Encyclopedia of Biological Chemistry by William J. Lennarz, M. Daniel Lane, Paul Modrich, Jack Dixon, Ernesto Carafoli, John Exton, Don Cleveland



Bibliographic Information:
Title: Encyclopedia of Biological Chemistry by William J. Lennarz, M. Daniel Lane, Paul Modrich, Jack Dixon, Ernesto Carafoli, John Exton, Don Cleveland
Editor: William J. Lennarz, M. Daniel Lane, Paul Modrich, Jack Dixon, Ernesto Carafoli, John Exton, Don Cleveland
Edition: 1st ed
Publisher: Elsevier
Length: 895 pages
Size: 24.43 MB
Language: English
Format: .pdf

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Table of Contents:
Cover Page......Page 895
Editors-in-Chief......Page 829
Associate Editors......Page 831
Preface......Page 834
Notes on the Subject Index......Page 835
Volume 1......Page 836
Volume 2......Page 844
Volume 3......Page 852
Volume 4......Page 860
Lipids, Carbohydrates, Membranes and Membrane Proteins......Page 865
Metabolism, Vitamins and Hormones......Page 867
Cell Architecture and Function......Page 869
Protein/Enzyme Structure Function and Degradation......Page 872
Bioenergetics......Page 875
Molecular Biology......Page 881
Signaling......Page 887
Techniques and Methodology......Page 894
Phylogeny......Page 1
Volume 4 (S-Z)......Page 0
Function and Diseases......Page 2
Structure and Biochemical Mechanism......Page 3
The Substrate Specificity of the ABC Multidrug Exporters......Page 4
Further Reading......Page 5
ABA Biosynthesis......Page 6
Role of ABA in Seed Development and Maturation......Page 7
Stomatal Closure Meditated by ABA......Page 8
ABA-Induced Modulation of Gene Expression......Page 10
Further Reading......Page 11
General Concepts in Actin Assembly/Disassembly......Page 12
Capping Proteins......Page 14
Cellular Aspects of Actin Assembly/Disassembly......Page 15
Further Reading......Page 17
Actin......Page 19
Pointed-End Binding and Branching......Page 20
Evolutionary and Structural Relationships between Some Severing and Severing/Barbed-End-Capping Proteins......Page 21
The Six Segment Proteins: Gelsolin, Villin, and Adseverin/Scinderin......Page 22
The Single Domain ADF/Cofilin Family......Page 23
Barbed-End-Capping Proteins......Page 24
Further Reading......Page 25
Prokaryotic Arps......Page 27
Conventional Actin......Page 30
Arp2 and Arp3......Page 31
Chromatin-Associated Conventional Actin......Page 32
Further Reading......Page 33
Sequence Similarity......Page 34
A1 Receptors......Page 35
Signaling Downstream of Adenosine Receptors......Page 36
A2A Receptors......Page 37
Glossary......Page 38
Further Reading......Page 39
Members of the Family......Page 40
Regulation of Adenylyl Cyclase Activity by G Proteins and Calcium......Page 41
Physiological Roles of Adenylyl Cyclases......Page 42
See Also the Following Articles......Page 44
Further Reading......Page 45
Classification and Mechanism of Action of Adrenergic Receptors......Page 46
Pharmacological and Molecular Characteristics of Alpha-1 Adrenergic Receptors......Page 47
Pharmacological and Molecular Characteristics of Beta Adrenergic Receptors......Page 48
Adrenergic Receptor Polymorphisms......Page 49
Further Reading......Page 50
Why and Where AC Works......Page 51
Activation of and Coupling to Carriers......Page 52
Adsorption......Page 53
AC and DNA Recombinant Techniques......Page 54
Glossary......Page 55
Further Reading......Page 56
Linker Peptide Composition......Page 57
Protein-Ligand Interaction Affinity Tags......Page 58
Antibody-Epitope Interaction Affinity Tags......Page 59
Glossary......Page 62
Further Reading......Page 63
The PKA Anchoring Hypothesis......Page 64
Anchoring Protein Targeting Regions......Page 65
Alternatively Spliced Scaffolds......Page 66
Further Reading......Page 67
The Hill n, a Measure of Cooperativity......Page 68
Two-State Models to Explain Cooperativity in Allosteric Proteins......Page 69
