Clark Molecular Biology

1. Auflage 2009
ISBN: 978-0-12-378590-9
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, 784 Seiten

Molecular Biology: Academic Cell Update provides an introduction to the fundamental concepts of molecular biology and its applications. It deliberately covers a broad range of topics to show that molecular biology is applicable to human medicine and health, as well as veterinary medicine, evolution, agriculture, and other areas. The present Update includes the study guide with online content, journal specific images, and test bank. It also offers vocabulary flashcards and online self-quizzing called Test Prep.
The book begins by defining some basic concepts in genetics such as biochemical pathways, phenotypes and genotypes, chromosomes, and alleles. It explains the characteristics of cells and organisms, DNA, RNA, and proteins. It also describes genetic processes such as transcription, recombination and repair, regulation, and mutations. The chapters on viruses and bacteria discuss their life cycle, diversity, reproduction, and gene transfer. Later chapters cover topics such as molecular evolution; the isolation, purification, detection, and hybridization of DNA; basic molecular cloning techniques; proteomics; and processes such as the polymerase chain reaction, DNA sequencing, and gene expression screening.
*Now with an online study guide with the most current, relevant research from Cell Press  *Full supplements including test bank, powerpoint and online self quizzing *Up to date description of genetic engineering, genomics, and related areas * Basic concepts followed by more detailed, specific applications * Hundreds of color illustrations enhance key topics and concepts * Covers medical, agricultural, and social aspects of molecular biology * Organized pedagogy includes running glossaries and keynotes (mini-summaries) to hasten comprehension

David P. Clark did his graduate work on bacterial antibiotic resistance to earn his Ph.D. from Bristol University, in the West of England. During this time, he visited the British Government's biological warfare facility at Porton Down and was privileged to walk inside the (disused) Black Death fermenter. He later crossed the Atlantic to work as a postdoctoral researcher at Yale University and then the University of Illinois. David Clark recently retired from teaching Molecular Biology and Bacterial Physiology at Southern Illinois University which he joined in 1981. His research into the Regulation of Alcohol Fermentation in E. coli was funded by the U.S. Department of Energy, from 1982 till 2007. From 1984-1991 he was also involved in a project to use genetically altered bacteria to remove contaminating sulfur from coal, jointly funded by the US Department of Energy and the Illinois Coal Development Board. In 1991 he received a Royal Society Guest Research Fellowship to work at Sheffield University, England while on sabbatical leave. He has supervised 11 master's and 7 PhD students and published approximately 70 articles in scientific journals. He has written or co-authored several textbooks, starting with Molecular Biology Made Simple and Fun (with Lonnie Russell; (Cache River Press, First edition, 1997) which is now in its fourth edition. Other books are Molecular Biology and Biotechnology (both published by Elsevier) He recently wrote a popular science book, Germs, Genes, & Civilization: How Epidemics Shaped Who We Are Today (2010, Financial Times Press/Pearson). David is unmarried, but his life is supervised by two cats, Little George and Mr Ralph.

Autoren/Hrsg.

Clark, David P.

Inhaltsverzeichnis

1;Front Cover ;4
2;Molecular biology: Academic Cell Update;4
