Molecular Biology

3rd Edition - November 2, 2018
Authors: David P. Clark, Nanette J. Pazdernik, Michelle R. McGehee
Language: English
Hardback ISBN:
9 7 8 - 0 - 1 2 - 8 1 3 2 8 8 - 3
eBook ISBN:
9 7 8 - 0 - 1 2 - 8 1 3 2 8 9 - 0

Molecular Biology, Third Edition, provides a thoroughly revised, invaluable resource for college and university students in the life sciences, medicine and related fields. This e… Read more

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Molecular Biology, Third Edition, provides a thoroughly revised, invaluable resource for college and university students in the life sciences, medicine and related fields. This esteemed text continues to meet the needs of students and professors by offering new chapters on RNA, genome defense, and epigenetics, along with expanded coverage of RNAi, CRISPR, and more ensuring topical content for a new class of students. This volume effectively introduces basic concepts that are followed by more specific applications as the text evolves.Moreover, as part of the Academic Cell line of textbooks, this book contains research passages that shine a spotlight on current experimental work reported in Cell Press articles. These articles form the basis of case studies found in the associated online study guide that is designed to tie current topics to the scientific community.

Cover image
Title page
Table of Contents
Copyright
Dedication
Preface to Third Edition
Changes in the Third Edition
Online Materials
Acknowledgments
Unit 1: Basic Chemical and Biological Principles
Chapter 1. Cells and Organisms
Abstract
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
Review Questions
Further Reading
Chapter 2. Basic Genetics
Abstract
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
Review Questions
Further Reading
Chapter 3. Nucleic Acids and Proteins
Abstract
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
Review Questions
Further Reading
Chapter 4. Genes, Genomes, and DNA
Abstract
1 Overview of Genome Organization
2 The Eukaryotic Genome
3 Palindromes, Inverted Repeats, and Stem and Loop Structures
4 Purine Rich DNA Structures
5 Supercoiling Is Necessary to Package Bacterial DNA
6 Separation of DNA Fragments by Electrophoresis
7 Alternative Helical Structures of DNA Occur
8 Packaging DNA in Eukaryotic Nuclei
Review Questions
Further Reading
Chapter 5. Manipulation of Nucleic Acids
Abstract
1 Cutting and Rejoining DNA
2 Chemical Synthesis of DNA
3 Measuring DNA and RNA Concentration 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
Review Questions
Further Reading
Unit 2: The Genome
Chapter 6. Polymerase Chain Reaction
Abstract
1 Fundamentals of PCR
2 Preventing Mispriming
3 Adding Sequences to PCR Amplicons
4 Degenerate PCR Primers
5 Inverse PCR
6 Reverse Transcriptase PCR
7 PCR in Genetic Engineering
8 Directed Mutagenesis
9 Engineering Deletions and Insertions by PCR
10 Real-Time PCR or Quantitative PCR (qPCR)
11 Molecular Beacons
12 Use of PCR in Forensics
13 PCR in Medical Diagnosis
14 Environmental DNA (eDNA) Analysis by PCR
15 Rescuing DNA from Extinct Life Forms by PCR
Review Questions
Further Reading
Chapter 7. Cloning Genes for Synthetic Biology
Abstract
1 Properties of Cloning Vectors
2 Adding Inserts to a Vector
3 Adding Vectors to Host Organisms With Transformation
4 Detecting Inserts in Vectors
5 Types of Cloning Vectors
6 Synthetic Biology Standardizes Vector Construction
7 A DNA Library Is a Collection of Genes
Review Questions
Further Reading
Chapter 8. DNA Sequencing
Abstract
1 DNA Sequencing—Overview of Chain Termination Sequencing
2 Automated Sequencing
3 Next Generation Sequencing
4 Targeted Sequencing
5 Third-Generation Sequencing
6 DNA Microarrays for Sequence Analysis
Review Questions
Further Reading
Chapter 9. Genomics and Systems Biology
Abstract
1 Large-Scale Mapping With Sequence Tags
2 Assembling Genomes by Shotgun Sequencing
3 Assembling the Human Genome
4 Survey of the Human Genome
5 Personal Genomics and Pharmacogenomics
6 Bioinformatics and Computer Analysis
7 Metagenomics and Community Sampling
Review Questions
Further Reading
Unit 3: The Central Dogma of Molecular Biology
Chapter 10. Cell Division and DNA Replication
Abstract
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 Chromosome Replication
11 The Concept of the Replicon
12 Replicating Linear DNA in Eukaryotes
13 Cell Division in Higher Organisms
Review Questions
Further Reading
Chapter 11. Transcription of Genes
Abstract
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
7 Transcription in Archaea
Review Questions
Further Reading
Chapter 12. Processing of RNA
Abstract
1 RNA Is Processed in Several Ways
2 Coding and Noncoding 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
Review Questions
Further Reading
Chapter 13. Protein Synthesis
Abstract
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
Review Questions