Ribonucleotide Reductase (RR)......Page 71
Further Reading......Page 72
Alternative Splicing of FGF-R2 Transcripts......Page 74
Exonic Splicing Enhancers......Page 75
Layers of Regulation......Page 76
Further Reading......Page 77
Details of the Hierarchy......Page 78
TRA: A Simple Blockage Model......Page 79
Sxl Autoregulation......Page 81
Alternative Splicing and Sex Determination in Other Species......Page 82
Further Reading......Page 83
FAD-Containing Monoamine Oxidases......Page 85
Cu/TPQ Amine Oxidases......Page 86
Further Reading......Page 88
Intestinal Metabolism......Page 90
Liver Metabolism......Page 91
Inter-Organ Exchanges......Page 92
Ureagenesis......Page 93
Catabolic Hormones......Page 94
Further Reading......Page 95
N-Terminal Cotranslational Processing......Page 96
Properties of MetAPs......Page 97
Further Reading......Page 98
History......Page 99
Physiological Factors in Amyloid Formation......Page 100
Evolved Amyloid......Page 101
Amyloid Assembly......Page 102
Glossary......Page 103
Further Reading......Page 104
Entry at Malate and Oxaloacetate......Page 105
Exit of Intermediates: Balancing Anaplerosis......Page 106
Expression and Activity of Proteins Regulating Anaplerosis......Page 107
Renal Ammonia Formation during Starvation......Page 108
Summary and Perspective......Page 109
Further Reading......Page 110
Ang I Binding Protein......Page 111
Ang II Receptors......Page 112
Ang IV......Page 114
Further Reading......Page 115
Control of DNA Looping......Page 116
The Discovery and Demonstration of DNA Looping......Page 117
History and Historical Significance......Page 118
Further Reading......Page 119
ARF-Related Proteins......Page 120
Regulators of ARF Activity......Page 121
Further Reading......Page 122
Structure......Page 123
Overall Structure......Page 124
Cancer......Page 125
Naturally Occurring Inhibitors......Page 126
Further Reading......Page 127
Mitochondrial Electron Transport Chain in Plants......Page 128
Substrates for ATP Synthesis......Page 129
Inhibitors of ATP Synthesis......Page 130
Nonphosphorylating Respiration......Page 131
Further Reading......Page 132
Cyanide-Resistant Respiration......Page 133
AOX Structure......Page 134
Physiological Role(s) of AOX......Page 136
Further Reading......Page 137
Macroautophagy in Mammals......Page 138
Macroautophagy in Yeast......Page 139
Glossary......Page 142
Further Reading......Page 143
The Cobalamin Cofactor......Page 144
Radical-Mediated Rearrangement Reactions......Page 145
Cobalamin-Dependent Methionine Synthase......Page 148
Further Reading......Page 149
Structure of Bcl2 Family Proteins......Page 151
Role of the Mitochondria......Page 152
Further Reading......Page 153
B-Cell Antigen Receptor Diversity......Page 154
Early Signaling Events......Page 155
The B-Cell Antigen Receptor and the Immune Response......Page 156
Further Reading......Page 157
Bile Salt Synthesis and its Regulation......Page 158
Bile Salt Transport and its Regulation......Page 160
Further Reading......Page 161
Mitochondrial Antigens and the Cellular Immune System......Page 163
Pathology......Page 164
Clinical Findings......Page 165
Treatment of the Underlying Disease Process......Page 166
Further Reading......Page 167
Gibbs Free Energy......Page 169
Redox Potentials......Page 170
The Thermodynamics of Bioenergetic Interconversions......Page 171
Further Reading......Page 172
Biotin Enzymes......Page 173
Biotin Domains......Page 174
Biotin Domain Structure......Page 175
E. coli Biotin Ligase, BirA......Page 176
Further Reading......Page 177
Biosynthesis and Degradation of Natively Biotinylated Proteins......Page 178
Clinical Application of Biotinylated Antibodies......Page 179
Further Reading......Page 180
B1 Receptor......Page 181
Regulation of B1 Receptor Induction......Page 182
B2 Receptor Knockout Animals......Page 183
Further Reading......Page 184
