Verfügbarkeit: Informational biopolymers of genes and gene expression

Informational biopolymers of genes and gene expression:

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Bibliographische Detailangaben
1. Verfasser:	Blake, Richard D. (VerfasserIn)
Format:	Buch
Sprache:	English
Veröffentlicht:	Sansalito, CA University Science Books 2005
Schlagworte:	aGenes aGene expression aInformation theory in biology Molekulargenetik Nucleinsäuren Genexpression Proteine
Online-Zugang:	Inhaltsverzeichnis
Beschreibung:	Includes bibliographical references and index
Beschreibung:	XXII, 778 S. Ill., graph. Darst.
ISBN:	1891389289

Internformat

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Datensatz im Suchindex

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adam_text	Informational Biopolymers of Genes and Gene Expression Properties and Evolution R D BLAKE UNIVERSITY SCIENCE BOOKS SAUSALITO, CALIFORNIA Contents Preface xix Chapter 1 Introduction to the Informational Biopolymers 1 1 1 Proteins 4 1 2 Nucleic Acids 8 121 The Special Fitness of the DNA Molecule 10 1 3 The Roles of the Informational Biopolymers in the Dissemination of Genetic Information 14 131 Central Dogma 14 132 Transcription 15 133 Translation 18 134 Replication 19 135 Genetic Variants and Mutants 22 1 4 The Cellular Imperative 23 141 Cell Types 23 1411 Prokaryotic Cells 23 1412 Eukaryotic Cells 25 Problems 27 References 28 Chapter 2 Forces Within and Between Biopolymers 31 2 1 Conformational Potential Energy 33 211 Bond-Length Stretching Potential 34 212 Bond Bending Potential 35 213 Bond Rotational Angle Potential 35 214 Nonbonding Potential 36 2 2 Dispersion and Exclusion Effects 38 2 3 Ionic Interactions 42 2 4 Dipole Interactions 45 2 5 van der Waals Forces 50 2 6 Hydrogen Bonds 50 2 7 Hydrophobic Bonds 54 2 8 Stacking Interactions 56 2 9 Modeling Structures by Computational Molecular Mechanics 57 Problems 58 References 59 V vi Contents Chapter 3 Proteins 63 3 1 Amino Acids 65 3 2 The Polypeptide Backbone 68 321 Conformation of the Polypeptide Backbone 68 3211 The Peptide Bond 68 3212 Pauling-Corey Rules 71 322 The Ramachandran Plot of Allowed Backbone Conformations 72 3 3 Secondary Structures 73 331 Thea-Helix 74 3311 Molecular Details 74 3312 Residue Chirality and Steric Conflicts 76 3313 Sequence Biases Determine Helix Orientations in Proteins 76 3314 Helix Propensities of Residues and Short Helices 78 332 The /3-Pleated Sheets 79 3 4 Thermodynamics of the a-Helix 81 341 Hydrogen Bonds 82 342 Backbone Dispersion Forces 83 343 Displacement of Bound Waters 83 344 Side-Chain Interactions and Conformational Entropy 83 345 Helix Dipole 83 346 End Effects 84 347 Structural and Energetic Cooperativity 85 348 Modeling of the Coil^Helix Transition—Multistate Model 87 349 Two-State Model 91 3 4 10 Helix Capping 92 3 5 Tertiary and Quaternary Structures 93 351 Fibrous Proteins 93 352 Globular Proteins 96 3 521 Single Crystal X-Ray Diffraction of Globular Proteins 96 3522 Structural Classification 103 3523 Mainly ar-Structures 104 3524 Alpha-Motifs or Coiled Coil Structures 106 3525 Mainly ^-Structures 106 352 6, a/p Structures 109 3527 FoldClassification Databases and Sequence-Structure Relationships 112 3 6 Protein Folding 112 361 Empirical Fold-Recognition Approaches to the Prediction of Protein Structure 116 3611 Case Study: The Relationship ofPlant and Animal Hemoglobins 117 3 7 Evolutionary Relationships from Primary Sequences 118 371 Phylogenetic Trees 119 Problems 121 References 124 Chapter 4 Covalent