Principles of Cell Biology, Third Edition

Cover Title Page Copyright Page Dedication Page Brief Contents Contents The Fourteen Principles of Cell Biology Preface Acknowledgments About the Cover About the Authors Chapter 1 Life Is a Team Sport 1.1 The Big Picture 1.2 Life Can Arise from Simple Ingredients Nonliving Substances Combine to Form Life Membrane Formation Requires Water Code Biology Helps Explain the Diversity of Life Evidence for the Possibility of Extraterrestrial Life 1.3 All Cells Are Built from the Same Common Molecular Building Blocks The Study of Cellular Chemistry Begins with an Examination of the Carbon Atom Complex Biomolecules Are Mostly Composed of Chemical Building Blocks Called Functional Groups Lipids Are Carbon-Rich Polymers That Are Insoluble in Water Sugars Are Simple Carbohydrates Amino Acids Form Carbon-Rich Molecules That Contain an Amino Acid Group and a Carboxylic Acid Group Nucleotides Are Complex Structures Containing a Sugar, a Phosphate Group, and a Base 1.4 Cells Must Cooperate to Succeed Prokaryotes Are the Simplest Forms of Cells Eukaryotes Are Complex Cells Capable of Forming Multicellular Organisms Biofilms Support Prokaryotic and Eukaryotic Symbiosis Macroorganismal Hosts Coevolve with Their Microbiomes to Create New Holobionts 1.5 Chapter Summary Chapter Study Questions Multiple-Choice Questions References Chapter 2 DNA Is the Instruction Book for Life 2.1 The Big Picture 2.2 All of the Information Necessary for Cells to Respond to Their External Environment Is Stored as DNA A Cell’s DNA Is Inherited DNA Must Be Read to Be Useful 2.3 DNA Is Carefully Packaged into Five Levels of Organization DNA Is a Linear Polymer of Deoxyribonucleotides Level 1: DNA Forms an Antiparallel Double Helix Level 2: DNA Is Bound to a Protein/RNA Scaffold Level 3: DNA Is Twisted to Form Fibers Level 4: DNA Fibers Attach to a Protein-RNA Scaffold Level 5: Chromatin Is Packaged into Highly Condensed Chromosomes 2.4 Cells Chemically Modify DNA and Its Scaffold to Control Packaging Chemical Modifications at Level 1 and Level 2 Can Affect DNA Packing Across All Levels of DNA Organization 2.5 Chapter Summary Chapter Study Questions Multiple-Choice Questions References Chapter 3 Proteins Are the Engines of Evolution 3.1 The Big Picture 3.2 Amino Acids Form Linear Polymers A Peptide Bond Joins Two Amino Acids Together Definitions: Proteins Versus Polypeptides Versus Peptides Versus Subunits 3.3 Protein Structure Is Classified into Four Categories Primary Structure Is Defined by the Linear Sequence of Amino Acids Secondary Structure Is Defined by Regions of Repetitive, Predictable Organization in the Primary Structure Tertiary Structure Is Defined by the Arrangement of the Secondary Structures in Three Dimensions Quaternary Structure Is Defined by the Three-Dimensional Arrangement of Polypeptide Subunits in a Multimeric Protein Five Classes of Chemical Bonds Stabilize Protein Structure 3.4 Changing Protein Shape and Protein Function All Proteins Adopt at Least Two Different Shapes Cells Chemically Modify Proteins to Control Their Shape and Function Classification of Proteins 3.5 Where Do Proteins Go to Die? Proteins in the Cytosol and Nucleus Are Broken Down in the Proteasome Proteins in Organelles Are Digested in Lysosomes Proteinases Digest Proteins in the Extracellular Space 3.6 Chapter Summary Chapter Study Questions Multiple-Choice Questions References Chapter 4 Membranes Are Complex Fluids That Define Compartments 4.1 The Big Picture 4.2 Phospholipids Are the Basic