Interorgan Relationships......Page 185
The Macromolecular Organization of the BCKD Complex......Page 187
Brain Neuropathology of BCKAs......Page 188
Further Reading......Page 189
Brassinosteroid Biosynthesis......Page 191
Campesterol to Brassinolide......Page 192
Receptor Kinases and BR Perception......Page 194
Downstream Components......Page 195
Further Reading......Page 196
Signaling Triggered by Cell-Cell Contact......Page 197
Mechanisms of Cadherin Signaling......Page 198
Rho Family GTPase Signaling......Page 199
Wnt/Beta-Catenin Signaling......Page 200
Phosphorylation and Dephosphorylation......Page 201
Further Reading......Page 202
Protocadherins......Page 203
Extracellular Domain Structure (cis- and trans-Dimers)......Page 204
Linkage to Beta-Catenin Family Members......Page 205
Roles of Cadherins in Cell and Tissue Morphogenesis......Page 206
See Also The Following Articles......Page 208
Further Reading......Page 209
CGRP Receptor-Selective Drugs and their Pharmacological Properties......Page 210
Cellular Signaling and RCP......Page 211
The Pathophysiology of CGRP and Adrenomedullin Receptors......Page 213
Further Reading......Page 214
Protein Structure......Page 215
Signaling......Page 216
CTR-Like Receptor (CTRLR)......Page 217
Further Reading......Page 218
Distribution and Localization......Page 219
Distribution and Localization......Page 220
Knockout Animals......Page 221
Further Reading......Page 222
Ca2+ Buffering in the ER Lumen......Page 224
Grp94 (Glucose-Regulated Protein)......Page 225
The Protein Disulfide Isomerase (PDI) Family of Proteins......Page 226
See Also the Following Articles......Page 227
Further Reading......Page 228
Mechanism of [Ca2+]c Oscillations......Page 229
Role and Functional Significance of [Ca2+]c Oscillations......Page 231
Further Reading......Page 232
Structure......Page 233
Intracellular Signaling Pathways Used by the CaR......Page 235
CaR in Hypercalcemia......Page 236
Further Reading......Page 237
Structure......Page 239
Substrate Specificity......Page 240
Regulation of Gene Expression......Page 241
Neuronal Functions......Page 242
Further Reading......Page 243
Cell-Cycle Regulators......Page 244
Oocyte Prophase and Metaphase Arrest......Page 245
Calcium and Meiosis......Page 246
Further Reading......Page 247
Tropomyosin Shift and Steric Blocking Model......Page 248
Molecular Organization of Troponin and its Ca2+-Induced Changes......Page 249
Ca2+-Induced Troponin Shift on the Thin Filaments......Page 251
Molecular Mechanism of Ca2+ Regulation......Page 252
Further Reading......Page 253
Calmodulin Interactions with Ca2+ and with NOS......Page 254
Ca2+/CaM Regulation of NOS......Page 255
Further Reading......Page 258
The Origins and the Fundamental Principles......Page 259
The Renaissance......Page 260
One (or Many) Roles......Page 261
Further Reading......Page 263
Mechanisms......Page 265
History, Roles, and Visualization......Page 266
Further Reading......Page 267
Soluble Complex Ions and Their Binding Strengths......Page 268
Concentrations and Selectivity of Binding in Organisms......Page 269
Overall Functional Fitness of Calcium Ions in Evolution......Page 270
Further Reading......Page 271
Neuronal CaMKII: Localization and Substrates......Page 272
Activation, Autoregulation, and Structure of CaMKII......Page 273
Ca2+/CaM-Dependent Autophosphorylation......Page 274
Autophosphorylation as an Index of Neuronal Activity......Page 275
CaMKII in LTP and Learning and Memory......Page 276
Glossary......Page 277
Further Reading......Page 278
Ca2+ Signaling......Page 279
Myosin Light Chain Kinase......Page 280
Ca2+/Calmodulin-Dependent Protein Kinase II......Page 281
Ca2+/Calmodulin-Dependent Protein Kinase IV......Page 282
Summary......Page 283
Further Reading......Page 284
Annexins......Page 285
Gelsolin......Page 286
C2-Domain Proteins......Page 288
Further Reading......Page 290
