LODISH • BERK • MATSUDAIRA • KAISE·R
`KRIEGER. SCOTT. ZIPURSKY. ~-D;RNELL
`
`Exhibit 1043
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`

`

`MOLECULAR CELL BIOLOGY
`
`Fl FTH 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
`
`Exhibit 1043
`Select Sires, et al. v. ABS Global
`
`

`

`SARA TENNEY
`PUBLISHER:
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`About the cover: The illustration depicts a diverse array of integral and peripheral membrane proteins.
`The phospholipid bilayer is derived from a molecular dynamics model. The protein structures (deter(cid:173)
`mined by x-ray crystallography), left to right from back cover to front, are aquaporin (bovine; PDB ID
`lj4n), rhodopsin (bovine; lf88), G protein (chimeric bovine and rat, ap subunits; l got), light-harvesting
`complex (bacterial; lkzu), potassium channel (bacterial; 1618), photosynthetic reaction center (bacterial;
`l prc), photosystem 1 (bacterial; ljb0), aquaporin (l j4n), ATP synthase (composite bovine [le79] and
`bacterial [lcl 7)). [Molecular dynamics model after H. Heller, M. Schaefer, and K. Schulten, 1993,
`Molecular dynamics simulation of 200 lipids in rbe gel and in the liquid-crystal phases, Phys. Chem.
`97:8343; H. Heller, 1993, Simulation einer Lipidrnembrao auf einem Parallelrechner, Ph.D. diss.,
`University of Munich, Germany.]
`
`Library of Congress Cataloging-in-Publication Data
`
`Molecular cell biology/Harvey Lodish ... [et al.].- 5th ed.
`p.cm.
`Includes bibliographical references and index.
`ISBN 0-7167-4366-3
`1. Cytology. 2. Molecular biology. I. Lodish, Harvey F.
`
`QH581.2.M655 2003
`571.6- dc21
`
`2003049089
`
`© 1986, 1990, 1995, 2000, 2004 by W. H . Freeman and Company. All rights reserved.
`
`Printed in the United States of America
`
`First printing 2003
`
`W. H . Freeman and Company
`41 Madison Avenue, New York, New York 10010
`Houndsmills, Basingstoke RG21 6XS, England
`
`www.whfreeman.com
`
`Exhibit 1043
`Select Sires, et al. v. ABS Global
`
`

`

`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
`1 Ill A Genome Perspective on Evolution
`
`Metabolic Proteins, the Genetic Code, and
`2
`Organelle Structures Are Nearly Universal
`4 Many Genes Controlling Development Are
`6
`Remarkably Similar in Humans and Other
`6
`Animals
`7
`Darwin's Ideas About the Evolution of Whole
`Animals Are Relevant to Genes
`Human Medicine Is Informed by Research '
`on Other Organisms
`
`8
`
`8
`
`CONTENTS
`
`D Chemical and Molecular
`Foundations
`
`1 I Life Begins with Cells
`m The Diversity and Commonality of Cells
`
`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
`
`m 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
`
`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
`
`DJ The Work of Cells
`
`Cells Build and Degrade Numerous Molecules
`and Structures
`Animal 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
`Ill 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
`
`2 1 Chemical Foundations
`Nucleic Acids Carry Coded Information for Making m Atomic Bonds and Molecular
`
`8
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`9
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`10
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`11
`12
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`13
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`14
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`15
`15
`16
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`16
`17
`
`Interactions
`Each Atom Has a Defined Number and Geometry
`of Covalent Bonds
`Electrons Are Shared Unequally in Polar
`Covalent Bonds
`Covalent Bonds Are Much Stronger and More
`Stable Than Noncovalent Interactions
`Ionic Interactions Are Attractions Between Oppositely
`Charged Ions
`Hydrogen Bonds Determine Water Solubility
`of Uncharged Molecules
`Van der Waals Interactions Are Caused by Transient
`Dipoles
`The Hydrophobic Effect Causes Nonpolar
`Molecules to Adhere to One Another
`Molecular Complementarity Permits Tight, Highly
`Specific Binding of Biomolecules
`
`18
`19 Ill Chemical Building Blocks of Cells
`20
`
`Amino Acids Differing Only in Their Side
`Chains Compose Proteins
`Five Different Nucleotides Are Used to Build
`N ucleic Acids
`Monosaccharides Joined by Glycosidic Bonds
`Form Linear and Branched Polysaccharides
`
`21
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`21
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`22
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`23
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`24
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`40
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`41
`
`xv
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`

