Acknowledgments, xiii

About the companion website, xv

Section 1: The Structure of the Cell, 1

1 A Look at Cells and Tissues, 3

Only Two Types of Cell, 3

Cell Division, 4

Viruses, 4

Origin of Eukaryotic Cells, 6

Cell Specialization in Animals, 8

Stem Cells and Tissue Replacement, 10

The Cell Wall, 11

Microscopes Reveal Cell Structure, 11

The Modern Light Microscope, 11

The Transmission Electron Microscope, 12

The Scanning Electron Microscope, 14

Fluorescence Microscopy, 14

Increasing the Resolution of Fluorescence Microscopes, 15

Fluorescent Proteins, 15

2 Membranes and Organelles, 21

Basic Properties of Cell Membranes, 21

Organelles Bounded by Double-Membrane Envelopes, 22

The Nucleus, 22

Mitochondria, 24

Organelles Bounded by Single Membranes, 24

Peroxisomes, 25

Endoplasmic Reticulum, 25

Golgi Apparatus, 25

Lysosomes, 25

The Connected Cell, 26

Organelle Junctions, 26

Cell Junctions, 26

Section 2: The Molecular Biology Of The Cell, 33

3 DNA Structure And The Genetic Code, 35

The Structure of DNA, 35

The DNA Molecule Is a Double Helix, 37

Hydrogen Bonds Form Between Base Pairs, 37

DNA Strands Are Antiparallel, 37

The Two DNA Strands Are Complementary, 39

DNA as the Genetic Material, 39

Packaging of DNA Molecules into Chromosomes, 39

Eukaryotic Chromosomes and Chromatin Structure, 39

Prokaryotic Chromosomes, 40

Plasmids, 41

Viruses, 42

The Genetic Code, 42

Amino Acids and Proteins, 42

Reading the Genetic Code, 42

Amino Acid Names Are Abbreviated, 44

The Code Is Degenerate but Unambiguous, 44

Start and Stop Codons and the Reading Frame, 45

The Code Is Nearly Universal, 45

Missense Mutations, 46

4 DNA As A Data Storage Medium, 51

DNA Replication, 51

The DNA Replication Fork, 51

Proteins Open up the DNA Double Helix During Replication, 51

DnaA Protein, 52

DnaB and DnaC Proteins, 52

Single-Stranded DNA-Binding Proteins, 52

Biochemistry of DNA Replication, 52

DNA Synthesis Requires an RNA Primer, 55

RNA Primers Are Removed, 55

The Self-Correcting DNA Polymerase, 55

Mismatch Repair Backs Up the Proofreading Mechanism, 55

DNA Repair after Replication, 56

Spontaneous and Chemically Induced Base Changes, 56

Repair Processes, 57

Gene Structure and Organization in Eukaryotes, 59

Introns and Exons – Additional Complexity in Eukaryotic Genes, 59

The Major Classes of Eukaryotic DNA, 60

Gene Nomenclature, 61

5 Transcription and the Control of Gene Expression, 67

Structure of RNA, 67

RNA Polymerase, 67

Gene Notation, 68

Bacterial RNA Synthesis, 69

Control of Bacterial Gene Expression, 71

Lac, an Inducible Operon, 71

Trp, a Repressible Operon, 74

Eukaryotic RNA Synthesis, 75

Messenger RNA Processing in Eukaryotes, 76

Control of Eukaryotic Gene Expression, 77

Glucocorticoids Cross the Plasma Membrane to Activate Transcription, 79

Noncoding RNAs and the Control of Eukaryotic Gene Expression, 80

Micro RNAs, 80

Long Noncoding RNAs, 81

Circular RNAs, 81

6 Manufacturing Protein, 85

Attachment of an Amino Acid to Its tRNA, 85

Transfer RNA, the Anticodon, and Wobble, 85

The Ribosome, 89

Bacterial Protein Synthesis, 89

Ribosome-Binding Site, 89

Chain Initiation, 90

Initiation Factor 2 Is a GTPase, 90

The 70S Initiation Complex, 91

Elongation of the Protein Chain in Bacteria, 92

The Polyribosome, 94

Termination of Protein Synthesis, 94

The Ribosome Is Recycled, 95

