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 THIRD EDITION

PRINCIPLES OF
Cell Biology

George Plopper, PhD

Senior Lead Associate/Regulatory Scientist
Booz Allen Hamilton
Rockville, MD

Diana Bebek Ivankovic, PhD

Director of the Center for Cancer Research
Anderson University
Anderson, SC

JONES & BARTLETT

LEARNING
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Copyright © 2021 by Jones & Bartlett Learning, LLC, an Ascend
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 To my family, colleagues, and former students for their
continued support and encouragement.
– Dr. George Plopper

To my husband, Miren, my parents Lori and Ante Bebek,

and our children, Sven, Andre, Nina, and Laura, who are
the source of my greatest inspiration and happiness.

– Dr. Diana Bebek Ivankovic

 Courtesy of Rhonda Reigers Powell.

Brief Contents
The Fourteen Principles of Cell Biology
Preface
Acknowledgments
About the Cover
About the Authors

Chapter 1 Life Is a Team Sport

Chapter 2 DNA Is the Instruction Book for Life
Chapter 3 Proteins Are the Engines of Evolution
Chapter 4 Membranes Are Complex Fluids That
Define Compartments
Chapter 5 The Cytoskeleton Forms the
Architectural Foundation for the
Structural Complexity of Life
Chapter 6 The Rise of Multicellularity
Chapter 7 The Nucleus Is the Brain of a Cell
Chapter 8 RNA Links the Information in DNA to
Actions Performed by Proteins
Chapter 9 The Endomembrane System Serves as
the Cellular Import/Export Machinery for
Most Macromolecules
Chapter 10 Chemical Bonds and Ion Gradients Are
Cellular Fuel
Chapter 11 Signaling Networks Are the Nervous
System of a Cell
Chapter 12 Protein Complexes Are Cellular
Decision-Making Devices
Chapter 13 Progression Through the Cell Cycle Is
the Most Vulnerable Period in a Cell’s
Life
Chapter 14 Human Activity Is Triggering a Paradigm
Shift in Evolution

Glossary
Answers
Index
 Courtesy of Rhonda Reigers Powell.

