Cell Biology: A Short Course, 3rd Edition

Preface xiii

1 Cells And Tissues 1

Principles of Microscopy 1

The Light Microscope 2

The Electron Microscope 3

The Scanning Electron Microscope 4

Only Two Types of Cell 7

Cell Division 8

Viruses 9

Origin of Eukaryotic Cells 10

Cell Specialization in Animals 11

Stem Cells and Tissue Replacement 13

The Cell Wall 14

2 Water and Macromolecules 17

The Chemical Bond: Sharing Electrons 17

Interactions with Water: Solutions 18

Ionic Compounds Will Dissolve Only in Polar Solvents 18

Acids are Molecules That Give H^₊ to Water 20

Bases are Molecules that Take H⁺ from Water 22

Isoelectric Point 22

A Hydrogen Bond Forms When a Hydrogen Atom is Shared 23

Biological Macromolecules 23

Carbohydrates: Candy and Canes 23

An Assortment of Sweets 24

Disaccharides 25

Out of the Sweet Comes Forth Strength 26

Modified Sugars 27

Oxidation and Reduction Involve the Movement of Electrons 31

Amino Acids, Polypeptides, and Proteins 32

Lipids 33

Hydrolysis 34

3 Membranes and Organelles 43

Basic Properties of Cell Membranes 43

Straight Through the Membrane: Diffusion Through the Bilayer 44

Cell Junctions 44

Organelles Bounded by Double-Membrane Envelopes 47

The Nucleus 47

Mitochondria 48

Organelles Bounded by Single Membranes 49

Peroxisomes 49

Endoplasmic Reticulum 49

Golgi Apparatus 50

Lysosomes 50

4 DNA Structure and The Genetic Code 53

The Structure of DNA 53

The DNA Molecule is a Double Helix 53

The Two DNA Chains are Complementary 55

Different Forms of DNA 55

DNA as the Genetic Material 55

Packaging of DNA molecules Into Chromosomes 57

Eukaryotic Chromosomes and Chromatin Structure 57

Prokaryotic Chromosomes 58

Plasmids 59

Viruses 59

The Genetic Code 59

Amino Acid Names are Abbreviated 60

The Code is Degenerate But Unambiguous 60

Start and Stop Codons and the Reading Frame 63

The Code is Nearly Universal 64

Missense Mutations 64

5 DNA as A Data Storage Medium 67

DNA Replication 67

The DNA Replication Fork 67

Proteins Open Up the DNA Double Helix During Replication 67

DnaA Protein 68

DnaB and DnaC Proteins 68

Single-Strand Binding Proteins 68

Biochemistry of DNA Replication 68

DNA Synthesis Requires an RNA Primer 69

RNA Primers are Removed 71

The Self-Correcting DNA Polymerase 71

Mismatch Repair Backs Up the Proofreading Mechanism 71

DNA Repair After Replication 72

Spontaneous and Chemically Induced Base Changes 72

Repair Processes 73

Gene Structure and Organization in Eukaryotes 75

Introns and Exons: Additional Complexity in Eukaryotic Genes 75

The Major Classes of Eukaryotic DNA 76

Gene Nomenclature 78

6 Transcription and The Control Of Gene Expression 81

Structure of RNA 81

RNA Polymerase 81

Gene Notation 81

Bacterial RNA Synthesis 82

Control of Bacterial Gene Expression 85

Lac, an Inducible Operon 85

trp, a Repressible Operon 90

Eukaryotic RNA Synthesis 91

Messenger RNA Processing in Eukaryotes 91

Control of Eukaryotic Gene Expression 92

Glucocorticoids Cross the Plasma Membrane to Activate Transcription 94

7 Recombinant DNA And Genetic Engineering 99

DNA Cloning 99

Creating the Clone 100

Introduction of Foreign DNA Molecules into Bacteria 100

Selection of cDNA Clones 103

Genomic DNA Clones 106

Uses of DNA Clones 109

DNA Sequencing 109

Southern Blotting 111

In situ Hybridization 112

Northern Blotting 113

Production of Mammalian Proteins in Bacteria 113

Protein Engineering 114

Polymerase Chain Reaction 116

Identifying the Gene Responsible for a Disease 116

Reverse Genetics 117

Transgenic and Knockout Mice 117

Ethics of DNA Testing for Inherited Disease 119

8 Manufacturing Protein 123

Attachment of an Amino Acid to Its tRNA 123

Transfer RNA, the Anticodon, and the Wobble 123

The Ribosome 124

Bacterial Protein Synthesis 127

Ribosome-Binding Site 127

Chain Initiation 128

The 70S Initiation Complex 128

Elongation of the Protein Chain in Bacteria 128

The Polyribosome 130

Termination of Protein Synthesis 130

The Ribosome is Recycled 131

Eukaryotic Protein Synthesis is a Little More Complex 131

Antibiotics and Protein Synthesis 132

Protein Destruction 133

9 Protein Structure 137

Naming Proteins 137

Polymers of Amino Acids 137

The Amino Acid Building Blocks 138

The Unique Properties of Each Amino Acid 141

Other Amino Acids are Found in Nature 143

The Three-Dimensional Structures of Proteins 143

Hydrogen Bonds 143

Electrostatic Interactions 143

van der Waals Forces 143

Hydrophobic Interactions 143

Disulfide Bonds 143

Levels of Complexity 144

The Primary Structure 144

The Secondary Structure 145

Tertiary Structure: Domains and Motifs 147

Quaternary Structure: Assemblies of Protein Subunits 150

Prosthetic Groups 150

The Primary Structure Contains All The Information Necessary To Specify Higher-Level Structures 151