Features of the Nucleic Acids 131 4 1 Nucleotide Sugar 131 411 /5-D-Ribofuranose 132 Indicates an optional section Contents vii 412 Sugar Configurations 134 4121 Sugar Chirality 134 413 Sugar Conformation 136 4131 The Reason for Sugar Pucker 136 4132A Continuum of Sugar Conformations: Pseudorotation Angle 138 4133 Three Main Sugar Conformations 138 4 2 Nucleotide Base 140 421 Tautomeric Forms of the Bases 142 422 Polarity of the Bases 144 423 Modified Bases 145 424 Electronic Absorption Spectra of the Bases 145 4241 Lambert-Beer Law 147 4242 Radiant Energy 148 4243 Spectra 151 4244 Molecular Orbital Theory and Aromaticity 151 4245 Electron Derealization and Transition Energy 152 4246 Effects of Solvent on Spectra 153 4247 Photochemical and Mutational Effects of Ultraviolet Light 154 4 3 The N-Glycosidic Bond 154 431 Preferred Conformations of the N-Glycosidic Bond 154 4 4 Phosphoester Bond 156 441 Phosphodiester Linkages 159 442 The Unusually Long Half-Life of the Phosphodiester Linkage 162 443 Nucleotide and Phosphodiester Conformations 163 444 Nucleotide Polymerization, Base Stacking, and the Hypochromic Effect 164 4 5 Pyrimidine and Nucleotide Cofactors 166 451 NAD+and Dehydrogenases 168 Problems 170 References 170 Chapter 5 Structure, Synthesis, and Function of RNA 175 5 1 The Preponderance of Ribosomal, Transfer, and Small Nuclear RNA in Cells 182 511 RibosomdRNA 183 5111 The Roles of Ribosomal RNA Species in the Assembly and Function ofRibosomes 184 512 Transfer RNA 186 513 Messenger RNA 187 514 Eukaryotic Small Nuclear, Nucleolar, and Cytoplasmic RNA Types 187 5 2 Primary Structures of RNA Species 187 521 Primary Structures of Transfer RNA 187 5211 Posttranscriptional Changes in Primary Structures of tRNA Species 189 522 Primary Structures of Ribosomal RNA Molecules 189 5221 Primary Sequences of Eukaryotic Crown Ribosomal RNA 192 523 Primary Structures of Messenger RNA Species 192 5231 Primary Sequences of Eukaryotic Messenger RNA 194 52311 Introns 195 52312 Did Introns Arise Early or Late in Evolution? 195 52313 Multigene Families 195 viii Contents 5 3 Secondary Structures of RNA Molecules 196 531 Major Sources of Stability of Secondary Structures 196 5311 Hydrogen Bonds 197 5312 Stacking Interactions 197 532 Probing Secondary Structure 199 533 RNA Secondary Structural Elements 199 5331 Some Qualitative Thermodynamic Considerations 200 5332 Contributions of Structural Elements to Conformational Cooperativity 200 5333 Single-Stranded Stacking Interactions 202 5334 Stem-Loops 204 53341 TheTetraloop 204 534 Case Study: Secondary Structure of Transfer RNA 204 535 Case Study: Secondary Structure of 55 rRNA Particles 205 536 Case Study: Secondary Structures of Small Subunit rRNA Particles 207 537 Predictions of RNA Secondary Structure 207 5 4 Tertiary Structures of RNA Species 209 541 Crystal Structure of Transfer RNA 209 5411 Binding of Water 211 5412 Binding of Divalent Cations 213 542 Crystal Structure of the Catalytic Core of the Tetrahymena Ribozyme 214 5 5 Protein-RNA Interactions 214 5 6 The Biosynthesis of RNA: Transcription 217 561 Structures of Structural Genes 217 562 The Initiation Stage of Transcription in Prokaryotes 218 5621E coli DNA-Dependent RNA Polymerase 218 5622 Initiation of Transcription in Prokaryotes 219 5623 Location of Promoter Sequences by RNA Polymerase in Prokaryotes 221 5624 The Structure of T7 RNA Polymerase in Complex with an Open Promoter 223 563 Transcription in Eukaryotes 224 564 Elongation by RNA Polymerase 227 565 Transcription of