`

`xvi CONTENTS
`
`Fatty Acids Are Precursors for Many Cellular
`Lipids
`Phospholipids Associate N oncovalently to Form
`the Basic Bilayer Structure of Biomembranes
`
`DJ Chemical Equilibrium
`
`Equilibrium Constants Reflect the Extent of a
`Chemical Reaction
`Chemical Reactions in Cells Are at Stead y State
`Dissociation Consta nts for Binding Reactions Reflect
`the Affinity of Interacting Molecules
`Biological Fluids Have Characteristic pH Values
`H ydrogen Ions Are Released by Acids and Taken Up
`by Bases
`Buffers Maintain the pH of Intracellular
`and Extracellular Fluids
`
`lfll Biochemical Energetics
`
`Ill 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
`46 M any Proteins Undergo Chemical Modification
`of Amino Acid Residues
`46
`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
`
`43
`
`44
`
`46
`
`47
`47
`
`48
`
`48
`
`so m Enzymes and the Chemical Work
`
`,
`
`of Cells
`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
`V max and Km Characterize an Enzymatic Reaction
`Enzymes in a Common Pathway Are Often Physically
`Associated with One Another
`
`Several Forms of Energy Are Important
`50
`in Bio logical Systems
`Cells Can Transform One Type of Energy into Another 50
`The Change in Free Energy Determines
`the Direction of a Chemical Reaction
`The t!i.G 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
`H ydrolysis of ATP Releases Substantial Free Energy
`and Drives Many Cellular Processes
`ATP Is Generated During Photosynthesis
`and Respiration
`NAD + and FAD Coup le Many Biological Ox idation
`and Reduction Reactions
`
`51
`
`52
`
`54
`
`52
`52 DI Molecular Motors and the Mechanical
`Work of Cells
`53
`Molecular Motors Convert Energy into Motion
`All Myosins H ave Head, Neck, and Tail Domains
`with Distinct Functions
`Conformational Changes in the M yosin Head
`Couple ATP H ydrolysis to Movement
`
`3 1 Protein Structure and Function
`ID Hierarchical Structure of Proteins
`
`T he Primary Structure of a Protein ls Its Linear
`Arrangement of Amino Acids
`Secondar y 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 M acromolecular Assemblies
`Members of Protein Families H ave a Common
`Evolutionary Ancestor
`
`59
`60 Ill Common Mechanisms for Regulating
`Protein Function
`Cooperative Binding Increases a Protein's Response
`to Small Changes in Ligand Concentration
`Ligand Binding Can Induce Allosteric Release
`of Catalytic Subunits or Transition to a State
`with Different Activity
`Calcium and GTP Are Widely Used to Modulate
`Protein Activity
`Cyclic Protein Phosphorylation and Dephosphorylation
`Regulate Many Cellular Functions
`Proteolytic Cleavage Irreversibly Activates
`or Inactivates Some Proteins
`Higher-Order Regulation Includes Control of Protein
`Location and Concentration
`
`60
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`61
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`62
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`63
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`64
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`66
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`