Temporal Buffering......Page 292
Structure of the EF-Hand......Page 293
Distribution of EF-Hand Domains......Page 294
Further Reading......Page 297
Structure and Function of Conventional Calpains......Page 298
Classifications......Page 301
Structure and Functions of Calpain Superfamily Members......Page 302
Further Reading......Page 303
Enzymatic Synthesis of Oligosaccharides......Page 305
Carbohydrate Chain Synthesis Utilizing Glycotransferases......Page 306
Chemical Synthesis of Oligosaccharides......Page 307
Solution Phase Chemical Oligosaccharide Synthesis......Page 308
See Also the Following Articles......Page 310
Further Reading......Page 311
Mitochondrial Beta-Oxidation......Page 312
Further Reading......Page 315
Structure and Active Site......Page 317
Mechanism of Action......Page 318
Sequence of Action......Page 319
Substrates during Apoptosis......Page 320
Inhibitors......Page 322
Pathological Implications......Page 323
Further Reading......Page 324
Regulators of G0 Exit and G1-S Progression......Page 326
Cell Growth Regulation......Page 328
Further Reading......Page 329
Initiation......Page 330
Cdc7 (DDK)......Page 331
Coupling Replication to the Cell-Cycle Engine......Page 332
CDK Inhibitors and Proteolysis......Page 333
Conclusions......Page 334
Further Reading......Page 335
G2/M Checkpoint......Page 336
Intra-S Checkpoint......Page 338
G1/S Checkpoint......Page 339
Protein Kinase of the PI3K Family......Page 340
Glossary......Page 341
Further Reading......Page 342
Molecular Components of the Mitotic Checkpoint......Page 343
Sequestration Model......Page 345
Direct Inhibitor Model......Page 346
Checkpoint Proteins Can Have Dual Functions......Page 347
Further Reading......Page 348
Executors of Ca2+ Death Signals......Page 350
Apoptosis, Necrosis, and Other Ca2+-Dependent Forms of Cell Death in Brain Ischemia......Page 351
See Also the Following Articles......Page 352
Further Reading......Page 353
The Actin Cytoskeleton......Page 354
Adhesion......Page 355
Microtubules and Cell Guidance......Page 357
Microtubules and Contractility......Page 358
Further Reading......Page 359
Adhesive Motifs......Page 360
Structure......Page 361
Conformational Changes......Page 362
Further Reading......Page 363
Heterochromatin Domain......Page 365
The Centromere as DNA......Page 366
The Centromere as Chromatin......Page 367
Further Reading......Page 369
Structure of the Centrosome......Page 370
GammaTuRC......Page 371
GammaTuRC-Mediated Microtubule Nucleation in Vivo......Page 372
Centrosome Abnormalities in Cancer......Page 373
Further Reading......Page 374
N-Terminal Region......Page 375
Myeloid Differentiation......Page 376
Small G Proteins......Page 377
PI3-K Pathway......Page 378
Further Reading......Page 379
Why the Need for Metal Trafficking?......Page 381
Delivering Copper to the Golgi: Pathways Involving the ATX1 Copper Chaperone......Page 382
Delivery of Copper to Mitochondrial Cytochrome Oxidase......Page 383
Further Reading......Page 384
Clp/Hsp100 Chaperones......Page 385
Structure of Clp ATPases and Their Associated Proteases......Page 386
Mechanism of Action of Clp Chaperones and Proteases......Page 387
Hsp90 Chaperones......Page 388
Further Reading......Page 389
Overall Mechanism......Page 391
Architecture......Page 393
Polypeptide Binding by Type I Chaperonins......Page 394
Substrate Proteins......Page 395
Further Reading......Page 396
Chemiluminescence: Fluorescence from a Chemical Reaction......Page 397
Bioluminescence: Chemiluminescence from a Biological Source......Page 400
Further Reading......Page 402
Protonmotive Force......Page 403
The Protonmotive Circuit......Page 404
Behavior of the Protonmotive Circuit......Page 405
Uncoupling Proteins......Page 406
Fourth Postulate - Ion Carriers and Channels......Page 407
The Sodium-Calcium Cycle......Page 408
Further Reading......Page 409
