Molecular Cell Biology 9th Edition by Harvey Lodish, Arnold Berk, Chris Kaiser, Monty Krieger, Anthony Bretscher, Hidde Ploegh, Kelsey ISBN‎ 1319208525 ‎ 978-1319208523

Chapter 1 Evolution: Molecules, Genes, Cells, and Organisms

1.1 The Molecules of Life

Proteins Give Cells Structure and Perform Most Cellular Tasks

Nucleic Acids Carry Coded Information for Making Proteins at the Right Time and Place

Phospholipids Are the Conserved Building Blocks of All Cellular Membranes

Quality Control of All Cellular Macromolecules Is Essential for Life

1.2 Prokaryotic Cell Structure and Function

Prokaryotes Comprise Two Kingdoms: Archaea and Eubacteria

Many Bacteria Including Escherichia coli Are Widely Used in Biological Research

1.3 Eukaryotic Cell Structure and Function

The Cytoskeleton Has Many Important Functions

The Nucleus Contains the DNA Genome, Apparatuses for Synthesis of DNA and RNA, and a Fibrous Matrix

The Endoplasmic Reticulum Is the Site of Synthesis of Most Membrane and Secreted Proteins as Well as Many Lipids

The Golgi Complex Sorts Secreted Proteins and Many Membrane Proteins to Their Final Destinations in the Cell

Endosomes Bring Proteins and Particles from the Outside into Cells

Lysosomes Are Cellular Recycling Centers

Plant Vacuoles Store Water, Ions, and Small-Molecule Nutrients Such as Sugars and Amino Acids

Peroxisomes and Plant Glyoxisomes Metabolize Fatty Acids and Other Small Molecules Without Producing ATP from ADP and Pi

Mitochondria Are the Principal Sites of ATP Production in Aerobic Cells

Chloroplasts Contain Internal Compartments in Which Photosynthesis Takes Place

Many Organelle-Like Structures Are Unbounded by a Membrane

All Eukaryotic Cells Use a Similar Cycle to Regulate Their Division

1.4 Unicellular Eukaryotic Organisms Widely Used in Cell Biology Research

Yeasts Are Used to Study Fundamental Aspects of Eukaryotic Cell Structure and Function

Mutations in Yeast Led to the Identification of Key Cell Cycle Proteins

Studies in the Alga Chlamydomonas reinhardtii Led to the Development of a Powerful Technique to Study Brain Function

The Parasite That Causes Malaria Has Novel Organelles That Allow It to Undergo a Remarkable Life Cycle

1.5 Metazoan Structure, Function, Evolution, and Differentiation

Multicellularity Requires Cell-Cell and Cell-Matrix Adhesions

Epithelia Originated Early in Evolution

Cells Are Organized into Tissues and Tissues into Organs

Genomics Has Revealed Important Aspects of Metazoan Evolution and Cell Function

Development Uses a Conserved Set of Master Transcription Factors and Involves Epigenetic Modifications to DNA and Its Associated Histone Proteins

1.6 Metazoan Organisms Widely Used in Cell Biology Research

Drosophila melanogaster and Caenorhabditis elegans Are Used to Identify Genes That Regulate Animal Development

Planaria Are Used to Study Stem Cells and Tissue Regeneration

Studies on Fish, Mice, and Other Vertebrate Organisms Inform the Study of Human Development and Disease

Human Genetic Diseases Elucidate Important Aspects of Cell Function

Unbiased Single Cell Sequencing Experiments Identify Altogether New Cell Types

The Following Chapters Present Many Experimental Techniques and Much Experimental Data That Explains How We Know What We Know About Cell Structure and Function

Chapter 2 Chemical Foundations

2.1 Covalent Bonds and Noncovalent Interactions

The Electronic Structure of an Atom Determines the Number and Geometry of the Covalent Bonds It Can Make

All Covalent Bonds Are Not Equal: Electrons May Be Shared Equally or Unequally in Covalent Bonds

Covalent Bonds Are Much Stronger and More Stable Than Noncovalent Interactions

Ionic Bonds Are Noncovalent Interactions Formed by the Electrostatic Attractions Between Oppositely Charged Ions