10 Intracellular Protein Trafficking 157

Three Modes of Intracellular Protein Transport 157

Targeting Sequences 158

Retention 159

Transport to and From The Nucleus 159

The Nuclear Pore Complex 159

Gated Transport Through the Nuclear Pore 159

GTPases and the GDP/GTP Cycle 160

GTPases in Nuclear Transport 162

Transport Across Membranes 163

Transport to Mitochondria 163

Chaperones and Protein Folding 164

Transport to Peroxisomes 164

Synthesis on the Rough Endoplasmic Reticulum 164

Glycosylation: The Endoplasmic Reticulum and Golgi System 165

Vesicular Trafficking Between Intracellular Compartments 166

The Principle of Fission and Fusion 167

Vesicle Formation 167

Coatomer-Coated Vesicles 167

Clathrin-Coated Vesicles 167

Trans Golgi Network and Protein Secretion 168

Targeting Proteins to the Lysosome 169

Fusion 170

11 How Proteins Work 175

How Proteins Bind Other Molecules 175

Dynamic Protein Structures 175

Allosteric Effects 175

Chemical Changes That Shift the Preferred Shape of a Protein 178

Enzymes are Protein Catalysts 179

The Initial Velocity of an Enzyme Reaction 182

Effect of Substrate Concentration on Initial Velocity 183

The Effect of Enzyme Concentration 184

The Specificity Constant 184

Cofactors and Prosthetic Groups 184

Enzymes can be Regulated 186

12 Energy Trading Within The Cell 191

Cellular Energy Currencies 191

Reduced Nicotinamide Adenine Dinucleotide (NADH) 192

Nucleoside Triphosphates (ATP plus GTP CTP TTP and UTP) 192

The Hydrogen Ion Gradient Across the Mitochondrial Membrane 193

The Sodium Gradient Across the Plasma Membrane 194

Energy Currencies are Interconvertible 194

Exchange Mechanisms Convert Between the Four Energy Currencies 195

Electron Transport Chain 196

ATP Synthase 198

Sodium/Potassium ATPase 199

ADP/ATP Exchanger 203

All Carriers Can Change Direction 203

13 Metabolism 207

The Krebs Cycle: The Central Switching Yard of Metabolism 208

From Glucose to Pyruvate: Glycolysis 209

Glycolysis Without Oxygen 211

Glycogen Can Provide Glucose for Glycolysis 212

Glucose May Be Oxidized to Produce Pentose Sugars 214

From Fats to Acetyl-CoA: β Oxidation 214

Amino Acids as Another Source of Metabolic Energy 215

Making Glucose: Gluconeogenesis 216

Making Glycogen: Glycogenesis 219

Making Fatty Acids, Glycerides, and Cholesterol 219

Synthesis of Amino Acids 221

Control of Energy Production 223

Feedback and Feedforward 223

Negative Feedback Control of Glycolysis 224

Feedforward Control in Muscle Cells 224

14 Ions and Voltages 229

The Potassium Gradient And The Resting Voltage 229

Potassium Channels Make the Plasma Membrane Permeable to Potassium Ions 229

Concentration Gradients and Electrical Voltage Can Balance 231

The Chloride Gradient 232

General Properties of Channels 233

General Properties of Carriers 236

The Glucose Carrier 236

The Sodium/Calcium Exchanger 236

Carriers with an Enzymatic Action: The Calcium ATPase 237

Electrical Signaling 238

The Pain Receptor Nerve Cell 238