Structure......Page 411
Signal Transduction......Page 412
Internalization......Page 413
HIV Entry......Page 414
Tumor Growth and Metastasis......Page 415
Further Reading......Page 416
Categories of Growth Based on the Nature of the Growth-Supporting Reductant......Page 417
Nitrifying Bacteria......Page 418
Generation of the Electrochemical Gradient and ATP Synthesis......Page 419
Release and Uptake of Protons in Chemolithotrophic Reactions......Page 420
Ecology......Page 421
Further Reading......Page 422
Receptors......Page 423
Chemotactic Peptide Receptors......Page 424
Effector Proteins......Page 425
Receptor Regulation......Page 426
Further Reading......Page 427
Spectroscopy......Page 428
Chemical Properties......Page 430
Spectroscopy......Page 431
Occurrence and Functions......Page 432
Glossary......Page 434
Further Reading......Page 435
The Hill Reaction......Page 436
Chloroplast Function......Page 437
Cyclic Electron Transport and Photophosphorylation......Page 438
State Transitions......Page 439
Transcriptional Control......Page 440
Mechanisms and Evolutionary Implications......Page 441
See Also The Following Articles......Page 442
Further Reading......Page 443
Envelope......Page 444
Thylakoid System......Page 445
Etioplasts......Page 446
Glossary......Page 447
Further Reading......Page 448
Diet and Lipoproteins......Page 449
Cholesterol Synthesis......Page 450
Statins......Page 452
Further Reading......Page 453
Remodeling Enzymes......Page 454
Remodeling Mechanisms......Page 455
Acetylation......Page 456
Methylation......Page 457
Ubiquitination......Page 458
Modification Crosstalk and the ‘‘Histone Code’’ Hypothesis......Page 459
Further Reading......Page 460
Posttranslational Modifications of Core Histones......Page 462
NHCPs......Page 463
Global Primary Structures-The Nucleosome Repeat Length (NRL)......Page 464
Tertiary and Higher Level Features......Page 465
Further Reading......Page 466
The Structure of Chromatin......Page 467
The Mitotic Chromosome......Page 470
Further Reading......Page 471
CoA as Donor of 4-Phosphopantetheine for Fatty Acid Synthase......Page 473
Metabolic Roles/Functions......Page 474
Further Reading......Page 475
Revised Definition of ‘‘Collagenases’’......Page 476
The Collagenases......Page 477
See Also the Following Articles......Page 478
Further Reading......Page 479
The Two Subtypes: The Fibrillar and Non-Fibrillar Collagens......Page 480
Why the Hydroxyproline......Page 483
Evolutionary Origins and Selective Pressures on (Gly-XY-)n Sequences......Page 484
Further Reading......Page 485
Identification and Properties of cAMP Receptors......Page 486
G Protein-Dependent Pathways......Page 488
G Protein-Independent Pathways......Page 489
See Also the Following Articles......Page 490
Further Reading......Page 491
Domain Structure of Class I PDEs......Page 492
C Domains of Class I PDEs......Page 493
Characteristics of cGMP-Specific Class I PDEs (PDEs 5, 6, and 9)......Page 495
Regulation of Class II PDEs......Page 496
Further Reading......Page 497
Molecular Diversity......Page 499
PDEs: Components of Spatially Organized Signaling Networks and Microdomains......Page 500
PDEs: Signal Integrators......Page 501
Glossary......Page 502
Further Reading......Page 503
Overall Structure of Cyclic Nucleotide-Dependent Protein Kinases......Page 504
PKA......Page 505
Cyclic Nucleotide-Binding Specificity and Affinity......Page 507
Negative Feedback and Feed-Forward Control of Cyclic Nucleotide Pathways......Page 508
Further Reading......Page 509
CNG Channels......Page 510
HCN Channels......Page 511
Further Reading......Page 512
Activation......Page 514
Bone Turnover......Page 516
Parasitic Proteinases......Page 517
Further Reading......Page 518
Composition and Structure......Page 519
The Rieske FeS-Protein......Page 520
Plastoquinol Oxidation - Q-Cycle and Fes-Domain Movement......Page 522