Ribosomal RNA 229 5651 Transcription-ofrRNA in E coli 229 5652 Posttranscriptional Processing of Primary rRNA Transcripts in E coli 230 5653 Transcription of rRNA in Eukaryotes 231 5654 Posttranscriptional Processing of Pre-rRNA in Eukaryotes 232 5655 Posttranscriptional Modification of Pre-mRNA in Eukaryotes 232 5656 Group I Introns and the Ribozyme-Catalyzed Self-Splicing of rRNA Transcripts 236 566 Transfer RNA Genes 236 5661 Processing of Pre-tRNA 236 5662 RNaseP 237 5 7 The Participation of RNAs in Protein Synthesis 237 571 Activation 238 5711 Aminoacyl-tRNA Synthetases and Their Complexes with Cognate tRNA 240 572 Initiation 243 Contents ix 5721E coli Methionyl-tRNA-^ Transformylase 243 5722 Formation of the 705 Initiation Complex 244 5723 Structure of the Bacterial Ribosome 246 573 Elongation 247 5731E coli Elongation Factor Tu (EF-Tu) 247 5732 Peptidyltransferase 250 574 Termination 251 575 Translation in Eukaryotic Cells 251 Problems 252 References 253 Chapter 6 Secondary Structure of Duplex DNA 263 6 1 Contributions of Fiber Diffraction to Our Knowledge of DNA Structure 263 611 Semicrystalline Fibers of DNA 264 612 Theory of Diffraction by Helical Fibers 264 613 Overcoming the Limitations of Fiber Diffraction 268 6 2 Prelude to the Watson-Crick Double Helix 268 621 The Watson-Crick Double-Helical DNA 271 6 3 Refined and Archetypal Structures 274 631 Terms Used in the Definition of Conformational States 275 632 B-DNA, the Structure at High Relative Humidity 277 633 A-DNA, the Structure at Low Relative Humidity 277 634 DNA • RNA Hybrids 283 635 Polymorphism of DNA Double Helices 284 6 4 Structural Features Common to All Nucleic Acid Helices 285 641 Base Pairs and Hydrogen Bonds 285 642 Stacking Interactions 287 643 Grooves 289 6 5 Structures from Single-Crystal Diffraction Analysis 290 651 Z-DNA Structure from a Single Crystal of an Oligonucleotide 290 652 B-DNA in Single Crystals 294 6521 Local Base-Pair and Base-Pair-Neighbor Parameters 298 6522 Drew-Dickerson B-DNA: Sequence-Dependent Variations 299 6523 Drew-Dickerson B-DNA: Correlations Among Torsional Bond Angles 299 6524 Drew-Dickerson B-DNA: Effects of Propeller on Grooves 302 6525 The Structure of Drew-Dickerson Dodecanucleotide at Very High Resolution 303 6526 Nelson-Klug Sequence: (dA • dT)„ Tracts and Bifurcated Hydrogen Bonds 303 6527 Nelson-Klug Sequence: Inherent Sequence-Dependent Curvature of the Helix Axis 304 6528 Sequence-Dependent Variations and Bending 304 653 A-DNA in Single Crystals 307 654 The DNA • RNA Hybrid Helix 308 6 6 DNA Structure in Solution 308 661 Spectroscopic Methods Often Provide a Superabundance of Structural Detail 309 662 Nuclear Magnetic Resonance Spectroscopy 310 6 621 One-Dimensional NMR 310 x Contents 6 622 Multidimensional NMR 314 663 UV Electronic Absorption Spectroscopy 314 6631 Light-Induced Electronic Transitions 315 6632 Hypochromism 315 664 Helical Repeat in Solution 316 6 7 Hydrogen Bonding in an Aqueous Environment 320 6 8 Molecular Dynamics of DNA 320 681A Molecular Dynamics Case Study of an Oligomeric B-DNA 321 682 Spontaneous Breathing of DNA 321 6 9 Denaturation and Thermodynamics of DNA 324 691 Cooperativity and Energetics of DNA Denaturation 325 692 DNA Stability and (G + C) Content 327 6921 Distribution of Nearest Neighbors 328 6922 DNA Length 329 6923 Conformational States of Neighboring Domains 329 693 Effects of Extrinsic Factors on DNA Stability 330 6931 Counter-Cation Type and Concentration 330 6932 Inhospitable Solvents 330 6933 pH 330 694 Statistical