Encyclopedia of Biological Chemistry N-R

Cover Page......Page 848
Editors-in-Chief......Page 782
Associate Editors......Page 784
Preface......Page 787
Notes on the Subject Index......Page 788
Volume 1......Page 789
Volume 2......Page 797
Volume 3......Page 805
Volume 4......Page 813
Lipids, Carbohydrates, Membranes and Membrane Proteins......Page 818
Metabolism, Vitamins and Hormones......Page 820
Cell Architecture and Function......Page 822
Protein/Enzyme Structure Function and Degradation......Page 825
Bioenergetics......Page 828
Molecular Biology......Page 834
Signaling......Page 840
Techniques and Methodology......Page 847
Volume 4 (S-Z)......Page 0
Atrial Natriuretic Peptide......Page 1
Brain Natriuretic Peptide......Page 2
Natriuretic Peptide Receptors......Page 3
Guanylyl Cyclase-Linked Natriuretic Peptide Receptors......Page 4
Further Reading......Page 5
The N-End Rule Pathway......Page 6
Further Reading......Page 9
Using Synthetic Carbohydrate Derivatives......Page 11
Use of Glycosyl Transferases......Page 12
Conjugation of Glycopeptides......Page 13
Further Reading......Page 14
Spatial Calcium Signaling in Synapse-to-Nucleus Communication......Page 16
NFAT and DREAM......Page 17
Nuclear Calcium Signals......Page 18
See Also the Following Articles......Page 19
Further Reading......Page 20
The Neurofilament Triplet Proteins......Page 21
Peripherin......Page 24
Further Reading......Page 25
The NPY Y1 Receptor......Page 26
The NPY Y2 Receptor......Page 27
The NPY Y4 Receptor......Page 28
The NPY Y5 Receptor......Page 29
Further Reading......Page 30
NTS1......Page 32
NTS3......Page 33
Neurotensin Receptor Implication in Brain Functions......Page 34
Glossary......Page 35
Further Reading......Page 36
Reuptake......Page 37
Structure and Function......Page 38
Further Reading......Page 39
Neurotrophin Activation of Trk Receptors......Page 41
Neurotrophin Activation of the p75NTR Receptor......Page 43
Interaction Between p75NTR and the Nogo Receptor......Page 44
Further Reading......Page 45
Structure-Function of the Substrate-Binding Domains......Page 46
Mechanism of Hydride Transfer......Page 48
The Proton Channel......Page 50
Physiological Role......Page 51
Further Reading......Page 52
The Extracellular Domain......Page 53
The Pore......Page 54
Central Nervous System......Page 55
Epilepsy......Page 56
Further Reading......Page 57
Nitric Oxide Synthase......Page 58
Chemistry of NO......Page 59
Non-cGMP NO-Signaling Pathways......Page 60
Further Reading......Page 61
Classification and Properties of Processing Alpha-Mannosidases......Page 62
Class-I Golgi Alpha1,2-Mannosidases......Page 63
Class II Golgi Alpha-Mannosidases......Page 64
Further Reading......Page 65
DNA-PKcs......Page 66
Roles of NHEJ......Page 67
Repair of Radiation Induced DSBs......Page 68
Role in Maintaining Genomic Stability......Page 69
Further Reading......Page 70
Types of Transposable Elements......Page 71
DDE Enzymes......Page 73
Non-DDE Transposases......Page 75
Target Choice......Page 76
Regulation......Page 77
Further Reading......Page 78
Transposons......Page 80
‘‘Cut-and-Paste’’ versus ‘‘Copy-and-Paste’’ Transposition......Page 81
Retrotransposons......Page 82
Site-Specific Non-LTR Retrotransposons......Page 84
Glossary......Page 85
Further Reading......Page 86
PML Nuclear Bodies, ND10......Page 87
Cajal (Coiled) Bodies and Gems......Page 89
The Compartmentalized Nucleus......Page 90
Further Reading......Page 91
Lamin Genes......Page 92
Nuclear Size......Page 93
Proteolysis......Page 94
Further Reading......Page 95
Regulation of NFB Activity......Page 96