3;Copyright Page;5
4;Dedication;6
5;Preface;8
6;Introduction;9
7;Table of Contents;10
8;Chapter One Basic Genetics;20
8.1;Gregor Mendel Was the Father of Classical Genetics;21
8.2;Genes Determine Each Step in Biochemical Pathways;22
8.3;Mutants Result from Alterations in Genes;23
8.4;Phenotypes and Genotypes;24
8.5;Chromosomes Are Long, Thin Molecules ThatCarry Genes;25
8.6;Different Organisms may Have Different Numbers of Chromosomes;26
8.7;Dominant and Recessive Alleles;27
8.8;Partial Dominance, Co-Dominance, Penetrance and Modifier Genes;28
8.9;Genes from Both Parents Are Mixed by Sexual Reproduction;30
8.10;Sex Determination and Sex-Linked Characteristics;32
8.11;Neighboring Genes Are Linked during Inheritance;34
8.12;Recombination during Meiosis Ensures Genetic Diversity;35
8.13;Escherichia coli is a Model for Bacterial Genetics;36
9;Chapter Two Cells and Organisms;40
9.1;What Is Life?;41
9.2;Living Creatures Are Made of Cells;42
9.3;Essential Properties of a Living Cell;42
9.4;Prokaryotic Cells Lack a Nucleus;46
9.5;Eubacteria and Archaebacteria Are Genetically Distinct;47
9.6;Bacteria Were Used for Fundamental Studies of Cell Function;48
9.7;Escherichia coli (E. coli) Is a Model Bacterium;50
9.8;Where Are Bacteria Found in Nature?;51
9.9;Some Bacteria Cause Infectious Disease, but Most Are Beneficial;53
9.10;Eukaryotic Cells Are Sub-Divided into Compartments;53
9.11;The Diversity of Eukaryotes;55
9.12;Eukaryotes Possess Two Basic Cell Lineages;55
9.13;Organisms Are Classified;57
9.14;Some Widely Studied Organisms Serve as Models;59
9.15;Yeast Is a Widely Studied Single-Celled Eukaryote;59
9.16;A Roundworm and a Fly Are Model Multicellular Animals;60
9.17;Zebrafish are used to Study Vertebrate Development;61
9.18;Mouse and Man;63
9.19;Arabidopsis Serves as a Model for Plants;63
9.20;Haploidy, Diploidy and the Eukaryote Cell Cycle;64
9.21;Viruses Are Not Living Cells;65
9.22;Bacterial Viruses Infect Bacteria;66
9.23;Human Viral Diseases Are Common;67
9.24;A Variety of Subcellular Genetic Entities Exist;68
10;Chapter Three DNA, RNA and Protein;70
10.1;Nucleic Acid Molecules Carry Genetic Information;71
10.2;Chemical Structure of Nucleic Acids;71
10.3;DNA and RNA Each Have Four Bases;73
10.4;Nucleosides Are Bases Plus Sugars; Nucleotides Are Nucleosides Plus Phosphate74
10.5;Double Stranded DNA Forms a Double Helix;75
10.6;Base Pairs are Held Together by Hydrogen Bonds;76
10.7;Complementary Strands Reveal the Secret of Heredity;78
10.8;Constituents of Chromosomes;79
10.9;The Central Dogma Outlines the Flow ofGenetic Information;82
10.10;Ribosomes Read the Genetic Code;84
10.11;The Genetic Code Dictates the Amino Acid Sequence of Proteins;86
10.12;Various Classes of RNA Have Different Functions;88
10.13;Proteins, Made of Amino Acids, Carry Out Many Cell Functions;89
10.14;The Structure of Proteins Has Four Levels of Organization;90
10.15;Proteins Vary in Their Biological Roles;92
11;Chapter Four Genes, Genomes and DNA;94
11.1;History of DNA as the Genetic Material;95
11.2;How Much Genetic Information Is Necessary to Maintain Life?;97
11.3;Non-Coding DNA;97
11.4;Coding DNA May Be Present within Non-coding DNA;99
11.5;Repeated Sequences Are a Feature of DNA in Higher Organisms;100
11.6;Satellite DNA Is Non-coding DNA in the Form of Tandem Repeats;102
11.7;Minisatellites and VNTRs;103
11.8;Origin of Selfish DNA and Junk DNA;103
11.9;Palindromes, Inverted Repeats and Stem and Loop Structures;105
11.10;Multiple A-Tracts Cause DNA to Bend;106
11.11;Supercoiling is Necessary for Packaging of Bacterial DNA;107
11.12;Topoisomerases and DNA Gyrase;108
11.13;Catenated and Knotted DNA Must Be Corrected;110
11.14;Local Supercoiling;110
11.15;Supercoiling Affects DNA Structure;110
