Molecular Biology 2nd Edition – David P. Clark

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Molecular Biology 2nd Edition

Molecular Biology 2Nd Edition Pdf

By David P. Clark and Nanette J. Pazdernik

Molecular Biology 2nd Edition PDF examines the basic concepts of molecular biology while incorporating primary literature from today’s leading researchers. This updated edition includes Focuses on Relevant Research sections that integrate primary literature from Cell Press and focus on helping the student learn how to read and understand research to prepare them for the scientific world.

The new Academic Cell Study Guide features all the articles from the text with concurrent case studies to help students build foundations in the content while allowing them to make the appropriate connections to the text. Animations provided deal with topics such as protein purification, transcription, splicing reactions, cell division and DNA replication and SDS-PAGE. The text also includes updated chapters on Genomics and Systems Biology, Proteomics, Bacterial Genetics and Molecular Evolution and RNA. An updated ancillary package includes flashcards, online self quizzing, references with links to outside content and PowerPoint slides with images.

This text is designed for undergraduate students taking a course in Molecular Biology and upper-level students studying Cell Biology, Microbiology, Genetics, Biology, Pharmacology, Biotechnology, Biochemistry, and Agriculture.

  • NEW: “Focus On Relevant Research” sections integrate primary literature from Cell Press and focus on helping the student learn how to read and understand research to prepare them for the scientific world.
  • NEW: Academic Cell Study Guide features all articles from the text with concurrent case studies to help students build foundations in the content while allowing them to make the appropriate connections to the text.
  • NEW: Animations provided include topics in protein purification, transcription, splicing reactions, cell division and DNA replication and SDS-PAGE
  • Updated chapters on Genomics and Systems Biology, Proteomics, Bacterial Genetics and Molecular Evolution and RNA
  • Updated ancillary package includes flashcards, online self quizzing, references with links to outside content and PowerPoint slides with images.
  • Fully revised art program
Table of Contents

