Molecular and cellular signaling

Series Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii Guide to Acronyms . . . . . . . . . . . . . . . . . . . . . . . . . . . xxv 1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.1 Prokaryotes and Eukaryotes . . . . . . . . . . . . . . . 1 1.2 The Cytoskeleton and Extracellular Matrix . . . . . . 2 1.3 Core Cellular Functions in Organelles . . . . . . . . . 3 1.4 Metabolic Processes in Mitochondria and Chloroplasts . . . . . . . . . . . . . . . . . . . . . . . . 4 1.5 Cellular DNA to Chromatin . . . . . . . . . . . . . . . 5 1.6 Protein Activities in the Endoplasmic Reticulum and Golgi Apparatus . . . . . . . . . . . . . . . . . . . . . . 6 1.7 Digestion and Recycling of Macromolecules . . . . . . 8 1.8 Genomes of Bacteria Reveal Importance of Signaling . . . . . . . . . . . . . . . . . . . . . . . . . . 9 1.9 Organization and Signaling of Eukaryotic Cell . . . . 10 1.10 Fixed Infrastructure and the Control Layer . . . . . . 12 1.11 Eukaryotic Gene and Protein Regulation . . . . . . . 13 1.12 Signaling Malfunction Central to Human Disease . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 1.13 Organization of Text . . . . . . . . . . . . . . . . . . . 16 2. The Control Layer . . . . . . . . . . . . . . . . . . . . . . . . . 21 2.1 Eukaryotic Chromosomes Are Built from Nucleosomes . . . . . . . . . . . . . . . . . . . . . . . . 22 2.2 The Highly Organized Interphase Nucleus . . . . . . . 23 2.3 Covalent Bonds Define the Primary Structure of a Protein . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 2.4 Hydrogen Bonds Shape the Secondary Structure . . . 27 2.5 Structural Motifs and Domain Folds: Semi-Independent Protein Modules . . . . . . . . . . 29 Contents xi 2.6 Arrangement of Protein Secondary Structure Elements and Chain Topology . . . . . . . . . . . . . . 29 2.7 Tertiary Structure of a Protein: Motifs and Domains . . . . . . . . . . . . . . . . . . . . . . . . . . 30 2.8 Quaternary Structure: The Arrangement of Subunits . . . . . . . . . . . . . . . . . . . . . . . . . . 32 2.9 Many Signaling Proteins Undergo Covalent Modifications . . . . . . . . . . . . . . . . . . . . . . . 33 2.10 Anchors Enable Proteins to Attach to Membranes . . . . . . . . . . . . . . . . . . . . . . . . 34 2.11 Glycosylation Produces Mature Glycoproteins . . . . 36 2.12 Proteolytic Processing Is Widely Used in Signaling . . . . . . . . . . . . . . . . . . . . . . . . . . 36 2.13 Reversible Addition and Removal of Phosphoryl Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 2.14 Reversible Addition and Removal of Methyl and Acetyl Groups . . . . . . . . . . . . . . . . . . . . . . . 38 2.15 Reversible Addition and Removal of SUMO Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 2.16 Post-Translational Modifications to Histones . . . . . 40 3. Exploring Protein Structure and Function . . . . . . . . . . . 45 3.1 Interaction of Electromagnetic Radiation with Matter . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 3.2 Biomolecule Absorption and Emission Spectra . . . . 49 3.3 Protein Structure via X-Ray Crystallography . . . . . 49 3.4 Membrane Protein 3-D Structure via Electron and Cryoelectron Crystallography . . . . . . . . . . . . . . 53 3.5 Determining Protein Structure Through NMR . . . . 53 3.6 Intrinsic Magnetic Dipole Moment of Protons and Neutrons . . . . . . . . . . . . . . . . . . . . . . . . . . 56 3.7 Using Protein Fluorescence to Probe Control Layer . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 3.8 Exploring Signaling with FRET . . . . . . . . . . . . . 58 3.9 Exploring Protein Structure with Circular Dichroism . . . . . . . . . . . . . . . . . . . . . . . . . 60 3.10 Infrared and Raman Spectroscopy to Probe Vibrational States . . . . . . . . . . . . . . . . . . . . . 61 3.11 A Genetic Method for Detecting Protein Interactions . . . . . . . . . . . . . . . . . . . . . . . . 61 3.12 DNA and Oligonucleotide Arrays Provide Information on Genes . . . . . . . . . . . . . . . . . . 