Page numbers followed by “f” indicate figures.
Page numbers followed by “t” indicate tables.
P bodies, 447, 457
P element, 243
P segments, 498
P16, 1164
p38 kinases, 746
p53, 907–908, 1020–1021, 1145, 1146, 1165–1166
P54 protein, 588, 588f
PABP. See Poly(A)-binding protein
PABPC. See Cytoplasmic poly(A)-binding protein
PABPC1. See Cytoplasmic poly(A)-binding protein
PAF. See Platelet-
PAGE. See Polyacrylamide gel electrophoresis
Pain receptors, 1062–1064
Palade, George Emil, 634
PALM. See Photo-
Palmitic acid, 51f
Palmitoyl CoA, 293, 295
Pancreas cells, 18f
Pancreatic β cells, 767, 767f
Pancreatic eIF2 kinase (PEK), 455
Paneth cells, 992, 994
Pannexins, 944
PAP. See Poly(A) polymerase
Pap smear, 1152
Papillae, 1064
Par proteins, 1006f
epithelial cell polarity and, 1007–1008, 1007f
nematode embryos and, 1003–1006
stem cells and, 1008, 1010, 1010f
Paracellular pathway, 941, 941f
Paracrine signaling, 675f, 676, 763
Paralogous sequences, 325
Parasites, 22, 24
eukaryotic, 1082
Parental types, 232
Parietal cells, 509–510, 509f
Parkin, 529
Parkinson’s disease, 87, 985f
Paroxetine, 1057
Passive immunization, 1089
I-
Passive transport, 476
Patch clamps, 500–501, 500f, 501f
Pathogens, 1079
entry routes, 1081–1082
mechanical and chemical boundaries against, 1083–1084
replication sites, 1081–1082
Patterning genes, 26
Pax6 gene, 364, 365f, 366
Paxil, 1057
PC. See Phosphatidylcholine
PC3 endoproteases, 657
P-
PCNA. See Proliferating cell nuclear antigen
PCP. See Planar cell polarity
PCR. See Polymerase chain reaction
PD-
PDE. See cGMP phosphodiesterase
PDE inhibitors, 716
PDGF. See Platelet-
PDI. See Protein disulfide isomerase
PD-
PDZ domains, 940
PE. See Phosphatidylethanolamine
Pectin, 969, 972
PEK. See Pancreatic eIF2 kinase
Pelizaeus-
Pemphigus vulgaris, 938
Penicillin, 137
Peptide bonds, 41, 69
planar, 81, 81f
synthesis of, 194
Peptide groups, 38f
planar, 81f
Peptide mass fingerprint, 118
Peptides
MHCs binding, 1107–1109, 1108f
phosphorylated, 684, 685f
Peptidoglycan, 47
Peptidyl-
Peptidyltransferase reaction, 194
Perforins, 1086f, 1094, 1122–1123, 1123f
Pericentriolar material, 825
Peripheral membrane proteins, 284, 292
Peripheral nervous system, 1026, 1044, 1045f
Perlecan, 945, 950
Permissive temperature, 21, 228, 229f
Peroxisomal oxidation, 537, 538f
Peroxisomal proteins
import of, 620f
incorporation pathways, 620f, 621
targeting of, 619–621
Peroxisomal-
Peroxisomes, 13f, 17
biogenesis and division, 621, 621f
fatty acid oxidation in, 537, 538f
Perutz, Max, 119
Pervasive transcription, 432–433
Petite mutations, 524, 525f
PH domain, 750
pH values, 55f
of biological fluids, 54–55, 54f
buffers and, 55–56, 56f
cytosolic, 485, 505–506
of endosomes, 662–663
enzyme activity dependent on, 95, 95f
in lysosomes, 489–491
in vacuoles, 489–491
Phages, 212
temperate, 216
Phagocytes, 1084
Phagocytosis, 16, 659, 776, 790–791
actin dynamics and, 792f
in apoptosis, 1012, 1012f
Phagosomes, 792f
Phalloidin, 792
Pharming, 561
Phase-
Phenotype, 224
mutant allele effects on, 225f
of transcription factor mutations, 355f
Phenylalanine, 43
Pheromones, 673
Philadelphia chromosome, 1156, 1156f
Phosphatases, 103, 856
exit from mitosis and, 902
in signaling pathways, 676–677
Phosphate, 44
Phosphatidylcholine (PC), 49f, 277f
Phosphatidylethanolamine (PE), 277f
Phosphatidylinositol (PI), 277f, 282, 709, 710f
Phosphatidylinositol-
Phosphatidylserine (PS), 277f, 282, 1015
Phosphoanhydride bonds, 61
Phosphodiester bonds, 41, 170, 170f
Phosphoenolpyruvate carboxylase, 577