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
BOX 1-1 TIP
1.2 Life Can Arise from Simple Ingredients
Nonliving Substances Combine to Form Life
BOX 1-2 FAQ: Are Viruses Alive?
BOX 1-3 TIP: Make Judicious Use of the Internet
Membrane Formation Requires Water
BOX 1-4 TIP: Quick Review of Darwinian Evolution
Code Biology Helps Explain the Diversity of Life
BOX 1-5 TIP: The World of Codes
BOX 1-6 The “Cell as a Busy City” Analogy
BOX 1-7 FAQ: Are Biological Codes the Product of
“Intelligent Design”?
Evidence for the Possibility of Extraterrestrial Life
1.3 All Cells Are Built from the Same Common
Molecular Building Blocks
BOX 1-8 TIP: Overcoming the Jargon Barrier
BOX 1-9 FAQ: How Much Chemistry Do I Need to
Know to Understand the Subjects in this Book?
The Study of Cellular Chemistry Begins with an
Examination of the Carbon Atom
BOX 1-10 Silicon as a Potential Substitute for Carbon
in Living Organisms
Complex Biomolecules Are Mostly Composed of
Chemical Building Blocks Called Functional Groups
BOX 1-11 TIP: Understanding Molecular Structure
Diagrams
Lipids Are Carbon-Rich Polymers That Are Insoluble in
Water
Sugars Are Simple Carbohydrates
BOX 1-12 Case Study: Why Can Adult Humans Drink
Milk?
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
BOX 1-13 FAQ: Is Uncertainty in the Mechanism of
Evolution Evidence That it Is Not True?
Biofilms Support Prokaryotic and Eukaryotic Symbiosis
BOX 1-14 Artificial Eukaryote-like Cells on the Horizon
Macroorganismal Hosts Coevolve with Their
Microbiomes to Create New Holobionts
BOX 1-15 Applied Cell Biology: Healing the Human
Holobiont with Prokaryotic Transplantation
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
BOX 2-1 TIP
BOX 2-2 The Library of Congress Analogy, Part 1
A Cell’s DNA Is Inherited
DNA Must Be Read to Be Useful
BOX 2-3 The Library of Congress Analogy, Part 2
BOX 2-4 FAQ: Is Cancer Inherited or Not?
2.3 DNA Is Carefully Packaged into Five Levels of
Organization
DNA Is a Linear Polymer of Deoxyribonucleotides
BOX 2-5 The Library of Congress Analogy, Part 3
BOX 2-6 TIP: Structure Before Jargon
BOX 2-7 TIP
BOX 2-8 TIP
BOX 2-9 TIP
BOX 2-10 TIP
BOX 2-11 TIP: Chemistry Nomenclature
BOX 2-12 The Holiday Lights Analogy
BOX 2-13 DNA Sequencing Technologies
BOX 2-14 The Library of Congress Analogy, Part 4
 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
BOX 2-15 FAQ: What is the Difference Between a
Nucleosome and a Chromatosome?
Level 4: DNA Fibers Attach to a Protein-RNA Scaffold
Level 5: Chromatin Is Packaged into Highly Condensed
Chromosomes
BOX 2-16 Case Study: Duchenne Muscular Dystrophy
in a Female Patient
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
BOX 3-1 TIP
A Peptide Bond Joins Two Amino Acids Together
Definitions: Proteins versus Polypeptides versus
Peptides versus Subunits
BOX 3-2 TIP: Exploring Protein Nomenclature
BOX 3-3 FAQ: Why Are There so Many Different Ways
to Draw a Protein?
BOX 3-4 FAQ: How is Protein Binding Defined?
BOX 3-5 TIP: Anthropomorphism in Analogies
BOX 3-6 TIP: Understanding Protein Names
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
BOX 3-7 Many “Disordered” Random Coils in Proteins
Are Functional
Tertiary Structure Is Defined by the Arrangement of the
Secondary Structures in Three Dimensions
BOX 3-8 The Personal Trainer Analogy
BOX 3-9 TIP: Beware of Overinterpreting Definitions of
“Domain” in Protein Structure
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
BOX 3-10 The “Cell as a Busy City” Analogy, Revisited
All Proteins Adopt at Least Two Different Shapes
Cells Chemically Modify Proteins to Control Their Shape
and Function
BOX 3-11 TIP
BOX 3-12 TIP
Classification of Proteins
BOX 3-13 The Advent of -Omics in Biotechnology
BOX 3-14 The “Cell as a Busy City” Analogy,
Continued
BOX 3-15 Practical Protein Technology: The Home
Pregnancy Test
BOX 3-16 FAQ: What is the Function of Fluorescent
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
BOX 3-17 The Incinerator Analogy
Proteinases Digest Proteins in the Extracellular Space
BOX 3-18 FAQ: Do Proteins Evolve?
BOX 3-19 Case Study: Flu Vaccines and Antiviral Drug
Designs
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
BOX 4-1 TIP: Beware of Falling Into the Jargon Trap
BOX 4-2 TIP: Drawing Phospholipids
The Amphipathic Nature of Phospholipids Allows Them
to Form Lipid Bilayers in Aqueous Solution
BOX 4-3 The Soap Bubble Demonstration
Phospholipid Bilayers Are Semipermeable Barriers
4.3 The Fluid-Mosaic Model Explains How
Phospholipids and Proteins Interact Within a
Cellular Membrane
BOX 4-4 TIP
BOX 4-5 The Edible Membrane Exercise
BOX 4-6 The Pool Analogy
Membrane Proteins Associate with Membranes in Three
Different Ways
BOX 4-7 TIP
Cellular Membranes Are Both Fluid and Static
BOX 4-8 The Hearty Goldfish
BOX 4-9 The Dance Floor Analogy
4.4 Cellular Membranes Maintain Chemical
Disequilibrium Between Compartments
Protein Channels, Carriers, and Pumps Regulate the
Transport of Most Small Molecules Across
Membranes
BOX 4-10 The Folded Hands Analogy
BOX 4-11 More Name Games
BOX 4-12 FAQ: What is the Difference Between Active,
Passive, and Coupled Transporters?
BOX 4-13 Case Study: Maintaining a Balanced
Disequilibrium
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
BOX 4-14 FAQ: What Is a “Protein Family”?
BOX 4-15 Technology at Work: Artificial Membranes
BOX 4-16 TIP: Exploring Cell Membranes Online
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
BOX 5-1 The Steel Cable/Highrise Building Analogy
The Primary Building Block of Intermediate Filaments Is a
Filamentous Subunit
Intermediate Filament Subunits Form Coiled-Coil Dimers
BOX 5-2 TIP: Revisiting the Protein/Subunit Issue
Heterodimers Overlap to Form Filamentous Tetramers
BOX 5-3 The Tetris Analogy
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
BOX 5-4 The Highway Network Analogy
Microtubule Assembly Begins at a Microtubule-
Organizing Center
BOX 5-5 TIP: Centrosomes versus MTOCs
The Growth and Shrinkage of Microtubules Is Called
Dynamic Instability
BOX 5-6 The Fishing Analogy
BOX 5-7 Case Study: Microtubules are Therapeutic
Targets for Cancer Patients
Microtubule-Associated Proteins Regulate the Stability
and Function of Microtubules
BOX 5-8 TIP: Definitions of the Word Polarity
Cilia and Flagella Are Specialized Microtubule-Based
Structures Responsible for Motility in Some Cells
BOX 5-9 FAQ: Are Prokaryotic Cilia and Flagella the
Same as Those in Eukaryotes?
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
BOX 5-10 The Clasping Hands Analogy
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
BOX 5-11 Clarifying the “Foot” versus “Hand”
Comparisons
BOX 5-12 Applied Cell Biology: Blood Pressure
Medications
5.7 Eukaryotic Cytoskeletal Proteins Arose from
Prokaryotic Ancestors
BOX 5-13 Exploring the Cytoskeleton Online
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
BOX 6-1 The Assembly-Line Analogy
BOX 6-2 TIP
Proteoglycans Provide Hydration to Tissues
BOX 6-3 Applied Cell Biology: Engineered ECM
BOX 6-4 Cell Walls Are Evolutionary “Shields” Against
Environmental Threats
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
BOX 6-5 TIP
BOX 6-6 Case Study: Can Gene Therapy Cure
Epidermolysis Bullosa?
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
BOX 6-7 TIP
Calcium-Dependent Cadherins Mediate Adhesion
Between Cells
Calcium-Independent NCAMs Mediate Adhesion Between
Neural Cells
Selectins Control Adhesion of Circulating Immune Cells
BOX 6-8 The Kayak Analogy
6.5 Chapter Summary
BOX 6-9 Explore the ECM and Cell Junctions Online
Chapter Study Questions
Multiple-Choice Questions
References