62 3.13 Gel Electrophoresis of Proteins . . . . . . . . . . . . . 63 3.14 Mass Spectroscopy of Proteins . . . . . . . . . . . . . . 64 xii Contents 4. Macromolecular Forces . . . . . . . . . . . . . . . . . . . . . . 71 4.1 Amino Acids Vary in Size and Shape . . . . . . . . . . 71 4.2 Amino Acids Behavior in Aqueous Environments . . . . . . . . . . . . . . . . . . . . . . . 72 4.3 Formation of H-Bonded Atom Networks . . . . . . . 74 4.4 Forces that Stabilize Proteins . . . . . . . . . . . . . . 74 4.5 Atomic Radii of Macromolecular Forces . . . . . . . . 75 4.6 Osmophobic Forces Stabilize Stressed Cells . . . . . . 76 4.7 Protein Interfaces Aid Intra- and Intermolecular Communication . . . . . . . . . . . . . . . . . . . . . . 77 4.8 Interfaces Utilize Shape and Electrostatic Complementarity . . . . . . . . . . . . . . . . . . . . . 78 4.9 Macromolecular Forces Hold Macromolecules Together . . . . . . . . . . . . . . . . . . . . . . . . . . 79 4.10 Motion Models of Covalently Bonded Atoms . . . . . 79 4.11 Modeling van der Waals Forces . . . . . . . . . . . . . 81 4.12 Molecular Dynamics in the Study of System Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . 83 4.13 Importance of Water Molecules in Cellular Function . . . . . . . . . . . . . . . . . . . . . . . . . . 84 4.14 Essential Nature of Protein Dynamics . . . . . . . . . 85 5. Protein Folding and Binding . . . . . . . . . . . . . . . . . . . 89 5.1 The First Law of Thermodynamics: Energy Is Conserved . . . . . . . . . . . . . . . . . . . . . . . . . 90 5.2 Heat Flows from a Hotter to a Cooler Body . . . . . . 91 5.3 Direction of Heat Flow: Second Law of Thermodynamics . . . . . . . . . . . . . . . . . . . . . 92 5.4 Order-Creating Processes Occur Spontaneously as Gibbs Free Energy Decreases . . . . . . . . . . . . . . 93 5.5 Spontaneous Folding of New Proteins . . . . . . . . . 94 5.6 The Folding Process: An Energy Landscape Picture . . . . . . . . . . . . . . . . . . . . . . . . . . . 96 5.7 Misfolded Proteins Can Cause Disease . . . . . . . . . 98 5.8 Protein Problems and Alzheimer’s Disease . . . . . . 99 5.9 Amyloid Buildup in Neurological Disorders . . . . . . 100 5.10 Molecular Chaperones Assist in Protein Folding in the Crowded Cell . . . . . . . . . . . . . . . . . . . 101 5.11 Role of Chaperonins in Protein Folding . . . . . . . . 102 5.12 Hsp 90 Chaperones Help Maintain Signal Transduction Pathways . . . . . . . . . . . . . . . . . . 103 5.13 Proteins: Dynamic, Flexible, and Ready to Change . . . . . . . . . . . . . . . . . . . . . . . . . . . 104 Contents xiii 6. Stress and Pheromone Responses in Yeast . . . . . . . . . . . 111 6.1 How Signaling Begins . . . . . . . . . . . . . . . . . . 112 6.2 Signaling Complexes Form in Response to Receptor-Ligand Binding . . . . . . . . . . . . . . . . . 113 6.3 Role of Protein Kinases, Phosphatases, and GTPases . . . . . . . . . . . . . . . . . . . . . . . . . . 115 6.4 Role of Proteolytic Enzymes . . . . . . . . . . . . . . . 116 6.5 End Points Are Contact Points to Fixed Infrastructure . . . . . . . . . . . . . . . . . . . . . . . 117 6.6 Transcription Factors Combine to Alter Genes . . . . 118 6.7 Protein Kinases Are Key Signal Transducers . . . . . . 119 6.8 Kinases Often Require Second Messenger Costimulation . . . . . . . . . . . . . . . . . . . . . . . 121 6.9 Flanking Residues Direct Phosphorylation of Target Residues . . . . . . . . . . . . . . . . . . . . . . 122 6.10 Docking Sites and Substrate Specificity . . . . . . . . . 123 6.11 Protein Phosphatases Are Prominent Components of Signaling Pathways . . . . . . . . . . . . . . . . . . . . 123 6.12 Scaffold and Anchor Protein Role in Signaling and Specificity . . . . . . . . . . . . . . . . . . . . . . . . . 124 6.13 GTPases Regulate Protein Trafficking in the Cell . . . 125 6.14 Pheromone Response Pathway Is Activated by Pheromones . . . . . . . . . . . . . . . . . . . . . . . . 