Mechanical Simulation of Melting from DNA Sequences 332 6 10 Higher Organization of DNA 333 6 10 1 Supercoiling 333 6 10 1 1 The Biological Importance of Supercoiled DNA 335 6 10 2 Energetics of Supercoiling 337 6 10 3 The Consequences of Supercoiling from Theoretical Studies 337 6 10 4 Unusual DNA Structures, Some Induced by Supercoiling 339 6 10 4 1 Cruciform Structures 339 6 10 4 2 Triple Helices and the H-Structure 340 6 11 Macromolecular Structure 343 Problems 346 References 347 Chapter 7 Primary Sequences of DNA 357 7 1 Base Compositions ofcProkaryotic DNA 357 711 Directional MutationPressures 359 712 Distributions of (G + C) Contents in Prokaryotes 360 7 1 3 Relationship to the Normal Distribution Function 360 714 Distribution of (G + C) in E coli 361 7 2 Base Compositions of Eukaryotic DNA 363 721 Distributions of (G + C) Compositions and Isochores 363 7 3 Dinucleotide (Nearest-Neighbor) Frequencies 365 731 Dinucleotide Frequencies by Direct Count 366 732 Dinucleotide Frequencies by Chemical Analysis 367 733 CG Instability 367 734 CpG Islands 368 7 4 Sequence Complexity 369 7 4 1 Sequence Complexity and Shannon Entropy 371 742 Sequence Complexity from Renaturation Kinetics 372 743 Second-Order Kinetics 373 744 Second-Order DNA Reassociation Kinetics 374 Contents xi 7 5 Primary Sequences in Prokaryotes 381 751 Codon Biases 383 7 6 Primary Sequence Elements in Eukaryotes 383 761 Genome Reorganization 386 762 Gene Sequences 387 7621 Codon Biases 389 763 Sequence Signals for Posttranscriptional Alterations 389 764 Introns 390 765 Pseudogenes 390 766 Computer Identification of Coding Sequences 391 7 7 Satellite DNA and Repetitive Sequences 391 771 Classification 391 772 Gene Duplication and the Origin of Tandem Repeats 394 773 Macrosatellites 396 774 Minisatellites 397 7741 Minisatellite DNA Fingerprinting (DNA Typing) 400 775 Microsatellites 401 7751 Trinucleotide Repeats and Genetic Disorders 403 776 Origins of Interspersed Repetitive Sequences 403 7761 Mammalian A/w SINEs 405 7762 LINEs 408 777 Specialized Repetitive Sequence Elements of the Functional Eukaryotic Chromosome 408 7771 Centromere 409 7772 Telomere 412 7773 Yeast Artificial Chromosome 413 778 Multigene or Repetitive Structural Gene Families 414 7781 Multicopy Gene Families for Increased Dosages of Gene Product 415 7782 Paralogous Multigene Families 417 77821 Hemoglobin 417 7 8 Primary Sequences of Mitochondrial DNA 418 7 9 Determining Evolutionary Relationships from Primary Sequences 422 7:9 1 -Phylogenetic Trees 423 7911 Base Substitutions 425 7912 The Neutral Theory of Evolution 425 7913 Primary Sequence Repositories 426 7914 Multiple Sequence Alignments 427 7915 Tree Building 427 7916 Vagaries of the Molecular Clock 429 7917 Selected Case Studies of Intra- and Interspecific Molecular Evolution ofHominoids 431 7918A Hominoid Tree from Stabilities of DNAA • DNAB Heteroduplexes 434 7919 Distances Within Populations: The Use of mtDNA and the Origins of Homo sapiens 435 791 10 Molecular Archaeology 436 Problems 439 References 440 xii Contents Chapter 8 Interactions of Water and Cations with DNA 449 8 1 The Unusual Character of Water 450 8 2 Hydration of Electrolytes 452 8 3 Interactions of Hydrated Ions in Solution 455 8 3 1 Electrostatic Potentials and the Debye-Hiickel Theory 456 8 4 Macroscopic Studies of DNA Hydration 459 841 Early Gravimetric and IR Studies of DNA Hydration 459 842 The Dependence of Buoyant Density on Base Composition 460 8 421 Density Gradient Centrifugation 462 843 The Dependence of Buoyant