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MOLECULAR CELL BIOLOGY FIFTH EDITION

Harvey Lodish Arnold Berk Paul Matsudaira Chris A. Kaiser Monty Krieger Matthew P. Scott S. Lawrence Zipursky James Darnell

W. H. Freeman and Company New York

H Cell Signaling

Q Chemical and Molecular Foundations 1 Life Begins with Cells

1

2 Chemical Foundations

29

3 Protein Structure and Function

59

4 Basic Molecular Genetic Mechanisms 101

533

14 Signaling Pathways That Control Gene Activity

571

15 Integration of Signals and Gene Controls

611

W] Membrane Trafficking

HI Cell Organization and Biochemistry 5 Biomembranes and Cell Architecture

147

6 Integrating Cells into Tissues

197

7 Transport of Ions and Small Molecules Across Cell Membranes 245 8 Cellular Energetics

13 Signaling at the Cell Surface

16 Moving Proteins into Membranes and Organelles

657

17 Vesicular Traffic, Secretion, and Endocytosis

701

18 Metabolism and Movement of Lipids

743

301

PfTI Cytoskeleton 19 Microfilaments and Intermediate Filaments

779

351

20 Microtubules

817

10 Molecular Stucture of Genes and Chromosomes

405

WM\ Cell-Cycle and Cell-Growth Control

11 Transcriptional Control of Gene Expression

447

mi Genetics and Molecular Biology 9 Molecular Genetic Techniques and.Genomics

12 Post-transcriptional Gene Control and Nuclear Transport

493

21 Regulating the Eukaryotic Cell Cycle

853

22 Cell Birth, Lineage, and Death

899

23 Cancer

935

XIII

CONTENTS D Chemical and Molecular Foundations

Genomics Reveals Differences in the Structure and Expression of Entire Genomes Developmental Biology Reveals Changes in the Properties of Cells as They Specialize Choosing the Right Experimental Organism for the Job

1 I Life Begins with Cells m The Diversity and Commonality of Cells

1

All Cells Are Prokaryotic or Eukaryotic Unicellular Organisms Help and Hurt Us Even Single Cells Can Have Sex Viruses Are the Ultimate Parasites We Develop from a Single Cell Stem Cells, Cloning, and Related Techniques Offer Exciting Possibilities but Raise Some Concerns

2 4 6 6 7

I1E| The Molecules of a Cell Small Molecules Carry Energy, Transmit Signals, and Are Linked into Macromolecules Proteins Give Cells Structure and Perform Most Cellular Tasks Nucleic Acids Carry Coded Information for Making Proteins at the Right Time and Place The Genome Is Packaged into Chromosomes and Replicated During Cell Division Mutations May Be Good, Bad, or Indifferent

10

n

The Work of Cells

Investigating Cells and Their Parts Cell Biology Reveals the Size, Shape, and Location of Cell Components Biochemistry Reveals the Molecular Structure and Chemistry of Purified Cell Constituents Genetics Reveals the Consequences of Damaged Genes

23 24

26 26

26 27 28

8

12 Cells Build and Degrade Numerous Molecules and Structures \nimal Cells Produce Their Own External Environment and Glues Cells Change Shape and Move Cells Sense and Send Information Cells Regulate Their Gene Expression to Meet Changing Needs Cells Grow and Divide Cells Die from Aggravated Assault or an Internal Program

A Genome Perspective on Evolution Metabolic Proteins, the Genetic Code, and Organelle Structures Are Nearly Universal Many Genes Controlling Development Are Remarkably Similar in Humans and Other Animals Darwin's Ideas About the Evolution of Whole Animals Are Relevant to Genes Human Medicine Is Informed by Research on Other Organisms

22

13 14 15 15 16 16 17 18

19 20 21 21

2 I Chemical Foundations

29

VMM Atomic Bonds and Molecular Interactions

30

Each Atom Has a Defined Number and Geometry of Covalent Bonds 30 Electrons Are Shared Unequally in Polar Covalent Bonds 32 Covalent Bonds Are Much Stronger and More Stable Than Noncovalent Interactions 32 Ionic Interactions Are Attractions Between Oppositely Charged Ions 33 Hydrogen Bonds Determine Water Solubility of Uncharged Molecules 33 Van der Waals Interactions Are Caused by Transient Dipoles 34 The Hydrophobic Effect Causes Nonpolar Molecules to Adhere to One Another 35 Molecular Complementarity Permits Tight, Highly Specific Binding of Biomolecules 36