Eukaryotic Protein Synthesis Is a Little More Complex, 95

Antibiotics and Protein Synthesis, 97

Protein Destruction, 98

7 Protein Structure, 103

Naming Proteins, 103

Polymers of Amino Acids, 104

The Amino Acid Building Blocks, 104

The Unique Properties of Each Amino Acid, 107

Other Amino Acids Are Found in Nature, 109

The Three-Dimensional Structures of Proteins, 109

Hydrogen Bonds, 109

Electrostatic Interactions, 109

Van der Waals Forces, 109

Hydrophobic Interactions, 109

Disulfide Bonds, 109

Levels of Complexity, 110

The Primary Structure, 110

The Secondary Structure, 111

Tertiary Structure: Domains and Motifs, 114

Quaternary Structure: Assemblies of Protein Subunits, 118

Prosthetic Groups, 118

The Primary Structure Contains all the Information Necessary to Specify Higher-Level Structures, 119

Protein–Protein Interactions Underlie all of Cell Biology, 119

8 Recombinant DNA Technology and Genetic Engineering, 123

DNA Cloning, 123

Creating the Clone, 124

Introduction of Foreign DNA Molecules into Bacteria, 124

Genomic DNA Clones, 126

Uses of DNA Clones, 128

Southern Blotting, 129

In-Situ Hybridization, 130

Northern Blotting, 130

Production of Mammalian Proteins in Bacteria and Eukaryotic Cells, 130

Polymerase Chain Reaction, 132

DNA Sequencing, 133

“Omics”, 135

Transcriptomics, 135

Microarrays, 135

RNA-Seq, 136

ChIP-Seq and Epigenomics, 136

Other “Omics”, 137

Identifying the Gene Responsible for a Disease, 137

Reverse Genetics, 137

Transgenic and Knockout Mice, 137

RNA Interference (RNAi), 139

CRISPR/Cas9, 139

Ethics of DNA Testing for Inherited Disease, 140

Section 3: Cell Communication, 145

9 Carriers, Channels, And Voltages, 147

Carriers, 147

The Glucose Carrier, 149

The Sodium/Calcium Exchanger, 150

The Sodium/Potassium ATPase, 150

The Calcium ATPase, 151

The Potassium Gradient and the Resting Voltage, 152

Potassium Channels Make the Plasma Membrane Permeable to Potassium Ions, 152

Concentration Gradients and Electrical Voltage Can Balance, 154

The Action Potential, 156

The Pain Receptor Neuron, 156

The Voltage-Gated Sodium Channel, 158

The Sodium Action Potential, 158

The Strength of a Signal Is Coded by Action Potential Frequency, 159

Myelination and Rapid Action Potential Transmission, 161

10 Signalling Through Ions, 165

Calcium as a Signaling Ion, 165

Calcium Can Enter Cells from the Extracellular Medium, 165

Calcium Can Be Released from Organelles, 166

Processes Activated by Cytosolic Calcium Are Extremely Diverse, 167

Return of Calcium to Resting Levels, 169

Propagating the Signal, 170

Transmitters Are Released at Synapses, 170

Ligand-Gated Ion Channels Respond to

Transmitters, 170

Rapid Communication: From Neurons to Their Targets, 171

Inhibitory Transmission, 172

Signaling at the Neuromuscular Junction, 175

11 Signalling Through Enzymes, 179

G Protein-Coupled Receptors and Second Messengers, 179

G Protein-Coupled Receptors Are an Abundant Class of Cell Surface Receptors, 179

Inositol Trisphosphate Controls Secretion in the Exocrine Pancreas, 179

Cyclic Adenosine Monophosphate Helps Us Smell, 181

Receptor Tyrosine Kinases and the Map Kinase Cascade, 183

Growth Factors Can Trigger a Calcium Signal, 185

Akt and the Glucose Carrier: How Insulin Works, 185

Cytokine Receptors, 187

Signaling Through Proteolysis, 188

Wnt Proteins Signal Through Receptors that Prevent Proteolysis of Beta Catenin, 188