Hydrogen Bonds Are Noncovalent Interactions That Determine the Properties of Water and the Water Solubility of Uncharged Molecules

Van der Waals Interactions Are Weak Attractive Interactions Caused by Transient Dipoles

The Hydrophobic Effect Causes Nonpolar Molecules to Adhere to One Another

Molecular Complementarity Due to Noncovalent Interactions Leads to a Lock-and-Key Fit Between Biomolecules

2.2 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 Covalently Assemble into Linear and Branched Polysaccharides

Phospholipids Associate Noncovalently to Form the Basic Bilayer Structure of Biomembranes

2.3 Chemical Reactions and Chemical Equilibrium

A Chemical Reaction Is in Equilibrium When the Rates of the Forward and Reverse Reactions Are Equal

The Equilibrium Constant Reflects the Extent of a Chemical Reaction

Chemical Reactions in Cells Are at Steady State

Dissociation Constants of 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

2.4 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 If a Chemical Reaction Will Occur Spontaneously

The ΔG°′ of a Reaction Can Be Calculated from Its Keq

The Rate of a Reaction Depends on the Activation Energy Necessary to Energize the Reactants into a Transition State

Life Depends on the Coupling of Energetically Unfavorable Chemical Reactions with Energetically Favorable Ones

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

End of Chapter

Key Terms

Review the Concepts

Chapter 3 Protein Structure and Function

3.1 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

Structural Motifs Are Regular Combinations of Secondary Structures

Tertiary Structure Is the Overall Folding of a Polypeptide Chain

Different Ways of Depicting the Conformation of Proteins Convey Different Types of Information

Domains Are Modules of Tertiary Structure

Comparing Protein Sequences and Structures Provides Insight into Protein Function and Evolution

There Are Four Broad Structural Categories of Proteins

Multiple Polypeptides Assemble into Quaternary Structures, Supramolecular Complexes, and Biomolecular Condensates

3.2 Protein Folding

Planar Peptide Bonds Limit the Shapes into Which Proteins Can Fold

Protein Folding Is Promoted by Proline Isomerases

The Amino Acid Sequence of a Protein Determines How It Will Fold

Folding of Proteins In Vivo Is Promoted by Chaperones

Abnormally Folded Proteins Can Form Amyloids That Are Implicated in Diseases

3.3 Protein Binding and Enzyme Catalysis

Specific Binding of Ligands Underlies the Functions of Most Proteins

Enzymes Are Highly Efficient and Specific Catalysts

An Enzyme’s Active Site Binds Substrates and Carries Out Catalysis

Serine Proteases Demonstrate How an Enzyme’s Active Site Works

Enzymes in a Common Pathway Are Often Physically Associated with One Another

3.4 Regulating Protein Function

Regulated Synthesis and Degradation of Proteins Is a Fundamental Property of Cells

The Proteasome Is a Molecular Machine Used to Degrade Proteins

Ubiquitin Marks Cytosolic Proteins for Degradation in Proteasomes

Noncovalent Binding Permits Allosteric, or Cooperative, Regulation of Proteins

Noncovalent Binding of Calcium and GTP Are Widely Used as Allosteric Switches to Control Protein Activity

Covalent Modification of Proteins Can Regulate their Activities

Phosphorylation and Dephosphorylation Covalently Regulate Protein Activity

The Structure and Function of Protein Kinase A Is Typical of Many Kinases

Protein Kinase Activity Is Often Regulated by Phosphorylation of the Kinase

Ubiquitinylation and Deubiquitinylation Covalently Regulate Protein Activity

Proteolytic Cleavage Irreversibly Activates or Inactivates Some Proteins

Higher Order Regulation Includes Control of Protein Location

3.5 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-to-Mass Ratio

Liquid Chromatography Resolves Proteins by Mass, Charge, or Affinity

Highly Specific Enzyme and Antibody Assays Can Detect Individual Proteins

Radioisotopes Are Indispensable Tools for Detecting Biological Molecules

Mass Spectrometry Can Determine the Mass and Sequence of Proteins

Protein Primary Structure Can Be Determined by Chemical Methods and from Gene Sequences