11.16;Alternative Helical Structures of DNA Occur;111
11.17;Histones Package DNA in Eukaryotes;114
11.18;Further Levels of DNA Packaging in Eukaryotes;115
11.19;Melting Separates DNA Strands; Cooling Anneals Them119
12;Chapter Five Cell Division and DNAReplication;122
12.1;Cell Division and ReproductionAre Not Always Identical;123
12.2;DNA Replication Is a Two-Stage Process Occurring at the Replication Fork;123
12.3;Supercoiling Causes Problems for Replication;124
12.4;Strand Separation Precedes DNA Synthesis;126
12.5;Properties of DNA Polymerase;126
12.6;Polymerization of Nucleotides;128
12.7;Supplying the Precursors for DNA Synthesis;128
12.8;DNA Polymerase Elongates DNA Strands;130
12.9;The Complete Replication Fork Is Complex;131
12.10;Discontinuous Synthesis of DNA Requires a Primosome;133
12.11;Completing the Lagging Strand;135
12.12;Chromosome Replication Initiates at oriC;137
12.13;DNA Methylation and Attachment to the Membrane Control Initiation of Replication;139
12.14;Chromosome Replication Terminates at terC;140
12.15;Disentangling the Daughter Chromosomes;141
12.16;Cell Division in Bacteria Occurs after Replication of Chromosomes;143
12.17;How Long Does It Take for Bacteria to Replicate?;143
12.18;The Concept of the Replicon;144
12.19;Replicating Linear DNA in Eukaryotes;145
12.20;Eukaryotic Chromosomes Have Multiple Origins;148
12.21;Synthesis of Eukaryotic DNA;149
12.22;Cell Division in Higher Organisms;149
13;Chapter Six Transcription of Genes;151
13.1;Genes are Expressed by Making RNA;152
13.2;Short Segments of the Chromosome Are Turned into Messages;153
13.3;Terminology: Cistrons, Coding Sequences and Open Reading Frames;153
13.4;How Is the Beginning of a Gene Recognized?;154
13.5;Manufacturing the Message;156
13.6;RNA Polymerase Knows Where to Stop;157
13.7;How Does the Cell Know Which Genes to Turn On?;159
13.8;What Activates the Activator?;160
13.9;Negative Regulation Results from the Action ofRepressors;162
13.10;Many Regulator Proteins Bind Small Molecules and Change Shape;163
13.11;Transcription in Eukaryotes Is More Complex;164
13.12;Transcription of rRNA and tRNA in Eukaryotes;165
13.13;Transcription of Protein-Encoding Genes in Eukaryotes;167
13.14;Upstream Elements Increase the Efficiency of RNA Polymerase II Binding;170
13.15;Enhancers Control Transcription at a Distance;171
14;Chapter Seven Protein Structure and Function;173
14.1;Proteins Are Formed from Amino Acids;174
14.2;Formation of Polypeptide Chains;174
14.3;Twenty Amino Acids Form Biological Polypeptides;174
14.4;Amino Acids Show Asymmetry around the Alpha-carbon;177
14.5;The Structure of Proteins Reflects Four Levels of Organization;179
14.6;The Secondary Structure of Proteins Relies on Hydrogen Bonds;179
14.7;The Tertiary Structure of Proteins;182
14.8;A Variety of Forces Maintain the 3-D Structure of Proteins;184
14.9;Cysteine Forms Disulfide Bonds;185
14.10;Multiple Folding Domains in Larger Proteins;185
14.11;Quaternary Structure of Proteins;186
14.12;Higher Level Assemblies and Self-Assembly;188
14.13;Cofactors and Metal Ions Are Often Associated with Proteins;188
14.14;Nucleoproteins, Lipoproteins and Glycoproteins Are Conjugated Proteins;191
14.15;Proteins Serve Numerous Cellular Functions;193
14.16;Protein Machines;196
14.17;Enzymes Catalyze Metabolic Reactions;196
14.18;Enzymes Have Varying Specificities;198
14.19;Lock and Key and Induced Fit Models Describe Substrate Binding;200
14.20;Enzymes Are Named and Classified According to the Substrate;200
14.21;Enzymes Act by Lowering the Energy of Activation;201
14.22;The Rate of Enzyme Reactions;203
14.23;Substrate Analogs and Enzyme Inhibitors Act at the Active Site;203