Building Blocks of Cellular Membranes Phospholipids Contain Four Structural Elements The Amphipathic Nature of Phospholipids Allows Them to Form Lipid Bilayers in Aqueous Solution Phospholipid Bilayers Are Semipermeable Barriers 4.3 The Fluid-Mosaic Model Explains How Phospholipids and Proteins Interact Within a Cellular Membrane Membrane Proteins Associate with Membranes in Three Different Ways Cellular Membranes Are Both Fluid and Static 4.4 Cellular Membranes Maintain Chemical Disequilibrium Between Compartments Protein Channels, Carriers, and Pumps Regulate the Transport of Most Small Molecules Across Membranes 4.5 The Smooth Endoplasmic Reticulum and Golgi Apparatus Build Most Eukaryotic Cellular Membrane Components Glycerol and Fatty Acids Are Synthesized in the Cytosol The Synthesis of Phosphoglycerides Begins at the Cytosolic Face of the SER Membrane Additional Membrane Lipids Are Synthesized in the Endoplasmic Reticulum and Golgi Apparatus Most Membrane Assembly Begins in the SER and Is Completed in the Target Organelle 4.6 Chapter Summary Chapter Study Questions Multiple-Choice Questions References Chapter 5 The Cytoskeleton Forms the Architectural Foundation for the Structural Complexity of Life 5.1 The Big Picture 5.2 The Cytoskeleton Is Represented by Three Functional Classes of Proteins 5.3 Intermediate Filaments Are the Strongest, Stablest Elements of the Cytoskeleton Intermediate Filaments Are Formed from a Family of Related Proteins The Primary Building Block of Intermediate Filaments Is a Filamentous Subunit Intermediate Filament Subunits Form Coiled-Coil Dimers Heterodimers Overlap to Form Filamentous Tetramers Assembly of a Mature Intermediate Filament from Tetramers Occurs in Three Stages Posttranslational Modifications Control the Shape of Intermediate Filaments 5.4 Microtubules Organize Movement Inside a Cell Microtubule Assembly Begins at a Microtubule-Organizing Center The Growth and Shrinkage of Microtubules Is Called Dynamic Instability Microtubule-Associated Proteins Regulate the Stability and Function of Microtubules Cilia and Flagella Are Specialized Microtubule-Based Structures Responsible for Motility in Some Cells 5.5 Actin Filaments Control the Movement of Cells The Building Block of Actin Filaments Is the Actin Monomer Actin Polymerization Occurs in Three Stages Actin Filaments Have Structural Polarity 5.6 Seven Classes of Proteins Bind to Actin to Control Its Polymerization and Organization Monomer-Binding Proteins Regulate Actin Polymerization Nucleating Proteins Regulate Actin Polymerization Capping, Depolymerizing, and Severing Proteins Affect the Length and Stability of Actin Filaments Crosslinking Proteins Organize Actin Filaments into Bundles and Networks Membrane Anchors and Cytoskeletal Linkers Bridge Actin Filaments to Other Structural Proteins Including Intermediate Filaments and Microtubules Myosins Exert Force on Actin Filaments to Induce Cell Movement Cell Migration Is a Complex, Dynamic Reorganization of an Entire Cell 5.7 Eukaryotic Cytoskeletal Proteins Arose from Prokaryotic Ancestors 5.8 Chapter Summary Chapter Study Questions Multiple-Choice Questions References Chapter 6 The Rise of Multicellularity 6.1 The Big Picture 6.2 Multicellularity Is an Evolutionary Response to Selective Pressure 6.3 The Extracellular Matrix Is a Complex Network of Molecules That Fills the Spaces Between Cells in a Multicellular Organism Glycoproteins Form Filamentous Networks Between Cells Proteoglycans Provide Hydration to Tissues Matricellular