Genes, Biogenesis, and Phylogeny......Page 523
Further Reading......Page 524
Protein Subunits......Page 526
Three-Dimensional Structure of the bc1 Complex......Page 528
The Protonmotive Q Cycle......Page 529
Proton Conduction Pathways......Page 530
Inhibitors......Page 531
Further Reading......Page 532
Attachment of the Heme Prosthetic Group to Cytochrome c Apoprotein......Page 533
Evolutionary Aspects......Page 534
Cytochrome c and Apoptosis......Page 535
Further Reading......Page 536
Structures......Page 537
Oxygen Binding and Reduction......Page 539
Proton Pumping......Page 540
Further Reading......Page 541
Cytochrome P-450-General Aspects......Page 542
Structural Organization of Cytochrome P-450 Systems......Page 543
Reaction Cycle......Page 544
Regulation of Cytochrome P-450 Systems......Page 545
Further Reading......Page 546
Regulated Expression......Page 548
Cytokines and the Innate Immune Response......Page 549
Cytokines and the Adaptive Immune Response......Page 550
JAK/STAT Signaling......Page 551
Glossary......Page 552
Further Reading......Page 553
Making the Plans: Coordinating Nuclear and Cytoplasmic Division in Animal Cells......Page 554
Assembling the Parts 2: Building the Central Spindle......Page 556
Pushing the Envelope: Membrane Fusion......Page 557
Getting the Timing Right......Page 558
Further Reading......Page 559
Biosynthesis......Page 560
Conjugation......Page 561
Signal Transduction......Page 562
Cell Cycle......Page 563
Further Reading......Page 564
Structure and Molecular Components of the Desmosome......Page 566
Desmosome Assembly and Maintenance......Page 567
Desmosome Function......Page 568
Structure and Molecular Components of the Hemidesmosome......Page 569
BP180......Page 570
Conclusion......Page 572
Further Reading......Page 573
Hydrophilic Groups (Headgroups)......Page 574
Critical Micelle Concentration (CMC)......Page 575
Temperature Effects......Page 576
Membrane Proteins......Page 577
Further Reading......Page 578
Type 1 Diabetes Mellitus......Page 579
Type 2 Diabetes Mellitus......Page 580
Other Specific Types......Page 582
Acute......Page 584
Chronic......Page 585
Weight Loss and Exercise......Page 587
Further Reading......Page 588
Regulation of DGK Activity......Page 590
PA as a Signal......Page 592
Further Reading......Page 593
Disulfide Bond Formation During Protein Folding......Page 595
Catalysis of Disulfide Formation......Page 596
The Thioredoxin Family......Page 597
Disulfide Formation as a Regulatory Mechanism......Page 598
Further Reading......Page 599
DNA Base Excision......Page 600
Backbone Incision......Page 602
Base Excision Repair in Mitochondria......Page 603
Further Reading......Page 604
Alkylating Agents and Mechanism of the Reaction with DNA......Page 606
Effect of DNA Conformation on the Alkylation......Page 607
Methods of Identification of Alkyl Derivatives of Nucleic Acids......Page 608
Cytotoxic and Mutagenic Effects of Alkylation: Methylation......Page 609
Further Reading......Page 610
Structural Superfamilies of DNA Glycosylases......Page 611
Base Flipping......Page 612
Catalytic Strategies for Glycosidic Bond Hydrolysis......Page 613
Further Reading......Page 614
Primary Structures......Page 615
‘‘Open’’ And ‘‘Closed’’ Conformations......Page 616
Single-Stranded DNA Translocation by Monomers of SF1 Helicases......Page 617
Active Versus Passive Mechanisms of DNA Unwinding......Page 618
Summary......Page 619
Further Reading......Page 620
Nucleic Acid Strand Separation Activity of Helicases......Page 621
Brownian Motor Model......Page 622
Mechanisms of Nucleic Acid Strand Separation......Page 623
Ring Structure......Page 624
Nucleic Acid Binding in the Central Channel......Page 625
Mechanism and Role of NTP Hydrolysis......Page 626
Conclusion......Page 627
Further Reading......Page 628
Structure......Page 629