Title

Copyright

Dedication

Acknowledgements

UNIT 1. Basic Chemical and Biological Principles

Chapter 1. Cells and Organisms

1 What Is Life?

2 Living Creatures Are Made of Cells

3 Eubacteria and Archaea Are Genetically Distinct

4 Eukaryotic Cells Are Subdivided into Compartments

5 The Diversity of Eukaryotes

6 Haploidy, Diploidy, and the Eukaryote Cell Cycle

7 Organisms Are Classified

8 Some Widely-Studied Organisms Serve as Models

9 Basic Characteristics of a Model Organism

10 Purifying DNA from Model Organisms

11 Viruses Are Not Living Cells

12 Bacterial Viruses Infect Bacteria

13 Human Viral Diseases Are Common

14 A Variety of Subcellular Genetic Entities Exist

Chapter 2. Basic Genetics

1 Gregor Mendel, The Father of Classical Genetics

2 Genes Determine Each Step in Biochemical Pathways

3 Mutants Result from Alterations in Genes

4 Phenotypes and Genotypes

5 Chromosomes Are Long, Thin Molecules That Carry Genes

6 Dominant and Recessive Alleles

7 Genes from Both Parents Are Mixed by Sexual Reproduction

8 Neighboring Genes Are Linked During Inheritance Unless the DNA Recombines

9 Identifying Genes that Cause Human Diseases

Chapter 3. DNA, RNA, and Protein

1 History of DNA as the Genetic Material

2 Nucleic Acid Molecules Carry Genetic Information

3 Chemical Structure of Nucleic Acids

4 Double-Stranded DNA Forms a Double Helix

5 Constituents of Chromosomes

6 The Central Dogma Outlines the Flow of Genetic Information

7 Ribosomes Read the Genetic Code

8 Various Classes of RNA Have Different Functions

9 Proteins Carry Out Many Cell Functions

Chapter 4. Genomes and DNA

1 Genome Organization

2 Repeated Sequences Are a Feature of Eukaryotic DNA

3 Palindromes, Inverted Repeats, and Stem and Loop Structures

4 Multiple A-Tracts Cause DNA to Bend

5 Supercoiling Is Necessary for Packaging of Bacterial DNA

6 Separation of DNA Fragments by Electrophoresis

7 Alternative Helical Structures of DNA Occur

8 Packaging DNA in Eukaryotic Nuclei

Chapter 5. Manipulation of Nucleic Acids

1 Manipulating DNA

2 Chemical Synthesis of DNA

3 Measuring the Concentration of DNA and RNA with Ultraviolet Light

4 Radioactive Labeling of Nucleic Acids

5 Fluorescence in the Detection of DNA and RNA

6 The Electron Microscope

7 Hybridization of DNA and RNA

UNIT 2. The Genome

Chapter 6. Polymerase Chain Reaction

1 Fundamentals of the Polymerase Chain Reaction

2 Inverse PCR

3 Randomly Amplified Polymorphic DNA (RAPD)

4 Reverse Transcriptase PCR

5 Differential Display PCR

6 Rapid Amplification of cDNA Ends (RACE)

7 PCR in Genetic Engineering

8 Directed Mutagenesis

9 Engineering Deletions and Insertions by PCR

10 Real-Time Fluorescent PCR

11 Molecular Beacons and Scorpion Primers

12 Use of PCR in Medical Diagnosis

13 Environmental Analysis by PCR

14 Rescuing DNA from Extinct Life Forms by PCR

Chapter 7. Cloning Genes for Analysis

1 Properties of Cloning Vectors

2 Detecting Insertions in Vectors

3 Moving Genes Between Organisms: Shuttle Vectors

4 Bacteriophage Lambda Vectors

5 Cosmid Vectors

6 Yeast Artificial Chromosomes

7 Bacterial and P1 Artificial Chromosomes

8 Recombineering Increases the Speed of Gene Cloning

9 A DNA Library is a Collection of Genes from One Source

10 Cloning Complementary DNA Avoids Introns

11 Chromosome Walking

12 Cloning by Subtractive Hybridization

13 Expression Vectors

Chapter 8. DNA Sequencing

1 DNA Sequencing—General Principles for Chain Termination Sequencing

2 Primer Walking Along a Strand of DNA

3 Automated Sequencing

4 Cycle Sequencing

5 The Emergence of DNA Chip Technology

6 Pyrosequencing

7 Second-Generation Sequencing

8 Third-Generation Sequencing

9 Nanopore Detectors for DNA

Chapter 9. Genomics & Systems Biology

1 Large-Scale Mapping with Sequence Tags

2 Assembling Small Genomes by Shotgun Sequencing

3 Race for the Human Genome

4 Survey of the Human Genome

5 Pharmacogenomics—Genetically-Individualized Drug Treatment

6 Personal Genomics and Comparative Genomics

7 Bioinformatics and Computer Analysis

8 Systems Biology

9 Metagenomics and Community Sampling

10 Epigenetics and Epigenomics

UNIT 3. The Central Dogma of Molecular Biology

Chapter 10. Cell Division and DNA Replication

1 Cell Division and Reproduction Are Not Always Identical

2 DNA Replication Occurs at the Replication Fork

3 Properties of DNA Polymerase

4 Nucleotides Are the Precursors for DNA Synthesis

5 DNA Polymerase Elongates DNA Strands

6 The Complete Replication Fork Is Complex

7 Discontinuous Synthesis of the Lagging Strand

8 Chromosome Replication Initiates at oriC

9 Chromosome Replication Terminates at terC

10 Cell Division in Bacteria Occurs after Replication of Chromosomes

11 The Concept of the Replicon

12 Replicating Linear DNA in Eukaryotes

13 Cell Division in Higher Organisms

Chapter 11. Transcription of Genes

1 Genes Are Expressed by Making RNA

2 How Is the Beginning of a Gene Recognized?

3 Manufacturing the Message

4 RNA Polymerase Knows Where to Stop

5 How Does the Cell Know Which Genes to Turn On?

6 Transcription in Eukaryotes Is More Complex

Chapter 12. Processing of RNA

1 RNA Is Processed in Several Ways

2 Coding and Non-Coding RNA

3 Processing of Ribosomal and Transfer RNA

4 Eukaryotic Messenger RNA Contains a Cap and a Tail

5 Introns Are Removed from RNA by Splicing

6 Alternative Splicing Produces Multiple Forms of RNA

7 Inteins and Protein Splicing

8 Base Modification of rRNA Requires Guide RNA

9 RNA Editing Alters the Base Sequence

10 Transport of RNA out of the Nucleus

11 Degradation of mRNA

Chapter 13. Protein Synthesis

1 Overview of Protein Synthesis