Protein Conformation Is Determined by Sophisticated Physical Methods

3.6 Proteomics

Proteomics Is the Study of All or a Large Subset of Proteins in a Biological System

Advanced Techniques in Mass Spectrometry Are Critical to Proteomic Analysis

End of Chapter

Key Terms

Review the Concepts

Chapter 4 Culturing and Visualizing Cells

4.1 Growing and Studying Cells in Culture

Culture of Animal Cells Requires Nutrient-Rich Media and Special Solid Surfaces

Primary Cell Cultures and Cell Strains Have a Finite Life Span

Transformed Cells Can Grow Indefinitely in Culture

Flow Cytometry Separates Different Cell Types

Growth of Cells in Two-Dimensional and Three-Dimensional Culture Mimics the In Vivo Environment

Stem Cells Can Differentiate in Culture to Make Organoids

Hybridomas Produce Abundant Monoclonal Antibodies

A Wide Variety of Cell Biological Processes Can Be Studied with Cultured Cells

Drugs Are Commonly Used in Cell Biological Research

4.2 Light Microscopy: Exploring Cell Structure and Visualizing Proteins Within Cells

The Resolution of the Conventional Light Microscope Is About 0.2 μm

Phase-Contrast and Differential-Interference-Contrast Microscopy Visualize Unstained Live Cells

Imaging Subcellular Details Often Requires That Specimens Be Fixed, Sectioned, and Stained

Fluorescence Microscopy Can Localize and Quantify Specific Molecules in Live Cells

Intracellular Ion Concentrations Can Be Determined with Ion-Sensitive Fluorescent Dyes

Immunofluorescence Microscopy Can Detect Specific Proteins in Fixed Cells

Tagging with Fluorescent Proteins Allows the Visualization of Specific Proteins in Live Cells

Deconvolution and Confocal Microscopy Enhance Visualization of Three-Dimensional Fluorescent Objects

Two-Photon Excitation Microscopy Allows Imaging Deep into Tissue Samples

TIRF Microscopy Provides Exceptional Imaging in One Focal Plane

FRAP Reveals the Dynamics of Cellular Components

FRET Measures Distance Between Fluorochromes

Optogenetics Allows Light to Regulate Events in a Spatial and Temporal Manner

Point Source Fluorescent Objects Can Be Located at Nanometer Resolution

Super-Resolution Microscopy Can Localize Proteins to Nanometer Accuracy

Light-Sheet Microscopy Can Rapidly Image Cells in Living Tissue

4.3 Electron Microscopy: High-Resolution Imaging

Single Molecules or Structures Can Be Imaged Using a Negative Stain or Metal Shadowing

Cells and Tissues Are Cut into Thin Sections for Viewing by Electron Microscopy

Immunoelectron Microscopy Localizes Proteins at the Ultrastructural Level

Cryoelectron Microscopy Allows Visualization of Specimens Without Fixation or Staining

Scanning Electron Microscopy of Metal-Coated Specimens Reveals Surface Features

4.4 Isolation of Cell Organelles

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

Proteomics Reveals the Protein Composition of Organelles

End of Chapter

Key Terms

Review the Concepts

Chapter 5 Fundamental Molecular Genetic Mechanisms

5.1 The Double-Helical Structure of DNA

Native DNA Is a Double Helix of Complementary Antiparallel Strands

DNA Can Undergo Reversible Strand Separation

DNA Molecules Can Acquire Torsional Stress

5.2 DNA Replication

DNA Polymerases Require a Template and a Primer to Replicate DNA

Duplex DNA Is Unwound, and Daughter Strands Are Formed at the DNA Replication Fork

A DNA Replication Fork Advances by Cooperation of Multiple Proteins

DNA Replication Occurs Bidirectionally from Each Origin

5.3 DNA Repair and Recombination

Chemical and Radiation Damage to DNA Can Lead to Mutations

High-Fidelity DNA Excision-Repair Systems Recognize and Repair Damage

Base Excision Repairs T-G Mismatches and Damaged Bases

Mismatch Excision Repairs Other Mismatches and Small Insertions and Deletions

Nucleotide Excision Repairs Chemical Adducts That Distort Normal DNA Shape

Two Systems Use Recombination to Repair Double-Strand Breaks in DNA

Homologous Recombination Can Repair DNA Damage and Generate Genetic Diversity

5.4 Transcription of Protein-Coding Genes and Formation of mRNA

A Template DNA Strand Is Transcribed into a Complementary RNA Strand by RNA Polymerase