NFAlphaB and Disease......Page 98
Further Reading......Page 99
Origin of Nuclear Gene Products with Functions in Mitochondria......Page 100
Nonessential PET Genes......Page 101
Essential PET Genes......Page 102
Glossary......Page 103
Further Reading......Page 104
Establishing a Zone......Page 105
Changes in Gene Expression Correlate with Shifting Zones......Page 106
Glossary......Page 107
Further Reading......Page 108
Targeting Signals......Page 109
Transport Receptors......Page 110
Transport Mechanisms: RNA Trafficking......Page 111
mRNA Export......Page 112
Further Reading......Page 113
DNA Supercoiling......Page 115
The Domain Structure of the Nucleoid......Page 116
Nucleoid-Associated Proteins......Page 117
Further Reading......Page 118
Amplified Nucleoli and Missing Nucleoli......Page 119
The Plurifunctional Nucleolus......Page 120
Further Reading......Page 122
Types of Damage Repaired by NER......Page 123
Excision of the Damaged Strand......Page 124
Replication of Damaged DNA......Page 125
Clinical Consequences of NER Deficiencies - Cancer......Page 126
Mouse Models of NER Deficiencies......Page 127
Glossary......Page 128
Further Reading......Page 129
Mechanism of Nucleotide Excision Repair......Page 130
Damage Recognition and Transcription-Coupled Repair......Page 131
Glossary......Page 132
Further Reading......Page 133
Genetics and Evolutionary Conservation of uvr Genes......Page 134
Properties of UvrA, UvrB, and UvrC Proteins......Page 136
Molecular Mechanism of Damage Recognition......Page 138
Dual Incision......Page 139
UvrD......Page 140
Transcription-Coupled Repair......Page 141
Further Reading......Page 142
Distribution in Nature......Page 143
Detection of NER in vivo and in vitro......Page 144
Kinetics of NER......Page 145
Further Reading......Page 146
Olfactory Receptors Segregate in Several Highly Divergent Groups......Page 148
Monogenic and Monoallelic Expression of Olfactory Receptor Genes......Page 149
Olfactory Receptor Gene Expression is Regulated by Proximal and Distal Control Regions......Page 150
Signal Transduction of Olfactory Receptors......Page 151
Further Reading......Page 153
Obtaining and Preparing Glycans for Mass Spectrometry......Page 154
Instrumentation for Glycoconjugate Mass Spectrometry......Page 155
Tandem Mass Spectrometry (MS/MS) and Sequential Mass Spectrometry (MSn)......Page 156
Further Reading......Page 159
Free Oligosaccharide Transport System from the Endoplasmic Reticulum to the Cytosol......Page 160
Free Oligosaccharides Formed in the Cytosol: Its Connection with Endoplasmic-Reticulum-Associated Degradation......Page 161
Concluding Remarks......Page 162
Further Reading......Page 163
Mitochondrial Biochemistry......Page 164
Further Reading......Page 165
Discovery of Multiple Opioid Receptors......Page 166
Distribution and Pharmacology of Multiple Opioid Receptors......Page 167
Opioid Ligands Selectivity for the Multiple Opioid Receptors......Page 168
Summary and Future Direction......Page 169
Further Reading......Page 170
Chemistry of the Cycle......Page 171
Physiological Aspects of the Cycle......Page 172
Short-Term Regulation......Page 173
Extra-Hepatic Expression of Ornithine Cycle Enzymes......Page 174
Inborn Errors of the Ornithine Cycle......Page 175
Further Reading......Page 176
Dioxygenases......Page 177
Molecular Oxygen as a Substrate......Page 178
Biological Function of Oxygenases......Page 179
Glossary......Page 180
Further Reading......Page 181
Release of ATP onto P2X Receptors......Page 182
Activation of P2X Receptor Ion Channels (P2X1 through P2X6)......Page 183