14.24;Enzymes May Be Directly Regulated;206
14.25;Allosteric Enzymes Are Affected by Signal Molecules;206
14.26;Enzymes May Be Controlled by Chemical Modification;208
14.27;Binding of Proteins to DNA Occurs in Several Different Ways;209
14.28;Denaturation of Proteins;213
15;Chapter Eight Protein Synthesis;216
15.1;Protein Synthesis Follows a Plan;217
15.2;Proteins Are Gene Products;217
15.3;Decoding the Genetic Code;218
15.4;Transfer RNA Forms a Flat Cloverleaf Shape and a Folded “L” Shape;219
15.5;Modified Bases Are Present in Transfer RNA;220
15.6;Some tRNA Molecules Read More Than One Codon;221
15.7;Charging the tRNA with the Amino Acid;223
15.8;The Ribosome: The Cell’s Decoding Machine;223
15.9;Three Possible Reading Frames Exist;227
15.10;The Start Codon Is Chosen;229
15.11;The Initiation Complexes Must Be Assembled;230
15.12;The tRNA Occupies Three Sites During Elongation of the Polypeptide;230
15.13;Termination of Protein Synthesis Requires Release Factors;232
15.14;Several Ribosomes Usually Read the Same Message at Once;233
15.15;Bacterial Messenger RNA Can Code for Several Proteins;234
15.16;Transcription and Translation Are Coupled in Bacteria;235
15.17;Some Ribosomes Become Stalled and Are Rescued;236
15.18;Differences between Eukaryotic and Prokaryotic Protein Synthesis;237
15.19;Initiation of Protein Synthesis in Eukaryotes;237
15.20;Protein Synthesis Is Halted When Resources Are Scarce;240
15.21;A Signal Sequence Marks a Protein for Export from the Cell;240
15.22;Molecular Chaperones Oversee Protein Folding;243
15.23;Protein Synthesis Occurs in Mitochondria and Chloroplasts;244
15.24;Proteins Are Imported into Mitochondria and Chloroplasts by Translocases;245
15.25;Mistranslation Usually Results in Mistakesin Protein Synthesis;245
15.26;The Genetic Code Is Not “Universal”;246
15.27;Unusual Amino Acids are Made in Proteins by Post-Translational Modifications;246
15.28;Selenocysteine: The 21st Amino Acid;246
15.29;Pyrrolysine: The 22nd Amino Acid;247
15.30;Many Antibiotics Work by Inhibiting Protein Synthesis;249
15.31;Degradation of Proteins;250
16;Chapter Nine Regulation of Transcriptionin Prokaryotes;253
16.1;Gene Regulation Ensures a Physiological Response;254
16.2;Regulation at the Level of Transcription Involves Several Steps;255
16.3;Alternative Sigma Factors in Prokaryotes Recognize Different Sets of Genes;257
16.4;Heat Shock Sigma Factors in Prokaryotes Are Regulated by Temperature;257
16.5;Cascades of Alternative Sigma Factors Occurin Bacillus Spore Formation;258
16.6;Anti-sigma Factors Inactivate Sigma; Anti-anti-sigma Factors Free It to Act261
16.7;Activators and Repressors Participate in Positive and Negative Regulation;262
16.8;The Operon Model of Gene Regulation;263
16.9;Some Proteins May Act as Both Repressors and Activators;265
16.10;Nature of the Signal Molecule;267
16.11;Activators and Repressors May Be Covalently Modified;271
16.12;Two-Component Regulatory Systems;272
16.13;Phosphorelay Systems;273
16.14;Specific versus Global Control;273
16.15;Crp Protein Is an Example of a Global Control Protein;274
16.16;Accessory Factors and Nucleoid Binding Proteins;275
16.17;Action at a Distance and DNA Looping;276
16.18;Anti-Termination as a Control Mechanism;277
17;Chapter Ten Regulation of Transcription in Eukaryotes;281
17.1;Transcriptional Regulation in Eukaryotes Is More Complex Than in Prokaryotes;282
17.2;Specific Transcription Factors Regulate Protein Encoding Genes;283
17.3;The Mediator Complex Transmits Information to RNA Polymerase;283
17.4;Enhancers and Insulator Sequences Segregate DNA Functionally;284
17.5;Matrix Attachment Regions Allow DNA Looping;287
17.6;Negative Regulation of Transcription Occurs in Eukaryotes;288