Proteins Are Nonadhesive Proteins That Regulate the Functions of Extracellular Matrix Proteins The Basal Lamina Is a Specialized Extracellular Matrix Most Integrins Are Receptors for Extracellular Matrix Proteins 6.4 Cells Adhere to One Another via Specialized Proteins and Junctional Complexes Tight Junctions Form Selectively Permeable Barriers Between Cells Adherens Junctions Link Adjacent Cells Desmosomes Are Intermediate Filament-Based Cell Adhesion Complexes Gap Junctions Allow Direct Transfer of Molecules Between Adjacent Cells Calcium-Dependent Cadherins Mediate Adhesion Between Cells Calcium-Independent NCAMs Mediate Adhesion Between Neural Cells Selectins Control Adhesion of Circulating Immune Cells 6.5 Chapter Summary Chapter Study Questions Multiple-Choice Questions References Chapter 7 The Nucleus Is the Brain of a Cell 7.1 The Big Picture 7.2 The Nucleus Carefully Protects a Eukaryotic Cell’s DNA The Nuclear Envelope Is a Double-Membrane Structure Nuclear Pore Complexes Regulate Molecular Traffic into and Out of the Nucleus The Interior of the Nucleus Is Highly Organized and Contains Many Subcompartments 7.3 DNA Replication Is a Complex, Tightly Regulated Process DNA Polymerases Are Enzymes That Replicate DNA DNA Replication Is Semidiscontinuous Cells Have Two Main DNA Repair Mechanisms Excision Systems Remove One Strand of Damaged DNA and Replace It 7.4 Mitosis Separates Replicated Chromosomes Mitosis Is Divided into Stages Prophase Prepares the Cell for Division Chromosomes Attach to the Mitotic Spindle During Prometaphase Arrival of the Chromosomes at the Spindle Equator Signals the Beginning of Metaphase Separation of Chromatids at the Metaphase Plate Occurs During Anaphase The Structural Rearrangements That Occur in Prophase Begin to Reverse During Telophase Cytokinesis Completes Mitosis by Partitioning the Cytoplasm to Form Two New Daughter Cells 7.5 Chapter Summary Chapter Study Questions Multiple-Choice Questions Additional Reading Chapter 8 RNA Links the Information in DNA to Actions Performed by Proteins 8.1 The Big Picture 8.2 Transcription Converts the DNA Genetic Code into RNA RNA Polymerases Transcribe Genes in a “Bubble” of Single-Stranded DNA Transcription Occurs in Three Stages In Eukaryotes, Messenger RNAs Undergo Processing Prior to Leaving the Nucleus 8.3 Proteins Are Synthesized by Ribosomes Using an mRNA Template Translation Occurs in Three Stages 8.4 At Least Five Different Mechanisms Are Required for Proper Targeting of Proteins in a Eukaryotic Cell Signal Sequences Code for Proper Targeting of Proteins The Nuclear Import/Export System Regulates Traffic of Macromolecules Through Nuclear Pores Proteins Targeted to the Peroxisome Contain Peroxisomal Targeting Signals (PTS) Secreted Proteins and Proteins Targeted to the Endomembrane System Contain an Endoplasmic Reticulum Signal Sequence Integration of Transmembrane Proteins Requires Specific Amino Acid Sequences 8.5 Chapter Summary Chapter Study Questions Multiple-Choice Questions References Chapter 9 The Endomembrane System Serves as the Cellular Import/Export Machinery for Most Macromolecules 9.1 The Big Picture 9.2 The Endomembrane System Is a Network of Organelles in Eukaryotic Cells The Endomembrane System Controls Molecular Transport into and out of a Cell Vesicles Shuttle Material Between Organelles in the Endomembrane System 9.3 Exocytosis Begins in the Endoplasmic Reticulum Newly Synthesized Proteins Begin Posttranslational Modification as ER-Resident Proteins Help Them Fold Properly COPII-Coated