Eukaryotic Precursor mRNAs Are Processed to Form Functional mRNAs

Alternative RNA Splicing Increases the Number of Proteins That Can Be Expressed from a Single Eukaryotic Gene

5.5 The Decoding of mRNA by tRNAs

Messenger RNA Carries Information from DNA in a Three-Letter Genetic Code

The Folded Structure of tRNA Promotes Its Decoding Functions

Nonstandard Base Pairing Often Occurs Between Codons and Anticodons

Amino Acids Are Linked to Their Cognate tRNAs with Great Accuracy

5.6 Stepwise Synthesis of Proteins on Ribosomes

Ribosomes Are Protein-Synthesizing Machines

Methionyl-tRNAiMet Recognizes the AUG Start Codon

Eukaryotic Translation Initiation Usually Occurs at the First AUG Downstream from the 5′ End of an mRNA

During Chain Elongation Each Incoming Aminoacyl-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

GTPase-Superfamily Proteins Function in Several Quality-Control Steps of Translation

Nonsense Mutations Can Be Bypassed by Suppressing tRNA Mutations

5.7 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

Lytic Viral Growth Cycles Lead to Death of Host Cells

Viral DNA Is Integrated into the Host-Cell Genome in Some Nonlytic Viral Growth Cycles

End of Chapter

Key Terms

Review the Concepts

Chapter 6 Molecular Genetic Techniques

6.1 Using 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 Whether They Are Dominant or Recessive

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 Same Gene

Double Mutants Are Useful in Assessing the Order in Which Proteins Function

Genetic Suppression and Synthetic Lethality Can Reveal Interacting or Redundant Proteins

Global Analysis of Double Mutant Combinations Can Reveal Networks of Gene Functions

6.2 DNA Cloning and Characterization

Restriction Enzymes and DNA Ligases Allow Insertion of DNA Fragments into Cloning Vectors

Isolated DNA Fragments Can Be Cloned into E. coli Plasmid Vectors

Yeast Genomic Libraries Can Be Constructed with Shuttle Vectors and Screened by Functional Complementation

cDNA Libraries Represent the Sequences of Protein-Coding Genes

The Polymerase Chain Reaction Amplifies a Specific DNA Sequence from a Complex Mixture

Cloned DNA Molecules Can Be Sequenced Rapidly by Methods Based on PCR

6.3 Using Sequence Information to Identify Genes and Deduce Their Function

Most Genes Can Be Readily Identified Within Genomic DNA Sequences

Bioinformatic Principles Can Be Used to Deduce the Likely Functional Consequences of Mutations

The Function and Evolutionary Origins of Genes and Proteins Can Be Deduced from Their Sequence

Comparison of Related Sequences from Different Species Can Give Clues to Evolutionary Relationships Among Proteins

Biological Complexity of an Organism Is Not Directly Related to the Number of Protein-Coding Genes in the Genome

6.4 Locating and Identifying Genes That Specify Human Traits

Monogenic Diseases Show One of Three Patterns of Inheritance

DNA Polymorphisms Are Used as Markers for Linkage Mapping of Human Mutations

Human Linkage Studies Can Map Disease Genes with a Resolution of About 1 Mbp

Further Analysis Is Needed to Locate a Disease Gene in Cloned DNA

Most Inherited Diseases Result from Multiple Genetic Defects

Identifying Component Genetic Risk Factors of Complex Traits

Medically Important Genes Can Be Identified by Alleles That Protect Against Disease

Identification of Causative Mutations in Cancer Cells

6.5 Using Cloned DNA Fragments to Study Gene Expression

In Situ Hybridization Techniques Permit Detection of Specific mRNAs

DNA Microarrays Can Be Used to Evaluate the Expression of Many Genes at Once

Cluster Analysis of Multiple Expression Experiments Identifies Co-Regulated Genes