P2X Receptors and Sympathetic Neurotransmission (P2X1 and P2X2 Receptors)......Page 184
P2X Receptors and Sensory Pathways (P2X3 and P2X2/3)......Page 185
Further Reading......Page 186
Extracellular Nucleotides as Signaling Molecules......Page 187
Functional Classification of the P2Y Receptors......Page 188
Important Physiological or Pathological Functions of P2Y Receptor Subtypes......Page 189
Further Reading......Page 190
Growth Arrest and Apoptosis......Page 191
p53 Regulation......Page 192
Protein-Protein Interactions......Page 193
Further Reading......Page 194
Roles of Nutrients and mTOR in Regulating p70 S6 Kinase......Page 195
Mechanisms Involved in the Activation of p70 S6 Kinase......Page 196
mTOR Signaling is Inhibited by the Immunosuppressant Drug, Rapamycin......Page 197
mTOR Signaling Is Regulated by Hormones and Nutrients......Page 198
Further Reading......Page 199
PTH......Page 200
Functional Domains of PTH(1-34) and PTHrP(1-34)......Page 202
The Ligand Interaction Mechanism in the PPR......Page 203
Blomstrand’s Chondrodysplasia......Page 205
Further Reading......Page 206
Applications......Page 207
Further Reading......Page 209
Shunt or Cycle......Page 210
Methods......Page 211
Further Reading......Page 214
Background......Page 215
Early Discoveries......Page 216
Post Second World War Discoveries of Reactions in the Nonoxidative Segment of the Pentose Pathway......Page 218
Finding a Reaction Sequence for the Nonoxidative Pentose Pathway......Page 219
The Search for a New Reaction Scheme for the Pentose Pathway......Page 220
Exposing the Problem of Assigning a Reaction Scheme to the Nonoxidative PP......Page 222
Glossary......Page 223
Further Reading......Page 224
Peptidylglycine Alpha-Hydroxylating Monooxygenase - PHM......Page 225
Evolutionary Relationships......Page 227
Impaired Peptide Amidation......Page 228
Further Reading......Page 229
Respiratory Electron Transport Systems......Page 230
Bacterial Periplasmic Respiratory Electron Transport Systems that are Dependent on the Cytochrome bc1 Complex......Page 231
Periplasmic Electron Transport Systems that do not Depend on the Cytochrome bc1 Complex......Page 232
Formate Dehydrogenase N......Page 233
Nitrate Reductase A......Page 234
Multi-Heme c-Type Cytochromes......Page 235
Synthesis of Periplasmic Electron Transport Systems......Page 236
Further Reading......Page 237
Peroxisome Proliferator-Activated Receptors......Page 238
PPAR (NR1C1)......Page 239
PPAR (NR1C3)......Page 242
PPAR (NR1C2)......Page 243
Further Reading......Page 244
Functions of Peroxisomes......Page 245
Peroxisomal Matrix Protein Import......Page 246
Glossary......Page 248
Further Reading......Page 249
Phagemid Vectors......Page 250
Construction of Libraries......Page 251
Design of Diversity Libraries......Page 252
Phage-Binding Analysis......Page 253
Further Reading......Page 254
Pheromone Receptors Stimulate a Signal Transduction Pathway......Page 255
Pheromone Receptor Synthesis Requires the Secretory Pathway......Page 257
Pheromone Receptors Bind Ligand via Contacts with the Extracellular Ends of the Transmembrane Segments......Page 258
Pheromone Receptors Promote G-Protein Activation via the Third Intracellular Loop......Page 259
Further Reading......Page 260
The PHO Genes and their Regulation......Page 261
Further Reading......Page 264
Synthesis......Page 265
Hydrolysis......Page 266
Cellular Function......Page 267
PtdIns-3,4,5-P3-Binding Proteins......Page 268
Cellular Function......Page 269
Further Reading......Page 270
Dephosphorylation of PtdIns(3)P......Page 271