Vesicles Shuttle Proteins from the ER to the Golgi Apparatus Resident ER Proteins Are Retrieved from the Golgi Apparatus 9.4 The Golgi Apparatus Modifies and Sorts Proteins in the Exocytic Pathway The Golgi Apparatus Is Subdivided into Cis, Medial, and Trans Cisternae The Trans-Golgi Network Sorts Proteins Exiting the Golgi Apparatus 9.5 Exocytosis Ends at the Plasma Membrane Cells Use Two Mechanisms for Controlling the Final Steps of Exocytosis 9.6 Endocytosis Begins at the Plasma Membrane Clathrin Stabilizes the Formation of Endocytic Vesicles 9.7 The Endosome Sorts Proteins in the Endocytic Pathway The Endosome Is Subdivided into Early and Late Compartments Proton Pump Proteins Play a Central Role in the Sorting and Activation of Endosomal Contents 9.8 Endocytosis Ends at the Lysosome Endogenous Proteins Destined for the Lysosome Are Tagged and Sorted by the Golgi Apparatus Digested Material Is Transported into the Cytosol Lysosomes Can Also Degrade Some Resident Organelles Peroxisomes Defy Classification 9.9 Chapter Summary Chapter Study Questions Multiple-Choice Questions References Chapter 10 Chemical Bonds and Ion Gradients Are Cellular Fuel 10.1 The Big Picture 10.2 Cells Store Energy in Many Forms The Laws of Thermodynamics Define the Rules for Energy Transfer Fats and Polysaccharides Are Examples of Long-Term Energy Storage in Cells High-Energy Electrons and Ion Gradients Are Examples of Short-Term Potential Energy in Cells Nucleotide Triphosphates Store Energy for Immediate Use Cells Couple Energetically Favorable and Unfavorable Reactions The Amount of Potential Energy Stored in an Ion Gradient Can Be Expressed as an Electrical Potential 10.3 Storage of Light Energy Occurs in the Chloroplast Chloroplasts Have Three Membrane-Bound Compartments Chloroplasts Convert Sunlight into the First Forms of Cellular Energy 10.4 Cells Use a Combination of Channel, Carrier, and Pump Proteins to Transport Small Molecules Across Membranes The Na+/K+ ATPase Maintains the Resting Potential Across the Plasma Membrane In the Vertebrate Gut, a Leaky K+ Channel, an Na+/Glucose Symporter, and a Passive Glucose Carrier Work Together to Move Glucose from the Gut Lumen to the Bloodstream 10.5 The First Phase of Glucose Metabolism Occurs in the Cytosol Why a Stepwise Method of Metabolizing Glucose Is Necessary The Ten Chemical Reactions in Glycolysis Convert a Glucose Molecule into Two Three-Carbon Compounds, Two NADH Molecules, and Two ATP Molecules Pyruvate Is Not an Endpoint in Glucose Metabolism 10.6 Aerobic Respiration Results in the Complete Oxidation of Glucose Aerobic Respiration Occurs in Four Stages 10.7 Chapter Summary Chapter Study Questions Multiple-Choice Questions References Chapter 11 Signaling Networks Are the Nervous System of a Cell 11.1 The Big Picture 11.2 Signaling Molecules Form Communication Networks Signaling Networks Are Composed of Signals, Receptors, Signaling Proteins, and Second Messenger Molecules 11.3 Cell-Signaling Molecules Transmit Information Between Cells Intercellular Signals Are Secreted into the Extracellular Space Six Classes of Receptors Are Sufficient to Detect a Vast Array of Environmental Stimuli 11.4 Intracellular Signaling Proteins Propagate Signals Within a Cell G Proteins Are Two Classes of Molecular Switches Protein Kinases Phosphorylate Downstream Signaling Proteins Lipid Kinases Phosphorylate Phospholipids Ion Channels Release Bursts of Ions Calcium Fluxes Control Calcium-Binding Proteins Adenylyl Cyclases Form Cyclic AMP Adaptors Facilitate