Low Oxygen Levels Are Sensed by Preventing Proteolysis of Hypoxia-Inducing Factor, 189

Intracellular Receptors, 190

Guanylate Cyclase Is a Receptor for Nitric Oxide, 190

Many Steroid Hormone Receptors Are Transcription Factors, 190

Crosstalk – Signaling Pathways or Signaling Webs?, 190

Signaling in the Control of Muscle Blood Supply, 192

The Blood Supply Is Under Local Control, 193

The Blood Supply Is Under Nervous System Control, 193

The Blood Supply Is Under Hormonal Control, 194

New Blood Vessels in Growing Muscle, 194

Section 4: The Mechanics Of The Cell, 199

12 Intracellular Trafficking, 201

Principles of Protein Transport, 201

Proteins Enter Organelles in Different Ways, 201

Vesicles Shuttle Proteins Around the Cell Through Fission and Fusion, 202

The Destination of a Protein Is Determined by Sorting Signals, 204

GTPases Are Master Regulators of Traffic, 205

Trafficking to the Endoplasmic Reticulum and Plasma Membrane, 205

Synthesis on the Rough Endoplasmic Reticulum, 205

Glycosylation: The Endoplasmic Reticulum and Golgi System, 206

Coatomer-Coated Vesicles, 207

Trans Golgi Network and Protein Secretion, 208

Trafficking to the Lysosome, 209

Endocytosis Is a Gateway into the Cell, 209

Clathrin-Coated Vesicles, 209

Delivery of Enzymes to Lysosomes, 209

Lysosomes Degrade Proteins from both Outside and Inside of the Cell: Autophagy, 210

Trafficking to and from the Nucleus, 210

The Nuclear Pore Complex, 211

Gated Transport Through the Nuclear Pore, 212

GTPases in Nuclear Transport, 212

Trafficking to Other Organelles, 212

Transport to Mitochondria, 212

Transport to Peroxisomes, 215

13 CELLULAR SCAFFOLDING, 219

Microtubules, 219

Functions of Microtubules, 222

Intracellular Transport and Cellular Architecture, 222

Cell Movement by Cilia and Flagella, 223

Microfilaments, 225

Functions of Microfilaments, 226

Muscle Contraction, 226

Microfilament-Based Cell Migration, 227

Intermediate Filaments, 228

Functions of Intermediate Filaments, 229

Anchoring Cell Junctions, 229

The Nuclear Lamina, 230

14 Controlling Cell Number, 233

M-phase, 235

Mitosis, 235

Cytokinesis, 236

Control of the Cell Cycle, 238

The Cell Cycle Is Driven by Kinase Activities, 238

Checkpoints Tell the Cell Cycle When to Stop and When to Go, 239

The Mitotic Checkpoint Determines When the Cell Cycle Ends, 241

Cell Cycle Control and Cancer, 241

Meiosis and Fertilization, 242

Meiosis, 242

Crossing Over and Linkage, 245

Cell Death, 246

Cell Stress Activates the Intrinsic Apoptotic Pathway, 246

Communication with the External Environment Can Activate the Extrinsic Apoptotic Pathway, 247

Default Death: Apoptosis as a Result of Absence of Growth Factors, 248

Section 5 Case Study, 253

15 Case Study: Cystic Fibrosis, 255

Cystic Fibrosis Is a Severe Genetic Disease, 255

The Fundamental Lesion in Cystic Fibrosis Lies in Chloride Transport, 256

Cloning the CFTR Gene, 256

The CFTR Gene Codes for a Chloride Ion Channel, 257

Replacing or Repairing the Gene, 259

Tailoring Treatment to the Patient’s Lesion, 260

New Treatments for CF, 261

Diagnostic Tests for CF, 261

Prenatal implantation diagnosis for CF, 262

Conclusion, 262

Answers to Review Questions, 265

Glossary, 273

Index, 307