Phosphofructokinase-
Phosphofructokinase-
Phosphoglycerides, 49, 49f, 50t, 276, 278
Phosphohistidine, 361
Phosphoinositide signaling pathways, 748–751
Phosphoinositides, 278, 748
Phospholipase A2, 290, 291f
Phospholipase C (PLC), 289, 692, 708, 710, 714, 749
second messengers from, 709–710, 710f, 712
Phospholipases, 282, 282f
Phospholipid anchors, 598–599
Phospholipid bilayers
biomembrane properties and composition of, 279
formation of, 273–274, 273f
gel and liquid phases of, 278–279, 279f
permeability of, 474, 474f
sealed compartment formed by, 274–276
Phospholipid molecules, 5f
Phospholipids, 9, 9f, 48–50, 49t
ABC proteins flipping, 493–494
annular, 287, 287f
fatty acid incorporation into, 294–295
flippases moving, 295
regulation of levels of, 763–766
synthesis and intracellular movement, 293–297, 294f
transport mechanisms, 296–297, 296f
Phosphoprotein phosphatase (PP), 703
Phosphoproteins, 103, 114, 1054
Phosphoproteomics, 124
Phosphoric acid, 56, 56f
Phosphorylated peptides, 684, 685f
Phosphorylated peptide-
Phosphorylation, 103f
in Ca2+ ATPase, 487f
CDKs and, 883, 886
of lamins, 866
of MAP kinase family, 744–745, 744f
mRNP export and, 441–442, 442f
oxidative, 515
in protein regulation, 102–103
of rhodopsin, 697–698
of Smad transcription factors, 724
substrate-
Phosphotyrosine, 730, 731f
Phosphotyrosine phosphatases, 732–733, 733f
Photo-
Photoelectron transport, 564–566, 564f
ROS protection in, 570
Photoinhibition, 570
Photomotility, 1046
Photophobia, 1046
Photophosphorylation, cyclic, 570–571
Photoreceptors, 740–741, 740f, 1061
Photorespiration, 576–578, 576f
Photosynthesis, 6, 62–
ATP in, 563
CO2 metabolism during, 573–578, 575f
rates of, 564f
stages of, 561–563, 562f
Photosystem I (PSI), 563, 568, 569f
cyclic electron flow through, 570–571, 571f
regulation of, 571–572, 572f
Photosystem II (PSII), 563, 568, 569f
oxygen-
regulation of, 571–572, 572f
Photosystems, 563–564
molecular analysis of, 567–572
proton-
Phragmoplast, 860
PI. See Phosphatidylinositol
PI-
PI-
PIC. See Preinitiation complex
Piezo channels, 1063, 1064f
Piezo1, 1063, 1064f
Piezo2, 1063, 1064f
PINK1, 529
Pioneer transcription factors, 395–396
PKA. See Protein kinase A
PKB. See Protein kinase B
PKCs. See Protein kinase Cs
PKG. See Protein kinase G
PKR. See Protein kinase RNA-
Placental alkaline phosphatase (PLAP), 289
Plakins, 867
Planar cell polarity (PCP), 1008, 1009f
I-
Planaria, 27–28, 988
Plant adhesion molecules, 971–972, 971f
Plant cell walls, 968–969, 968f
Plant cells, 4f
mitosis of, 860
stem cells, 996–999, 998f, 999f
Plant tissues, 968–972
Plant vacuoles, 17–18, 17f, 507
PLAP. See Placental alkaline phosphatase
Plaque assay, 213, 215f
Plaques, amyloid, 87, 88f
Plasma, 1082
Plasma cells, 1102
Plasma membrane, 9f, 13f, 271, 272f, 473
in bacteria, 10
depolarization of, 1034, 1035f
domains of, 657–658
electric potential across, 497, 498f
in myocardial infarction, 807
PI 3-phosphates in, 750
protein anchoring in, 289f
protein degradation, 665, 666f
protein sorting and, 657–658, 658f
retroviruses budding from, 666–667, 668f
store-
targeting to, 585
Plasmalogens, 278
Plasma-
Plasmid cloning vectors, 236–237
Plasmid expression vectors, 251–253
gene and protein tagging, 252–253
retroviral systems, 252, 252f
transfection, 251–252
Plasmids, 10, 236
Plasmodesmata, 13f, 24, 969–970, 970f
Plasmodium falciparum, 22, 24, 525
Plasmodium species, 23f
Plastocyanin, 569
Platelet-
Platelet-
Platelets, 964
PLC. See Phospholipase C
Pleated sheet, 71
Plectin, 867, 868f
PLP. See Proteolipid protein