Protein Domains that Bind to PtdIns(3)P......Page 272
PtdIns(3)P in Phagocytosis and Bacterial Invasion......Page 273
Further Reading......Page 274
Enzymology of PFK-2......Page 276
Regulation and Physiological Roles of Specific Isoforms in Specific Tissues......Page 277
Glossary......Page 278
Further Reading......Page 279
Activation and Regulation of PI 3-Kinases......Page 280
Class I PI 3-Kinases......Page 281
Signaling Downstream of PI 3-Kinases......Page 283
Inflammatory Disease......Page 284
Further Reading......Page 285
Cellular Functions......Page 286
Type II PIP Kinases......Page 287
Type III PIP Kinases......Page 288
Phosphoinositide 5-Phosphatases......Page 289
Further Reading......Page 290
Protein Kinase B/Akt......Page 291
PDK1 and the Regulation of the AGC Kinases......Page 292
Regulators of Cellular Growth - mTOR and S6K1......Page 293
Further Reading......Page 294
PLA2 Enzymes Using a Catalytic Histidine (sPLA2s)......Page 296
PLA2 Enzymes Utilizing a Catalytic Serine......Page 297
Further Reading......Page 298
Structure of PLC......Page 300
PLC-Beta......Page 301
PLC-Gamma......Page 302
See Also the Following Articles......Page 303
Further Reading......Page 304
PLD Structure......Page 305
Regulation of Mammalian Phospholipase D......Page 306
Biophysical role......Page 309
Mammals......Page 310
Further Reading......Page 311
Diacylglycerophospholipids......Page 313
Biosynthesis of Ether Glycerophospholipids......Page 316
Glossary......Page 318
Further Reading......Page 319
CDP-DAG Pathway......Page 320
CDP-Choline and CDP-Ethanolamine (Kennedy) Pathways......Page 321
Regulation of Phospholipid Synthesis......Page 322
Biochemical Regulation......Page 323
Further Reading......Page 324
Phototransduction......Page 325
Pineal Photoreceptors......Page 327
Further Reading......Page 328
Energy Capture......Page 329
Electron Transport and ATP Synthesis......Page 330
Benson-Calvin Cycle......Page 331
C4 Photosynthesis......Page 332
Further Reading......Page 333
Carboxylation Phase......Page 335
Regeneration Phase......Page 336
Regulation of the Calvin Cycle......Page 337
Direct Targeting of Calvin Cycle......Page 338
Glossary......Page 339
Further Reading......Page 340
Function of PS I......Page 341
The Proteins......Page 342
The Electron Transport Chain......Page 343
The Antenna System......Page 344
Further Reading......Page 346
Photosystem I: The Best-Studied Type I Reaction Center......Page 347
Geometry and Oxidation States......Page 348
FX, the Interpolypeptide [4Fe-4S] Cluster Bound by PsaA and PsaB......Page 350
FA and FB, the [4Fe-4S] Clusters Bound by PsaC......Page 351
Resolution of the Sequence of Electron Transfer: FX>FA>FB......Page 352
Further Reading......Page 354
Structure and Function of LHCII......Page 356
The Need for Control of the Light Reactions of Photosynthesis......Page 357
Energy-Dependent Quenching, qE......Page 358
The Nature of the Quenched State of LHCII......Page 359
See Also the Following Articles......Page 360
Further Reading......Page 361
Cooperation Between Chloroplast and Nucleus......Page 362
PSII Photoinactivation and the D1 Protein Damage......Page 363
PSII Photoinhibition Repair Cycle......Page 364
Further Reading......Page 365
QA......Page 366
PsbC-CP43......Page 367
PsbE and PsbF......Page 368
PsbH......Page 369
PsbO......Page 370
PsbV......Page 371
Further Reading......Page 372
The Photosystem II Complex......Page 374
The Water Splitting Enzyme......Page 375
The Redox Potential of the Different S States......Page 376
The Mechanism of Water Oxidation......Page 377
Glossary......Page 378
Further Reading......Page 379