125 6.15 Osmotic Stresses Activate Glycerol Response Pathway . . . . . . . . . . . . . . . . . . . . . . . . . . 128 6.16 Yeasts Have a General Stress Response . . . . . . . . 129 6.17 Target of Rapamycin (TOR) Adjusts Protein Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . 131 6.18 TOR Adjusts Gene Transcription . . . . . . . . . . . . 133 6.19 Signaling Proteins Move by Diffusion . . . . . . . . . 134 7. Two-Component Signaling Systems . . . . . . . . . . . . . . . 139 7.1 Prokaryotic Signaling Pathways . . . . . . . . . . . . . 140 7.2 Catalytic Action by Histidine Kinases . . . . . . . . . 141 7.3 The Catalytic Activity of HK Occurs at the Active Site . . . . . . . . . . . . . . . . . . . . . . . . . 143 7.4 The GHKL Superfamily . . . . . . . . . . . . . . . . . 144 7.5 Activation of Response Regulators by Phosphorylation . . . . . . . . . . . . . . . . . . . . . . 145 7.6 Response Regulators Are Switches Thrown at Transcriptional Control Points . . . . . . . . . . . . . . 146 7.7 Structure and Domain Organization of Bacterial Receptors . . . . . . . . . . . . . . . . . . . . 147 7.8 Bacterial Receptors Form Signaling Clusters . . . . . 148 xiv Contents 7.9 Bacteria with High Sensitivity and Mobility . . . . . . 149 7.10 Feedback Loop in the Chemotactic Pathway . . . . . 150 7.11 How Plants Sense and Respond to Hormones . . . . . 152 7.12 Role of Growth Plasticity in Plants . . . . . . . . . . . 154 7.13 Role of Phytochromes in Plant Cell Growth . . . . . . 154 7.14 Cryptochromes Help Regulate Circadian Rhythms . . . . . . . . . . . . . . . . . . . . . . . . . . 156 8. Organization of Signal Complexes by Lipids, Calcium, and Cyclic AMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161 8.1 Composition of Biological Membranes . . . . . . . . . 162 8.2 Microdomains and Caveolae in Membranes . . . . . . 163 8.3 Lipid Kinases Phosphorylate Plasma Membrane Phosphoglycerides . . . . . . . . . . . . . . . . . . . . . 165 8.4 Generation of Lipid Second Messengers from PIP2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165 8.5 Regulation of Cellular Processes by PI3K . . . . . . . 167 8.6 PIPs Regulate Lipid Signaling . . . . . . . . . . . . . . 168 8.7 Role of Lipid-Binding Domains . . . . . . . . . . . . . 169 8.8 Role of Intracellular Calcium Level Elevations . . . . 170 8.9 Role of Calmodulin in Signaling . . . . . . . . . . . . . 171 8.10 Adenylyl Cyclases and Phosphodiesterases Produce and Regulate cAMP Second Messengers . . . . . . . . 172 8.11 Second Messengers Activate Certain Serine/ Threonine Kinases . . . . . . . . . . . . . . . . . . . . 173 8.12 Lipids and Upstream Kinases Activate PKB . . . . . . 174 8.13 PKB Supplies a Signal Necessary for Cell Survival . . . . . . . . . . . . . . . . . . . . . . . . . . . 176 8.14 Phospholipids and Ca2+ Activate Protein Kinase C . . . . . . . . . . . . . . . . . . . . . . . . . . 177 8.15 Anchoring Proteins Help Localize PKA and PKC Near Substrates . . . . . . . . . . . . . . . . . . . . . . 178 8.16 PKC Regulates Response of Cardiac Cells to Oxygen Deprivation . . . . . . . . . . . . . . . . . . . 179 8.17 cAMP Activates PKA,Which Regulates Ion Channel Activities . . . . . . . . . . . . . . . . . . . . . 180 8.18 PKs Facilitate the Transfer of Phosphoryl Groups from ATPs to Substrates . . . . . . . . . . . . . . . . . 182 9. Signaling by Cells of the Immune System . . . . . . . . . . . . 187 9.1 Leukocytes Mediate Immune Responses . . . . . . . . 188 9.2 Leukocytes Signal One Another Using Cytokines . . . . . . . . . . . . . . . . . . . . . . . . . . 190 9.3 APC and Naïve T Cell Signals Guide Differentiation into Helper T Cells . . . . . . . . . . . 192 Contents xv 9.4 Five Families of Cytokines and Cytokine Receptors . . . . . . . . . . . . . . . . . . . . . . . . . 193 9.5 Role of NF-kB/Rel in Adaptive Immune Responses . . . . . . . . . . . . . . . . . . . . . . . . . 194 9.6 Role of MAP Kinase Modules in Immune Responses . . . . . . . . . . . . . . . . . . . . . . . . . 196 9.7 Role of TRAF and DD Adapters . . . . . . . . . . . . 