Pluripotent cells, 976
Pluripotent stem cells, 988. See also Induced pluripotent stem cells
PML. See Promyelocytic leukemia
P-
Podophyllotoxin, 830
Podosomes, 961
Point mutations, 204, 204f, 225, 1151
disease gene location and, 257
mRNA and, 257
Point-
Pol I. See RNA polymerase I
Pol II. See RNA polymerase II
Pol III. See RNA polymerase III
Pol β. See DNA polymerase β
Pol δ. See DNA polymerase δ
Pol ε. See DNA polymerase ε
Polar bonds, 34
Polar microtubules, 852
Polarity, 824
cell, 776, 776f, 1000–1010
cell division and, 1002–1003, 1002f
hyperpolarized state, 693
membrane depolarization, 1039–1040, 1042
plasma membrane depolarization, 1034, 1035f
Polarized cells, 931, 977
Polarized membrane traffic, 1003, 1007
Poliovirus, 1130
Polo kinase, 897, 916
Poly(A) polymerase (PAP), 180, 431, 452
Poly(A) sites, 303
Poly(A) tail, 180
Poly(A)-binding protein (PABP), 195, 196f, 431
in mRNP remodeling, 441, 441f
Polyacrylamide gel electrophoresis (PAGE), 108
kinase study with, 684
Polyacrylamide gels, 246
Polyadenylation
alternative, 450
cytoplasmic, 451–452, 452f
of pre-
3′ cleavage and, 419, 430–432, 431f
Polyclonal antibodies, 144
Polycomb proteins, 406–407, 408f, 409, 982
Polycystic kidney disease, autosomal dominant, 849
Polydactyly, 354
Polygenic diseases, 258
Polyglutamine, 311
Polyglutamylation, 843, 843f
Polyglycylation, 843, 843f
Poly-
Polylinkers, 237
Polymerase chain reaction (PCR), 234, 239–243, 241f
gene sequencing and, 243–244, 244f, 245f
isolation of specific segments of DNA, 241–242, 242f
Polymers, 6, 41, 169
Polypeptides, 70
binding to ER, 589
chaperonins and folding, 85, 86f
in ER, 590–591
MHC molecules binding to, 1108–1109
structure of, 69f
synthesizing chains of, 194
translocon allowing passage of, 590, 590f
Polyploid organisms, 224
Polyribosomes, 195
Polysaccharides, 7, 41, 46–48
Polysomes, 195
Polyspermy, 979
Polytene chromosomes, 343–345, 345f
Polytenization, 344
Polyubiquitiny chains, 760
Polyubiquitinylation, 103, 104f
Polyunsaturated fatty acids, 49
Porins, 288, 288f, 523
Positive feedback mechanisms, 876
intrinsic polarity program and, 1000–1002, 1001f
Postmitotic cells, 876
Postsynaptic cell dendrites, 1028
Postsynaptic density (PSD), 1050
Postsynaptic target cells, 1048
Post-
cytoplasmic mechanisms, 445–460
Post-
Potential energy, 57
Power stroke
dynein, 839f
myosins, 800, 801f
PP. See Phosphoprotein phosphatase
PP1. See Protein phosphatase 1
PP2A. See Protein phosphatase 2A
PPARγ, 770, 771f
PRC1 complex, 407, 408f
PRC2 complex, 407, 408f, 982
Pre-
Pre-
Precancerous polyps, 1153
Precursor cells, 988
Precursor mRNAs (pre-
nuclear exoribonucleases degrading, 432
processing of eukaryotic, 419–433
proteins associating with, 421–422
regulation of processing, 435–440
snRNAs base pairing with, 424, 425f, 426
spliceosome and, 426–427, 443
SR proteins and exon definition in, 428–429, 429f
3′ cleavage and polyadenylation of, 430–432, 431f
Precursor rRNA (pre-
nucleolar organization and, 461–462, 462f
processing of, 462–465, 464f
transcription units, 462, 462f
Precursor tRNA (pre-
modification in nucleus, 466–468
processing of, 467, 467f
Preinitiation complex (PIC), 191, 192f, 374, 375f, 376f
pre-
pre-
Prenyl anchors, 289
Prenylation, 288
Preprophase band, 860
pre-
Pre-
Presenilin 1 (PS1), 762
Presynaptic neurons, 1048, 1049–1050
Presynaptic terminal, 1054
pre-
Primary cell cultures, 131–132
Primary cell walls, 969
Primary cilium, 757, 847–848, 848f
defects in, 848–849
Primary electron acceptor, 563
Primary lymphoid organs, 1082