Tomato and Tobacco Hydroxyproline-Rich Glycosylated Defense Signals......Page 380
CLAVATA3......Page 381
Concluding Remarks......Page 382
Further Reading......Page 383
Plasma-Membrane Calcium Pump Structure......Page 384
Mechanistic Aspects......Page 385
Regulation......Page 386
Glossary......Page 387
Further Reading......Page 388
The Structure of Cyt f......Page 389
The Structure of PSI......Page 390
Involvement of The PsaF Subunit in Electrostatic Interaction Between PC and PSI in Higher Plants and Green Algae......Page 391
Further Reading......Page 392
Platelet-Activating Factor......Page 393
PAF Receptor Structure......Page 394
PAF Receptor Signal Transduction......Page 396
Further Reading......Page 397
PDGF Receptors......Page 398
Proteins Associated with the PDGF Receptors and PDGF-Driven Signaling Pathways......Page 399
Proliferation......Page 400
Chemotaxis......Page 402
Dephosphorylation by PTPs......Page 403
Further Reading......Page 404
Polysialic Acid inMolecular Medicine......Page 406
Embryonic and Adult Forms of N-CAM......Page 407
Expression and Function of Polysialic Acid on Extraneural Cells......Page 408
Prokaryotic-Derived Reagentsfor the Detection and Analysisof PolySia......Page 409
Evidence for the Role of Polysialic Acid in Cancer Metastasis......Page 410
Rationale for Chemotherapeutic Inhibition of PolySia Biosynthesis......Page 411
Further Reading......Page 412
-Aminolevulinic Acid to Uroporphyrinogen III......Page 414
Heme and Chlorophyll Biosynthesis......Page 415
Regulation......Page 416
Herbicides......Page 417
Further Reading......Page 418
Enzymatic Processing of tRNA Precursors......Page 419
Primary Processing......Page 420
Generation of Mature rRNAs......Page 421
Processing Differences among Various Bacterial Species......Page 422
Further Reading......Page 423
Removal of Precursor-Specific Sequences......Page 424
Changes in Nucleotide Sequence of the Mature Domain......Page 425
Removal of the Spacer Regions......Page 426
Further Reading......Page 430
Prion Domains and Functional Domains......Page 431
Yeast, Fungal Prions [PSI+], [URE3], and [Het-s] are Self-Propagating Amyloidoses......Page 432
Prion Generation......Page 433
Chaperones and Prion Propagation......Page 434
Further Reading......Page 435
Replication Cycle......Page 436
Physiopathology of Prion Diseases......Page 437
Glossary......Page 438
Further Reading......Page 439
Processivity Clamp Loaders......Page 440
E. Coli Clamp Loader, Gama-Complex......Page 441
See Also the Following Articles......Page 444
Further Reading......Page 445
Propionyl CoA Carboxylase......Page 446
Propionic Acidemia/Aciduria (PA)......Page 447
Further Reading......Page 449
PGHS Catalysis and Inhibition......Page 451
PGHS-1 and PGHS-2 Gene Expression......Page 452
5-Lipoxygenase Activating Protein (FLAP)......Page 453
Leukotriene Metabolism......Page 454
Further Reading......Page 455
The Role of Thrombin......Page 456
Similarity to Trypsin......Page 458
Further Reading......Page 461
Subunit Composition......Page 463
Structure......Page 464
The 19S Regulator and its Subcomplexes......Page 465
Glossary......Page 466
Further Reading......Page 467
The 26S Proteasome......Page 468
Physiological Importance......Page 469
REGs or PA28s......Page 470
PA200......Page 471
Further Reading......Page 472
Introduction......Page 473
Ras-Related and Heterotrimeric G Protein......Page 474
Protein Phosphatase 2A......Page 475
Further Reading......Page 476
Primary Data Acquisition - The PDB......Page 477
Data Dissemination......Page 478
Secondary Sources......Page 479