Sequencing of cDNAs Allows Analysis of Gene Expression in Individual Cells

E. coli Expression Systems Can Produce Large Quantities of Proteins from Cloned Genes

Plasmid Expression Vectors Can Be Designed for Use in Animal Cells

6.6 Altering the Function of Specific Genes by Design

Normal Yeast Genes Can Be Replaced with Mutant Alleles by Homologous Recombination

Engineered CRISPR Systems Allow Precise Genome Editing

Somatic Cell Recombination Can Inactivate Genes in Specific Tissues of Mice

RNA Interference Causes Gene Inactivation by Destroying the Corresponding mRNA

End of Chapter

Key Terms

Review the Concepts

Chapter 7 Genes, Chromatin, and Chromosomes

7.1 Eukaryotic Gene Structure and Organization

Most Genes of Multicellular Eukaryotes Contain Introns and Produce mRNAs Encoding Single Proteins

Simple and Complex Transcription Units Are Found in Eukaryotic Genomes

Protein-Coding Genes May Be Solitary or Belong to a Gene Family

Heavily Used Gene Products Are Encoded by Multiple Copies of Genes

Nonprotein-Coding Genes Encode Functional RNAs

7.2 Chromosomal Organization of Genes and Noncoding DNA

Genomes of Many Organisms Contain a Large Fraction of Noncoding DNA

Most Simple-Sequence DNAs Are Concentrated in Specific Chromosomal Locations

DNA Fingerprinting Depends on Differences in Length of Simple-Sequence DNAs

Unclassified Intergenic DNA Occupies a Significant Portion of the Genome

7.3 Transposable (Mobile) DNA Elements

Movement of Mobile Elements Involves a DNA or an RNA Intermediate

Most Mobile Elements in Bacteria Are DNA Transposons Known as Insertion Sequences

Eukaryotic DNA Transposons Move Using a Cut-and-Paste Process

LTR Retrotransposons Behave Like Intracellular Retroviruses

Non-LTR Retrotransposons Transpose by a Distinct Mechanism

Other Retroposed RNAs Are Found in Genomic DNA

Mobile DNA Elements Have Significantly Influenced Evolution

7.4 Structural Organization of Eukaryotic Chromatin and Chromosomes

Chromatin Structure

Chromatin Structure Is Conserved Among Eukaryotes

Chromatin Is a Disordered Chain of Nucleosomes Packed Together at Different Concentration Densities in the Nucleus

Modifications of Histone Tails Control Chromatin Condensation and Function

Additional Nonhistone Proteins Regulate Transcription and Replication

7.5 Morphology and Functional Elements of Eukaryotic Chromosomes

Chromosome Number, Size, and Shape at Metaphase Are Species-Specific

During Metaphase, Chromosomes Can Be Distinguished by Banding Patterns and Chromosome Painting

Chromosome Painting and DNA Sequencing Reveal the Evolution of Chromosomes

Interphase Polytene Chromosomes Arise by DNA Amplification

Three Functional Elements Are Required for Replication and Stable Inheritance of Chromosomes

Centromere Sequences Vary Greatly in Length and Complexity

Addition of Telomeric Sequences by Telomerase Prevents Shortening of Chromosomes

End of Chapter

Key Terms

Chapter 8 Transcriptional Control of Gene Expression

8.1 Overview of Eukaryotic Transcription

Regulatory Elements in Eukaryotic DNA Are Found Both Close to and Many Kilobases Away from Transcription Start Sites

Three Eukaryotic Nuclear RNA Polymerases Catalyze Formation of Different RNAs

The Clamp Domain Enables RNA Polymerase II to Transcribe Long Stretches of DNA

The Largest Subunit in RNA Polymerase II Has an Essential Carboxy-Terminal Repeat

8.2 RNA Polymerase II Promoters and General Transcription Factors

RNA Polymerase II Initiates Transcription at DNA Sequences Corresponding to the 5′ Cap of mRNAs

The TATA Box, Initiators, and CpG Islands Function as Promoters in Eukaryotic DNA