Primary structure, 70
I-
Primary transcripts, 417
Primase, 199
Primer, 198, 200f
Prions, 87
Pro-
Procaspases, 1015, 1018, 1126
Processed pseudogenes, 321
Procollagen molecules, 951
Proenzymes, 656
Professional APCs, 1105–1106
Profilin, 784–785
Progenitor cells, 988
Progeria, 866
Progesterone, 879, 879f, 1157
Programmed cell death, 906, 977, 1011, 1011f, 1012–1013, 1012f
Prohormone, 104
Proinsulin, 656f
Projection neurons, 1067
Prokaryotic cells
DNA transposons in, 314, 315f
gene organization, 179, 180f
structure and function of, 10–12, 10f
Prolactin, 727
Proliferating cell nuclear antigen (PCNA), 200
Proline, 44
Proline isomerases, 86, 87f
Prometaphase, 851, 853–854, 855f
Promoter fusion, 253
Promoter-
Promoters, 176, 364, 731
experimentally regulated, 260–261
RNA polymerase II, 371–373
Promyelocytic leukemia (PML), 469
Promyelocytic leukemia nuclear bodies, 469
Proofreading, 188, 203, 204f, 528, 528f
Prophage, 216
Prophase, 850, 875
Proprioceptive neurons, 1017, 1017f
Proproteins, 656
Prostaglandin E1, 701
Prostate cancer, 1155
Prosthetic groups, 95, 540, 540t
Proteases, 76
ADAM and, 763
metalloproteases, 960
MMP, 761, 763, 960
serine, 92–96, 94f
Proteasome, 97–99, 98f
immunoproteasome, 1111
ubiquitin and, 99–100
Proteasome inhibitors, 99
Protein binding, 89–96
ligands in, 89, 90f
Protein cleavage-
Protein coats, 638–639
Protein Data Bank, 119, 121
Protein degradation, 97
plasma membrane, 665, 666f
proteasome and, 97–99
signaling pathways controlled by, 751–760
ubiquitin and, 99–100
Protein disulfide isomerase (PDI), 603–604, 604f
Protein expression profiling, 122
Protein family, 306
Protein folding, 81–89, 82f
abnormal, 87, 88f
amino acid sequence and, 81–82
catalysts in, 606–607
chaperone-
chaperones promoting, 82–86
chaperonin-
in ER, 601–608
ER proteins and, 604–606, 605f
improper, 606–607
isomerizations and, 606
oil drop model for, 72, 73f
planar peptide bonds and, 81, 81f
proline isomerases promoting, 86, 87f
Protein fusion, 253
Protein kinase A (PKA), 679
activation of, 701–702, 702f, 703–704
anchoring proteins localizing, 705–706, 706f
cell types and activation of, 703–704, 704t
gene transcription and, 704–705, 705f
glycogen metabolism regulation by, 702–703, 703f
signal amplification and, 704
signal suppression, 706–707
structure of, 702f
Protein kinase B (PKB), 748, 750–751, 750f, 767, 1019f
Protein kinase Cs (PKCs), 709, 714, 748
Protein kinase G (PKG), 714–716, 715f
Protein kinase RNA-
Protein kinases, 874. See also specific protein kinases
in signaling pathways, 676–677
Protein modification, in ER, 601–608
Protein phosphatase 1 (PP1), 899
Protein phosphatase 2A (PP2A), 900, 916
Protein phosphatases, in signaling pathways, 676–677
Protein regulation, 97–105
allosteric, 100–101
high-
phosphorylation and dephosphorylation in, 102–103, 103f
proteolytic cleavage in, 104–105
ubiquitinylation and deubiquitinylation in, 103–104
Protein self-
Protein sorting, 583
pathways for, 583–584, 584f
plasma membrane and, 657–658, 658f
trans-Golgi and, 657–658, 658f
Protein structure
categories of, 72–73
comparing, 79–80
determining, 118
function and, 68f
hierarchical, 69–80
motifs, 75–76, 76f, 325
primary, 69–70
quaternary, 78
secondary, 70–71, 71f, 72f
tertiary, 72
Protein synthesis
AUG start codon in, 190–191
cell-
chain elongation, 193–195, 193f
completion of, 195
global regulation of, 452–455
GTPase superfamily role in, 195–196
microsomes and, 587–588, 587f
nonsense mutations and, 196–197
ribosomes and, 188–197
RNA roles, 183, 183f