17.7;Heterochromatin Causes Difficulty for Access to DNA in Eukaryotes;289
17.8;Methylation of DNA in Eukaryotes Controls Gene Expression;292
17.9;Silencing of Genes Is Caused by DNA Methylation;294
17.10;Genetic Imprinting in Eukaryotes Has Its Basis in DNA Methylation Patterns;294
17.11;X-Chromosome Inactivation Occurs in Female XX Animals;296
18;Chapter Eleven Regulation at the RNA Level;300
18.1;Regulation at the Level of RNA;301
18.2;Binding of Proteins to mRNA Controls The Rate of Degradation;301
18.3;Some mRNA Molecules Must Be Cleaved Before Translation;302
18.4;Some Regulatory Proteins May Cause Translational Repression;303
18.5;Some Regulatory Proteins Can Activate Translation;306
18.6;Translation May Be Regulated by Antisense RNA;307
18.7;Regulation of Translation by Alterations to the Ribosome;309
18.8;RNA Interference (RNAi);310
18.9;Amplification and Spread of RNAi;311
18.10;Experimental Administration of siRNA;312
18.11;PTGS in Plants and Quelling in Fungi;313
18.12;Micro RNA—A Class of Small Regulatory RNA;314
18.13;Premature Termination Causes Attenuation of RNA Transcription;316
18.14;Riboswitches—RNA Acting Directly as a Control Mechanism;318
19;Chapter Twelve Processing of RNA;321
19.1;RNA is Processed in Several Ways;322
19.2;Coding and Non-Coding RNA;323
19.3;Processing of Ribosomal and Transfer RNA;324
19.4;Eukaryotic Messenger RNA Contains a Cap and a Tail;324
19.5;Capping is the First Step in Maturation of mRNA;325
19.6;A Poly(A) Tail is Added to Eukaryotic mRNA;327
19.7;Introns are Removed from RNA by Splicing;329
19.8;Different Classes of Intron Show Different Splicing Mechanisms;333
19.9;Alternative Splicing Produces Multiple Forms of RNA;334
19.10;Inteins and Protein Splicing;337
19.11;Base Modification of rRNA Requires Guide RNA;341
19.12;RNA Editing Involves Altering the Base Sequence;343
19.13;Transport of RNA out of the Nucleus;346
19.14;Degradation of mRNA;346
19.15;Nonsense Mediated Decay of mRNA;347
20;Chapter Thirteen Mutations;352
20.1;Mutations Alter the DNA Sequence;353
20.2;The Major Types of Mutation;354
20.3;Base Substitution Mutations;355
20.4;Missense Mutations May Have Major or Minor Effects;355
20.5;Nonsense Mutations Cause Premature Polypeptide Chain Termination;357
20.6;Deletion Mutations Result in Shortened or Absent Proteins;359
20.7;Insertion Mutations Commonly Disrupt Existing Genes;360
20.8;Frameshift Mutations Sometimes Produce Abnormal Proteins;362
20.9;DNA Rearrangements Include Inversions,Translocations, and Duplications;362
20.10;Phase Variation Is Due to Reversible DNA Alterations;364
20.11;Silent Mutations Do Not Alter the Phenotype;365
20.12;Chemical Mutagens Damage DNA;367
20.13;Radiation Causes Mutations;369
20.14;Spontaneous Mutations Can Be Caused by DNA Polymerase Errors;370
20.15;Mutations Can Result from Mispairing and Recombination;372
20.16;Spontaneous Mutation Can Be the Result of Tautomerization;372
20.17;Spontaneous Mutation Can Be Caused by Inherent Chemical Instability;372
20.18;Mutations Occur More Frequently at Hot Spots;374
20.19;How Often Do Mutations Occur?;377
20.20;Reversions Are Genetic Alterations That Change the Phenotype Back to Wild-type;378
20.21;Reversion Can Occur by Compensatory Changes in Other Genes;380
20.22;Altered Decoding by Transfer RNA May Cause Suppression;381
20.23;Mutagenic Chemicals Can Be Detected by Reversion;382
20.24;Experimental Isolation of Mutations;383
20.25;In Vivo versus In Vitro Mutagenesis;384
20.26;Site-Directed Mutagenesis;385
21;Chapter Fourteen Recombination and Repair ;387
21.1;Overview of Recombination;388
21.2;Molecular Basis of Homologous Recombination;389
21.3;Single-Strand Invasion and Chi Sites;390
21.4;Site-Specific Recombination;392