Data Reduction......Page 480
The Future......Page 481
Further Reading......Page 482
Endocytic-Lysosomal Pathway......Page 483
Lysosomes......Page 484
Ubiquitin-Proteasome Pathway......Page 485
Ubiquitin Conjugation......Page 486
Protein Degradation......Page 487
Proteolysis in Mitochondria......Page 489
Selection of Substrates......Page 490
Further Reading......Page 491
Levinthal’s Paradox......Page 492
Folding Intermediates......Page 493
More Complex Folding Reactions......Page 494
Disulfide-Coupled Folding......Page 495
Assembly of Oligomeric Proteins......Page 496
Protein Folding Pathologies......Page 497
Further Reading......Page 498
Mechanism of Action of Glycosylation Inhibitors......Page 499
Mechanism of Action and Effect of Glycoprotein Processing Inhibitors......Page 500
Further Reading......Page 502
The Protein Carbohydrate Linkage......Page 503
O-Linked Glycosylation......Page 504
Protective......Page 506
Glossary......Page 507
Further Reading......Page 508
Transport to and Across the Outer Membrane......Page 509
The TOM Translocase......Page 510
The TIM23 Complex......Page 511
Protein Folding and Assembly......Page 512
Further Reading......Page 513
The PI3K/PKB Signaling Pathway......Page 515
Apoptosis and Cell Survival......Page 517
Regulation of proliferation......Page 519
Further Reading......Page 520
Protein Kinase C Phosphorylation......Page 522
Protein Kinase C Translocation......Page 523
Protein Kinase C Signaling......Page 524
Further Reading......Page 525
Function of N-Myristoylation......Page 526
Reaction Mechanism......Page 527
Therapeutics......Page 528
Further Reading......Page 529
Palmitoyltransferases......Page 531
Palmitoylation and Protein Function......Page 532
Further Reading......Page 533
Intracellular PTPs......Page 535
Involvement of PTPs in Mammalian Biology and Disease......Page 536
PTPs as Drug Targets......Page 539
Further Reading......Page 540
Agonist Peptides......Page 542
Northern Blot Analysis......Page 543
In SituHybridization to Detect Receptor mRNA......Page 544
Tissue Bioassays (Contraction or Relaxation)......Page 545
See Also the Following Articles......Page 546
Further Reading......Page 547
Glycosaminoglycans......Page 548
Secreted And Matrix Proteoglycans......Page 550
Membrane-Bound Proteoglycans......Page 552
Glossary......Page 553
Further Reading......Page 554
Distribution of Pterins in Nature......Page 555
The Aromatic Amino Acid Hydroxylases (AAHs)......Page 556
Molybdopterin-Containing Enzymes......Page 557
Tetrahydrobiopterin and Human Disease......Page 558
Further Reading......Page 559
General Structure of Group IB P-Type ATPases......Page 560
Physiological Roles......Page 561
Regulation......Page 562
Further Reading......Page 563
The Alpha-Subunit of Gastric H+, K+-ATPase......Page 564
The Beta-Subunit of Gastric H+, K+-ATPase......Page 565
Kinetics and Conformational Changes of the Gastric H+, K+-ATPase......Page 566
Functional Residues of the H+, K+-ATPase......Page 567
See Also the Following Articles......Page 568
Further Reading......Page 569
E1- and E2-Conformations of the Na+/K+ Pump......Page 570
Na+/K+ Pumps in Epithelial Cells of Kidney, Intestine, Lung, and Glands......Page 572
Na+/K+ Pump Isoform Expression and Regulation in Muscle and Central Nervous System......Page 573
Further Reading......Page 574
Structure......Page 576
Reaction Mechanism......Page 577
Biogenesis......Page 578
Regulation......Page 579
Further Reading......Page 580
Reaction Center......Page 581
Properties of Reaction Center Cofactors......Page 582
Ubiquinol-Cytochrome c Oxidoreductase (Cytochrome bc1 Complex)......Page 583