Domains Constituting the Core Catalytic Domain......Page 630
Biological Functions......Page 631
Genetic Recombination and Recombinational Repair......Page 632
Further Reading......Page 633
Overall Structure of DNA Ligases......Page 634
Mechanism of Nucleotidyl Transfer......Page 637
Glossary......Page 639
Further Reading......Page 640
Molecular Recognition of the Presence of the Methyl Groups on the DNA......Page 641
The Molecular Logic of DNA Methylation......Page 642
Chemistry of DNA Methylation......Page 643
Reaction Mechanism of N-MTases......Page 644
Mechanism of Base Flipping......Page 645
Mechanism of DNA Recognition......Page 646
Mechanism of Target Site Location and Processivity of DNA Methylation......Page 647
Further Reading......Page 648
Prokaryotes......Page 649
Eukaryotes......Page 650
Tertiary Structure......Page 652
Chemistry......Page 653
AdoMet and DNA Binding......Page 655
Further Reading......Page 656
Dam-Directed Mismatch Repair......Page 657
Altered Gene Expression......Page 659
See Also the Following Articles......Page 660
Further Reading......Page 661
Generalized Mismatch Repair in Eukaryotes......Page 662
Anti-Recombination Activity in Escherichia coli......Page 663
Anti-Recombination Activity in Saccharomyces cerevisae......Page 664
DNA Sequence Divergence, Mismatch Repair, Loss of Heterozygosity, and Cancer......Page 665
Evolutionary Role of the Control of Homologous Recombination by Mismatch Repair......Page 666
Further Reading......Page 667
Mismatch Repair Function is Required for Drug Cytotoxicity......Page 668
Mismatch Repair Proteins Promote DNA Damage-Induced Cell Cycle Arrest and Apoptosis......Page 669
Mismatch Repair-Mediated Apoptosis Eliminates Damaged Cells from Tumorigenesis......Page 670
Further Reading......Page 671
MutS Homologue Proteins Involved in Mismatch Repair......Page 672
Other Proteins Implicated in Mismatch Repair......Page 674
Defects in Mismatch Repair Cause Increased Cancer Susceptibility......Page 675
Glossary......Page 677
Further Reading......Page 678
Mechanism of E. coli Long-Patch Mismatch Repair......Page 679
Initiation of Mismatch Repair......Page 680
Excision and Repair Synthesis of Mismatch Repair......Page 681
MutY Repair Pathway......Page 682
Further Reading......Page 683
MutS and Some of Its Homologs Recognize Mismatches......Page 684
Orchestration of Mismatch Correction in Mammals......Page 685
How is Directional Excision Initiated and Controlled......Page 686
Further Reading......Page 687
Biochemistry of Vsr......Page 688
Structure and Biochemistry of MBD4......Page 689
Further Reading......Page 690
Oxidants and Antioxidants......Page 691
Carcinogenesis......Page 692
GO System......Page 693
Further Reading......Page 694
Primary Structure and Chromophores......Page 695
Reaction Mechanism......Page 696
See Also The Following Articles......Page 698
Further Reading......Page 699
DNA Primase Activity and Mechanisms of Primer Synthesis......Page 700
Residues Responsible for Interactions with the Metal Ion-dNTP Complex......Page 701
Checkpoint Activation......Page 702
Glossary......Page 703
Further Reading......Page 704
Pol Domain Organization......Page 705
Lyase Domain......Page 706
Polymerase Domain......Page 707
Glossary......Page 708
Further Reading......Page 709
Processivity Factor......Page 710
Further Reading......Page 711
Biochemical Character......Page 713
Role at Replication Fork......Page 714
Glossary......Page 715
Further Reading......Page 716
Domain Structure and Relation to Other Polymerases......Page 717
Substrate Binding......Page 718
DNA Polymerase Reaction Specificity......Page 719
3-5 Exonuclease......Page 720
Glossary......Page 721
Further Reading......Page 722
DNA Polymerase II: Structure and Biochemical Functions......Page 723
Biological Function: Replication Restart......Page 724
Further Reading......Page 725
