
spliceosome 321F
separated chromosomes 466F
see also yeasts, budding
salamanders 1194–1195
Salmonella enterica 1268, 1281, 1282F,
1284F, 1285, 1290
Salmonella ssp.
as Gram-negative 1267F
use of phase variation 294
SAM complex (sorting and assembly
machinery) 659, 660F, 662
Sanger sequencing see dideoxy
sequencing
Sar1 proteins 703, 704–705F
sarcomas 1092
sarcomeres 918–920, 948
sarcoplasmic reticulum (SR)
Ca 2+ pump 606–607, 608F, 632F, 633,
920
in muscle cells 671, 920, 921F
satellite cells, skeletal muscle 1234
scaffold proteins 126
cullins as 160, 164
Dishevelled as 870
in intracellular signaling complexes
822, 823F, 857
membrane bending 594
in protein machines and biochemical
factories 164, 332F
septins as 949, 999
in tight junctions 1049–1050
scaffold RNA molecules 165, 435
scanning electron microscopy see SEM
SCAP (SREBP cleavage activation protein
656F
SCF (stem cell factor)/Steel protein 1187,
1244
SCF ubiquitin ligase 159–160, 164,
167–168, 971, 972F, 973, 1004
schistosomes 1302F
schizophrenia 494
Schizosaccharomyces (S. pombe)
microtubule +TIP proteins 935F
mitochondrial genome 801F, 805F
as a model organism 966, 1271
mutant phenotype 21F
Schmidtea mediterranea 1247–1249
Schwann cells 625
Sciara 987F
SCN cells (suprachiasmatic nucleus) 877
“scramblases” 574, 690
SDS-PAGE (sodium dodecyl
sulfate-polyacrylamide-gel
electrophoresis) 452, 453F, 454F,
584
SDS (sodium dodecyl sulfate) 583, 584F
sea urchin embryo 403F, 524
sealing strands 1047–1048, 1049F, 1050
Sec61 complex 676–678
Sec pathway 665F
Sec23/Sec24 and Sec 13/31 proteins
705F
SecA ATPase 677, 678F
second-generation sequencing methods
479–480
second law of thermodynamics 52, 53F,
60, 102–103
second messengers 819–820, 824, 827,
833
in intracellular signal amplification 848
IP 3 and diacylglycerol as 837, 838F
secondary cell walls 1082–1083,
1085–1086
secretion systems, bacterial 1271, 1278,
1281, 1282F, 1285–1286
secretory and endocytic pathways
constitutive and regulated secretory
pathways 741, 742F