Chapter 7 The Nucleus Is the Brain of a Cell

7.1 The Big Picture
BOX 7-1 Analogies of the Nucleus, Extended
7.2 The Nucleus Carefully Protects a Eukaryotic
Cell’s DNA
The Nuclear Envelope Is a Double-Membrane Structure
BOX 7-2 TIP: Lamins versus Laminins versus Lamina
Nuclear Pore Complexes Regulate Molecular Traffic into
and Out of the Nucleus
The Interior of the Nucleus Is Highly Organized and
Contains Many Subcompartments
BOX 7-3 Cell Biology Depends on Microscopy
BOX 7-4 TIP: More Subunit Issues
7.3 DNA Replication Is a Complex, Tightly Regulated
Process
DNA Polymerases Are Enzymes That Replicate DNA
BOX 7-5 TIP
DNA Replication Is Semidiscontinuous
BOX 7-6 FAQ: Is Animal Research Ethical?
BOX 7-7 The Library of Congress Analogy, Revisited
Cells Have Two Main DNA Repair Mechanisms
Excision Systems Remove One Strand of Damaged DNA
and Replace It
BOX 7-8 Case Study: Xeroderma Pigmentosum
7.4 Mitosis Separates Replicated Chromosomes
 Mitosis Is Divided into Stages
BOX 7-9 The Centromere
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
BOX 7-10 Explore More Online
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
BOX 8-1 TIP: Transcription versus Translation
RNA Polymerases Transcribe Genes in a “Bubble” of
Single-Stranded DNA
Transcription Occurs in Three Stages
BOX 8-2 TIP
BOX 8-3 The Rope Analogy
 In Eukaryotes, Messenger RNAs Undergo Processing
Prior to Leaving the Nucleus
BOX 8-4 Gene Splicing in Medicine
8.3 Proteins Are Synthesized by Ribosomes Using an
mRNA Template
Translation Occurs in Three Stages
BOX 8-5 A (True) Cell Biology Joke
BOX 8-6 Applied Cell Biology: Next-Generation
Sequencing and Pharmacogenomics
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
BOX 8-7 The “Cell As a Busy City” Analogy, Revisited
BOX 8-8 The Ticket Analogy
The Nuclear Import/Export System Regulates Traffic of
Macromolecules Through Nuclear Pores
BOX 8-9 Case Study: Nuclear Export as a Cancer
Therapy Target
Proteins Targeted to the Peroxisome Contain
Peroxisomal Targeting Signals (PTS)
BOX 8-10 TIP: Monoubiquitin versus Polyubiquitin
Secreted Proteins and Proteins Targeted to the
Endomembrane System Contain an Endoplasmic
Reticulum Signal Sequence
BOX 8-11 GTP is a Multipurpose Molecule
Integration of Transmembrane Proteins Requires Specific
Amino Acid Sequences
BOX 8-12 Explore More Online
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
BOX 9-1 The Balloon Analogy
BOX 9-2 The Car Engine Analogy
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
BOX 9-3 TIP
Digested Material Is Transported into the Cytosol
Lysosomes Can Also Degrade Some Resident Organelles
Peroxisomes Defy Classification
BOX 9-4 Applied Cell Biology: The Power of
Antibodies
BOX 9-5 Case Study: Orphan Diseases
BOX 9-6 Explore Further
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
BOX 10-1 TIP
10.2 Cells Store Energy in Many Forms
The Laws of Thermodynamics Define the Rules for
Energy Transfer
BOX 10-2 FAQ: What About Deep-Sea Vents?
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
BOX 10-3 TIP
Nucleotide Triphosphates Store Energy for Immediate
Use
Cells Couple Energetically Favorable and Unfavorable
Reactions
BOX 10-4 The Falling Water Analogy
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
BOX 10-5 TIP
BOX 10-6 TIP
BOX 10-7 Applied Cell Biology: Mobile Sensors of
Metabolic Function
BOX 10-8 Case Study: Manipulating the Mitochondrial
Genome
BOX 10-9 Explore Online
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
BOX 11-1 Analogies Galore
11.2 Signaling Molecules Form Communication
Networks
Signaling Networks Are Composed of Signals,
Receptors, Signaling Proteins, and Second
Messenger Molecules
BOX 11-2 FAQ: What’s the Difference Between a
Protein that Functions as a Signal and a
Signaling Protein?
BOX 11-3 Memorization Warning
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
BOX 11-4 FAQ: How Is the Phosphate Placed Back on
the GDP?
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
BOX 11-5 TIP
Protein Tyrosine Kinase Signaling Pathways Control
Cell Growth and Migration
BOX 11-6 TIP: Capitalization and Italicization of Names
in Signal Transduction
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
BOX 11-7 Applied Cell Biology: Studying Protein
Activity
BOX 11-8 Explore More Online
BOX 11-9 Case Study: Combating the Spread of
Cancer Cells via Signal Transduction
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
BOX 12-1 TIP
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
BOX 12-2 Case Study: Stem Cells and the Amazing
Regenerating Liver
BOX 12-3 Applied Cell Biology: Are Personalized
Tissue and Organ Implants in Our Future?
BOX 12-4 Explore More Online
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
BOX 13-1 FAQ: Haven’t Scientists Already Created
Artificial Life?
The Cell Cycle Is Divided into Five Phases
The G1/S Checkpoint Is the Point of No Return
BOX 13-2 TIP
The G2/M Checkpoint Is the Trigger for Large-Scale
Rearrangement of Cellular Architecture
BOX 13-3 TIP
Activation of Cyclin-CDK Complexes Begins in G1
Phase
BOX 13-4 TIP: Overcoming Complicated Signaling
Diagrams
DNA Replication Occurs in S Phase
G2 Phase Prepares Cells for Mitosis
Mitosis and Cytokinesis Occur in M Phase
BOX 13-5 TIP
13.3 Multicellular Organisms Contain a Cell Self-
Destruct Program That Keeps Them Healthy
Two Different Types of Cellular Death: Necrosis and
Apoptosis
BOX 13-6 FAQ: How is Apoptosis Pronounced in
English?
BOX 13-7 Case Study: Progeria
BOX 13-8 Applied Cell Biology: Flow Cytometry and
Cell Sorting
BOX 13-9 Explore More Online
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
BOX 14-1 Tip
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
BOX 14-2 Beating the Odds
BOX 14-3 TIP
BOX 14-4 Case Study: Brain Plasticity and
Schizencephaly
14.3 Gene Editing Is a Revolutionary Advance in
Artificial Selection
CRISPR/Cas9 Is a Promising, Efficient Additive to
Traditional Anti-HIV Treatments
BOX 14-5 Artificial Selection of Humans Raises
Serious Ethical Concerns
14.4 Gametogenesis, Fertilization, and
Embryogenesis Form a Complex Developmental
Program That Is Subject to Human Intervention
BOX 14-6 Medical Ethics Disclaimer
Meiosis Creates Gametes, Which Are the Two Essential
Precursors of a Diploid Life
BOX 14-7 TIP: Autosomes versus Sex Chromosomes
BOX 14-8 Artificial Selection at Work: Human Birth
Control
BOX 14-9 Applied Cell Biology: In Vitro Fertilization
Artificially Selects and Supports the Creation of
Life
14.5 Chapter Summary
Chapter Study Questions
Multiple-Choice Questions
References

Glossary
Answers
Index
 Courtesy of Rhonda Reigers Powell.