RE8 Chemical Building Blocks of Cells Amino Acids Differing Only in Their Side Chains Compose Proteins Five Different Nucleotides Are Used to Build Nucleic Acids Monosaccharides Joined by Glycosidic Bonds Form Linear and Branched Polysaccharides

37 38 40 41 XV

XVI

CONTENTS

Fatty Acids Are .Precursors for Many Cellular Lipids Phospholipids Associate Noncovalently to Form the Basic Bilayer Structure of Biomembranes

Hfe^jp Chemical Equilibrium Equilibrium Constants Reflect the Extent of a Chemical Reaction Chemical Reactions in Cells Are at Steady State Dissociation Constants for Binding Reactions Reflect the Affinity of Interacting Molecules Biological Fluids Have Characteristic pH Values Hydrogen Ions Are Released by Acids and Taken Up by Bases Buffers Maintain the pH of Intracellular and Extracellular Fluids

Biochemical Energetics Several Forms of Energy Are Important in Biological Systems Cells Can Transform One Type of Energy into Another The Change in Free Energy Determines the Direction of a Chemical Reaction The AG 0 ' of a Reaction Can Be Calculated from Its Keq An Unfavorable Chemical Reaction Can Proceed If It Is Coupled with an Energetically Favorable Reaction Hydrolysis of ATP Releases Substantial Free'Energy and Drives Many Cellular Processes ATP Is Generated During Photosynthesis and Respiration NAD + and FAD Couple Many Biological Oxidation and Reduction Reactions

3 I Protein Structure and Function Hierarchical Structure of Proteins The Primary Structure of a Protein Is Its Linear Arrangement of Amino Acids Secondary Structures Are the Core Elements of Protein Architecture , Overall Folding of a Polypeptide Chain Yields Its Tertiary Structure Motifs Are Regular Combinations of Secondary Structures Structural and Functional Domains Are Modules of Tertiary Structure Proteins Associate into Multimeric Structures and Macromolecular Assemblies Members of Protein Families Have a Common Evolutionary Ancestor

43 44

46 46 46 47 47 48 48

50 50 50 51 52

52 52 53 54

59 60 60 61 62 63 64 66 67

tW Folding, Modification, and Degradation of Proteins The Information for Protein Folding Is Encoded in the Sequence Folding of Proteins in Vivo Is Promoted by Chaperones Many Proteins Undergo Chemical Modification of Amino Acid Residues Peptide Segments of Some Proteins Are Removed After Synthesis Ubiquitin Marks Cytosolic Proteins for Degradation in Proteasomes Digestive Proteases Degrade Dietary Proteins Alternatively Folded Proteins Are Implicated in Slowly Developing Diseases

H E 1 Enzymes and the Chemical Work of Cells

68 68 69 70 70 71 72 72

73

Specificity and Affinity of Protein-Ligand Binding Depend on Molecular Complementarity Enzymes Are Highly Efficient and Specific Catalysts An Enzyme's Active Site Binds Substrates and* Carries Out Catalysis y m a x and Km Characterize an Enzymatic Reaction Enzymes in a Common Pathway Are Often Physically Associated with One Another ME1 Cholesterol: A Multifunctional Membrane Lipid Cholesterol Is Synthesized by Enzymes in the Cytosol and ER Membrane Many Bioactive Molecules Are Made from Cholesterol and Its Biosynthetic Precursors Cholesterol and Phospholipids Are Transported Between Organelles by Golgi-Independent Mechanisms

745 745 746 747 748

750 751 752

752

• I : * I Lipid Movement into and out of Cells 754 Cell-Surface Transporters Aid in Moving Fatty Acids Across the Plasma Membrane 755 ABC Proteins Mediate Cellular Export of Phospholipids and Cholesterol 755 Lipids Can Be Exported or Imported in Large Well-Defined Lipoprotein Complexes 757