Density on Sequence 464 844 Variations in Densities of Water Molecules Bound to DNA 465 845 Summary of Macroscopic Analyses of Hydration in Aqueous Solution 466 8 5 Microscopic Studies of DNA Hydration: Single-Crystal Diffraction 467 851 Summary Analysis of Hydration in Single Crystals 471 8 6 Interactions of Cations with DNA 474 861 The Physiologically Important Microcations 476 862 Interactions of Inorganic Cations with DNA 476 8621 Nonspecific Counterion Condensation of Microcations by DNA 476 8622 The Dependence of DNA Stability on Cation Concentration 477 86221 Effects of Condensed Microcations on Helix-Coil Equilibria: A Case Study 480 8623 The Fractional Occupancy of Microcations at Sites in Grooves 482 8624 Specific Site Binding by Metal Ions 483 863 Interactions of Biochemical Cations with DNA 485 8631 Protamines in Eukaryotic Sperm 485 8632 Basic Histones of Eukaryotic Chromosomes 486 8633 Histonelike Proteins of Prokaryotes 486 8634 Polyamines 486 Problems 488 References 489 Chapter 9 Interactions of Proteins with DNA 493 9 1 Modes of Interaction 493 911 Noncovalent Interactions Involved in Binding 496 912 Conformational Transitions Associated with Binding 497 9 2 Methods of Analysis 497 921A Popular Thermodynamic Binding Isotherm for the Binding of Proteins to DNA 498 9 3 Principles of Sequence-Specific DNA-Binding Proteins 500 931 Target-Site Specificity 500 932 Target-Site Recognition in the Major Groove 501 933 Energetics of Site-Specific Association 502 934 The Principal DNA-Binding Motifs 503 935 The or-Helix, a Common Structural Element of DNA-Binding Motifs 504 9 4 DNA-Binding Proteins of the Structural Class 506 941 Nonspecific Binding of Proteins That Reduce the Lineal Dimensions of DNA 506 9411 Prokaryotic HU Protein 506 9412 Eukaryotic Nucleosome 509 Contents xiii 9 5 DNA-Binding Proteins of the Enzymatic Class 510 951 Topoisomerases 513 9511 The Structure of Human DNA Topoisomerase I 513 952 Enzymes of Nucleic Acid Digestion 516 9521 Bovine Pancreatic DNase I 516 9 6 DNA-Binding Proteins of the Regulatory Class 516 961 Group 1 Helix-Turn-Helix Proteins 516 9611 Variations in the Relationship Between DNA and Recognition Helix 2 Are Small 521 9612k cl and Cro Proteins, Well-Characterized Case Studies of DNA Binding Through the HTH Motif 521 96121 Developmental Control of k Depends on Sequence-Specific Repressor Protein-DNA Interactions 525 962 Group 2 Zinc-Coordinating Proteins 528 9621 The Role of Zinc 528 9622 Four Classes of Zinc-Coordinating Proteins 530 963 Class I Zinc-Finger DNA-Binding Proteins 531 9631 The Example of TFIIA 531 9632 TFIIA Regulates the Transcription of 55 Ribosomal RNA 532 9633 Structure of a TFIIA-DNA Complex 532 964 Class II Zinc-Finger DNA-Binding Proteins 533 9641 Nuclear Receptor Proteins: Ligand-Inducible Transcription Factors 533 9642 Structures of Glucocorticoid- and Estrogen Receptor-DNA Complexes 534 96421 The Class II Zinc-Finger DNA-Binding Domain 536 96422 The Class II (Hormone) Ligand-Binding Domain 537 9643 Origins and Evolution of Nuclear Receptor Proteins 540 965 Class III Zinc-Finger DNA-Binding Proteins 541 966 Class IV Zinc-Finger DNA-Binding Proteins 542 967 Group 3 Zipper Coiled Coil Proteins 545 9671 Transcription Regulatory Proteins of the Zipper Group 3 545 9672 Many Zipper Proteins Are the Expression Products of Proto-Oncogenes 545 9673 Specific Binding to DNA of NFAT-Fos-Jun Proteins, Members of the Zipper Family 548 9674 Specific Binding to DNA of the Max Protein, Member of the Helix-Loop-Helix Family 