196 9.8 Toll/IL-1R Pathway Mediates Innate Immune Responses . . . . . . . . . . . . . . . . . . . . . . . . . 198 9.9 TNF Family Mediates Homeostasis, Death, and Survival . . . . . . . . . . . . . . . . . . . . . . . . . . . 199 9.10 Role of Hematopoietin and Related Receptors . . . . 200 9.11 Role of Human Growth Hormone Cytokine . . . . . . 202 9.12 Signal-Transducing Jaks and STATs . . . . . . . . . . . 203 9.13 Interferon System: First Line of Host Defense in Mammals Against Virus Attacks . . . . . . . . . . . . . 205 9.14 Chemokines Provide Navigational Cues for Leukocytes . . . . . . . . . . . . . . . . . . . . . . . . . 206 9.15 B and T Cell Receptors Recognize Antigens . . . . . 207 9.16 MHCs Present Antigens on the Cell Surface . . . . . 208 9.17 Antigen-Recognizing Receptors Form Signaling Complexes with Coreceptors . . . . . . . . . . . . . . 209 9.18 Costimulatory Signals Between APCs and T Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . 211 9.19 Role of Lymphocyte-Signaling Molecules . . . . . . . 212 9.20 Kinetic Proofreading and Serial Triggering of TCRs . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213 10. Cell Adhesion and Motility . . . . . . . . . . . . . . . . . . . . 221 10.1 Cell Adhesion Receptors: Long Highly Modular Glycoproteins . . . . . . . . . . . . . . . . . . . . . . . 221 10.2 Integrins as Bidirectional Signaling Receptors . . . . . 223 10.3 Role of Leukocyte-Specific Integrin . . . . . . . . . . 224 10.4 Most Integrins Bind to Proteins Belonging to the ECM . . . . . . . . . . . . . . . . . . . . . . . . . . 225 10.5 Cadherins Are Present in Most Cells of the Body . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226 10.6 IgCAMs Mediate Cell–Cell and Cell–ECM Adhesion . . . . . . . . . . . . . . . . . . . . . . . . . . 228 10.7 Selectins Are CAMs Involved in Leukocyte Motility . . . . . . . . . . . . . . . . . . . . . . . . . . . 229 10.8 Leukocytes Roll, Adhere, and Crawl to Reach the Site of an Infection . . . . . . . . . . . . . . . . . . 230 10.9 Bonds Form and Break During Leukocyte Rolling . . . . . . . . . . . . . . . . . . . . . . . . . . . 231 xvi Contents 10.10 Bond Dissociation of Rolling Leukocyte as Seen in Microscopy . . . . . . . . . . . . . . . . . . . . . . . . . 232 10.11 Slip and Catch Bonds Between Selectins and Their Carbohydrate Ligands . . . . . . . . . . . . . . . 233 10.12 Development in Central Nervous System . . . . . . . 234 10.13 Diffusible, Anchored, and Membrane-Bound Glycoproteins in Neurite Outgrowth . . . . . . . . . . 235 10.14 Growth Cone Navigation Mechanisms . . . . . . . . . 236 10.15 Molecular Marking by Concentration Gradients of Netrins and Slits . . . . . . . . . . . . . . . . . . . . . . 237 10.16 How Semaphorins, Scatter Factors, and Their Receptors Control Invasive Growth . . . . . . . . . . 239 10.17 Ephrins and Their Eph Receptors Mediate Contact-Dependent Repulsion . . . . . . . . . . . . . 239 11. Signaling in the Endocrine System . . . . . . . . . . . . . . . . 247 11.1 Five Modes of Cell-to-Cell Signaling . . . . . . . . . . 248 11.2 Role of Growth Factors in Angiogenesis . . . . . . . . 249 11.3 Role of EGF Family in Wound Healing . . . . . . . . 250 11.4 Neurotrophins Control Neuron Growth, Differentiation, and Survival . . . . . . . . . . . . . . . 251 11.5 Role of Receptor Tyrosine Kinases in Signal Transduction . . . . . . . . . . . . . . . . . . . . . . . . 252 11.6 Phosphoprotein Recognition Modules Utilized Widely in Signaling Pathways . . . . . . . . . . . . . . . . . . . 254 11.7 Modules that Recognize Proline-Rich Sequences Utilized Widely in Signaling Pathways . . . . . . . . . 256 11.8 Protein–Protein Interaction Domains Utilized Widely in Signaling Pathways . . . . . . . . . . . . . . . . . . . 256 11.9 Non-RTKs Central in Metazoan Signaling Processes and Appear in Many Pathways . . . . . . . . . . . . . 258 11.10 Src Is a Representative NRTK . . . . . . . . . . . . . 