XXX

CONTENTS

Lipoproteins Are Made in the ER, Exported by the Secretory Pathway, and Remodeled in the Circulation Cells Use Several Protein-Mediated Mechanisms to Import Lipoprotein Lipids Analysis of Familial Hypercholesterolemia Revealed the Pathway for Receptor-Mediated Endocytosis of LDL Particles Cholesteryl Esters in Lipoproteins Can Be Selectively Taken Up by the Receptor SR-BI

» g : g | Feedback Regulation of Cellular Lipid Metabolism ER-to-Golgi Transport and Proteolytic Activation Control the Activity of SREBP Transcription Factors Multiple SREBPs Regulate Expression of Numerous Lipid-Metabolizing Proteins. Members of the Nuclear Receptor Superfamily Contribute to Cellular and Whole-Body Lipid Regulation

•t:*°1 The Cell Biology of Atherosclerosis, Heart Attacks, and Strokes Arterial Inflammation and Cellular Import of Cholesterol Mark the Early Stages of Atherosclerosis Atherosclerotic Plaques Can Impede Blood Flow, Leading to Heart Attacks and Strokes LDLR-Independent Uptake of LDL (Bad Cholesterol) Leads to Formation of Foam Cells Reverse Cholesterol Transport by HDL (Good Cholesterol) Protects Against Atherosclerosis Two Treatments for Atherosclerosis Are Based on SREBP-Regulated Cellular Cholesterol Metabolism

758 759 / 760 762

763

BMEJ The Dynamics of Actin Assembly

784

Actin Polymerization in Vitro Proceeds in Three Steps Actin Filaments Grow Faster at ( + ) End Than at(-)End Toxins Perturb the Pool of Actin Monomers Actin Polymerization Is Regulated by Proteins That Bind G-Actin Filament-Binding Severing Proteins Create New ; Actin Ends Actin-Capping Proteins Stabilize F-Actin Arp2/3 Assembles Branched Filaments Intracellular Movements and Changes in Cell Shape Are Driven by Actin Polymerization

784

liflfcl Myosin-Powered Cell Movements 764 765

766

767 768 769 770 770 771

EH Cytoskeleton

Myosins Are a Large Superfamily of Mechanochemical Motor Proteins Myosin Heads Walk Along Actin Filaments in Discrete Steps Myosin-Bound Vesicles Are Carried Along Actin Filaments Actin and Myosin II Form Contractile Bundles in Nonmuscle Cells . Organized Thick and Thin Filaments in Skeletal Muscle Slide Past One Another During Contraction Contraction of Skeletal Muscle Is Regulated by Ca 2 + and Actin-Binding Proteins Myosin-Dependent Mechanisms Regulate Contraction in Smooth Muscle and Nonmuscle Cells

Cell Locomotion Cell Movement Coordinates Force Generation with Cell Adhesion Ameboid Movement Entails Reversible Gel-Sol Transitions of Actin Networks External Signals and Various Signaling Pathways Coordinate Events That Lead to Cell Migration

•Mt>1 Intermediate Filaments

19

Microfi la merits and Intermediate Filaments Actin Structures

Actin Is Ancient, Abundant, and Highly Conserved G-Actin Monomers Assemble into Long, Helical F-Actin Polymers F-Actin Has Structural and Functional Polarity CH-Domain and Other Proteins Organize Microfilaments into Bundles and Networks

779 780 780 781 782 782

Intermediate Filaments Differ in Stability, Size, and Structure from Other Cytoskeletal Fibers IF Proteins Are Classified According to Their Distributions in Specific Tissues All IF Proteins Have a Conserved Core Domain and Are Organized Similarly into Filaments Intermediate Filaments Are Dynamic Various Proteins Cross-Link Intermediate Filaments to One Anther and to Other Cell Structures IF Networks Form Various Supportive Structures and Are Connected to Cellular Membranes Disruption of Keratin Networks Causes Blistering