`

`ID Purifying, Detecting, and Characterizing
`
`Proteins
`Centrifugation Can Separate Particles and Molecules
`That Differ in Mass or Density
`Electrophoresis Separates Molecules on the Basis
`of Their Charge: Mass Ratio
`Liquid Chromatography Resolves Proteins by Mass,
`Charge, or Binding Affinity
`Highly Specific Enzyme and Antibody Assays Can
`Detect Individual Proteins
`Radioisotopes Are Indispensable Tools for Detecting
`Biological Molecules
`Mass Spectrometry Measures the Mass of Proteins
`and Peptides
`Protein Primary Structure Can Be Determined
`by Chemical Methods and from Gene Sequences
`Peptides with a Defined Sequence Can Be
`Synthesized Chemically
`Protein Conforma tion Is Determined by Sophisticated
`Physical Methods
`
`86
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`86
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`87
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`90
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`92
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`93
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`94
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`95
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`95
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`95
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`41 Basic Molecular Genetic
`
`Mechanisms
`ID Structure of Nucleic Acids
`
`A Nucleic Acid Strand Is a Linear Polymer
`with End-to-End Directionality
`Native DNA Is a Double Helix of Complementary
`Antiparallel Strands
`DNA Can Undergo Reversible Strand Separation
`Many DNA Molecules Are Circular
`Different Types of RNA Exhibit Various
`Conformations Related to Their Functions
`
`101
`
`102
`
`103
`
`103
`105
`106
`
`107
`
`ID Transcription of Protein-Coding Genes
`and Formation of Functional mRNA
`A Template DNA Strand Is Transcribed into a
`Complementary RNA Chain by RNA Polymerase 109
`Organization of Genes Differs in Prokaryotic
`and Eukaryotic DNA
`Eukaryotic Precursor mRNAs Are Processed to Form
`Functional mRNAs
`Alternative RNA Splicing Increases the Number of
`Proteins Expressed from a Single Eukaryotic Gene 113
`
`111
`
`112
`
`108
`
`ID Control of Gene Expression
`in Prokaryotes
`Initiation of lac Operon Transcription Can Be
`Repressed and Activated
`
`115
`
`115
`
`Contents xvii
`
`Small Molecules Regulate Expression of Many Bacterial
`Genes via DNA-Binding Repressors
`116
`Transcription by cr54-RNA Polymerase Is Controlled
`by Activators That Bind Far from the Promoter
`Many Bacterial Responses Are Controlled
`by Two-Component Regulatory Systems
`
`116
`
`117
`
`Ill The Three Roles of RNA in Translation 119
`
`Messenger RNA Carries Information from DNA
`in a Three-Letter Genetic Code
`The Folded Structure of tRNA Promotes Its
`Decoding Functions
`,
`Nonstandard Base Pair ing Often Occurs Between
`Codons and Anticodons
`Aminoacyl-tRNA Synthetases Activate Amino Acids
`by Covalently Linking Them to tRNAs
`Ribosomes Are Protein-Synthesizing Machines
`
`119
`
`121
`
`122
`
`123
`123
`
`Ill Stepwise Synthesis of Proteins ,
`125
`on Ribosomes
`Methionyl-tRNAf"1e' Recognizes the AUG Start Codon 125
`Translation Initiation Usually Occurs Near the First
`AUG Closest to the 5' End of an mRNA
`During Chain Elongation Each Incoming Arninoacyl-
`tRNA Moves Through Three Ribosomal Sites
`Translation Is Terminated by Release Factors When
`a Stop Codon Is Reached
`Polysomes and Rapid Ribosome Recycling Increase
`the Efficiency of Translation
`
`127
`
`129
`
`130
`
`126
`
`Ill DNA Replication
`
`DNA Polymerases Require a Primer to Initiate
`Replication
`Duplex DNA Is Unwound, and Daughter Strands
`Are Formed at DNA Replication Fork
`Helicase, Primase, DNA Polymerases, and Other
`Proteins Participate in DNA Replication
`DNA Replication Generally Occurs Bidirectionally
`from Each Origin
`
`ID Viruses: Parasites of the Cellular
`Genetic System
`Most Viral Host Ranges Are Narrow
`Viral Capsids Are Regular Arrays of One or a Few
`Types of Protein
`Viruses Can Be Cloned and Counted
`in Plaque Assays
`Lytic Viral Growth Cycles Lead to Death
`of H ost Cells
`Viral DN A Is Integrated into Host-Cell Genome
`in Some Nonlytic Viral Growth Cycles
`
`131
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`132
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`133
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`