General Transcription Factors Position RNA Polymerase II at Transcription Start Sites and Assist in Initiation

Elongation Factors Regulate the Initial Stages of Transcription in the Promoter-Proximal Region

8.3 Regulatory Sequences for Protein-Coding Genes and the Proteins Through Which They Function

Promoter-Proximal Elements Help Regulate Eukaryotic Genes

Distant Enhancers Often Stimulate Transcription by RNA Polymerase II

Most Eukaryotic Genes Are Regulated by Multiple Transcription-Control Elements

DNase I Footprinting and EMSA Detect Protein-DNA Interactions

Activators Are Composed of Distinct Functional Domains

Repressors Are the Functional Converse of Activators

DNA-Binding Domains Can Be Classified into Numerous Structural Types

Structurally Diverse Activation and Repression Domains Regulate Transcription

Transcription Factor Interactions Increase Gene-Control Options

Multiprotein Complexes Form on Enhancers

8.4 Molecular Mechanisms of Transcription Repression and Activation

Formation of Heterochromatin Silences Gene Expression at Telomeres, near Centromeres, and in Other Regions

Repressors Can Direct Histone Deacetylation at Specific Genes

Activators Can Direct Histone Acetylation at Specific Genes

Chromatin-Remodeling Complexes Help Activate or Repress Transcription

Pioneer Transcription Factors Initiate the Process of Gene Activation During Cellular Differentiation

The Mediator Complex Forms a Molecular Bridge Between Activation Domains and Pol II

Transcriptional Condensates Greatly Increase the Rate of Transcription Initiation

Transcription Occurs in Bursts

8.5 Regulation of Transcription-Factor Activity

DNase I Hypersensitive Sites Reflect the Developmental History of Cellular Differentiation

Nuclear Receptors Are Regulated by Lipid-Soluble Hormones

All Nuclear Receptors Share a Common Domain Structure

Nuclear-Receptor Response Elements Contain Inverted or Direct Repeats

Hormone Binding to a Nuclear Receptor Regulates Its Activity as a Transcription Factor

Metazoans Regulate the RNA Polymerase II Transition from Initiation to Elongation

Termination of Transcription Is Also Regulated

8.6 Epigenetic Regulation of Transcription

DNA Methylation Regulates Transcription

Methylation of Specific Histone Lysines Is Linked to Epigenetic Mechanisms of Gene Repression

Epigenetic Control by Polycomb and Trithorax Complexes

Long Noncoding RNAs Direct Epigenetic Repression in Metazoans

8.7 Other Eukaryotic Transcription Systems

Transcription Initiation by Pol I and Pol III Is Analogous to That by Pol II

End of Chapter

Key Terms

Review the Concepts

Chapter 9 Post-Transcriptional Gene Control

9.1 Processing of Eukaryotic Pre-mRNA

The 5′ Cap Is Added to Nascent RNAs Shortly After Transcription Initiation

Chain Elongation by RNA Polymerase II Is Coupled to the Presence of RNA Processing Factors

A Diverse Set of Proteins with Conserved RNA-Binding Domains Associate with Pre-mRNAs

Splicing Occurs at Short, Conserved Sequences in Pre-mRNAs via Two Transesterification Reactions

During Splicing, snRNAs Base-Pair with Pre-mRNA to Select Splice Sites and Guide the Transesterification Reactions

Spliceosomes Catalyze Pre-mRNA Splicing

3′ Cleavage and Polyadenylation of Pre-mRNAs Are Tightly Coupled

9.2 Regulation of Pre-mRNA Processing

Additional Nuclear Proteins Contribute to Splice-Site Selection in the Long Pre-mRNAs of Humans and Other Vertebrates

Expression and Function of Related K+-Channel Protein Isoforms in Vertebrate Inner Ear Hair Cells

Regulation of RNA Splicing Through Splicing Enhancers and Silencers Controls Drosophila Sexual Differentiation

Splicing Repressors and Activators Control Splicing at Alternative Sites

Expression of Dscam Isoforms in Drosophila Retinal Neurons

Abnormal RNA Splicing and Disease

Self-Splicing Group II Introns Provide Clues to the Evolution of snRNAs

Nuclear Exonucleases and the Exosome Degrade RNA That Is Processed out of Pre-mRNAs