549 968 Group 5 ^-Sheet Proteins 549 969 Group 6 -Hairpin Proteins 549 Problems 553 References 554 Chapter 10 Cellular Replication of DNA 561 10 1 Stages of Replication 561 10 1 1 Enzymes and Proteins of DNA Replication 562 10 2 Origin Locus of Replication 563 10 2 1 DNAHelicase 565 10 211 The Structure of a Helicase Bound to a Single-Stranded DNA 565 xiv Contents 10 2 2 Primase 566 10 221 X-ray Structure of E coli Primase 567 10 2 3 Stabilization of Single-Stranded Regions at the Replication Fork 568 10 231 Crystal Structure of T4 SSB Protein 569 10 3 Condensation of dNTP and Elongation of DNA 570 10 3 1 Thermodynamics of Phosphate Esters 571 10 3 2 dNTP Pools and Isochores 573 10 3 3 Rates of Replication 573 10 3 4 Mechanism of DNA Replication by DNA Polymerase 574 10 3 5 Proofreading 576 10 3 6 Error Frequencies 577 10 3 7 Replicative Accuracy 577 10 3 8 Replicative Accuracy and Genome Size 578 10 3 9 Atomic Structures of DNA Polymerases 579 10 391E coli DNA Polymerase HI Holoenzyme 579 10 392 Structure of the p Subunit of E coli Pol III 580 10 393E coli Pol I 580 10 394 Crystal Structure and Mechanism of Action of E coli Pol I 582 10 395 Crystal Structures of Other Polymerases 584 10 396 Eukaryotic DNA Polymerases 584 10 4 Auxiliary Replicative Processes 585 10 4 1 Removal of Primer 585 10 411 Crystal Structure of M janeschii RNase HII 585 10 412 DNA • RNA Hybrid and Chimeric Structures 587 10 4 2 Joining of Okazaki Pieces 588 10 421 Crystal Structure of the ATP-Dependent T7 DNA Ligase 589 10 4 3 The Role of Topoisomerases During Elongation 589 10 5 Replication of the Ends of Linear Eukaryotic DNA by Telomerase 591 10 5 1 Evolution of Telomerase 593 10 5 2 The Quadruplex Secondary Structure of Telomeric DNA 595 Problems 596 References 596 Mutations, Unscheduled Decay, Reactivity, and Interactions of DNA 603 Mutations 604 ~—— 11 1 1 Mutation Background 605 11 1 2 Causes of Mutations 605 11 1 3 Germinal Mutations and Inborn Errors of Metabolism 607 11 1 4 Somatic Mutations and Cancer 608 11 1 5 Specificities of Different Mutagens on the p53 Tumor-Suppressor Gene 611 * 11 1 6 Mutagenicity Assays 611 11 2 Point Mutations 611 11 2 1 Types of Point Mutations 612 11 211 Transitions 613 11 212 Transversions 613 11 213 Insertions and Deletions 614 11 2 2 Effects of Point Mutations on Coding Sequences 614 11 3 Relative Rates of Point Mutation 615 11 3 1 Steady-State Differences of Mutation Rates in Humans 619 11 311 Neighbor-Dependent Mutation Rates 620 Chapter 11 Contents xv 11 312 Neighbor-Pair-Dependent Mutation Rates Contribute to the Formation of Nonrandom Sequences in DNA 622 11 313 Computer Simulation of Replication with Mutations 623 11 4 Molecular Basis of Mutagenesis 623 11 4 1 Keto^EnoI and Amino^Imino Tautomerization of the Bases 623 11 4 2 Wobble Mispairs 626 11 421 The Structure of the (G • Twobb/e) Mispair 628 11 422 The Structure of the (A • CwobbIe) Mispair 631 11 423 The Structure of the (G • A) Mispair 632 11 4 3 Spontaneous Lesions 634 11 431 Depurination and Depyrimidination 634 11 432 Deamination 634 11 433 Lability of the Phosphodiester Bond at AP Sites 636 11 5 Reactions with Endogenous Agents 636 11 5 1 Endogenous Sources of Reactive Oxygen 636 11 5 2 Reactions of Endogenous Electrophiles with DNA 639 11 6 Reactions of Exogenous Agents with DNA 640 11 6 1 Reactive Oxygen Generated by Solar Radiation 640 11 6 2 PyroPyr and Hydrate Photoproducts Caused by UV Radiation 641 11 621 Xeroderma Pigmentosum 643 11 6 3 Psoralen, a Photosensitizing Agent That Reacts