259 11.11 Roles of Focal Adhesion Kinase Family of NRTKs . . . . . . . . . . . . . . . . . . . . . . . . . . . 261 11.12 GTPases Are Essential Regulators of Cellular Functions . . . . . . . . . . . . . . . . . . . . . . . . . . 262 11.13 Signaling by Ras GTPases from Plasma Membrane and Golgi . . . . . . . . . . . . . . . . . . . . . . . . . . 263 11.14 GTPases Cycle Between GTP- and GDP-Bound States . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264 11.15 Role of Rho, Rac, and Cdc42, and Their Isoforms . . . 266 11.16 Ran Family Coordinates Traffic In and Out of the Nucleus . . . . . . . . . . . . . . . . . . . . . . . . . . . 267 11.17 Rab and ARF Families Mediate the Transport of Cargo . . . . . . . . . . . . . . . . . . . . . . . . . . . . 268 Contents xvii 12. Signaling in the Endocrine and Nervous Systems Through GPCRs . . . . . . . . . . . . . . . . . . . . . . . . . . 275 12.1 GPCRs Classification Criteria . . . . . . . . . . . . . . 276 12.2 Study of Rhodopsin GPCR with Cryoelectron Microscopy and X-Ray Crystallography . . . . . . . . 278 12.3 Subunits of Heterotrimeric G Proteins . . . . . . . . . 279 12.4 The Four Families of Ga Subunits . . . . . . . . . . . . 280 12.5 Adenylyl Cyclases and Phosphodiesterases Key to Second Messenger Signaling . . . . . . . . . . . . . . . 281 12.6 Desensitization Strategy of G Proteins to Maintain Responsiveness to Environment . . . . . . . . . . . . . 282 12.7 GPCRs Are Internalized, and Then Recycled or Degraded . . . . . . . . . . . . . . . . . . . . . . . . . . 284 12.8 Hormone-Sending and Receiving Glands . . . . . . . 285 12.9 Functions of Signaling Molecules . . . . . . . . . . . . 288 12.10 Neuromodulators Influence Emotions, Cognition, Pain, and Feeling Well . . . . . . . . . . . . . . . . . . 289 12.11 Ill Effects of Improper Dopamine Levels . . . . . . . 291 12.12 Inadequate Serotonin Levels Underlie Mood Disorders . . . . . . . . . . . . . . . . . . . . . . . . . . 292 12.13 GPCRs’ Role in the Somatosensory System Responsible for Sense of Touch and Nociception . . . . . . . . . . . . . . . . . . . . . . . . 292 12.14 Substances that Regulate Pain and Fever Responses . . . . . . . . . . . . . . . . . . . . . . . . . 293 12.15 Composition of Rhodopsin Photoreceptor . . . . . . . 295 12.16 How G Proteins Regulate Ion Channels . . . . . . . . 297 12.17 GPCRs Transduce Signals Conveyed by Odorants . . . . . . . . . . . . . . . . . . . . . . . . . . 297 12.18 GPCRs and Ion Channels Respond to Tastants . . . . . . . . . . . . . . . . . . . . . . . . . . . 299 13. Cell Fate and Polarity . . . . . . . . . . . . . . . . . . . . . . . 305 13.1 Notch Signaling Mediates Cell Fate Decision . . . . . 306 13.2 How Cell Fate Decisions Are Mediated . . . . . . . . 307 13.3 Proteolytic Processing of Key Signaling Elements . . . . . . . . . . . . . . . . . . . . . . . . . . 308 13.4 Three Components of TGF-b Signaling . . . . . . . . 311 13.5 Smad Proteins Convey TGF-b Signals into the Nucleus . . . . . . . . . . . . . . . . . . . . . . . . . . . 313 13.6 Multiple Wnt Signaling Pathways Guide Embryonic Development . . . . . . . . . . . . . . . . . . . . . . . 314 13.7 Role of Noncanonical Wnt Pathway . . . . . . . . . . 317 13.8 Hedgehog Signaling Role During Development . . . . 317 13.9 Gli Receives Hh Signals . . . . . . . . . . . . . . . . . 318 xviii Contents 13.10 Stages of Embryonic Development Use Morphogens . . . . . . . . . . . . . . . . . . . . . . . . 320 13.11 Gene Family Hierarchy of Cell Fate Determinants in Drosophila . . . . . . . . . . . . . . . . . . . . . . . . . 321 13.12 Egg Development in D. Melanogaster . . . . . . . . . 322 13.13 Gap Genes Help Partition the Body into Bands . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323 13.14 Pair-Rule Genes Partition the Body into Segments . . . . . . . . . . . . . . . . . . . . . . . . . . 324 13.15 Segment Polarity Genes Guide Parasegment Development . . . . . . . . . . . . . . . . . . . . . . . 