Further Reading......Page 584
Subunit Composition and Molecular Characterization......Page 585
Kinetics......Page 588
Mutants......Page 589
Quinone Reduction and Protonation......Page 591
Cytochrome c2 Oxidation......Page 592
Further Reading......Page 593
The Variety of PLP-Dependent Reactions......Page 594
Chemical Mechanisms......Page 596
Further Reading......Page 597
Regulation......Page 599
Deficiency and Interference......Page 600
Formation of Cytidine and Thymidine Nucleotides......Page 601
Regulation......Page 602
Deficiency and Interference......Page 603
Further Reading......Page 604
Control of Gluconeogenesis......Page 605
Control by Substrate Supply......Page 607
Breakdown of Amino Acids in Muscle and the ‘‘Glucose-Alanine Cycle’’......Page 608
Further Reading......Page 609
Components and Structure of PDH......Page 610
Role of PDH in Metabolism......Page 611
Regulation of Activity by Phosphorylation......Page 612
Extrinsic Regulation of PDH......Page 613
Further Reading......Page 614
Phosphorylation/Dephosporylation......Page 615
Crystallographic Studies......Page 616
Regulation of ChREBP in Response to Glucose and cAMP......Page 617
Further Reading......Page 618
Chemistry and Distribution......Page 619
Functions of Coenzyme Q......Page 621
Biological Naphthoquinones: Menaquinone and Vitamin K......Page 624
Further Reading......Page 625
Primary Structure and Evolution......Page 626
Cellular Localization......Page 627
Functional Cycle......Page 628
Rabs and Diseases......Page 629
Further Reading......Page 631
The Cellular Gradient of RanGTP......Page 632
Nuclear Transport......Page 633
Regulation of Spindle and Nuclear Envelope Assembly at Mitosis......Page 635
Further Reading......Page 636
The GDP/GTP Cycle and Ras Mutations......Page 637
H-, K-, and N-Ras......Page 638
Rap1 and 2......Page 639
Other Ras Family Members......Page 640
Further Reading......Page 641
RecA Strand Transfer......Page 642
Mismatch Repair Mediates Heteroduplex Formation......Page 643
Glossary......Page 644
Further Reading......Page 645
Structure......Page 646
Three-Strand Exchange Reaction......Page 647
Mediator Proteins......Page 648
Further Reading......Page 649
RDR Pathways in Bacteriophage......Page 651
Demonstration of RDR in Escherichia coli and Yeast......Page 652
RDR as a Backup Mechanism to Complete DNA Replication......Page 653
Replication Fork Failure and Direct Restart Pathways......Page 654
Further Reading......Page 656
Bloom Syndrome......Page 657
Functional Clues Provided by In vitro Studies......Page 658
Potential Functions for recQ Helicases in Replication-Associated DNA Repair......Page 659
Glossary......Page 660
Further Reading......Page 661
Sterol Regulatory Element-Binding Proteins (SREBPs)......Page 662
ATF6 and RseA......Page 664
Amyloid Precursor Protein (APP)......Page 665
Rip Mediated by Rhomboid......Page 666
Further Reading......Page 667
Complex I (NADH-Ubiquinone Oxidoreductase)......Page 668
Complex IV (Ferrocytochrome c - Oxygen Oxidoreductase or Cytochrome c Oxidase)......Page 669
Other Ubiquinol Oxidizing Enzymes (The Alternative Oxidase)......Page 670
Mechanism of ATP Synthesis......Page 671
Further Reading......Page 672
Assembly Factors......Page 673
The Hydrogenase Module......Page 674
Proton Pumping......Page 675
Poisoning of Complex I......Page 676
Further Reading......Page 677
Structural Classification......Page 678
Overall Description of the Structure......Page 679
The Integral Membrane Subunit(s) C (and D) and the Sites of Quinol Oxidation/Quinone Reduction......Page 681