Binding of Multiple Signaling Proteins Mutations in Signaling Networks Are Common in Cancer Cells 11.5 A Brief Look at Some Common Signaling Pathways Protein Tyrosine Kinase Signaling Pathways Control Cell Growth and Migration Heterotrimeric G Protein Signaling Pathways Regulate a Great Variety of Cellular Behaviors Phospholipid Kinase Pathways Work in Cooperation with Protein Kinase and G Protein Pathways Steroid Hormones Control Long-Term Cell Behavior by Altering Gene Expression 11.6 Chapter Summary Chapter Study Questions Multiple-Choice Questions References Chapter 12 Protein Complexes Are Cellular Decision-Making Devices 12.1 The Big Picture 12.2 Many Signaling Proteins Enter the Nucleus Nuclear Receptors Translocate from the Cytosol to the Nucleus During Signaling Notch Is a Transmembrane Scaffold Receptor That Enters the Nucleus G Protein Coupled Receptors and GPCR Fragments Signal in the Nucleus Heterotrimeric G Proteins Target Many Cellular Compartments, Including the Nucleus Several Elements of Phosphatidylinositol Signaling Pathways Are Present in the Nucleus Receptor Protein Tyrosine Kinases Signal in the Nucleus Some Protein Kinases Phosphorylate Nuclear Proteins PTEN Is a Nuclear Phosphatase An ATP-Binding Calcium Ion Channel Is Present in the Plasma Membrane and Nuclear Envelope in Some Neurons An Adenylyl Cyclase Is Present in the Nucleus 12.3 Effector Proteins in the Nucleus Are Grouped into Three Classes Cohesins and Condensins Help Control the Packaging State of Chromatin Histone Modifiers Control the Structure of Nucleosomes Transcription Factors Promote the Expression of Genes Epigenetic Mechanisms Alter Gene Expression Without Modifying DNA Sequences 12.4 Signal Transduction Pathways and Gene-Expression Programs Form Feedback Loops 12.5 Chapter Summary Chapter Study Questions Multiple-Choice Questions References Chapter 13 Progression Through the Cell Cycle Is the Most Vulnerable Period in a Cell’s Life 13.1 The Big Picture 13.2 New Cells Arise from Parental Cells That Complete the Cell Cycle The Cell Cycle Is Divided into Five Phases The G1/S Checkpoint Is the Point of No Return The G2/M Checkpoint Is the Trigger for Large-Scale Rearrangement of Cellular Architecture Activation of Cyclin-CDK Complexes Begins in G1 Phase DNA Replication Occurs in S Phase G2 Phase Prepares Cells for Mitosis Mitosis and Cytokinesis Occur in M Phase 13.3 Multicellular Organisms Contain a Cell Self-Destruct Program That Keeps Them Healthy Two Different Types of Cellular Death: Necrosis and Apoptosis 13.4 Chapter Summary Chapter Study Questions Multiple-Choice Questions References Chapter 14 Human Activity Is Triggering a Paradigm Shift in Evolution 14.1 The Big, Big Picture: A Review of Chapters 1–13 14.2 The Neuromuscular System Is an Emerging Target for Human Intervention and Artificial Selection Neurons Transmit Signals via Action Potentials Muscle Cells Are Effectors of Nerve Signals Skeletal Muscle Cells Are Multinucleated, Highly Specialized Cells Amyotrophic Lateral Sclerosis Describes a Range of Neuromuscular Diseases 14.3 Gene Editing Is a Revolutionary Advance in Artificial Selection CRISPR/Cas9 Is a Promising, Efficient Additive to Traditional Anti-HIV Treatments 14.4 Gametogenesis, Fertilization, and Embryogenesis Form a Complex Developmental Program That Is Subject to Human Intervention Meiosis Creates Gametes, Which Are the Two Essential Precursors of a Diploid Life 14.5 Chapter Summary Chapter Study Questions Multiple-Choice Questions References Glossary Answers Index