Further Reading
Chapter 14. Protein Structure and Function
Abstract
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
Review Questions
Further Reading
Chapter 15. Proteomics: The Global Analysis of Proteins
Abstract
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
9 Protein Arrays
10 Metabolomics
Review Questions
Further Reading
Unit 4: Regulating Gene Expression
Chapter 16. Regulation of Transcription in Prokaryotes
Abstract
1 Gene Regulation Ensures a Physiological Response
2 Regulation at the Level of Transcription Involves Several Steps
3 Alternative Sigma Factors Recognize Different Sets of Genes
4 Activators, Repressors and Operons
5 Two-Component Regulatory Systems
6 Specific Versus Global Control
7 Accessory Factors and Nucleoid-Binding Proteins
8 Antitermination As a Control Mechanism
Review Questions
Further Reading
Chapter 17. Regulation of Transcription in Eukaryotes
Abstract
1 Transcriptional Regulation in Eukaryotes Is More Complex Than in Prokaryotes
2 Specific Transcription Factors Regulate Protein-Encoding Genes
3 Negative Regulation of Transcription in Eukaryotes
4 Heterochromatin Blocks Access to DNA in Eukaryotes
5 Methylation of Eukaryotic DNA Controls Gene Expression
Review Questions
Further Reading
Chapter 18. Regulation of Protein Synthesis
Abstract
1 Regulation at the Level of mRNA
2 Regulation by Cleavage of mRNA
3 Regulation by mRNA-Binding Proteins
4 Regulation by Antisense RNA
5 Regulation by mRNA Upstream and Downstream Regions
6 Premature Termination Causes Attenuation of Transcription
7 Riboswitches—RNA Acting Directly As a Control Mechanism
8 Regulation of mRNA by Methylation
Review Questions
Further Reading
Chapter 19. Noncoding RNA
Abstract
1 Survey of RNA Classes
2 Ribozymes and the Enzyme Activity of RNA
3 RNA in Prokaryotes Versus Eukaryotes
4 Short Regulatory RNA
5 tRNA Fragments
6 Long Noncoding RNA
7 Circular RNA
Review Questions
Further Reading
Chapter 20. Genome Defense
Abstract
1 Introduction to Genome Defense
2 The Multifaceted Approach to Defending the Genome
3 Principles of RNA Interference (RNAi)
4 Delivery of siRNA and Applications of RNAi
5 CRISPR: Antiviral Defense in Bacteria
6 CRISPR Systems Are Functionally and Structurally Classified
7 Applications Using CRISPR
8 Other Genome Editing Tools
Review Questions
Further Reading
9 Glossary
Chapter 21. Analysis of Gene Expression
Abstract
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)
Review Questions
Further Reading
Chapter 22. Epigenetics and Epigenomics
Abstract
1 Defining Epigenetics and Epigenomics
2 Epigenetics of Bacteria
3 Methylation of DNA
4 Protein and RNA-Based Epigenetic Regulation
5 Structural Inheritance
6 Epigenetics of Humans and Other Mammals
7 Epigenetics of Insects
8 Epigenetics of Plants
9 Epigenetics of Protozoa
Review Questions
Further Reading
Unit 5: Subcellular Genetic Elements
Chapter 23. Plasmids
Abstract
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 2 Micron Plasmid of Yeast
8 Certain DNA Elements May Behave As Viruses or Plasmids
Review Questions
Further Reading
Chapter 24. Viruses, Viroids, and Prions
Abstract
1 Viruses Are Infectious Packages of Genetic Information
2 The Classification of Viruses
3 The Great Diversity of Viruses
4 Giant Viruses
5 Viruses With RNA Genomes Have Very Few Genes
6 Retroviruses Use Both RNA and DNA
7 Subviral Infectious Agents
8 Prions Are Infectious Proteins
Review Questions
Further Reading
Chapter 25. Mobile DNA
Abstract
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 Hybrids Combine Properties of Multiple Genetic Elements
6 Mobile DNA That Is Not Transposable
7 Junk DNA and Selfish DNA
Review Questions
Further Reading
Unit 6: Changing the DNA Blueprint
Chapter 26. Mutations and Repair
Abstract
1 Mutations Alter the DNA Sequence
2 The Major Types of Mutation
3 Chemical Mutagens Damage DNA
4 Overview of DNA Repair
5 Reversions Are Genetic Alterations That Change the Phenotype Back to Wild Type
6 Site-Directed Mutagenesis
7 Glossary
Review Questions
Further Reading
Chapter 27. Recombination
Abstract
1 Overview of Recombination
2 Molecular Basis of Homologous Recombination
3 Site-Specific Recombination
4 Recombination in Higher Organisms
5 Gene Conversion
Review Questions
Further Reading
Chapter 28. Bacterial Genetics
Abstract
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
Review Questions
Further Reading
Chapter 29. Molecular Evolution
Abstract
1 Getting Started—Formation of the Earth
2 The Chemical Origin of Life
3 Origin of Informational Macromolecules
4 Ribozymes and the RNA World
5 The Autotrophic Theory of the Origin of Life
6 Evolution of DNA and Encoded Proteins
7 Ribosomal RNA and the Three Domains
8 Symbiotic Origin of Eukaryotic Cells
9 DNA Sequencing and Biological Classification
10 Evolving Sideways: Horizontal Gene Transfer
Review Questions
Further Reading
Index