Electron Transfer......Page 682
Glossary......Page 683
Further Reading......Page 684
Background......Page 685
Prosthetic Groups......Page 686
Protein Structure......Page 687
Proton Transfer Pathways......Page 688
The Catalytic Cycle and Proton Pumping......Page 689
Further Reading......Page 691
Electron Transport Chains......Page 692
Genetic Regulation of Respiration and Photosynthesis in Facultative Phototrophs......Page 693
Electron Transport Pathways in Oxygenic Phototrophs......Page 694
Further Reading......Page 696
The RB Tumor Suppressor......Page 697
The Rb Pathway......Page 698
Glossary......Page 699
Further Reading......Page 700
Retinoic Acid-Binding Domain......Page 701
Retinoic Acid Receptor Function......Page 702
Glossary......Page 703
Further Reading......Page 704
Retrovirus Genome......Page 705
Activities Associated with the Reverse Transcriptase......Page 706
Fidelity......Page 707
The Role of RT in Reverse Transcription......Page 708
See Also the Following Articles......Page 709
Further Reading......Page 710
GTPase-Activating Proteins......Page 711
Rho Effectors......Page 712
Rac Effectors......Page 713
Cell Migration......Page 714
Further Reading......Page 715
Assembly of Bacterial Ribosomes in vitro......Page 716
Synthesis, Modification, and Processing of rRNA......Page 717
Ribosome Assembly......Page 719
See Also the Following Articles......Page 720
Further Reading......Page 721
Fundamental Activities of the Ribosome......Page 722
Distinguishing Structural Features of the Ribosome......Page 723
Struggling with Ribosome Structure......Page 724
General Features of Ribosomal Architecture Revealed from the Subunit Structures......Page 725
High-Resolution Structure of the Small Subunit......Page 726
Medium-Resolution Structure of the 70S Ribosome......Page 727
Further Reading......Page 728
Chemical Structure of RNA......Page 730
Ribonuclease P......Page 731
Small Ribozymes that do not Require Divalent Metals......Page 732
Further Reading......Page 734
Secondary Structure......Page 735
The Guanosine-Binding Site......Page 736
Helix P1 and 5 Splice-Site Recognition......Page 737
Further Reading......Page 739
Tertiary Structure......Page 740
Comparison with Other Ribozymes......Page 742
Further Reading......Page 743
Classes of Natural Ribozymes......Page 744
Unnatural Ribozymes......Page 746
SELEX......Page 748
Further Reading......Page 749
RNA Substrates that Undergo A-to-I Editing......Page 750
Adenosine Deaminases that Act on RNA......Page 751
Editosome Complex......Page 752
Substitution Editing of Viral RNAs......Page 753
Roles of RNA Editing......Page 754
Further Reading......Page 755
The RNA Polymerase Molecules......Page 756
Alu Genes and Retrotransposition......Page 757
Glossary......Page 758
Further Reading......Page 759
Structure and Catalytic Activity of RNA Polymerase II......Page 760
Roles of the Basal Factors in Transcription Initiation by Pol II......Page 761
Further Reading......Page 762
Elongation Maintenance Factors......Page 763
N-TEFs and Termination Factors......Page 764
Integration of Elongation Control and Gene Expression......Page 765
Further Reading......Page 766
Transcription Cycle......Page 767
Initiation......Page 768
Elongation......Page 769
Glossary......Page 770
Further Reading......Page 771
Transcription Initiation......Page 772
Transcription Elongation......Page 774
Transcription Termination......Page 775
Further Reading......Page 776
Structure of the Core Enzyme......Page 778
Structure of the Holoenzyme......Page 779
Structure of a Single Subunit Phage RNAP......Page 780
Further Reading......Page 781