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:38 Index
Salmonella enterica and 1285F
phalloidins 904, 916F, 953–954F, 957F
pharmaceutical production through DNA
cloning 484, 506
see also drug discovery
phase, light waves 531, 532F
phase-contrast microscopes 533–535,
591F
phase transitions, lipid bilayers 571, 572F
phase variation, bacteria 294, 1290
phencyclidine 636
phenobarbital 1022
phenotypes
behavioral changes 488
defined 485–486
stochastic effects on 523–524
synthetic 491
phenylalanine
structure 113
tRNA for 335F
pheromones 844, 857
Philadelphia chromosome 1093, 1094F,
1095, 1135
phosphate bonds
bond energies 78, 79F
phosphates and phosphoanhydrides
65–66F, 78, 79F, 91, 101
phosphates, position in nucleotides 100
phosphatidylcholine 567, 570F, 571T,
572F, 573
synthesis 689
phosphatidylethanolamine 566–567,
571T, 574, 689–690
phosphatidylinositol (PI) 574, 577F
interconversion with PIPs 700, 701F,
737, 859
phosphatidylserine 566–567, 571T, 574,
689–690
and phagocytosis 740, 1030–1031
and PKC 837
phosphodiester bonds
reformation by DNA ligase 246F,
269–270
reformation by DNA topoisomerase
251–252
in RNA 302F
phosphodiesterases see cyclic AMP;
cyclic GMP
phosphoenolpyruvate 79F, 85F, 105
phosphofructokinase 104
phosphoglucose isomerase 104
3-phosphoglycerate 76, 77–78F, 85F, 105,
785
phosphoglycerate kinase 77F, 78, 105
phosphoglycerate mutase 105
phosphoglycerides, cell membrane
566–567
phosphoinositide phosphatases 859
phosphoinositides
AP2 binding to 699
marking organelles and membrane
domains 700
membrane bending and 594
in signaling complex formation 822,
823F
phospholipases 574
phospholipase C 574
phospholipase C-β (PLCβ) 836, 837T,
838F, 840F, 859, 862F
phospholipase C-γ (PLCγ) 852, 853F,
859, 862F
phospholipase C-ζ (PLCζ) 839F
phospholipid exchange/transfer proteins
691
phospholipid translocators 570, 574, 690
phospholipids
G protein signaling through 836–838
mobility 569–571
in plasma membranes 9, 98
sites of synthesis 760
spontaneous bilayer formation
568–569
structures 566–567
phosphorylation
autophosphorylation 364F, 688, 841,
842F
in the cell-cycle control system 968,
970F
initiation factors 423–425
nuclear localization signals 655
regulating protein degradation 360
regulating protein function 153–156,
165T
regulating signal responses 826
self-phosphorylation of P-type pumps
607
of serine in RNA polymerase tails 312,
316–317
of serine in the nucleosome 196–197
phosphorylation cycles 156
phosphotyrosine docking/binding sites
824F, 850, 852–853, 863
photoactivation, fluorescent dyes 544,
546F
photochemical reaction centers 783–784,
788–790, 793, 796
photolyases 885
photoproteins 884
photoreceptors, rod and cone 844–846,
848
photorespiration, peroxisomes in 667,
668F
photoswitchable probes 551
photosynthesis
and atmospheric oxygen 796–797
ATP production by 753
categories of reaction 783–784
charge-separation in 788–789,
792–793
as complementary to respiration 55
electron-transfer process 788
energetics of 54F
green sulfur bacteria 796
role of chloroplasts in 782–799
thylakoid membrane as site of
786–787
see also chloroplasts
photosynthetic reaction centers 588
photosystems
in photosynthetic organisms 754–755,
789F
of the thylakoid membrane 786
photosystem I 755F, 789, 790F, 792–793,
794F
photosystem II 755F, 789–791, 792F, 793,
794F
photosystem II complex 588, 791F
phototrophic organisms 11, 13, 14F
phototropin 885
phragmoplasts 1000, 1001F
phylogenetic classification of bacteria
1267
phylogenetic trees (tree of life) 218–220,
221F
construction 10
genomic analysis and 14
primary branches 14–15, 220
phytochromes 883–885
PI 3-kinase/Akt/mTOR signaling pathway
1114–1115
PI 3-kinase-Akt signaling pathway
860–861, 1030F
TOR and 861, 1017
see also RTK/Ras/PI3K pathway
PI 3-kinase (phosphoinositide 3-kinase)
and cell survival 860–861
in chemotaxis 958–959
classes 1a and 1b 859
as a growth factor 1017
signaling protein recruitment 574, 852
pili 1267, 1277
pilin gene/protein 1290
pinch 1079
pineal gland 877
Pink1 protein kinase 727
pinocytosis 730–732
macropinocytosis 725, 732, 733F, 738
PIPs (phosphatidylinositol phosphates)
700, 701F, 703
PI(3)P 701F, 707, 737
PI(3,4)P 2 701F
PI(3,4,5)P 3 701F, 739, 740F, 859–860,
958, 1017F, 1115, 1117F
PI(4)P 701F
PI(4,5)P 2 701–702, 733, 739,
836–837, 859–860, 959,
1017F, 1078F
PI(5)P 701F
piRNAs (Piwi-interacting RNAs) 305T,
429, 433
pituitary glands 1196
Pitx1 gene expression 1174–1175
PKA (protein kinase A) see cyclic-AMPdependent
protein kinase
PKB (protein kinase B) see Akt
PKC see protein kinase C
plague 1276, 1281
plakins 948–949, 959
plakoglobin (γ-catenin) 1037T, 1042,
1046F
plakophilin 1037T, 1046F
planar cell polarity 1189–1190
planar polarity pathway 869
planarian worms 1247–1249
plant growth regulators 881, 1087
plants
cell growth and cell wall orientation
1085–1087
cell size and ploidy 1194
cell walls 26, 1000, 1053, 1081–1087
cytokinesis in 1000–1001
energy storage as starch 80–81
flowering times 1182–1184
intracellular signaling pathways 880–
885
model organism 32
and nitrogen-fixing bacteria 12
peroxisomes in 667, 668F
receptor serine/threonine kinases in
881
regeneration in culture 442
RNAi and viruses 431
transgenic plants 507–508