Subunits and Subassembly of Pol III Holoenzyme......Page 726
Tau-Subunit and Pol III......Page 727
Concurrent DNA Synthesis of Leading and Lagging Strands......Page 728
Further Reading......Page 730
Selectivity Contributions of Each Step......Page 731
Measurement of the Kinetics of Incorporation......Page 732
Structural Determinants of Fidelity......Page 733
Selectivity of the Proofreading Exonuclease......Page 734
Glossary......Page 735
Further Reading......Page 736
DNA Polymerase Holoenzymes......Page 737
Primosomes......Page 738
Lagging-Strand Synthesis......Page 739
Further Reading......Page 741
Replication Protein A (RPA)......Page 742
Polymerase Accessory Proteins......Page 743
Topoisomerases......Page 744
Further Reading......Page 745
Protein......Page 746
Mammalian mtDNA......Page 747
Glossary......Page 748
Further Reading......Page 749
The Generic DNA Replication Origin......Page 750
Metazoan Replication Origins......Page 752
The Origin Recognition Complex......Page 753
Regulating ORC Activity: The ORC Cycle......Page 754
Further Reading......Page 756
The E. coli Replication Origin, oriC......Page 758
DnaA Protein and the DnaA Box......Page 759
Functional Domains of DnaA Protein......Page 760
Regulation of DNA Replication in E. coli......Page 761
Interaction of DnaA with Hda and the -Subunit of DNA Polymerase III Holoenzyme......Page 762
Further Reading......Page 763
Genes and Protein Structure......Page 764
The Sequence Specificity Subunit......Page 765
Assembly and Control of the Type I Restriction Enzyme......Page 766
Cleavage of DNA......Page 767
Further Reading......Page 768
Discovery of New Restriction-Modification Systems......Page 769
Recognition Sequences......Page 770
Protein Structures......Page 771
Subsets of Type II Restriction Enzymes......Page 772
The Methyltransferase Enzymes......Page 773
Further Reading......Page 774
Substrate Requirements......Page 775
Organization of Genes and Regulation of Restriction Activity......Page 776
Other Type III RM Systems......Page 777
Further Reading......Page 778
Structure......Page 779
Biology......Page 780
Biology......Page 781
Cruciforms......Page 782
Further Reading......Page 783
Reading Heads......Page 785
The Helix-Turn-Helix Motif......Page 786
The Leucine Zipper Motif......Page 788
Diverse Structural Strategies are Employed by Proteins for DNA Recognition......Page 789
Further Reading......Page 790
Quantitative Relationship between Twist and Supercoil......Page 791
Handedness and the Sign of Tw and Wr......Page 792
Biological Effects of Supercoiling and Enzymes That Can Change DNA Supercoiling......Page 793
Further Reading......Page 794
Classification, Nomenclature and General Properties......Page 795
Protein Domains......Page 796
Reverse Gyrase Mechanism......Page 797
Crystal Structure of Human Topoisomerase I......Page 798
Cellular Roles......Page 799
Transcription......Page 800
Glossary......Page 801
Further Reading......Page 802
DNA Topoisomerases......Page 803
Enzyme Mechanism......Page 804
Enzyme Domain Structures and Isoforms......Page 805
Topoisomerase IV......Page 806
Anticancer Drugs......Page 807
Further Reading......Page 808
RecQ Helicases......Page 809
Physical Association......Page 810
The Recombination Connection......Page 811
RecQ Helicases and Human Disease......Page 812
Further Reading......Page 813
D1-Like and D2-Like Receptor Subfamilies......Page 814
Dopamine Receptor Signaling......Page 815
Dopamine Receptor Variants......Page 818
Further Reading......Page 819
Functions Associatedwith Dynein-Based Motility......Page 820
Dynein-Independent Functions......Page 821
Binding Activities......Page 822
Further Reading......Page 823
The Dynein Heavy Chain......Page 824
Cytoplasmic Dynein......Page 825
Flagellar Dyneins......Page 826
Glossary......Page 827
Further Reading......Page 828




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