The Fourteen Principles of

Cell Biology
Principle 1. Life is a Team Sport
Principle 2. DNA is the Instruction Book for Life
Principle 3. Proteins are the Engines of Evolution
Principle 4. Membranes are Complex Fluids that Define
Compartments
Principle 5. The Cytoskeleton Forms the Architectural
Foundation for the Structural Complexity of Life
Principle 6. The Rise of Multicellularity Was a Watershed
Moment in Evolution
Principle 7. The Nucleus is the Brain of a Cell
Principle 8. RNA Links the Information in DNA to Actions
Performed by Proteins
Principle 9. The Endomembrane System Serves as the
Cellular Import/Export Machinery for Most
Macromolecules
Principle 10. Chemical Bonds and Ion Gradients are Cellular
Fuel
Principle 11. Signaling Networks are the Nervous System of
a Cell
Principle 12. Protein Complexes are Cellular Decision-
Making Devices
Principle 13. Progression through the Cell Cycle is the Most
Vulnerable Period in a Cell’s Life
Principle 14. Human Activity is Triggering a Paradigm Shift
in Evolution
Another random document with
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 “My other conditions are,” continued Fontrailles, “that you make
no complaint of my search this morning—that you tell his eminence,
should you chance to meet him, that by advising Monsieur De Pontis
to surrender a portion to me, who, you are aware, had, even before
the Spaniard’s death, asked the future droit of the cardinal, that you
secured thereby the remainder to your friend.”
“Well! I do not object to building a bridge for Monseigneur’s
retreat,” observed the advocate.
“It would be ridiculous toward one of your profession, and, above
all, age, to offer the satisfaction accorded to a gentleman who has
received violence at the hands of another,” said the count; “I,
therefore, beg pardon of Monsieur Giraud for the same.”
The advocate bowed. It were, perhaps, better, he said, to allow it
to pass thus, though the count must be aware that he had shown no
want of courage. Fontrailles assented, remarking that he believed
their business was now concluded—at least the preliminaries—and
that he would call on the advocate on the morrow, when he hoped
everything would be prepared.
Giraud was not sorry to see the exterior of the Hôtel De
Fontrailles. The count had, however, made better terms for himself
than he thought to have granted—still, it was true, as Fontrailles
remarked, that, whatever became of him, through the cardinal
listening to the tale of Pedro Olivera, De Pontis would be none the
richer. The pride of Richelieu was touched by the veteran obtaining
the sign-manual without his knowledge or intervention, and it was
very probable that, if Fontrailles were disgraced, the droit d’aubaine
would be destined to another favorite.
Giraud had foreseen this difficulty from the commencement, yet it
was hard to part with so many thousand livres, especially to one who
had almost choked him. On second consideration, the advocate
thought it wiser to withhold this portion of the adventure from De
Pontis and his daughter—the blood of the militaire would rise at the
insult and imposition of hands offered to a kinsman, and fresh
difficulties, perhaps, be thrown in the way of what was, after all, a
very peaceful and happy termination of the affairs of the old soldier.
The count had confessed the injury, and sued for pardon, and what
more could he do? With this consolation, the advocate quieted
himself.
The glad news was imparted to Marguerite that evening, and
when the houblieur rang his bell, and was admitted, the maiden was
more gracious than on the former occasion—the youth more
thoughtful. As might be expected, from the previous intimacy shown
relative to the secret affairs of the Palais Cardinal, its inmates and
visiters, much of what had occurred was already known to the youth
—the remainder he heard from the lips of Marguerite. She was
charged by Giraud to reclaim the packet; it would be wanted on the
morrow. That same night it was placed in her hands, the seal
unbroken, and, before she retired to rest, it was again in the keeping
of the zealous, faithful advocate.
Giraud was seated in his office. A night’s repose had calmed his
spirits, refreshed the wearied frame. Fontrailles had kept the
appointment, bringing an authenticated relinquishment of the suit of
Pedro Olivera—also a notification from the procureur général that he
had abandoned the prosecution of the decree of sequestration—and,
lastly, a duplicate of Richelieu’s order to the warden of the
Conciergerie to release the Sieur De Pontis. The count claimed and
received satisfaction on the conditions insisted on—reference to the
prisoner was not necessary, as Giraud had, on the committal of De
Pontis, received a legal power to act as representative, and affix by
procuration his signature to any act deemed necessary. As the
cardinal’s seal was removed from the ware-rooms, and attachment
withdrawn from the banker where the moneys of the deceased were
lodged, there was no impediment to the prompt payment of the
count’s subsidy—a matter, seemingly, of the utmost importance to
Monseigneur.
Giraud, as we have said, was seated in his office, and alone. But
presently there arrived visiters—the Sieur De Pontis, and the fair
heroine, Marguerite. Congratulations and thanks exhausted,
business recited and discussed, there ensued a pause—their hearts
were full.
“There are but three here,” said Giraud, looking archly at
Marguerite, “I should wish to see a fourth. There is a friend,
Monsieur De Pontis, who has wonderfully aided our endeavors for
your release, and to whom we owe many thanks. Shall we never see
the unknown’s face?”
“Marguerite has my sanction to introduce him to Monsieur Giraud
whenever she pleases,” said the veteran.
“Hah! then I have been forestalled in her confidence,” cried the
advocate, “but I did not deserve the neglect!”
The day subsequent to the liberation of De Pontis, Louis was
promenading alone his customary path in the garden of the Tuileries.
The old soldier presented himself—he bent his knee to majesty.
“Rise, my good friend,” said the monarch, “I hear you have been
better served than Louis could have wrought for you, though he had
not forgotten his word, or his old servant.”
After a few remarks, the king complimented him on the
perseverance and heroism of Marguerite adding that she was
deserving of all honor.
“With your majesty’s permission, I believe I am about to marry
her,” remarked De Pontis.
“To whom? I hope to a subject of mine!” exclaimed the monarch.
“François De Romainville, if it please your majesty,” replied the
veteran.
“I know the youth,” said Louis, “our cardinal’s page, of good
lineage, though accounted wild and reckless—the cardinal
complains of his habits, but loves the page’s intelligence and
capacity. We must see what can be done for this youth, also for
Monsieur Giraud when the opportunity offers.”
He might have added, “when the cardinal permits,” thought the
veteran, with a sigh.
“For yourself, De Pontis,” continued the royal personage, “I hope
all will go well in future.”
“I intend to put it out of fortune’s power to do me further harm,”
answered the militaire—“your majesty’s late bounty I shall settle on
my daughter and her husband; for, though I hope a true man in the
tented field, yet I do believe that, whether from my own fault, or an
unlucky destiny, I should lose, or mismanage the fairest estate in
your realm.”
At that moment, the cardinal and his suite were seen in the
distance—the countenance of Louis fell, and De Pontis taking hasty
leave—much to the royal satisfaction—glided through a side-walk.
 MY MOTHER—A DREAM.
———
BY MRS. BALMANNO.
———

Oh mother! sacred! dear! in dreams of thee,

I sat, again a child, beside thy knee,
Nestling amidst thy robe delightedly!
And all was silent in the sunny room,
Save bees that humm’d o’er honeysuckle bloom.

I gazed upon thy face, so mild, so fair,

I heard thy holy voice arise in prayer;
Oh mother! mother! thou thyself wert there!
Thou, by the placid brow, the thoughtful eye,
The clasping hand, the voice of melody.

I clung around thy neck—thy tears fell fast,

Like rain in summer, yet the sorrow past;
And smiles, more beautiful than e’en the last,
Play’d on thy lip, dear mother! such it wore
To bless our early home in days of yore.

