Molecular Biology

Molecular Biology

2nd Edition - February 13, 2012

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  • Authors: David Clark, Nanette Pazdernik
  • eBook ISBN: 9780123785954

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Molecular Biology, Second Edition, 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.

Key Features

  • 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


Undergraduate students taking a course in Molecular Biology; upper-level students studying Cell Biology, Microbiology, Genetics, Biology, Pharmacology, Biotechnology, Biochemistry and Agriculture

Table of Contents

  • Dedication

    Preface to second edition


    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



Product details

  • No. of pages: 928
  • Language: English
  • Copyright: © Academic Cell 2012
  • Published: February 13, 2012
  • Imprint: Academic Cell
  • eBook ISBN: 9780123785954

About the Authors

David Clark

David Clark
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.

Affiliations and Expertise

Southern Illinois University, Carbondale, Illinois, USA

Nanette Pazdernik

Nanette Pazdernik
Nanette J. Pazdernik, Ph.D. is a co-author of Biotechnology, 2nd edition and Molecular Biology, 2nd edition, with Dr. David Clark. The second edition of Molecular Biology won a Texty award from the Textbook and Academic Authors Association in 2013. She has also authored an on-line study guide to accompany the update edition of Molecular Biology. She has taught courses in General Biology, Genetics, as well as Anatomy and Physiology at Southwestern Illinois College, McKendree University, and Harris-Stowe University. She received her BA in Biology from Lawrence University in Appleton, Wisconsin, in 1990 and her PhD in Molecular, Cellular, Developmental Biology and Genetics from the University of Minnesota in 1996. Her doctoral thesis studied how alterations in the structure of lactose permease affect its ability to transport sugar across the membrane of E. coli. Following her degrees, she investigated the IL-1 and TNF signal transduction pathways that control apoptosis and immunity at Indiana University School of Medicine. She has most recently studied the various molecules that maintain the stem cell fate in C. elegans at Washington University School of Medicine in St. Louis, MO. She is married and the mother of three children, ages 15, 12, and 8, which always make her realize the role biology plays in personality and development!

Affiliations and Expertise

Washington University School of Medicine, St. Louis, Missouri, USA

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