`xviii CONTENTS
`
`m Cell Organization and Biochemistry
`51 Biomembranes and Cell
`m Biomembranes: Lipid Composition
`
`Architecture
`
`147
`
`149
`and Structural Organization
`Three Classes of Lipids Are Found in Biomembranes 150
`Most Lipids and Many Proteins Are Laterally Mobile
`in Biomembranes
`Lipid Composition Influences the Physical Properties
`of Membranes
`Membrane Lipids Are Usually Distributed Unequally
`in the Exoplasmic and Cytosolic Leaflets
`Cholesterol and Sphingolipids Cluster with Specific
`Proteins in Membrane Microdomains
`
`152
`
`153
`
`155
`
`156
`
`DI Biomembranes: Protein Components
`and Basic Functions
`Proteins Interact with Membranes in Three
`Different Ways
`Membrane-Embedded a Helices Are the Primary
`Secondary Structures in Most Transmembrane
`Proteins
`Multiple 13 Strands in Porins Form Membrane(cid:173)
`Spanning "Barrels"
`Covalently Attached Hydrocarbon Chains Anchor
`Some Proteins to Membranes
`All Transmembrane Proteins and Glycolipids Are
`Asymmetrically Oriented in the Bilayer
`Interactions with the Cytoskeleton Impede
`the Mobility of Integral Membrane Proteins
`Lipid-Binding Motifs Help Target Peripheral Proteins
`to the Membrane
`The Plasma Membrane Has Many Common
`Functions in All Cells
`
`Ill Organelles of the Eukaryotic Cell
`
`Endosomes Take Up Soluble Macromolecules
`from the Cell Exterior
`Lysosomes Are Acidic Organelles That Contain
`a Battery of Degradative Enzymes
`Peroxisomes Degrade Fatty Acids and Toxic
`Compounds
`The Endoplasmic Reticulum Is a Network
`of Interconnected Internal Membranes
`The Golgi Complex Processes and Sorts Secreted
`and Membrane Proteins
`Plant Vacuoles Store Small Molecules and Enable
`a Cell to Elongate Rapidly
`
`157
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`157
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`158
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`160
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`160
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`161
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`162
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`162
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`164
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`165
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`165
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`165
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`168
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`168
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`169
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`170
`
`The Nucleus Contains the DNA Genome, RNA
`Synthetic Apparatus, and a Fibrous Matrix
`Mitochondria Are the Principal Sites of ATP
`Production in Aerobic Cells
`Chloroplasts Contain Internal Compartments
`in Which Photosynthesis Takes Place
`
`171
`
`171
`
`172
`
`Ill The Cytoskeleton: Components
`and Structural Functions
`Three Types of Filaments Compose the
`Cytoskeleton
`,
`Cytoskeletal Filaments Are Organized into Bundles
`and Networks
`Microfilaments and Membrane-Binding Proteins Form
`a Skeleton Underlying the Plasma Membrane
`Intermediate Filaments Support the Nuclear
`Membrane and Help Connect Cells into Tissues
`Microtubules Radiate from Centrosomes and
`Organize Certain Subcellular Structures
`
`173
`
`174
`
`176
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`176
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`177
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`177
`
`DI Purification of Cells and Their Parts
`
`Flow Cytometry Separates Different Cell Types
`Disruption of Cells Releases Their Organelles
`and Other Contents
`Centrifugation Can Separate Many Types
`of Organelles
`Organelle-Specific Antibodies Are Useful in Preparing
`Highly Purified Organelles
`Proteins Can Be Removed from Membranes by
`Detergents or High-Salt Solutions
`
`ID Visualizing Cell Architecture
`
`A Microscope Detects, Magnifies, and Resolves
`Small Objects
`Samples for Microscopy Must Be Fixed, Sectioned,
`and Stained to Image Subcellular Details
`Phase-Contrast and Differential Interference Contrast
`Microscopy Visualize Unstained Living Cells
`Fluorescence Microscopy Can Localize and Quantify
`Specific Molecules in Fixed and Live Cells
`Confocal Scanning and Deconvolution Microscopy
`Provide Sharp Images of Three-Dimensional
`Objects
`Resolution of Transmission Electron Microscopy Is
`Vastly Greater Than That of Light Microscopy
`Electron Microscopy of Metal-Coated Specimens
`Can Reveal Surface Features of Cells and Their
`Components
`Three-Dimensional Models Can Be Constructed from
`Microscopy Images
`
`178
`178
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`192
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`
`