Then wild and grand arose my native hills⁠—

I heard the leaping torrents, and the thrills
Of birds that hymn the sun; the charm that fills
Old Haddon’s vales, and haunts its river side⁠—
What time the Fays pluck king-cups by its tide.
Methought ’twas hawthorn time—the jolly May⁠—
For o’er far plains bright figures seemed to stray,
Gath’ring the buds, and calling me away!
I waked, but ah! to weep—no eye of thine,
Sweet mother! beam’d its gentle light on mine.
 BAINBRIDGE.
———
BY J. FENIMORE COOPER, AUTHOR OF “THE SPY,” “THE PIONEERS,” ETC.
———

Dr. Harris, in his “Life and Services” of this distinguished officer,

says that “The ancestor of Commodore Bainbridge, who, in the year
1600, settled in the province of New Jersey, was the son of Sir
Arthur Bainbridge, of Durham county, England.” As no portion of the
old United States was settled as early as 1600, and the province of
New Jersey, in particular, was organized only about the middle of the
seventeenth century, the date, in this instance, is an oversight, or a
misprint; though the account of the ancestor is probably accurate.
The family of the late Commodore Bainbridge was of respectable
standing, beyond a question, both in the colony and state of New
Jersey, and its connections were principally among persons of the
higher classes of society. His father was a physician of local
eminence, in the early part of his life, who removed to New York
about the commencement of the Revolution, where he left a fair
professional and personal reputation.
The fourth son of Dr. Bainbridge was William, the subject of our
memoir. He was born at Princeton, New Jersey, then the residence
of his father, May 7th, 1774. His birth must have occurred but a short
time before the removal of the family to New York. The maiden name
of Mrs. Bainbridge, the mother of William, was Taylor; a lady of
Monmouth county, in the same colony; and her father, a man of
considerable estate, undertook to superintend the education of the
child.
Young Bainbridge was of an athletic manly frame, and early
showed a bold spirit, and a love of enterprise. This temperament was
likely to interfere with studies directed toward a liberal education,
and, at the early age of fifteen, his importunities prevailed on his
friends to allow him to go to sea. This must have been about the time
when the present form of government went first into operation, and
the trade and navigation of the country began to revive. In that day
the republic had no marine; the old Alliance frigate, the favorite ship
of the Revolution, then sailing out of the port at which young
Bainbridge first embarked, as an Indiaman.
Philadelphia, for many years after the peace of 1783, produced
the best seamen of America. Other ports, doubtless, had as hardy
and as adventurous mariners, but the nicety of the art was better
taught and practiced on the Delaware than in any other portion of the
country. This advantage was thought to be owing to the length of the
river and bay, which required more elaborate evolutions to take a
ship successfully through, than ports that lay contiguous to the sea.
The same superiority has long been claimed for London, and for the
same reason, each place having a long and intricate navigation,
among shoals, and in a tide’s way, before its wharves can be
reached. The comparative decline of the navigation of these two
towns is to be attributed to the very difficulties which made expert
seamen, though the vast amount of supplies required by the English
capital, for its own consumption, causes great bodies of shipping still
to frequent the Thames. It is also probable that the superiority
formerly claimed for the seamen of these two towns, was in part
owing to the circumstances that, being the capitals of their respective
countries, they were then in advance of other ports, both as to the
arts, generally, and as to the wealth necessary to exhibit them.
Young Bainbridge, consequently, enjoyed the advantage of being
trained, as a seaman, in what was then the highest American school.
Singularly handsome and prepossessing in his appearance, of a
vigorous, and commanding frame, with the foundation of a good
education, all aided by respectable connections, he was made an
officer in the third year of his service. When eighteen, he sailed as
chief mate of a ship in the Dutch trade, and on his first voyage, in
this capacity, he recovered the vessel from the hands of mutineers,
by his personal intrepidity, and physical activity. In the following year,
when barely nineteen, the owners gave him command of the same
ship. From this time down to the period of his joining the navy,
Bainbridge continued in command of different merchant vessels, all
of which were employed in the European trade, which was then
carried on, by this country, in the height and excitement of the war
that succeeded the French revolution.
Occasions were not wanting, by which Bainbridge could prove his
dauntless resolution, even in command of a peaceful and slightly
armed merchantman. In 1796, whilst in command of the Hope, of
Philadelphia, he was lying in the Garonne, and was hailed by
another American to come and aid in quelling a mutiny. This he did
in person; though his life had nearly been the sacrifice, owing to an
explosion of gunpowder. The same season, while shaping his course
for one of the West India islands, the Hope was attacked by a small
British privateer, of eight guns and thirty men, being herself armed
with four nines, and having a crew of only eleven souls before the
mast—an equipment then permitted, by the laws, for the purposes of
defence only. The privateer commenced the engagement without
showing any colors; but, receiving a broadside from the Hope, she
hoisted English, in the expectation of intimidating her antagonist. In
this, however, the assailant was mistaken; Bainbridge, who had his
colors flying from the first, continued his fire until he actually
compelled the privateer to lower her flag. The latter was much cut
up, and lost several men. The Hope escaped with but little injury.
Although he had compelled his assailant to submit, it would not have
been legal for Bainbridge to take possession of the prize. He even
declined boarding her, most probably keeping in view the feebleness
of his own complement; but, hailing the privateer, he told her
commander to go to his employers and let them know they must
send some one else to capture the Hope if they had occasion for that
ship. It was probably owing to this little affair, as well as to his
general standing as a ship-master, that Bainbridge subsequently
entered the navy with the rank he obtained.
Not long after the action with the privateer, while homeward
bound again, a man was impressed from Bainbridge’s ship, by an
English cruiser. The boarding officer commenced by taking the first
mate, on account of his name, Allen M’Kinsey, insisting that the man
must be a Scotchman! This singular species of logic was often
applied on such occasions, even historians of a later day claiming
such men as M’Donough and Conner, on the supposition that they
must be Irish, from their family appellations. Mr. M’Kinsey, who was a
native Philadelphian, on a hint from Bainbridge, armed himself, and
refused to quit his own ship; whereupon the English lieutenant
seized a foremast hand and bore him off, in spite of his protestations
of being an American, and the evidence of his commander.
Bainbridge was indignant at this outrage—then, however, of almost
daily occurrence on the high seas—and, finding his own
remonstrances disregarded, he solemnly assured the boarding
officer that, if he fell in with an English vessel, of a force that would
allow of such a retaliation, he would take a man out of her to supply
the place of the seaman who was then carried away. This threat was
treated with contempt, but it was put in execution within a week;
Bainbridge actually seizing a man on board an English merchant-