2 Proteins Are Chains of Amino Acids

3 Decoding the Genetic Information

4 The Ribosome: The Cell’s Decoding Machine

5 Three Possible Reading Frames Exist

6 The tRNA Occupies Three Sites During Elongation of the Polypeptide

7 Bacterial mRNA Can Code for Several Proteins

8 Some Ribosomes Become Stalled and Are Rescued

9 Differences between Eukaryotic and Prokaryotic Protein Synthesis

10 Protein Synthesis Is Halted When Resources Are Scarce

11 A Signal Sequence Marks a Protein for Export from the Cell

12 Protein Synthesis Occurs in Mitochondria and Chloroplasts

13 Mistranslation Usually Results in Mistakes in Protein Synthesis

14 Many Antibiotics Work by Inhibiting Protein Synthesis

15 Post-Translational Modifications of Proteins

16 Selenocysteine and Pyrrolysine: Rare Amino Acids

17 Degradation of Proteins

Chapter 14. Protein Structure and Function

1 The Structure of Proteins Reflects Four Levels of Organization

2 Determining Protein Structures

3 Nucleoproteins, Lipoproteins, and Glycoproteins Are Conjugated Proteins

4 Proteins Serve Numerous Cellular Functions

5 Protein (Nano)-Machines

6 Enzymes Catalyze Metabolic Reactions

7 Binding of Proteins to DNA Occurs in Several Different Ways

8 Denaturation of Proteins

Chapter 15. Proteomics

1 The Proteome

2 Antibodies Are Essential Proteomics Tools

3 Western Blotting of Proteins

4 Isolating Proteins with Chromatography

5 Mass Spectrometry for Protein Identification

6 Protein-Tagging Systems

7 Selection by Phage Display

8 Protein Interactions: The Yeast Two-Hybrid System

9 Protein Interaction by Co-Immunoprecipitation

10 Protein Arrays

11 Metabolomics

UNIT 4. Regulating Gene Expression

Chapter 16. Regulation of Transcription in Prokaryotes

1 Gene Regulation Ensures a Physiological Response

2 Regulation at the Level of Transcription Involves Several Steps

3 Alternative Sigma Factors in Prokaryotes Recognize Different Sets of Genes

4 Activators and Repressors Participate in Positive and Negative Regulation

5 Two-Component Regulatory Systems

6 Specific versus Global Control

7 Accessory Factors and Nucleoid-Binding Proteins

8 Anti-Termination as a Control Mechanism

Chapter 17. Regulation of Transcription in Eukaryotes

1 Transcriptional Regulation in Eukaryotes Is More Complex Than in Prokaryotes

2 Specific Transcription Factors Regulate Protein-Encoding Genes

3 Negative Regulation of Transcription Occurs in Eukaryotes

4 Heterochromatin Blocks Access to DNA in Eukaryotes

5 Methylation of Eukaryotic DNA Controls Gene Expression

6 X-Chromosome Inactivation Occurs in Female XX Animals

Chapter 18. Regulation at the RNA Level

1 Regulation at the Level of mRNA

2 Basic Principles of RNA Interference (RNAi)

3 Long Non-coding Regulatory RNA

4 CRISPR: Anti-Viral Defense in Bacteria

5 Premature Termination Causes Attenuation of RNA Transcription

6 Riboswitches—RNA Acting Directly As a Control Mechanism

Chapter 19. Analysis of Gene Expression

1 Monitoring Gene Expression

2 Reporter Genes for Monitoring Gene Expression

3 Deletion Analysis of the Upstream Region

4 DNA-Protein Complexes Can Be Isolated by Chromatin Immunoprecipitation

5 Location of the Start of Transcription by Primer Extension

6 Transcriptome Analysis

7 DNA Microarrays for Gene Expression

8 TaqMan Quantitative PCR to Assay Gene Expression

9 Serial Analysis of Gene Expression (SAGE)

UNIT 5. Subcellular Life Forms

Chapter 20. Plasmids

1 Plasmids as Replicons

2 General Properties of Plasmids

3 Plasmid DNA Replicates by Two Alternative Methods

4 Many Plasmids Help Their Host Cells

5 Plasmids May Provide Aggressive Characters

6 Ti Plasmids Are Transferred from Bacteria to Plants

7 The 2μ Plasmid of Yeast

8 Certain DNA Molecules May Behave as Viruses or Plasmids

Chapter 21. Viruses

1 Viruses Are Infectious Packages of Genetic Information

2 The Great Diversity of Viruses

3 Viruses with RNA Genomes Have Very Few Genes

4 Retroviruses Use Both RNA and DNA

5 Subviral Infectious Agents

Chapter 22. Mobile DNA

1 Subcellular Genetic Elements as Gene Creatures

2 Most Mobile DNA Consists of Transposable Elements

3 Retroelements Make an RNA Copy

4 The Multitude of Transposable Elements

5 Junk DNA and Selfish DNA

UNIT 6. Changing the DNA Blueprint

Chapter 23. Mutations and Repair

1 Mutations Alter the DNA Sequence

2 The Major Types of Mutation

3 Chemical Mutagens Damage DNA

4 Overview of DNA Repair

5 Mutations Occur More Frequently at Hotspots

6 Reversions Are Genetic Alterations That Change the Phenotype Back to Wild-Type

7 Site-Directed Mutagenesis

Chapter 24. Recombination

1 Overview of Recombination

2 Molecular Basis of Homologous Recombination

3 Site-Specific Recombination

4 Recombination in Higher Organisms

5 Gene Conversion

Chapter 25. Bacterial Genetics

1 Reproduction versus Gene Transfer

2 Fate of the Incoming DNA after Uptake

3 Transformation Is Gene Transfer by Naked DNA

4 Gene Transfer by Virus—Transduction

5 Transfer of Plasmids between Bacteria

6 Gene Transfer among Gram-Positive Bacteria

7 Archaeal Genetics

8 Whole-Genome Sequencing

Chapter 26. Molecular Evolution

1 Getting Started—Formation of the Earth

2 Oparin’s Theory of the Origin of Life

3 Origin of Informational Macromolecules

4 The Autotrophic Theory of the Origin of Metabolism

5 Evolution of DNA, RNA, and Protein Sequences

6 Different Proteins Evolve at Very Different Rates

7 Symbiotic Origin of Eukaryotic Cells

8 DNA Sequencing and Biological Classification

9 Evolving Sideways: Horizontal Gene Transfer

Glossary

Index

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