secretory proteins, 587, 588–589, 589f
translation efficiency, 195, 196f
translation initiation, 191, 192f, 193
translation termination, 194f, 195
Protein targeting, 583
to endoplasmic reticulum, 585–592
to lysosomes, 653–655, 653f
to mitochondria and chloroplasts, 608–617
Protein transport
assaying, through secretory pathway, 634–635, 635f
COPI vesicle-
COPII vesicle-
from trans-Golgi, 651–652
Protein-
number of, in genome, 326–327, 326f
transcription of, 176–182
Protein-
Proteins, 2, 7f, 41. See also specific proteins
accessory, 805
alternative RNA splicing and, 181–182
amino acids in formation of, 7, 42–45, 43f
anchoring, 705–706
biomembrane, 284–292
bonding, 40, 40f
cell cycle, 21–22
in cell structure and tasks, 7
chimeric, 130, 612–613, 612f
cholesterol and sphingolipids clustering with, 282–283
cognate, 380
cross-
cytoskeletal, 7
cytosolic, 99–100
delivery of, 583
depicting conformation of, 74–75, 75f
determining conformation, 119, 120f, 121
DNA interaction with, 172, 172f
in DNA replication, 199–201
domains, 76–78
double mutants in studying function order, 230–231
enzyme and antibody assays detecting, 111–114, 113f
evolutionary relationships among, 325
fluorescent, 146–147, 146f
functions of, 68
GPI-
I-
GTP-
homology among, 80
integral membrane, 72–74, 284, 292
interacting, 231–232, 232f
lipid-
liquid chromatography of, 109–111
mass spectrometry of, 116, 116f, 117f, 119
membrane interaction with, 284–285
membrane transport, 68
misfolded, 87, 88f
motor, 68
multimeric membrane, 287, 287f, 601
order of functioning of, 230–231, 231f
peripheral membrane, 284
production from cloned genes, 250–251, 250f
purifying, detecting, and characterizing, 105–121
redundant, 231–232, 232f
regulation of activity of, 677, 677f
regulation of concentrations of, 354, 354f
regulation of transcription and replication, 339
regulatory, 68
removal from membranes, 290–292, 291f, 292f
scaffold, 67, 805
sequence comparison, 79–80
signaling, 68
stabilizing, 805
stepwise synthesis on ribosomes, 188–197
tail-
transmembrane, 285–287, 285f, 286f, 289–290
Proteoglycans, 723, 925, 945, 950, 951, 953–956
aggregate, 956, 957f
diversity of, 955–956
Proteolipid protein (PLP), 1044
Proteolysis, 98f, 1111, 1113–1114
Proteolytic cleavage, 104–105, 656f
Proteolytic processing, 656–657, 657f
Proteomics, 122–124
mass spectrometry in, 123–124, 123f, 124f
of organelles, 164
Protofibril, 861
Protofilaments, 823–824, 828, 861
Proton pumping, 539–540, 540f, 542–546
stoichiometry of, 549–550
Proton translocation, 556
Proton-
ATP synthesis and, 551–559
ATP-
heat generation with, 558–559
in mitochondria, 550
photosystem electron flow generating, 568–569
Proton/sucrose antiporter, 507, 507f
Proto-
apoptosis regulation genes as, 1163
gain-
MYC, 1145
viruses activating, 1152
Protostomes, 26
Protozoans, 22, 23f, 24
splicing in, 428
Provirus, 217, 444
Prozac, 1057
PS1. See Presenilin 1
PSD. See Postsynaptic density
PSD95, 1051, 1051f
Pseudogenes, 307
processed, 321
Pseudomonas fluorescens, 215f
Pseudosubstrate domain, 701
PSI. See Photosystem I
PSII. See Photosystem II
Psoriasis, 681
PTEN gene, 751, 1163
PTEN phosphatase, 751, 1156
PTS1. See Peroxisomal-
Pull-
Pulse-
Puma, 1019f, 1020–1021
Pumps, 476
ATP-
Ca2+, 486–489
electrogenic, 490
F-
K+, 476f
Na+K+, 476, 476f, 486
P-
regulation of, 489
V-
Purines, 45, 46f
Purkinje neurons, 4f, 1071f
Purple bacteria, 567, 568f
P-
Pyranoses, 47
Pyrimidines, 45, 46f, 170
Pyrophosphate, 46
Pyruvate, 518, 519f, 533
Pyruvate dehydrogenase, 533
Pyruvate kinase, 516