man, and that, too, of a force quite equal to his own, and carrying
him into an American port. The ship which impressed the man
belonging to the Hope, was the Indefatigable, Sir Edward Pellew.
All these little affairs contributed to give Bainbridge a merited
reputation for spirit; for, however illegal may have been his course in
impressing the Englishman, the sailor himself was quite content to
receive higher wages, and there was a natural justice in the measure
that looked down the policy of nations and the provisions of law.
Shortly after this incident the aggressions of France induced the
establishment of the present navy, and the government, after
employing all the old officers of the Revolution who remained, and
who were fit for service, was compelled to go into the mercantile
marine to find men to fill the subordinate grades. The merchant
service of America has ever been relatively much superior to that of
most other countries. This has been owing, in part, to the greater
diffusion of education; in part, to the character of the institutions,
which throws no discredit around any reputable pursuit; and in part,
to the circumstance that the military marine has not been large
enough to give employment to all of the maritime enterprise and
spirit of the nation. Owing to these united causes, the government of
1798 had much less difficulty in finding proper persons to put into its
infant navy, than might have been anticipated; although it must be
allowed that some of the selections, as usual, betrayed the influence
of undue recommendations, as well as of too partial friendships.
 The navy offering a field exactly suited to the ambition and
character of Bainbridge, he eagerly sought service in it, on his return
from a voyage to Europe; his arrival occurring a short time after the
first appointments had been made. The third vessel which got to sea,
under the new armament, was the Delaware 20, Capt. Stephen
Decatur, the father of the illustrious officer of the same name; and
this vessel, a few days out, had captured Le Croyable 14, a French
privateer that she found cruising in the American waters. Le
Croyable was condemned, and purchased by the navy department;
being immediately equipped for a cruiser, under the name of the
Retaliation. To this vessel Bainbridge was appointed, with the
commission of lieutenant commandant; a rank that was
subsequently and unwisely dropped; as the greater the number of
gradations in a military service, while they are kept within the limits of
practical necessity, the greater is the incentive for exertion, the more
frequent the promotions, and the higher the discipline. First
lieutenants, lieutenants commandant, exist, and must exist in fact, in
every marine; and it is throwing away the honorable inducement of
promotion, as well as some of the influence of a commission, not to
have the rank while we have the duties. It would be better for the
navy did the station of first lieutenant, or lieutenant commandant,
now exist, those who held the commissions furnishing officers to
command the smallest class of vessels, and the executive officers of
ships of the line and frigates.
The Retaliation sailed for the West India station, in September,
1798. While cruising off Guadaloupe, the following November, the
Montezuma, sloop of war, Capt. Murray, and the brig Norfolk, Capt.
Williams, in company, three sail were made in the eastern board,
that were supposed to be English; and two more strangers
appearing to the westward, Capt. Murray, who was the senior officer,
made sail for the latter, taking the Norfolk with him; while the
Retaliation was directed to examine the vessels to the eastward.
This separated the consorts, which parted on nearly opposite tacks.
Unfortunately two of the vessels to the eastward proved to be French
frigates, le Volontier 36, Capt. St. Laurent, and l’Insurgente 32, Capt.
Barreault. The first of these ships carried 44 guns, French eighteens,
and the latter 40, French twelves. L’Insurgente was one of the fastest
ships that floated, and, getting the Retaliation under her guns,
Bainbridge was compelled to strike, as resistance would have been
madness.
The prisoner was taken on board le Volontier, the two frigates
immediately making sail in chase of the Montezuma and Norfolk.
L’Insurgente again out-stripped her consort, and was soon a long
distance ahead of her. Capt. St. Laurent was the senior officer, and,
the Montezuma being a ship of some size, he felt an uneasiness at
permitting the Insurgente to engage two adversaries, of whose force
he was ignorant, unsupported. In this uncertainty, he determined to
inquire the force of the American vessels of his prisoner. Bainbridge
answered coolly that the ship was a vessel of 28 long twelves, and
the brig a vessel of 20 long nines. This was nearly, if not quite,
doubling the force of the two American cruisers, and it induced the
French commodore to show a signal of recall to his consort. Capt.
Barreault, an exceedingly spirited officer, joined his commander in a
very ill humor, informing his superior that he was on the point of
capturing both the chases, when he was so inopportunely recalled.
This induced an explanation, when the ruse practiced by Bainbridge
was exposed. In the moment of disappointment, the French officers
felt much irritated, but, appreciating the conduct of their prisoner
more justly, they soon recovered their good humor, and manifested
no further displeasure.
The Retaliation and her crew were carried into Basseterre. On
board the Volontier was Gen. Desfourneaux, who was sent out to
supersede Victor Hughes in his government. This functionary was
very diplomatic, and he entered into a negotiation with Bainbridge of
a somewhat equivocal character, leaving it a matter of doubt whether
an exchange of prisoners, an arrangement of the main difficulties
between the two countries, or a secret trade with his own island, and
for his own particular benefit, was his real object. Ill treatment to the
crew of the Retaliation followed; whether by accident or design is not
known; though the latter has been suspected. It will be remembered
that no war had been declared by either country, and that the
captures by the Americans were purely retaliatory, and made in self-
defence. Gen. Desfourneaux profited by this circumstance to effect
his purposes, affecting not to consider the officers and people of the
Retaliation as prisoners at all. To this Bainbridge answered that he
regarded himself, and his late crew, not only as prisoners of war, but
as ill-treated prisoners, and that his powers now extended no farther
than to treat of an exchange. After a protracted negotiation,
Bainbridge and his crew were placed in possession of the Retaliation
again, all the other American prisoners in Guadaloupe were put on
board a cartel, and the two vessels were ordered for America.
Accompanying the Americans, went a French gentleman, ostensibly
charged with the exchange; but who was believed to have been a
secret diplomatic agent of the French government.
The conduct of Bainbridge, throughout this rude initiation into the
public service, was approved by the government, and he was
immediately promoted to the rank of master commandant, and given
the Norfolk 18, the brig he had saved from capture by his address. In
this vessel he joined the squadron under Com. Truxtun, who was
cruising in the vicinity of St. Kitts. While on that station, the Norfolk
fell in with and chased a heavy three-masted schooner, of which she
was on the point of getting alongside, when both topmasts were lost
by carrying sail, and the enemy escaped. The brig went into St. Kitts
to repair damages, and here she collected a convoy of more than a
hundred sail, bound home. Bainbridge performed a neat and delicate
evolution, while in charge of this large trust. The convoy fell in with
an enemy’s frigate, when a signal was thrown out for the vessels to