David P. Clark

David P. Clark did his graduate work on bacterial antibiotic resistance to earn his Ph.D. from Bristol University, England. He later crossed the Atlantic to work as a postdoctoral researcher at Yale University and then the University of Illinois. Dr 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. In 1991 he received a Royal Society Guest Research Fellowship to work at Sheffield University, England while on sabbatical leave.

Affiliations and expertise

Southern Illinois University

Nanette J. Pazdernik

Nanette J. Pazdernik has devoted her career to the understanding of molecular biology and biotechnology, and then disseminating that knowledge by writing and teaching. She is a co-author of Biotechnology, 2nd edition and Molecular Biology, 3rd edition, with Dr. David P. Clark and Dr. Michelle McGehee. Both the second and third edition of Molecular Biology won a Texty award from the Textbook and Academic Authors Association. 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, and her PhD in Molecular, Cellular, Developmental Biology and Genetics from the University of Minnesota. Her doctoral thesis studied protein structure-function relationships. Following her degrees, she investigated the signal transduction pathways that control apoptosis and immunity at Indiana University School of Medicine. In a second post-doctoral position, she studied the various molecules that maintain the stem cell niche in the Department of Genetics at Washington University School of Medicine in St. Louis, MO. Currently, Dr. Pazdernik works in the biotech industry as a scientific writer.

Affiliations and expertise

Integrated DNA Technologies

Michelle R. McGehee

Michelle R. McGehee earned a BA in Microbiology in 2000 and a PhD in Molecular Biology, Microbiology, and Biochemistry in 2005, both from Southern Illinois University in Carbondale, USA. Her graduate research focused on the genetic and biochemical regulation of lactate fermentation in Escherichia coli. Michelle is currently an assistant academic dean and biology professor at a college in Texas, where she teaches courses in both microbiology and genetics.

Affiliations and expertise

Blinn College

Life Sciences

Physical Sciences & Engineering

Social Sciences & Humanities

Health

Molecular Biology

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Innovate. Sustain. Transform.

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Resources

David P. Clark

Nanette J. Pazdernik

Michelle R. McGehee