21.5;Recombination in Higher Organisms;395
21.6;Overview of DNA Repair;397
21.7;DNA Mismatch Repair System;398
21.8;General Excision Repair System;400
21.9;DNA Repair by Excision of Specific Bases;402
21.10;Specialized DNA Repair Mechanisms;403
21.11;Photoreactivation Cleaves Thymine Dimers;406
21.12;Transcriptional Coupling of Repair;406
21.13;Repair by Recombination;407
21.14;SOS Error Prone Repair in Bacteria;407
21.15;Repair in Eukaryotes;410
21.16;Double-Strand Repair in Eukaryotes;411
21.17;Gene Conversion;411
22;Chapter Fifteen Mobile DNA;415
22.1;Sub-Cellular Genetic Elements as Gene Creatures;416
22.2;Most Mobile DNA Consists of Transposable Elements;416
22.3;The Essential Parts of a Transposon;417
22.4;Insertion Sequences—the Simplest Transposons;419
22.5;Movement by Conservative Transposition;420
22.6;Complex Transposons Move by Replicative Transposition;421
22.7;Replicative and Conservative Transposition are Related;425
22.8;Composite Transposons;425
22.9;Transposition may Rearrange Host DNA;427
22.10;Transposons in Higher Life Forms;429
22.11;Retro-Elements Make an RNA Copy;431
22.12;Repetitive DNA of Mammals;433
22.13;Retro-Insertion of Host-Derived DNA;434
22.14;Retrons Encode Bacterial Reverse Transcriptase;435
22.15;The Multitude of Transposable Elements;436
22.16;Bacteriophage Mu is a Transposon;436
22.17;Conjugative Transposons;439
22.18;Integrons Collect Genes for Transposons;439
22.19;Junk DNA and Selfish DNA;441
22.20;Homing Introns;442
23;Chapter Sixteen Plasmids;444
23.1;Plasmids as Replicons;445
23.2;General Properties of Plasmids;446
23.3;Plasmid Families and Incompatibility;447
23.4;Occasional Plasmids are Linear or Made of RNA;447
23.5;Plasmid DNA Replicates by Two Alternative Methods;449
23.6;Control of Copy Number by Antisense RNA;451
23.7;Plasmid Addiction and Host Killing Functions;454
23.8;Many Plasmids Help their Host Cells;455
23.9;Antibiotic Resistance Plasmids;455
23.10;Mechanisms of Antibiotic Resistance;457
23.11;Resistance to Beta-Lactam Antibiotics;457
23.12;Resistance to Chloramphenicol;458
23.13;Resistance to Aminoglycosides;459
23.14;Resistance to Tetracycline;460
23.15;Resistance to Sulfonamides and Trimethoprim;461
23.16;Plasmids may Provide Aggressive Characters;461
23.17;Most Colicins Kill by One of Two Different Mechanisms;463
23.18;Bacteria are Immune to their own Colicins;464
23.19;Colicin Synthesis and Release;465
23.20;Virulence Plasmids;465
23.21;Ti-Plasmids are Transferred from Bacteria to Plants;466
23.22;The 2-Micron Plasmid of Yeast;469
23.23;Certain DNA Molecules may Behave as Viruses or Plasmids;470
24;Chapter Seventeen Viruses;443
24.1;Viruses are Infectious Packages of Genetic Information;473
24.2;Life Cycle of a Virus;474
24.3;Bacterial Viruses are Known as Bacteriophage;477
24.4;Lysogeny or Latency by Integration;479
24.5;The Great Diversity of Viruses;481
24.6;Small Single-Stranded DNA Viruses of Bacteria;482
24.7;Complex Bacterial Viruses with Double Stranded DNA;484
24.8;DNA Viruses of Higher Organisms;485
24.9;Viruses with RNA Genomes Have Very Few Genes;486
24.10;Bacterial RNA Viruses;488
24.11;Double Stranded RNA Viruses of Animals;488
24.12;Positive-Stranded RNA Viruses Make Polyproteins;488
24.13;Strategy of Negative-Strand RNA Viruses;489
24.14;Plant RNA Viruses;489
24.15;Retroviruses Use both RNA and DNA;491
24.16;Genome of the Retrovirus;496
24.17;Subviral Infectious Agents;496
24.18;Satellite Viruses;498
24.19;Viroids are Naked Molecules of Infectious RNA;499
24.20;Prions are Infectious Proteins;500
25;Chapter Eighteen Bacterial Genetics;503
25.1;Reproduction versus Gene Transfer;504
25.2;Fate of the Incoming DNA after Uptake;504
25.3;Transformation is Gene Transfer by Naked DNA;506