disperse. The Norfolk occupied the frigate, and induced her to
chase, taking care to lead her off from the merchantmen. That night
the brig gave her enemy the slip, and made sail on her course,
overtaking and collecting the whole fleet the following day. It is said
not a single vessel, out of one hundred and nineteen sail, failed of
the rendezvous!
It was August, 1799, before the Norfolk returned to New York.
Here Bainbridge found that no less than five lieutenants had been
made captains, passing the grades of commanders and lieutenants
commandant altogether. This irregularity could only have occurred in
an infant service, though it was of material importance to a young
officer in after life. Among the gentlemen thus promoted, were Capts.
Rodgers, and Barron, two names that, for a long time, alone stood
between Bainbridge and the head of the service. Still, it is by no
means certain that injustice was done, such circumstances
frequently occurring in so young a service, to repair an original
wrong. At all events, no slight was intended to Bainbridge, or any
other officer who was passed; though the former ever maintained
that he had not his proper rank in the navy.
After refitting the Norfolk, Bainbridge returned to the West Indies,
where he was put under the orders of Capt. Christopher R. Perry, the
father of the celebrated Commodore Oliver H. Perry, who sent him to
cruise off Cape François. The brig changed her cruising ground,
under different orders, no opportunity occurring for meeting an
enemy of equal force. Indeed, it was highly creditable to the maritime
enterprise of the French that they appeared at all in those seas,
which were swarming with English and American cruisers; this
country alone seldom employing fewer than thirty sail in the West
Indies, that year; toward the close of the season it had near, if not
quite forty, including those who were passing between the islands
and the home coast.
On the 31st October, however, the Norfolk succeeded in
decoying an armed barge within reach of her guns. The enemy
discovered the brig’s character in time to escape to the shore,
notwithstanding; though he was pursued and the barge was
captured. Six dead and dying were found in, or near the boat.
In November, Bainbridge took a small lugger privateer, called Le
Républicain, with a prize in company. The former was destroyed at
sea, and the latter sent in. The prize of the lugger was a sloop. She
presented a horrible spectacle when taken possession of by the
Americans. Her decks were strewed with mangled bodies, the
husbands and parents of eleven women and children, who were
found weeping over them at the moment of recapture. The murders
had been committed by some brigands in a barge, who slew every
man in the sloop, and were proceeding to further outrages when the
lugger closed and drove them from their prey. An hour or two later,
Bainbridge captured both the vessels. His treatment of the
unfortunate females and children was such as ever marked his
generous and manly character.
 Shortly after, Capt. Bainbridge received an order, direct from the
Navy Department, to go off the neutral port of the Havana, to look
after the trade in that quarter. Here he was joined by the Warren 18,
Capt. Newman, and the Pinckney 18, Capt. Heyward. Bainbridge
was the senior officer, and continued to command this force to the
great advantage of American commerce, by blockading the enemy’s
privateers, and giving convoy, until March, 1800, when, his cruise
being up, he returned home, anchoring off Philadelphia early in the
month of April. His services, especially those before Havana, were
fully appreciated, and May 2d, of the same year, he was raised to the
rank of captain. Bainbridge had served with credit, and had now
reached the highest grade which existed in the navy, when he
wanted just five days of being twenty-six years old. He had carried
with him into the marine the ideas of a high-class Philadelphia
seaman, as to discipline, and these were doubtless the best which
then existed in the country. In every situation he had conducted
himself well, and the promise of his early career as a master of a
merchantman was likely to be redeemed, whenever occasion should
offer, under the pennant of the republic.
Among the vessels purchased into the service during the war of
1798, was an Indiaman called the George Washington. This ship
was an example of the irregularity in rating which prevailed at that
day; being set down in all the lists and registers of the period as a
24, when her tonnage was 624; while the Adams, John Adams, and
Boston, all near one sixth smaller, are rated as 32s. The George
Washington was, in effect, a large 28, carrying the complement and
armament of a vessel of that class. To this ship Bainbridge was now
appointed, receiving his orders the month he was promoted; or, in
May, 1800. The destination of the vessel was to carry tribute to the
Dey of Algiers! This was a galling service to a man of her
commander’s temperament, as, indeed, it would have proved to
nearly every other officer in the navy; but it put the ship quite as
much in the way of meeting with an enemy as if she had been sent
into the West Indies; and it was sending the pennant into the
Mediterranean for the first time since the formation of the new navy.
Thus the United States 44, first carried the pennant to Europe, in
1799; the Essex 32, first carried it round the Cape of Good Hope, in
1800, and around Cape Horn, in 1813; and this ship, the George
Washington 28, first carried it into the classical seas of the old world.
Bainbridge did not get the tribute collected and reach his port of
destination, before the month of September. Being entirely without
suspicion, and imagining that he came on an errand which should
entitle him, at least, to kind treatment, he carried the ship into the
mole, for the purpose of discharging with convenience. This duty,
however, was hardly performed, when the Dey proposed a service
for the George Washington, that was as novel in itself as it was
astounding to her commander.
It seems that this barbarian prince had got himself into discredit
at the Sublime Porte, and he felt the necessity of purchasing favor,
and of making his peace, by means of a tribute of his own. The
Grand Seignor was at war with France, and the Dey, his tributary
and dependant, had been guilty of the singular indiscretion of making
a separate treaty of peace with that powerful republic, for some
private object of his own. This was an offence to be expiated only by
a timely offering of certain slaves, various wild beasts, and a round
sum in gold. The presents to be sent were valued at more than half a
million of our money, and the passengers to be conveyed amounted
to between two and three hundred. As the Dey happened to have no
vessel fit for such a service, and the George Washington lay very
conveniently within his mole, and had just been engaged in this very
duty, he came to the natural conclusion she would answer his
purpose.
The application was first made in the form of a civil request,
through the consul. Bainbridge procured an audience, and
respectfully, but distinctly, stated that a compliance would be such a
departure from his orders as to put it out of the question. Hereupon
the Dey reminded the American that the ship was in his power, and
that what he now asked, he might take without asking, if it suited his
royal pleasure. A protracted and spirited discussion, in which the
consul joined, now followed, but all without effect. The Dey offered
the alternatives of compliance, or slavery and capture, for the frigate
and her crew, with war on the American trade. One of his arguments
is worthy of being recorded, as it fully exposes the feeble policy of
submission to any national wrong. He told the two American
functionaries, that their country paid him tribute, already, which was
