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:36 Index
nucleosome assembly factors 976
nucleosome core particles
DNA packaging in 188–190
histone proteins in 187–188, 189F
susceptible sites to DNA damage
267F
nucleosome mark recognition 199F
nucleosome sliding 190, 191F
nucleosomes
assembly behind replication forks
261–265
as basic chromosome structures
187–188
chromatin remodeling and 190–193,
380
cooperative binding and 379–380
DNA replication and 254
fibroblast reprogramming as iPS 1256
histone H1 binding 193F
nucleotide excision repair 266T, 270–271
nucleotide-gated channels 614
nucleotide sequences see DNA
sequences
nucleotide-sugar intermediates, in
glycosylation 684
nucleotides
in activated carriers 69
biosynthesis 86
complementarity 3F
functions 101
in the nitrogen cycle 85–86
nomenclature 101
as nucleic acid monomers 3
number in human genome 28
number in the nucleosome 188
as phosphorylated nucleosides 101
structures 3–4, 100–101
see also bases
nucleus see nuclei
nullcline analyses 518, 519F
numerical aperture and resolution 532,
533F
numerical integration 512
O
O-linked glycosylation 719
O-linked oligosaccharides 684, 718, 868
O 6 -methylguanine 271
obesity 1115, 1128F, 1129, 1264
occludin 1049–1050
Oct4 transcription regulators 398–399F,
506F, 1254–1255
see also OSKM factors
β-octylglucoside 583, 584F
ocular dominance columns 1212
Okazaki fragments 241–242, 243F,
245–250, 253–254, 255F, 261
oleic acid 98
olfactory neurons 943, 1227
olfactory receptors 832, 843–844, 846T,
1250F
oligodendrocytes 625
oligonucleotides, affinity chromatography
449
oligosaccharides 97
glucose trimming 683F, 684–685
mannose trimming 686
N-linked 683
processing in the ER and Golgi
apparatus 718F
processing in the Golgi apparatus
716–718
oligosaccharyltransferases 677, 683F,
684, 717F
Omi protein 1029
OMPLA protein 581F
oncogene dependence 1135
oncogenes
collaborative action 1118
discovery 1105–1107
DNA sequence changes 1110F
gain-of-function mutations and 1104
v-Ras 1106
from viruses 1131–1132
see also proto-oncogenes
oocytes see eggs
open reading frames (ORFs) 424, 457,
482
ribosome profiling technique 505–506
operons 380–385. 385
Lac operon 381F, 382–383
opportunistic pathogens 1265, 1268,
1276
opsin 845
opsonization 1301F
optic cup 1258F
optic tectum 1204–1206, 1207F
optical isomers, amino acids 112
optical microscopy see light microscopy
optical sections 540
optical techniques, protein interactions
458
optogenetics 624–625
OR logic 521F
ORC (origin recognition complex)
259–261, 974–975, 976F
order
in biological structures 51F
disorder as entropy 52–53, 60, 103
thermodynamics of 52–54
organelles
biparental and maternal inheritance
807
endosymbiont hypothesis 800
energy-converting 753
four families of 645
gene transfer to the nucleus 801–802
growth and proliferation 648, 658,
800, 806
lipid droplets 573
membrane-enclosed 565, 641–649,
889, 896, 938–939, 1001
not constructed de novo 648, 658
protein movements between 645–647
Rab family GTPases in 706T
secretory and endocytic pathways
646F
from subcellular fractionation 445
volumes in a liver cell 643T
organic chemistry
biological importance 47
chemical bonds and groups 47,
90–91
organisms
shared proteins 482
size differences 1010
see also species
Organizer signaling center 1167–1168
organoids 1223
organotrophic organisms 11
organs
generation from stem cells
1256–1257, 1258F, 1266–1267
grafted/transplanted 1329, 1331
growth of animals and 1193–1198
regeneration of 1247–1249
size regulation 1226
sizes of transplanted 1193
transcription regulators and creation of
1170–1171
see also lymphoid organs
origins of replication see replication origins
orphan receptors 832, 875
orthologs 17–18, 36
oscillations
Ca 2+ waves 838–840, 842, 843F
circadian clocks 876–878
metaphase chromosomes 991
negative feedback effects 516, 517F,
829F, 830, 875F, 876–878
NFκB activation 874, 875F
and robustness 520
vertebrate segmentation 1177
OSKM factors (Oct4, Sox2, Klf4, and Myc)
1254–1255, 1256F
osmium tetroxide 555–556, 716F
osmotic equilibrium 1083
osmotic gradients 612
osmotic pressure 612, 619–620, 724
osmotic stress 857, 1115
osteoblasts 1057, 1229–1232
osteoclasts 1230–1232, 1239, 1243F
osteocytes 1229–1230
osteoporosis 1232
ovarian cancer 1113, 1116
OXA complex (cytochrome oxidase
activity) 659, 660F, 663F, 664
oxaloacetate 70F, 83–84, 85F, 87,
106–107
oxidation
as an electron transfer 55–56
DNA damage from 267T
of organic molecules 54–55
oxidative phosphorylation 84–85, 86F,
753, 759F, 761–763
in cancer cells 1098
in plants 786
oxidative stress 1115
oxygen
C-O chemical groups 91
carbonyl oxygen atoms 612, 618,
619F
detoxification 796
origins of atmospheric 11, 26,
796–797
utilization in peroxisomes 666
see also molecular oxygen
oxygen-carrying molecules, evolution
229–230
P
P-bodies (processing bodies) 427–428,
430
P 680 chlorophyll 790, 791F, 794F
P element, Drosophila 416, 486
P-glycoprotein (MDR) 610, 1293
P-granules 1002F
32 P labeling 466–467
p21 protein 1014, 1116
p27 protein 971F, 973T, 1004