Both Noncovalently and Covalently with DNA 643 11 6 4 Direct and Indirect Production of DNA Adducts by Alkylating Agents 645 11 641 Specificities of Alkylating Agents 645 11 642 Specificities of the Reactive Sites on the DNA 645 11 643 Alkylation of Guanine N7 Often Leads to Depurination 647 11 644 Bifunctional Alkylating Agents: The Sulfur and Nitrogen Mustards 648 11 6 5 Indirect-Acting Alkylating Agents 649 11 651 Benzo[a]pyrene, a Case Study 649 11 652 Aflatoxin Blf another Case Study 650 11 653 N-Nitroso Compounds 650 11 6 6 Nonalkylating Agents 653 11 6 7 Interactions with Dyes and Drugs 654 11 671 Structural and Energetic Consequences of Intercalation 655 11 672 Actinomycin D Binds DNA by Intercalation 657 11 673 Bleomycin and Pepleomycin Bind DNA by Intercalation 659 11 674 Netropsin Binds to (A * T) Tracts in the Narrow Minor Groove 660 11 675 Cisplatin Forms Guanine Adducts That Crosslink DNA 661 11 6 8 Metal Ion Binding 661 Problems 664 References 666 Chapter 12 Repair and Recombination of DNA 677 12 1 Multifunctional Repair Enzymes 678 12 2 Multiple Pathways for the Repair of Damage Caused by UV Radiation 679 12 3 Mismatch Repair 681 12 3 1 Summary of Biochemical Events During Mismatch Repair 683 12 3 2 Methyl-Directed Discrimination Between Standard but Noncomplementary Base Mispairs 684 xvi Contents 12 3 3 Long-Patch Mismatch Repair 685 12 331 Crystal Structures of MutS-DNA 687 12 3 4 Excision of the Section (Patch) Containing the Mismatch 688 12 3 5 Very Short Patch Repair 689 12 4 Excision Repair 689 12 4 1 Base Excision Repair 690 12 411 DNA Glycosylases 694 12 412 Crystal Structure of Human Uracil-DNA Glycosylase 695 12 4 2 Apurinic/Apyrimidinic Sites 697 12 4 3 Apurinic/Apyrimidinic Endonuclease 699 12 4 4 Apurinic/Apyrimidinic Endonuclease IV 700 12 441 Crystal Structure of E coli AP Endonuclease IV 700 12 4 5 Nucleotide Excision Repair 702 12 451 NER in E coli 702 12 4511 Structure of UvrB 703 12 452 NER in Eukaryotes 704 12 5 Direct Reversal of Certain Lesions 705 12 6 The SOS Repair System 706 12 7 Recombination and Recombination Repair 706 12 7 1 Homologous Recombination 708 12 7 2 Proposed Mechanism of Homologous Recombination 708 12 721 Molecular Structure of the Holliday Junction 714 12 7 3 Double-Strand Breaks and Recombination Repair 715 12 7 4 Gene Duplication 715 12 7 5 Tandemly Repetitive Sequences 717 12 7 6 Site-Specific Recombination 717 12 761 Transposable Genetic Elements 717 12 7 7 Nonspecific Recombination 718 Problems 718 References 719 Prebiotic Origins The Physical Age of the Universe 729 13 1 1 Origin of theJJniverse and Bioelements 729 Formation of Earth 730 13 2 1 Conditions on Primitive Earth 730 The Age of Chemistry 731 13 3 1 Favorable Attributes of the Primary Bioelements 732 * 13 311 Carbon in the Central Role of Biogenesis 732 * 13 312 Oxygen, Nitrogen, and the Importance of Polarity 732 * 13 313 Phosphorous 733 * 13 314 Water as Both Solvent and Reactant 738 Thermodynamic Precepts for Origins and Order: Dissipative Processes 739 13 4 1 Laws of Thermodynamics and Time-Independent Equilibrium States 13 4 2 Irreversible Time-Dependent Processes 742 13 4 3 Origins of Order Under Far-from-Equilibrium Conditions 743 13 4 4 Conditions Favorable for Dissipative Processes and Biogenesis 745 Hypercycles 746 13 5 1 Defining Characteristics of Hypercycles 748 Chapter 13 * Contents xvii 13 6 Age of Abiotic Chemistry: Synthesis of Pi and Alpha Molecules 748 13 6 1 Abiotic Amino Acid Synthesis 750 13 6 2 Abiotic Synthesis of Purines and Pyrimidines 751 13 6 3 Abiotic Synthesis of Sugars and Sugar Phosphates 752 13 7 Abiotic Synthesis of Beta Monomelic Units of D-Ribose 754 13 7 1 How Important Is Sugar Chirality? 