325 13.16 Hox Genes Guide Patterning in Axially Symmetric Animals . . . . . . . . . . . . . . . . . . . . . . . . . . 326 14. Cancer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331 14.1 Several Critical Mutations Generate a Transformed Cell . . . . . . . . . . . . . . . . . . . . . 332 14.2 Ras Switch Sticks to “On” Under Certain Mutations . . . . . . . . . . . . . . . . . . . . . . . . . 334 14.3 Crucial Regulatory Sequence Missing in Oncogenic Forms of Src . . . . . . . . . . . . . . . . . . . . . . . . 336 14.4 Overexpressed GFRs Spontaneously Dimerize in Many Cancers . . . . . . . . . . . . . . . . . . . . . . . 336 14.5 GFRs and Adhesion Molecules Cooperate to Promote Tumor Growth . . . . . . . . . . . . . . . . . 337 14.6 Role of Mutated Forms of Proteins in Cancer Development . . . . . . . . . . . . . . . . . . . . . . . 338 14.7 Translocated and Fused Genes Are Present in Leukemias . . . . . . . . . . . . . . . . . . . . . . . . . 339 14.8 Repair of DNA Damage . . . . . . . . . . . . . . . . . 340 14.9 Double-Strand-Break Repair Machinery . . . . . . . . 342 14.10 How Breast Cancer (BRCA) Proteins Interact with DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . 344 14.11 PI3K Superfamily Members that Recognize Double-Strand Breaks . . . . . . . . . . . . . . . . . . 345 14.12 Checkpoints Regulate Transition Events in a Network . . . . . . . . . . . . . . . . . . . . . . . . . . 346 14.13 Cyclin-Dependent Kinases Form the Core of Cell-Cycle Control System . . . . . . . . . . . . . . . . 347 14.14 pRb Regulates Cell Cycle in Response to Mitogenic Signals . . . . . . . . . . . . . . . . . . . . . 347 14.15 p53 Halts Cell Cycle While DNA Repairs Are Made . . . . . . . . . . . . . . . . . . . . . . . . . . . . 349 14.16 p53 and pRb Controllers Central to Metazoan Cancer Prevention Program . . . . . . . . . . . . . . . 350 Contents xix 14.17 p53 Structure Supports Its Role as a Central Controller . . . . . . . . . . . . . . . . . . . . . . . . . 352 14.18 Telomerase Production in Cancer Cells . . . . . . . . . 354 15. Apoptosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 359 15.1 Caspases and Bcl-2 Proteins Are Key Mediators of Apoptosis . . . . . . . . . . . . . . . . . . . . . . . . . 360 15.2 Caspases Are Proteolytic Enzymes Synthesized as Inactive Zymogens . . . . . . . . . . . . . . . . . . . . 361 15.3 Caspases Are Initiators and Executioners of Apoptosis Programs . . . . . . . . . . . . . . . . . . . 362 15.4 There Are Three Kinds of Bcl-2 Proteins . . . . . . . . 363 15.5 How Caspases Are Activated . . . . . . . . . . . . . . 365 15.6 Cell-to-Cell Signals Stimulate Formation of the DISC . . . . . . . . . . . . . . . . . . . . . . . . . . . . 366 15.7 Death Signals Are Conveyed by the Caspase 8 Pathway . . . . . . . . . . . . . . . . . . . . . . . . . . 367 15.8 How Pro- and Antiapoptotic Signals Are Relayed . . . . . . . . . . . . . . . . . . . . . . . . . . . 368 15.9 Bcl-2 Proteins Regulate Mitochondrial Membrane Permeability . . . . . . . . . . . . . . . . . . . . . . . . 369 15.10 Mitochondria Release Cytochrome c in Response to Oxidative Stresses . . . . . . . . . . . . . . . . . . . . . 371 15.11 Mitochondria Release Apoptosis-Promoting Agents . . . . . . . . . . . . . . . . . . . . . . . . . . . 372 15.12 Role of Apoptosome in (Mitochondrial Pathway to) Apoptosis . . . . . . . . . . . . . . . . . . . . . . . . . 373 15.13 Inhibitors of Apoptosis Proteins Regulate Caspase Activity . . . . . . . . . . . . . . . . . . . . . . . . . . . 374 15.14 Smac/DIABLO and Omi/HtrA2 Regulate IAPs . . . 375 15.15 Feedback Loops Coordinate Actions at Various Control Points . . . . . . . . . . . . . . . . . . . . . . . 375 15.16 Cells Can Produce Several Different Kinds of Calcium Signals . . . . . . . . . . . . . . . . . . . . . . 376 15.17 Excessive [Ca2+] in Mitochondria Can Trigger Apoptosis . . . . . . . . . . . . . . . . . . . . . . . . . 377 15.18 p53 Promotes Cell Death in Response to Irreparable DNA Damage . . . . . . . . . . . . . . . . . . . . . . . 