785 786 786 787 788 788. 789

791 791 793 794 796

797 798 799

800 801 803 803

805 806 806 808 809 810 810 811

Contents

20 I Microtubules ED Microtubule Organization and Dynamics Heterodimeric Tubulin Subunits Compose the Wall of a Microtubule Microtubule Assembly and Disassembly Take Place Preferentially at the (+) End Dynamic Instability Is an Intrinsic Property of Microtubules Numerous Proteins Regulate Microtubule Dynamics and Cross-Linkage to Other Structures |Xolchicine and Other Drugs Disrupt Microtubule Dynamics jMTOCs Orient Most Microtubules and Determine Cell Polarity he 7-Tubulin Ring Complex Nucleates I, Polymerization of Tubulin Subunits ytoplasmic Organelles and Vesicles Are Organized by Microtubules

Kinesin- and Dynein-Powered Movements xonal Transport Along Microtubules Is in Both Directions H|?iesin I Powers Anterograde Transport of Vesicles fin Axons lost Kinesins Are Processive (+) Enddirected Motor Proteins jtpsolic Dyneins Are (—) End-Directed Motor Broteins That Bind Cargo Through Dynactin Multiple Motor Proteins Sometimes Move the Same

817

818

. : , . . .

848

Cell-Cycle and Cell-Growth Control 822 823

825 825 827

828

829 829 831 832 833

838

IifiltSlitotic Apparatus Is a Microtubule Machine for Sarating Chromosomes 839 Jpinetochore Is a Centromere-Based Protein [jlomplex That Captures and Helps Transport bromosomes . 841 Centrosomes Align and Begin Separating of the Metaphase Mitotic Spindle quires Motor Proteins and Dynamic itrotubules ...

847

820

fearyotic Cilia and Flagella Contain a Core of doublet Microtubules Studded with Axonemal l%yneins 835 SiUary and Flagellar Beating Are Produced by sntrolled Sliding of Outer Doublet Microtubules 837

frophase

845

819

834

Microtubule Dynamics and Motor Proteins in Mitosis

Anaphase Chromosomes Separate and the Spindle Elongates Microtubules and Microfilaments Work Cooperatively During Cytokinesis Plant Cells Reorganize Their Microtubules and Build a New Cell Wall in Mitosis

xxxi

841

843

21

Regulating the Eukaryotic Cell Cycle 853 Overview of the Cell Cycle and Its Control

The Cell Cycle Is an Ordered Series of Events Leading to Cell Replication Regulated Protein Phosphorylation and Degradation Control Passage Through the Cell Cycle Diverse Experimental Systems Have Been Used to Identify and Isolate Cell-Cycle Control Proteins

W1WM Biochemical Studies with Oocytes, Eggs, and Early Embryos Maturation-Promoting Factor (MPF) Stimulates Meiotic Maturation of Oocytes and Mitosis in Somatic Cells Mitotic Cyclin Was First Identified in Early Sea Urchin Embryos Cyclin B Levels and Kinase Activity of MitosisPromoting Factor (MPF) Change Together in Cycling Xenopus Egg Extracts Anaphase-Promoting Complex (APC) Controls Degradation of Mitotic Cyclins and Exit from Mitosis

E f l U Genetic Studies with 5. pombe A Highly Conserved MPF-like Complex Controls Entry into Mitosis in S. pombe Phosphorylation of the CDK Subunit Regulates the Kinase Activity of MPF Conformational Changes Induced by Cyclin Binding and Phosphorylation Increase MPF Activity Other Mechanisms Also Control Entry into Mitosis by Regulating MPF Activity

854 854 855 856

858

859 860

861

862

864 865 865 866 867

Molecular Mechanisms for Regulating Mitotic Events 868 Phosphorylation of Nuclear Lamins and Other Proteins Promotes Early Mitotic Events Unlinking of Sister Chromatids Initiates Anaphase

868 870

XXXII

CONTENTS

875

Cultured Embryonic Stem Cells Can Differentiate into Various Cell Types Tissues Are Maintained by Associated Populations of Stem Cells Cell Fates Are Progressively Restricted During Development The Complete Cell Lineage of C. elegans Is Known Heterochronic Mutants Provide Clues About Control of Cell Lineage ,

878

i M M Cell-Type Specification in Yeast

Reassembly of the Nuclear Envelope and Cytokinesis Depend on Unopposed Constitutive Phosphatase Activity . 873