25.4;Transformation as Proof that DNA is the Genetic Material;507
25.5;Transformation in Nature;510
25.6;Gene Transfer by Virus—Transduction;512
25.7;Generalized Transduction;512
25.8;Specialized Transduction;513
25.9;Transfer of Plasmids between Bacteria;514
25.10;Transfer of Chromosomal Genes Requires Plasmid Integration;515
25.11;Gene Transfer among Gram-Positive Bacteria;520
25.12;Archaebacterial Genetics;523
25.13;Whole Genome Sequencing;525
26;Chapter Nineteen Diversity of Lower Eukaryotes;527
26.1;Origin of the Eukaryotes by Symbiosis;528
26.2;The Genomes of Mitochondria and Chloroplasts;529
26.3;Primary and Secondary Endosymbiosis;530
26.4;Is Malaria Really a Plant?;531
26.5;Symbiosis: Parasitism versus Mutualism;534
26.6;Bacterial Endosymbionts of Killer Paramecium;534
26.7;Is Buchnera an Organelle or a Bacterium?;536
26.8;Ciliates have Two Types of Nucleus;536
26.9;Trypanosomes Vary Surface Proteins to Outwit the Immune System;539
26.10;Mating Type Determination in Yeast;544
26.11;Multi-Cellular Organisms and Homeobox Genes;549
27;Chapter Twenty Molecular Evolution;552
27.1;Getting Started—Formation of the Earth;553
27.2;The Early Atmosphere;553
27.3;Oparin’s Theory of the Origin of Life;554
27.4;The Miller Experiment;555
27.5;Polymerization of Monomers to Give Macromolecules;557
27.6;Enzyme Activities of Random Proteinoids;558
27.7;Origin of Informational Macromolecules;559
27.8;Ribozymes and the RNA World;559
27.9;The First Cells;561
27.10;The Autotrophic Theory of the Origin of Metabolism;563
27.11;Evolution of DNA, RNA and Protein Sequences;564
27.12;Creating New Genes by Duplication;566
27.13;Paralogous and Orthologous Sequences;568
27.14;Creating New Genes by Shuffling;569
27.15;Different Proteins Evolve at Very Different Rates;569
27.16;Molecular Clocks to Track Evolution;571
27.17;Ribosomal RNA—A Slowly Ticking Clock;571
27.18;The Archaebacteria versus the Eubacteria;573
27.19;DNA Sequencing and Biological Classification;574
27.20;Mitochondrial DNA—A Rapidly Ticking Clock;578
27.21;The African Eve Hypothesis;579
27.22;Ancient DNA from Extinct Animals;581
27.23;Evolving Sideways: Horizontal Gene Transfer;583
27.24;Problems in Estimating Horizontal Gene Transfer;584
28;Chapter Twenty-one Nucleic Acids: Isolation,Purification, Detection, and Hybridization;502
28.1;Isolation of DNA;587
28.2;Purification of DNA;587
28.3;Removal of Unwanted RNA;588
28.4;Gel Electrophoresis of DNA;589
28.5;Pulsed Field Gel Electrophoresis;591
28.6;Denaturing Gradient Gel Electrophoresis;592
28.7;Chemical Synthesis of DNA;593
28.8;Chemical Synthesis of Complete Genes;599
28.9;Peptide Nucleic Acid;599
28.10;Measuring the Concentration of DNA and RNA withUltraviolet Light;601
28.11;Radioactive Labeling of Nucleic Acids;602
28.12;Detection of Radio-Labeled DNA;602
28.13;Fluorescence in the Detection of DNA and RNA;604
28.14;Chemical Tagging with Biotin or Digoxigenin;606
28.15;The Electron Microscope;607
28.16;Hybridization of DNA and RNA;609
28.17;Southern, Northern, and Western Blotting;611
28.18;Zoo Blotting;614
28.19;Fluorescence in Situ Hybridization (FISH);614
28.20;Molecular Beacons;617
29;Chapter Twenty-Two Recombinant DNA Technology;618
29.1;Introduction;619
29.2;Nucleases Cut Nucleic Acids;619
29.3;Restriction and Modification of DNA;619
29.4;Recognition of DNA by Restriction Endonucleases;620
29.5;Naming of Restriction Enzymes;620
29.6;Cutting of DNA by Restriction Enzymes;621
29.7;DNA Fragments are Joined by DNA Ligase;622
29.8;Making a Restriction Map;623
29.9;Restriction Fragment Length Polymorphisms (RFLPs);626
29.10;Properties of Cloning Vectors;627
29.11;Multicopy Plasmid Vectors;629
29.12;Inserting Genes into Vectors;629