`

`6 f Integrating Cells into Tissues
`m Cell-Cell and Cell-Matrix Adhesion:
`
`An Overview
`Cell-Adhesion Molecules Bind to One Another and
`to Intracellular Proteins
`The Extracellular Matrix Participates in Adhesion
`and Other Functions
`Diversity of Animal Tissues Depends on Evolution
`of Adhesion Molecules with Various Properties
`
`rlJI Sheetlike Epithelial Tissues: Junctions
`and Adhesion Molecules
`Specialized Junctions Help Define the Structure
`and Function of Epithelial Cells
`Ca2 + -Dependent Homophilic Cell-Cell Adhesion in
`Adherens Junctions and Desmosomes Is Mediated
`by Cadherins
`Tight Junctions Seal Off Body Cavities and Restrict
`Diffusion of Membrane Components
`Differences in Permeability of Tight Junctions
`Can Control Passage of Small Molecules
`Across Epithelia
`Many Cell-Matrix and Some Cell-Cell Interactions
`Are Mediated by Integrins
`
`Ill The Extracellular Matrix of Epithelial
`Sheets
`The Basal Lamina Provides a Foundation
`for Epithelial Sheets
`Sheet-Forming Type IV Collagen Is a Major
`Structural Component in Basal Laminae
`Laminin, a Multiadhesive Matrix Protein, Helps
`Cross-link Components of the Basal Lamina
`Secreted and Cell-Surface Proteoglycans Are
`Expressed by Many Cell Types
`Modifications in Glycosaminoglycan (GAG) Chains
`Can Determine Proteoglycan Functions
`
`199
`
`199
`
`201
`
`201
`
`201
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`202
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`204
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`206
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`208
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`212
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`213
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`215
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`216
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`217
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`217
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`218
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`219
`
`219
`
`Ill The Extracellular Matrix
`of Nonepithelial Tissues
`Fibrillar Collagens Are the Major Fibrous Proteins
`in the Extracellular Matrix of Connective Tissues
`Formation of Collagen Fibrils Begins in the
`Endoplasmic Reticulum and Is Completed Outside
`the Cell
`Type I and II Collagens Form Diverse Structures and
`Associate with Different Nonfibrillar Collagens
`Hyaluronan Resists Compression and Facilitates Cell
`Migration
`Association of Hyaluronan and Proteoglycans Forms
`Large, Complex Aggregates
`
`197
`
`Fibronectins Connect Many Cells to Fibrous
`Collagens and Other Matrix Components
`
`220
`
`Contents xix
`
`Bl Adhesive Interactions
`and Nonepithelial Cells
`Integrin-Containing Adhesive Structures Physically
`and Functionally Connect the ECM and
`Cytoskeleton in Nonepithelial Cells
`Diversity of Ligand-Integrin Interactions Contributes
`to Numerous Biological Processes
`Cell-Matrix Adhesion Is Modulated by Changes in
`the Binding Activity and Numbers of Integrins
`Molecular Connections between the ECM and the
`Cytoskeleton Are Defective in Muscular Dystrophy 226
`Ca2 + -Independent Cell-Cell Adhesion in Neuronal
`and Other Tissues Is Mediated by CAMs in the
`Immunoglobulin Superfamily
`Movement of Leukocytes into Tissues Depends on
`a Precise Sequence of Combinatorially Diverse
`Sets of Adhesive Interactions
`Gap Junctions Composed of Connexins Allow Small
`Molecules to Pass Between Adjacent Cells
`
`m Plant Tissues
`
`The Plant Cell WaH Is a Laminate of Cellulose Fibrils
`in a Matrix of Glycoproteins
`Loosening of the Cell Wall Permits Elongation
`of Plant Cells
`Plasmodesmata Directly Connect the Cytosols
`of Adjacent Cells in Higher Plants
`Only a Few Adhesive Molecules Have Been
`Identified in Plants
`
`IIJ Growth and Use of Cultured Cells
`
`223
`
`223
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`225
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`225
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`227
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`22 7
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`229
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`231
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`232
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`232
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`233
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`234
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`235
`
`Culture of Animal Cells Requires Nutrient-Rich
`Media and Special Solid Surfaces
`Primary Cell Cultures and Cell Strains Have a Finite
`236
`Life Span
`Transformed Cells Can Grow Indefinitely in Culture 236
`Hybrid Cells Called Hybridomas Produce Abundant
`Monoclonal Antibodies
`HAT Medium Is Commonly Used to Isolate Hybrid
`Cells
`
`237
`
`239
`
`235
`
`7 Transport of Ions and Small
`Molecules Across Cell
`Membranes
`
`m Overview of Membrane Transport
`
`Few Molecules Cross Membranes by Passive
`Diffusion
`
`245
`
`246
`
`246
`
`Exhibit 1043
`Select Sires, et al. v. ABS Global
`
`