378 15.19 Anti-Cancer Drugs Target the Cell’s Apoptosis Machinery . . . . . . . . . . . . . . . . . . . . . . . . . 379 16. Gene Regulation in Eukaryotes . . . . . . . . . . . . . . . . . 385 16.1 Organization of the Gene Regulatory Region . . . . . 386 16.2 How Promoters Regulate Genes . . . . . . . . . . . . 387 16.3 TFs Bind DNA Through Their DNA-Binding Domains . . . . . . . . . . . . . . . . . . . . . . . . . . 389 xx Contents 16.4 Transcriptional Activation Domains Initiate Transcription . . . . . . . . . . . . . . . . . . . . . . . . 392 16.5 Nuclear Hormone Receptors Are Transcription Factors . . . . . . . . . . . . . . . . . . . . . . . . . . . 393 16.6 Composition and Structure of the Basal Transcription Machinery . . . . . . . . . . . . . . . . . 393 16.7 RNAP II Is Core Module of the Transcription Machinery . . . . . . . . . . . . . . . . . . . . . . . . . 394 16.8 Regulation by Chromatin-Modifying Enzymes . . . . . . . . . . . . . . . . . . . . . . . . . . 395 16.9 Multiprotein Complex Use of Energy of ATP Hydrolysis . . . . . . . . . . . . . . . . . . . . . . . . . 397 16.10 Protein Complexes Act as Interfaces Between TFs and RNAP II . . . . . . . . . . . . . . . . . . . . . 398 16.11 Alternative Splicing to Generate Multiple Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . 399 16.12 Pre-Messenger RNA Molecules Contain Splice Sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 400 16.13 Small Nuclear RNAs (snRNAs) . . . . . . . . . . . . . 401 16.14 How Exon Splices Are Determined . . . . . . . . . . . 403 16.15 Translation Initiation Factors Regulate Start of Translation . . . . . . . . . . . . . . . . . . . . . . . . . 404 16.16 eIF2 Interfaces Upstream Regulatory Signals and the Ribosomal Machinery . . . . . . . . . . . . . . . . 406 16.17 Critical Control Points for Protein Synthesis . . . . . . 407 17. Cell Regulation in Bacteria . . . . . . . . . . . . . . . . . . . . 411 17.1 Cell Regulation in Bacteria Occurs Primarily at Transcription Level . . . . . . . . . . . . . . . . . . . . 412 17.2 Transcription Is Initiated by RNAP Holoenzymes . . . . . . . . . . . . . . . . . . . . . . . 412 17.3 Sigma Factors Bind to Regulatory Sequences in Promoters . . . . . . . . . . . . . . . . . . . . . . . . . 414 17.4 Bacteria Utilize Sigma Factors to Make Major Changes in Gene Expression . . . . . . . . . . . . . . 414 17.5 Mechanism of Bacterial Transcription Factors . . . . . 416 17.6 Many TFs Function as Response Regulators . . . . . . 417 17.7 Organization of Protein-Encoding Regions and Their Regulatory Sequences . . . . . . . . . . . . . . . 418 17.8 The Lac Operon Helps Control Metabolism in E. coli . . . . . . . . . . . . . . . . . . . . . . . . . . . . 419 17.9 Flagellar Motors Are Erected in Several Stages . . . . 421 17.10 Under Starvation Conditions, B. subtilis Undergoes Sporulation . . . . . . . . . . . . . . . . . . . . . . . . . 422 17.11 Cell-Cycle Progression and Differentiation in C. crescentus . . . . . . . . . . . . . . . . . . . . . . . . 424 Contents xxi xxii Contents 17.12 Antigenic Variation Counters Adaptive Immune Responses . . . . . . . . . . . . . . . . . . . . . . . . . 426 17.13 Bacteria Organize into Communities When Nutrient Conditions Are Favorable . . . . . . . . . . . . . . . . 426 17.14 Quorum Sensing Plays a Key Role in Establishing a Colony . . . . . . . . . . . . . . . . . . . . . . . . . . . 428 17.15 Bacteria Form Associations with Other Bacteria on Exposed Surfaces . . . . . . . . . . . . . . . . . . . . . 430 17.16 Horizontal Gene Transfer (HGT) . . . . . . . . . . . . 430 17.17 Pathogenic Species Possess Virulence Cassettes . . . . 431 17.18 Bacterial Death Modules . . . . . . . . . . . . . . . . . 433 17.19 Myxobacteria Exhibit Two Distinct Forms of Social Behavior . . . . . . . . . . . . . . . . . . . . . . 434 17.20 Structure Formation by Heterocystous Cyanobacteria . . . . . . . . . . . . . . . . . . . . . . . 