§^gj| Genetic Studies with S. cerevisiae A Cyclin-Dependent Kinase (CDK) Is Critical for S-Phase Entry in S. cerevisiae Three Gi Cyclins Associate with S. cerevisiae to Form S Phase-Promoting Factors Degradation of the S-Phase Inhibitor Triggers DNA Replication Multiple Cyclins Direct the Kinase Activity of S. cerevisiae During Different Cell-Cycle Phases Cdcl4 Phosphatase Promotes Exit from Mitosis Replication at Each Origin Is Initiated Only Once During the Cell Cycle

874 /

874

878 879 879

HH Cell-Cycle Control in Mammalian Cells 881 Mammalian Restriction Point Is Analogous to START in Yeast Cells Multiple CDKs and Cyclins Regulate Passage of Mammalian Cells Through the Cell Cycle Regulated Expression of Two Classes of Genes Returns Go Mammalian Cells to the Cell Cycle Passage Through the Restriction Point Depends on Phosphorylation of the Tumor-Suppressor Rb Protein Cyclin A Is Required for DNA Synthesis and CDK1 for Entry into Mitosis ' Two Types of Cyclin-CDK Inhibitors Contribute to Cell-Cycle Control in Mammals

WSWM Checkpoints in Cell-Cycle Regulation The Presence of Unreplicated DNA Prevents Entry into Mitosis Improper Assembly of the Mitotic Spindle Prevents . the Initiation of Anaphase Proper Segregation of Daughter Chromosomes Is Monitored by the Mitotic ExirNetwork Cell-Cycle Arrest of Cells with Damaged DNA Depends on Tumor Suppressors

882 883 883

884 885 886

886

Transcription Factors Encoded at the MAT Locus Act in Concert with MCM1 to Specify Cell Type MCM1 and a l - M C M l Complexes Activate Gene Transcription a2-MCMl and a2-al Complexes Repress Transcription Pheromones Induce Mating of a and a Cells to Generate a Third Cell Type

E M U Specification and Differentiation of Muscle Embryonic Somites Give Rise to Myoblasts, the Precursors of Skeletal Muscle Cells Myogenic Genes Were First Identified in Studies with Cultured Fibroblasts Muscle-Regulatory Factors (MRFs) and MyocyteEnhancing Factors (MEFs) Act in Concert to Confer Myogenic Specificity Terminal Differentiation of Myoblasts Is Under ( Positive and Negative Control Cell-Cell Signals Are Crucial for Muscle Cell-Fate Determination and Myoblast Migration b H L H Regulatory Proteins Function in Creation of Other Tissues

901 902 906 907 908

910 910 911 912 912

913 914 '• 9141

915 ; 9161 9171 9181

888

E H Regulation o f Asymmetric Cell Division

i & & | Meiosis: A Special Type of Cell Division 890 Repression of Gx Cyclins and Meiosis-Specific Ime2 Prevents DNA Replication in Meiosis II 890 Crossing Over and Meiosis-Specific Rec8 Are Necessary for Specialized Chromosome Segregation in Meiosis I 891

22 I Cell Birth, Lineage, and Death 899 g £ U The Birth of Cells

900

Stem Cells Give Rise to Stem Cells and to Differentiating Cells

900

Yeast Mating-Type Switching Depends upon Asymmetric Cell Division Critical Asymmetry-Regulating Proteins Are Localized at Opposite Ends of Dividing Neuroblasts in Drosophila Orientation of the Mitotic Spindle Is Linked to Cytoplasmic Cell-Asymmetry Factors

9191 9201

92l| 923J

WH.1 Cell Death and Its Regulation

924]

Programmed Cell Death Occurs Through Apoptosis Neurotrophins Promote Survival of Neurons A Cascade of Caspase Proteins Functions in One Apoptotic Pathway Pro-Apoptotic Regulators Permit Caspase Activation in the Absence of Trophic Factors

9241 925J 9271 928;

Contents

Some Trophic Factors Induce Inactivation of a ProApoptotic Regulator Tumor Necrosis Factor and Related Death Signals Promote Cell Murder by Activating Caspases

23 I Cancer

929 930

935

fgg] Tumor Cells and the Onset of Cancer

936

Metastatic Tumor Cells Are Invasive and Can Spread Cancers Usually Originate in Proliferating Cells Tumor Growth Requires Formation of New Blood Vessels i Cultured Cells Can Be Transformed into Tumor Cells |