29.13;Detecting Insertions in Vectors;631
29.14;Moving Genes between Organisms: Shuttle Vectors;634
29.15;Bacteriophage Lambda Vectors;635
29.16;Cosmid Vectors;636
29.17;Yeast Artificial Chromosomes;639
29.18;Bacterial and P1 Artificial Chromosomes;639
29.19;A DNA Library Is a Collection of Genesfrom One Organism;640
29.20;Screening a Library by Hybridization;642
29.21;Screening a Library by Immunological Procedures;642
29.22;Cloning Complementary DNA Avoids Introns;643
29.23;Chromosome Walking;645
29.24;Cloning by Subtractive Hybridization;647
29.25;Expression Vectors;650
30;Chapter Twenty-Three The Polymerase Chain Reaction;653
30.1;Fundamentals of the Polymerase Chain Reaction;654
30.2;Cycling Through the PCR;657
30.3;Degenerate Primers;659
30.4;Inverse PCR;660
30.5;Adding Artificial Restriction Sites;661
30.6;TA Cloning by PCR;662
30.7;Randomly Amplified Polymorphic DNA (RAPD);662
30.8;Reverse Transcriptase PCR;665
30.9;Differential Display PCR;666
30.10;Rapid Amplification of cDNA Ends (RACE);668
30.11;PCR in Genetic Engineering;668
30.12;Directed Mutagenesis;670
30.13;Engineering Deletions and Insertions by PCR;670
30.14;Use of PCR in Medical Diagnosis;671
30.15;Environmental Analysis by PCR;672
30.16;Rescuing DNA from Extinct Life Forms by PCR;673
30.17;Realtime Fluorescent PCR;674
30.18;Inclusion of Molecular Beacons in PCR—Scorpion Primers;675
31;Chapter Twenty-Four Genomics and DNA Sequencing;652
31.1;Introduction to Genomics;682
31.2;DNA Sequencing—General Principle;682
31.3;The Chain Termination Method for Sequencing DNA;682
31.4;DNA Polymerases for Sequencing DNA;687
31.5;Producing Template DNA for Sequencing;687
31.6;Primer Walking along a Strand of DNA;689
31.7;Automated Sequencing;689
31.8;The Emergence of DNA Chip Technology;691
31.9;The Oligonucleotide Array Detector;691
31.10;Pyrosequencing;693
31.11;Nanopore Detectors for DNA;695
31.12;Large Scale Mapping with Sequence Tags;695
31.13;Mapping of Sequence Tagged Sites;696
31.14;Assembling Small Genomes by Shotgun Sequencing;699
31.15;Race for the Human Genome;699
31.16;Assembling a Genome from Large Cloned Contigs;702
31.17;Assembling a Genome by Directed Shotgun Sequencing;702
31.18;Survey of the Human Genome;702
31.19;Sequence Polymorphisms: SSLPs and SNPs;705
31.20;Gene Identification by Exon Trapping;707
31.21;Bioinformatics and Computer Analysis;709
32;Chapter Twenty-Five Analysis of Gene Expression;712
32.1;Introduction;713
32.2;Monitoring Gene Expression;713
32.3;Reporter Genes for Monitoring Gene Expression;713
32.4;Easily Assayable Enzymes as Reporters;715
32.5;Light Emission by Luciferase as a Reporter System;715
32.6;Green Fluorescent Protein as Reporter;718
32.7;Gene Fusions;718
32.8;Deletion Analysis of the Upstream Region;721
32.9;Locating Protein Binding Sites in the Upstream Region;721
32.10;Location of the Start of Transcription byPrimer Extension;725
32.11;Location of the Start of Transcription by S1 Nuclease;726
32.12;Transcriptome Analysis;728
32.13;DNA Microarrays for Gene Expression;728
32.14;Serial Analysis of Gene Expression (SAGE);732
33;Chapter Twenty-Six Proteomics: The Global Analysis of Proteins;736
33.1;Introduction to Proteomics;737
33.2;Gel Electrophoresis of Proteins;738
33.3;Two Dimensional PAGE of Proteins;739
33.4;Western Blotting of Proteins;741
33.5;Mass Spectrometry for Protein Identification;741
33.6;Protein Tagging Systems;745
33.7;Full-Length Proteins Used as Fusion Tags;745
33.8;Self Cleavable Intein Tags;748
33.9;Selection by Phage Display;748
33.10;Protein Interactions: The Yeast Two-Hybrid System;751
33.11;Protein Interaction by Co-Immunoprecipitation;756
33.12;Protein Arrays;760
33.13;Metabolomics;760
34;Glossary;764
35;Index;790