`

`xx CONTENTS
`
`Membrane Proteins Mediate Transport of Most
`Molecules and All Ions Across Biomembranes
`Several Features Distinguish Uniport Transport from
`Passive Diffusion
`GLUTl Uniporter Transports Glucose into Most
`Mammalian Cells
`The Human Genome Encodes a Family of Sugar-
`Transporting GLUT Proteins
`Transport Proteins Can Be Enriched Within Artificial
`Membranes and Cells
`
`fll ATP-Powered Pumps and the
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`Na + -Linked Anti porter Exports Ca2+ from Cardiac
`Muscle Cells
`Several Cotransporters Regulate Cytosolic pH
`Numerous Transport Proteins Enable Plant Vacuoles
`to Accumulate Metabolites and Ions
`
`Ill Movement of Water
`
`Osmotic Pressure Causes Water to Move Across
`Membranes
`Different Cells Have Various Mechanisms for
`Controlling CeJI Volume
`Aquaporins Increase the Water Permeability of Cell
`Membranes
`
`252 ID Transepithelial Transport
`
`Intracellular Ionic Environment
`Different Classes of Pumps Exhibit Characteristic
`Structural and Functional Properties
`ATP-Driven Ion Pumps Generate and Maintain Ionic
`Gradients Across Cellular Membranes
`Muscle Ca2 + ATPase Pumps Ca2+ Ions from
`the Cytosol into the Sarcoplasmic Reticulum
`Calmodulin-Mediated Activation of Plasma-Membrane
`Ca2+ ATPase Leads ro Rapid Ca2+ Export
`Na+ /K+ ATPase Maintains the Intracellular Na +
`and K+ Concentrations in Animal Cells
`V-Class H + ATPases Pump Protons Across
`257 DJ Voltage-Gated Ion Channels and
`Lysosomal and Vacuolar Membranes
`Bacterial Permeases Are ABC Proteins That Import
`the Propagation of Action Potentials
`a Variety of Nutrients from the Environment
`in Nerve Cells
`About 50 ABC Small-Molecule Pumps Are Known
`in Mammals
`Specialized Regions of Neurons Carry Out Different
`Functions
`ABC Proteins That Transport Lipid-Soluble
`Substrates May Operate by a Flippase Mechanism 259 Magnitude of the Action Potential Is Close to ENa
`Ill Nongated Ion Channels and the
`Sequential Opening and Closing of Voltage-Gated
`Na + and K+ Channels Generate Action
`Potentials
`Action Potentials Are Propagated Unidirectionally
`Without Diminution
`Nerve Cells Can Conduct Many Action Potentials
`in the Absence of ATP
`All Voltage-Gated Ion Channels Have Similar
`Structures
`Voltage-Sensing S4 a. Helices Move in Response to
`Membrane Depolarization
`Movement of the Channel-Inactivating Segment
`into the Open-Pore Blocks Ion Flow
`Myelination Increases the Velocity of Impulse
`Conduction
`Action Potentials "Jump" from Node to ode in
`Myelinated Axons
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`253 Multiple Transport Proteins Are Needed to Move
`Glucose and Amino Acids Across Epithelia
`Simple Rehydration Therapy Depends on the
`Osmotic Gradient Created by Absorption of
`Glucose and Na+
`Parietal Cells Acidify the Stomach Contents While
`Maintaining a Neutral Cytosolic pH
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`Resting Membrane Potential
`Selective Movement of Ions Creates a
`Transmembrane Electric Potential Difference
`The Membrane Potential in Animal Cells Depends
`Largely on Resting K+ Channels
`Ion Channels Contain a Selectivity Filter Formed
`from Conserved Transmembrane a. Helices
`and P Segments
`Patch Clamps Permit Measurement of Ion
`Movements Through Single Channels
`Novel Ion Channels Can Be Characterized by
`a Combination of Oocyte Expression
`and Patch Clamping
`Na+ Entry into Mammalian Cells Has a Negative
`Change in Free Energy (~G)
`1,11 Cotransport by Symporters
`and Antiporters
`Na+ -Linked Symporters Import Amino Acids and
`Glucose into Animal Cells Against High
`Concentration Gradients
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`m Neurotransmitters and Receptor
`
`and Transport Proteins in Signal
`Transmission at Synapses
`Neurotransmitters Are Transported into Synaptic
`Vesicles by H + -Linked Anti port Proteins
`
`Exhibit 1043
`Select Sires, et al. v. ABS Global
`
`