435 17.21 Rhizobia Communicate and Form Symbiotic Associations with Legumes . . . . . . . . . . . . . . . 436 18. Regulation by Viruses . . . . . . . . . . . . . . . . . . . . . . . 441 18.1 How Viruses Enter Their Host Cells . . . . . . . . . . 442 18.2 Viruses Enter and Exit the Nucleus in Several Ways . . . . . . . . . . . . . . . . . . . . . . . . 442 18.3 Ways that Viruses Exit a Cell . . . . . . . . . . . . . . 443 18.4 Viruses Produce a Variety of Disorders in Humans . . . . . . . . . . . . . . . . . . . . . . . . . . 444 18.5 Virus–Host Interactions Underlie Virus Survival and Proliferation . . . . . . . . . . . . . . . . . . . . . . . . 445 18.6 Multilayered Defenses Are Balanced by Multilayered Attacks . . . . . . . . . . . . . . . . . . . 446 18.7 Viruses Target TNF Family of Cytokines . . . . . . . . 447 18.8 Hepatitis C Virus Disables Host Cell’s Interferon System . . . . . . . . . . . . . . . . . . . . . . . . . . . 447 18.9 Human T Lymphotropic Virus Type 1 Can Cause Cancer . . . . . . . . . . . . . . . . . . . . . . . . . . . 449 18.10 DNA and RNA Viruses that Can Cause Cancer . . . 450 18.11 HIV Is a Retrovirus . . . . . . . . . . . . . . . . . . . . 452 18.12 Role of gp120 Envelope Protein in HIV . . . . . . . . 453 18.13 Early-Acting tat, rev, and nef Regulatory Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 454 18.14 Late-Acting vpr, vif, vpu, and vpx Regulatory Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 456 18.15 Bacteriophages’ Two Lifestyles: Lytic and Lysogenic . . . . . . . . . . . . . . . . . . . . . . . . . . 457 18.16 Deciding Between Lytic and Lysogenic Lifestyles . . . 458 18.17 Encoding of Shiga Toxin in E. coli . . . . . . . . . . . 459 19. Ion Channels . . . . . . . . . . . . . . . . . . . . . . . . . . . . 465 19.1 How Membrane Potentials Arise . . . . . . . . . . . . 466 19.2 Membrane and Action Potentials Have Regenerative Properties . . . . . . . . . . . . . . . . . . . . . . . . . 468 19.3 Hodgkin–Huxley Equations Describe How Action Potentials Arise . . . . . . . . . . . . . . . . . . . . . . 470 19.4 Ion Channels Have Gates that Open and Close . . . . 472 19.5 Families of Ion Channels Expressed in Plasma Membrane of Neurons . . . . . . . . . . . . . . . . . . 474 19.6 Assembly of Ion Channels . . . . . . . . . . . . . . . . 476 19.7 Design and Function of Ion Channels . . . . . . . . . 478 19.8 Gates and Filters in Potassium Channels . . . . . . . . 478 19.9 Voltage-Gated Chloride Channels Form a Double-Barreled Pore . . . . . . . . . . . . . . . . . . 479 19.10 Nicotinic Acetylcholine Receptors Are Ligand-Gated Ion Channels . . . . . . . . . . . . . . . . . . . . . . . . 480 19.11 Operation of Glutamate Receptor Ion Channels . . . 483 20. Neural Rhythms . . . . . . . . . . . . . . . . . . . . . . . . . . 487 20.1 Heartbeat Is Generated by Pacemaker Cells . . . . . 487 20.2 HCN Channels’ Role in Pacemaker Activities . . . . . 489 20.3 Synchronous Activity in the Central Nervous System . . . . . . . . . . . . . . . . . . . . . . . . . . . 492 20.4 Role of Low Voltage-Activated Calcium Channels . . . . 492 20.5 Neuromodulators Modify the Activities of Voltage-Gated Ion Channels . . . . . . . . . . . . . . . 494 20.6 Gap Junctions Formed by Connexins Mediate Rapid Signaling Between Cells . . . . . . . . . . . . . 495 20.7 Synchronization of Neural Firing . . . . . . . . . . . . 497 20.8 How Spindling Patterns Are Generated . . . . . . . . 498 20.9 Epileptic Seizures and Abnormal Brain Rhythms . . . 498 20.10 Swimming and Digestive Rhythms in Lower Vertebrates . . . . . . . . . . . . . . . . . . . . . . . . . 499 20.11 CPGs Have a Number of Common Features . . . . . 502 20.12 Neural Circuits Are Connected to Other Circuits and Form Systems . . . . . . . . . . . . . . . . . . . . . . . 504 20.13 A Variety of Neuromodulators Regulate Operation of the Crustacean STG . . . . . . . . . . . . . . . . . . 505 20.14 Motor Systems Adapt to Their Environment and Learn . . . . . . . . . . . . . . . . . . . . . . . . .