RNA Processing Solves the Problem of Pervasive Transcription of the Genome in Mammalian Cells

RNA Editing Alters the Sequences of Some Pre-mRNAs

9.3 Transport of mRNA Across the Nuclear Envelope

SR Proteins Mediate Nuclear Export of mRNA

Pre-mRNAs Associated with Spliceosomes Are Not Exported from the Nucleus

HIV Rev Protein Regulates the Transport of Unspliced Viral mRNAs

9.4 Cytoplasmic Mechanisms of Post-Transcriptional Control

The Concentration of an mRNA in the Cytoplasm Is Determined by Its Rate of Synthesis and Its Rate of Degradation

Degradation of mRNAs in the Cytoplasm Occurs by Several Mechanisms

MicroRNAs Repress Translation and Induce Degradation of Specific mRNAs

RNA Interference Induces Degradation of Precisely Complementary mRNAs

Cytoplasmic Polyadenylation Promotes Translation of Some mRNAs

Protein Synthesis Can Be Globally Regulated

Sequence-Specific RNA-Binding Proteins Control Specific mRNA Translation

Surveillance Mechanisms Prevent Translation of Improperly Processed mRNAs

Localization of mRNAs Permits Production of Proteins at Specific Regions Within the Cytoplasm

9.5 Processing of rRNA and tRNA

Pre-rRNA Genes Are Similar in All Eukaryotes and Function as Nucleolar Organizers

Small Nucleolar RNAs Assist in Processing Pre-rRNAs

Self-Splicing Group I Introns Were the First Examples of Catalytic RNA

Pre-tRNAs Undergo Extensive Modification in the Nucleus

9.6 Nuclear Bodies Are Functionally Specialized Nuclear Domains

Cajal Bodies

Nuclear Speckles

Nuclear Paraspeckles

Promyelocytic Leukemia (PML) Nuclear Bodies

Nucleolar Functions in Addition to Ribosomal Subunit Synthesis

End of Chapter

Key Terms

Review the Concepts

Chapter 10 Biomembrane Structure

10.1 The Lipid Bilayer: Composition and Structural Organization

Phospholipids Spontaneously Form Bilayers

Phospholipid Bilayers Form a Sealed Compartment Surrounding an Internal Aqueous Space

Biomembranes Contain Three Principal Classes of Lipids

Most Lipids and Many Proteins Are Laterally Mobile in Biomembranes

Lipid Composition Influences the Physical Properties of Membranes

Lipid Composition Is Different in the Exoplasmic and Cytosolic Leaflets

Cholesterol and Sphingolipids Cluster with Specific Proteins in Membrane Microdomains

Cells Store Excess Lipids in Lipid Droplets

10.2 Membrane Proteins: Structure and Basic Functions

Proteins Interact with Membranes in Three Different Ways

Most Transmembrane Proteins Have Membrane-Spanning α Helices

Multiple β Strands in Porins Form Membrane-Spanning “Barrels”

Covalently Attached Lipids Anchor Some Proteins to Membranes

All Transmembrane Proteins and Glycolipids Are Asymmetrically Oriented in the Bilayer

Lipid-Binding Motifs Help Target Peripheral Proteins to the Membrane

Proteins Can Be Removed from Membranes by Detergents or High-Salt Solutions

10.3 Phospholipids, Sphingolipids, and Cholesterol: Synthesis and Intracellular Movement

Fatty Acids Are Assembled from Two-Carbon Building Blocks by Several Important Enzymes

Small Cytosolic Proteins Facilitate Movement of Fatty Acids

Fatty Acids Are Incorporated into Phospholipids Primarily on the ER Membrane

Flippases Move Phospholipids from One Membrane Leaflet to the Opposite Leaflet

Cholesterol Is Synthesized by Enzymes in the Cytosol and ER Membrane

Cholesterol and Phospholipids Are Transported Between Organelles by Several Mechanisms

End of Chapter

Key Terms

Review the Concepts