`

`Influx of Ca2 + Through Voltage-Gated Ca2 +
`Channels Triggers Release of Neurotransmitters
`Signaling at Synapses Usually Is Terminated ~y
`Degradation or Reuptake of Neurotransmitters
`Opening of Acetylcholine-Gated Cation Channels
`Leads to Muscle Contraction
`All Five Subunits in the Nicotinic Acetylcholine
`Receptor Contribute to the Ion Channel
`Nerve Cells Make an All-or-None Decision
`to Generate an Action Potential
`The Nervous System Uses Signaling Circuits
`Composed of Multiple Neurons
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`81 Cellular Energetics
`Ill Oxidation of Glucose and Fatty Acids
`to CO2
`Cytosolic Enzymes Convert Glucose into Pyruvate
`in Glycolysis
`Anaerobic Metabolism of Each Glucose Molecule
`Yields Only Two ATP Molecules
`Mitochondria Possess Two Structurally
`and Functionally Distinct Membranes
`Acetyl CoA Derived from Pyruvate Is Oxidized
`to Yield CO2 and Reduced Coenzymes
`in Mitochondria
`Transporters in the Inner Mitochondrial
`Membrane Allow the Uptake of Electrons
`from Cytosolic NADH
`Mitochondrial Oxidation of Fatty Acids Is Coupled
`to ATP Formation
`Peroxisomal Oxidation of Fatty Acids Generates
`No ATP
`The Rate of Glucose Oxidation Is Adjusted to Meet
`the Cell's Need for ATP
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`Ill Electron Transport and Generation of
`the Proton-Motive Force
`The Proton-Motive Force in Mitochondria Is Due
`Largely to a Voltage Gradient Across the Inner
`Membrane
`Electron Transport in Mitochondria Is Coupled
`to Proton Translocation
`Electrons Flow from FADH2 and NADH to 0 2
`Through a Series of Four Multiprotein
`Complexes
`Reduction Potentials of Electron Carriers Favor
`Electron Flow from NADH to 0 2
`CoQ and Three Electron-Transport Complexes
`Pump Protons Out of the Mitochondrial Matrix
`The Q Cycle Increases the Number of Protons
`Translocated as Electrons Flow Through
`the CoQHi-Cytochrome c Reductase Complex
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`Contents xxi
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`Ill Harnessing the Proton-Motive Force
`for Energy-Requiring Processes
`Bacterial Plasma-Membrane Proteins Catalyze
`Electron Transport and Coupled ATP Synthesis
`ATP Synthase Comprises Two Multiprotein
`Complexes Termed F0 and F1
`Rotation of the F1 -y Subunit, Driven by Proton
`Movement Through F0 , Powers ATP Synthesis
`ATP-ADP Exchange Across the Inner Mitochondrial
`Membrane Is Powered by the Proton-Motive
`Force
`Rate of Mitochondrial Oxidation Normally Depends
`on ADP Levels
`Brown-Fat Mitochondria Contain an Uncoupler
`of Oxidative Phosphorylation
`
`Ill Photosynthetic Stages and
`Light-Absorbing Pigments
`Thylakoid Membranes Are the Sites
`of Photosynthesis in Plants
`Three of the Four Stages in Photosynthesis Occur
`Only During Illumination
`Each Photon of Light Has a Defined Amount
`of Energy
`Photosystems Comprise a Reaction Center and
`Associated Light-Harvesting Complexes
`Photoelectron Transport from Energized Reaction-
`Center Chlorophyll a Produces a Charge
`Separation
`Light-Harvesting Complexes Increase the Efficiency
`of Photosynthesis
`
`Ill Molecular Analysis of Photosystems
`
`The Single Photosystem of Purple Bacteria Generates
`a Proton-Motive Force but No 0 2
`Chloroplasts Contain Two Functionally and Spatially
`Distinct Photosystems
`Linear Electron Flow Through Both Plant
`Photosystems, PSII and PSI, Generates a
`Proton-Motive Force, 0 2 , and NADPH
`An Oxygen-Evolving Complex Is Located on the
`Luminal Surface of the PSII Reaction Center
`Cyclic Electron Flow Through PSI Generates a
`Proton-Motive Force but No NADPH or 0 2
`Relative Activity of Photosystems I and II Is
`Regulated
`
`Ill CO2 Metabolism During
`Photosynthesis
`CO2 Fixation Occurs in the Chloroplast Stroma
`Synthesis of Sucrose Incorporating Fixed CO2 Is
`Completed in the Cytosol
`Light and Rubisco Activase Stimulate CO2 Fixation
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`Exhibit 1043
`Select Sires, et al. v. ABS Global
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`