The Voltage-Gated Sodium Channel 240

The Sodium Action Potential 241

The Strength of a Signal is Coded by Action Potential Frequency 242

Myelination and Rapid Action Potential Transmission 244

15 Intracellular Signaling 251

Calcium 251

Calcium Can Enter from the Extracellular Medium 251

Calcium Can Be Released from the Endoplasmic Reticulum 253

Processes Activated by Cytosolic Calcium are Extremely Diverse 254

Return of Calcium to Resting Levels 257

Cyclic Adenosine Monophosphate 257

Cyclic Guanosine Monophosphate 259

Multiple Messengers 259

Biochemical Signaling 260

Receptor Tyrosine Kinases and the MAP Kinase Cascade 260

Growth Factors Can Trigger a Calcium Signal 262

Protein Kinase B and the Glucose Carrier: How Insulin Works 262

Cytokine Receptors 264

Crosstalk—Signaling Pathways or Signaling Webs? 264

16 Intercellular Communication 269

Classifying Transmitters and Receptors 269

Ionotropic Cell Surface Receptors 269

Metabotropic Cell Surface Receptors 269

Intracellular Receptors 270

Classification by Transmitter Lifetime 270

Rapid Communication: From Nerve Cells To Their Targets 271

Inhibitory Transmission: Chloride-Permeable Ionotropic Receptors 273

How Nerve Cells Control the Body 273

Paracrine Transmitters and the Control of Muscle Blood Supply 276

The Blood Supply is Also Under Hormonal Control 277

New Blood Vessels in Growing Muscle 277

Chemotaxis 278

Signaling During Development 278

Intrinsic Cues 279

Inductive Signaling 279

17 Mechanical Molecules 283

Microtubules 283

Microtubule-Based Motility 285

Cilia and Flagella 286

Intracellular Transport 287

Microfilaments 288

Muscle Contraction 289

Cell Locomotion 289

Intermediate Filaments 291

Anchoring Cell Junctions 292

18 Cell Cycle and The Control Of Cell Number In Eukaryotes 297

Stages of Mitosis 297

Meiosis and Fertilization 299

Meiosis 299

Fertilization and Inheritance 301

Crossing Over and Linkage 302

Control of the Cell Division Cycle 303

Checkpoints Tell the Cell Cycle When to Stop and When to Go 306

Ending the Cycle 306

The Cell Cycle and Cancer 307

Recruiting Blood Vessels 308

Apoptosis 308

Instructed Death: Death Domain Receptors 309

Default Death: Absence of Growth Factors 309

The Sick are Left to Die: Stress-Activated Apoptosis 311

19 The Cell Biology Of The Immune System 315

Cells of The Immune System 315

B Cells and Antibodies 315

Other Antibody Isoforms 317

The Genetic Basis of Antibody Structure 317

T Cells 321

The Action of CD8+ T Cells 322

The Action of CD4+ T Cells 323

Autoimmune Disease 325

20 Case Study: Cystic Fibrosis 329

Cystic Fibrosis is a Severe Genetic Disease 329

The Fundamental Lesion in Cystic Fibrosis Lies in Chloride Transport 330

Homing in on the CF Gene 330

Cloning the GENE for CF 331

The CFTR Gene Codes for a Chloride Ion Channel 331

Novel Therapies for CF 331

Diagnostic Tests for CF 333

Prenatal Implantation Diagnosis for CF 334

The Future 334

Appendix 339

Glossary 343

Answers to Review Questions 381

Index 395