755 13 7 2 Diastereoselective Synthesis of Sugars 755 13 7 3 Abiotic Synthesis of Sugar and Nucleoside Phosphate Esters 756 13 8 Alpha Monomelic Units of Ribose Analogs 756 13 8 1 Flexible Prochiral Analogs of D-Ribose 756 13 8 2 Hexose Nucleotide Analogs 757 13 8 3 The Age of Prebiotic Chemistry 757 13 9 The RNA World 760 * 13 9 1 The Life Cycle of Q/3 760 13 9 2 In vivo Replication and Quasi Species of Q^vRNA and Q/JmvRNA 761 13 9 3 In vitro Darwinian Experiments with Q/8 RNA Replicase 762 Problems 763 References 764 Index 769
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id	DE-604.BV019812221
illustrated	Illustrated
indexdate	2024-07-09T20:06:41Z
institution	BVB
isbn	1891389289
language	English
lccn	2004043051
oai_aleph_id	oai:aleph.bib-bvb.de:BVB01-013137617
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owner	DE-M49 DE-BY-TUM DE-11
owner_facet	DE-M49 DE-BY-TUM DE-11
physical	XXII, 778 S. Ill., graph. Darst.
publishDate	2005
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publisher	University Science Books
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spelling	Blake, Richard D. Verfasser aut Informational biopolymers of genes and gene expression R.D. Blake Sansalito, CA University Science Books 2005 XXII, 778 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references and index aGenes aGene expression aInformation theory in biology Molekulargenetik (DE-588)4039987-4 gnd rswk-swf Nucleinsäuren (DE-588)4172117-2 gnd rswk-swf Genexpression (DE-588)4020136-3 gnd rswk-swf Proteine (DE-588)4076388-2 gnd rswk-swf Nucleinsäuren (DE-588)4172117-2 s Molekulargenetik (DE-588)4039987-4 s DE-604 Proteine (DE-588)4076388-2 s Genexpression (DE-588)4020136-3 s HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=013137617&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis
spellingShingle	Blake, Richard D. Informational biopolymers of genes and gene expression aGenes aGene expression aInformation theory in biology Molekulargenetik (DE-588)4039987-4 gnd Nucleinsäuren (DE-588)4172117-2 gnd Genexpression (DE-588)4020136-3 gnd Proteine (DE-588)4076388-2 gnd
subject_GND	(DE-588)4039987-4 (DE-588)4172117-2 (DE-588)4020136-3 (DE-588)4076388-2
title	Informational biopolymers of genes and gene expression
title_auth	Informational biopolymers of genes and gene expression
title_exact_search	Informational biopolymers of genes and gene expression
title_full	Informational biopolymers of genes and gene expression R.D. Blake
title_fullStr	Informational biopolymers of genes and gene expression R.D. Blake
title_full_unstemmed	Informational biopolymers of genes and gene expression R.D. Blake
title_short	Informational biopolymers of genes and gene expression
title_sort	informational biopolymers of genes and gene expression
topic	aGenes aGene expression aInformation theory in biology Molekulargenetik (DE-588)4039987-4 gnd Nucleinsäuren (DE-588)4172117-2 gnd Genexpression (DE-588)4020136-3 gnd Proteine (DE-588)4076388-2 gnd
topic_facet	aGenes aGene expression aInformation theory in biology Molekulargenetik Nucleinsäuren Genexpression Proteine
url	http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=013137617&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
work_keys_str_mv	AT blakerichardd informationalbiopolymersofgenesandgeneexpression

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