`

`xxii CONTENTS
`
`Photorespiration, Which Competes with
`Photosynthesis, Is Reduced in Plants That Fix
`CO2 by the C4 Pathway
`Sucrose Is Transported from Leaves Through
`the Phloem to All Plant Tissues
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`DII Genetics and Molecular Biology
`
`9 Molecular Genetic Techniques
`and Genomics
`DJ Genetic Analysis of Mutations to
`Identify and Study Genes
`Recessive and Dominant Mutant Alleles Generally
`Have Opposite Effects on Gene Function
`Segregation of Mutations in Breeding Experiments
`Reveals Their Dominance or Recessivity
`Conditional Mutations Can Be Used to Study
`Essential Genes in Yeast
`Recessive Lethal Mutations in Diploids Can Be
`Identified by Inbreeding and Maintained in
`Heterozygotes
`Complementation Tests Determine Whether
`Different Recessive Mutations Are in the Sarne
`Gene
`Double Mutants Are Useful in Assessing the Order
`in Which Proteins Function
`Genetic Suppression and Synthetic Lethality Can
`Reveal Interacting or Redundant Proteins
`
`DJI DNA Cloning by Recombinant DNA
`Methods
`Restriction Enzymes and DNA Ligases Allow
`Insertion of DNA Fragments into Cloning
`Vectors
`E. coli Plasmid Vectors Are Suitable
`for Cloning Isolated DNA Fragments
`Bacteriophage X. Vectors Permit Efficient
`Construction of Large DNA Libraries
`cDNAs Prepared by Reverse Transcription
`of Cellular mRNAs Can Be Cloned to Generate
`cDNA Libraries
`DNA Libraries Can Be Screened by Hybridization
`to an Oligonucleotide Probe
`Oligonucleotide Probes Are Designed Based
`on Partial Protein Sequences
`Yeast Genomic Libraries Can Be Constructed with
`Shuttle Vectors and Screened by Functional
`Complementation
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`DJ Characterizing and Using Cloned
`DNA Fragments
`Gel Electrophoresis Allows Separation of Vector
`DNA from Cloned Fragments
`Cloned DNA Molecules Are Sequenced Rapidly
`by the Dideoxy Chain-Termination Method
`The Polymerase Chain Reaction Amplifies a Specific
`DNA Sequence from a Complex Mixture
`Blotting Techniques Permit Detection of Specific
`DNA Fragments and mRNAs with DNA Probes
`E. coli Expression Systems Can Produce Large
`Quantities of Proteins' from Cloned Genes
`Plasmid Expression Vectors Can Be Designed for
`Use in Animal Cells
`
`Ill Genomics: Genome-wide Analysis
`of Gene Structure and Expression
`Stored Sequences Suggest Functions of Newly
`,
`Identified Genes and Proteins
`Comparison of Related Sequences from Different
`Species Can Give Clues to Evolutionary
`Relationships Among Proteins
`Genes Can Be Identified Within Genomic DNA
`Sequences
`The Size of an Organism's Genome Is Not Directly
`Related to Its Biological Complexity
`DNA Microarrays Can Be Used to Evaluate the
`Expression of Many Genes at One Time
`Cluster Analysis of Multiple Expression Experiments
`Identifies Co-regulated Genes
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`358 DI Inactivating the Function of Specific
`Genes in Eukaryotes
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`Normal Yeast Genes Can Be Replaced with Mutant
`Alleles by Homologous Recombination
`Transcription of Genes Ligated to a Regulated
`Promoter Can Be Controlled Experimentally
`Specific Genes Can Be Permanently Inactivated
`in the Germ Line of Mice
`Somatic Cell Recombination Can Inactivate Genes
`in Specific Tissues
`Dominant-Negative Alleles Can Functionally Inhibit
`Some Genes
`Double-Stranded RNA Molecules Can Interfere
`with Gene Function by Targeting mRNA
`for Destruction
`
`m Identifying and Locating Human
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`Disease Genes
`368 Many Inherited Diseases Show One of