an admission of their inferiority, as well as of their duty to obey him;
and he chose to order this particular piece of service, in addition to
the presents which he had just received.
Bainbridge finally consented to do as desired. He appears to
have been influenced in this decision, by the reasoning of Mr.
O’Brien, the consul, who had himself been a slave in Algiers, not
long before, and probably retained a lively impression of the power
of the barbarian, on his own shores. It is not to be concealed,
however, that temporizing in all such matters, had been the policy of
America, and it would have required men of extraordinary moral
courage to have opposed the wishes of the Dey, by a stern assertion
of those principles, which alone can render a nation great. “To ask
for nothing but what is right, and to submit to nothing that is wrong,”
is an axiom more easily maintained on paper than in practice, where
the chameleon-like policy of trade interferes to color principles; and
O’Brien, a merchant in effect, and Bainbridge, who had so lately
been in that pursuit himself, were not likely to overlook the besetting
weakness of the nation. Still, it may be questioned if there was a
man in the navy who felt a stronger desire to vindicate the true
maxims of national independence than the subject of this memoir.
He appears to have yielded solely to the arguments of the consul,
and to his apprehensions for a trade that certainly had no other
protection in that distant sea, than his own ship; and she would be
the first sacrifice of the Dey’s resentment. It ought to be mentioned,
too, that a base and selfish policy prevailed, in that day, on the
subject of the Barbary Powers, among the principal maritime states
of Europe. England, in particular, was supposed to wink at their
irregularities, in the hope that it might have a tendency to throw a
monopoly of the foreign navigation of the Mediterranean into the
hands of those countries which, by means of their great navies, and
their proximity to the African coast, were always ready to correct any
serious evil that might affect themselves. English policy had been
detected in the hostilities of the Dey, a few years earlier, and it is by
no means improbable that Mr. O’Brien foresaw consequences of this
nature, that did not lie absolutely on the surface.
 Yielding to the various considerations which were urged,
Bainbridge finally consented to comply with the Dey’s demand. The
presents and passengers were received on board, and on the 19th
of October, or about a month after her arrival at Algiers, the George
Washington was ready to sail for Constantinople. When on the very
eve of departing a new difficulty arose, and one of a nature to show
that the Dey was not entirely governed by rapacity, but that he had
rude notions of national honor, agreeably to opinions of the school in
which he had been trained. As the George Washington carried his
messenger, or ambassador, and was now employed in his service,
he insisted that she should carry the Algerine flag at the main, while
that of the republic to which the ship belonged, should fly at the fore.
An altercation occurred on this point of pure etiquette, the Dey
insisting that English, French, and Spanish commanders, whenever
they had performed a similar service for him, had not hesitated to
give this precedency to his ensign. This was probably true, as well
as the fact that vessels of war of those nations had consented to
serve him in this manner, in compliance with the selfish policy of their
respective governments; though it may be doubted whether English,
or French ships, had been impressed into such a duty. Dr. Harris,
whose biography of Bainbridge is much the most full of any written,
and to which we are indebted for many of our own details, has cited
an instance as recently as 1817, when an English vessel of war
conveyed presents to Constantinople for the Dey; though it was
improbable that any other inducement for the measure existed, than
a desire in the English authorities to maintain their influence in the
regency. Bainbridge, without entering into pledges on the subject,
and solely with a view to get his ship beyond the reach of the
formidable batteries of the mole, hoisted the Algerine ensign, as
desired, striking it, as soon as he found himself again the
commander of his own vessel.
The George Washington had a boisterous and weary passage to
the mouth of the Dardanelles, the ship being littered with Turks, and
the cages of wild beasts. This voyage was always a source of great
uneasiness and mortification to Bainbridge, but he occasionally
amused his friends with the relation of anecdotes that occurred
during its continuance. Among other things he mentioned that his
passengers were greatly puzzled to keep their faces toward Mecca,
in their frequent prayers; the ship often tacking during the time thus
occupied, more especially after they got into the narrow seas. A man
was finally stationed at the compass to give the faithful notice when it
was necessary to “go-about,” in consequence of the evolutions of the
frigate.
Bainbridge had great apprehensions of being detained at the
Dardanelles, for want of a firman, the United States having no
diplomatic agent at the Porte, and commercial jealousy being known
to exist, on the subject of introducing the American flag into those
waters. A sinister influence up at Constantinople might detain him for
weeks, or even prevent his passage altogether, and having come so
far, on his unpleasant errand, he was resolved to gather as many of
its benefits as possible. In the dilemma, therefore, he decided on a
ruse of great boldness, and one which proved that personal
considerations had little influence, when he thought the interests of
his country demanded their sacrifice.
The George Washington approached the castles with a strong
southerly wind, and she clewed up her light sails, as if about to
anchor, just as she began to salute. The works returned gun for gun,
and in the smoke sail was again made, and the ship glided out of the
range of shot before the deception was discovered; passing on
toward the sea of Marmora under a cloud of canvass. As vessels
were stopped at only one point, and the progress of the ship was too
rapid to admit of detention, she anchored unmolested under the
walls of Constantinople, on the 9th November, 1800; showing the
flag of the republic, for the first time, before that ancient town.
Bainbridge was probably right in his anticipation of difficulty in
procuring a firman to pass the castles, for when his vessel reported
her nation, an answer was sent off that the government of Turkey
knew of no such country. An explanation that the ship came from the
new world, that which Columbus had discovered, luckily proved
satisfactory, when a bunch of flowers and a lamb were sent on
board; the latter as a token of amity, and the former as a welcome.
The George Washington remained several weeks at
Constantinople, where Bainbridge and his officers were well
received, though the agents of the Dey fared worse. The Capudan
Pacha, in particular, formed a warm friendship for the commander of
the George Washington, whose fine personal appearance, frank
address and manly bearing were well calculated to obtain favor. This
functionary was married to a sister of the Sultan, and had more
influence at court than any other subject. He took Bainbridge
especially under his own protection, and when they parted, he gave
the frigate a passport, which showed that she and her commander
enjoyed this particular and high privilege. In fact, the intercourse
between this officer and the commander of the George Washington
was such as to approach nearly to paving the way for a treaty, a step
that Bainbridge warmly urged on the government at home, as both
possible and desirable. It has been conjectured even, that Capt.
Bainbridge was instructed on this subject; and that, in consenting to
go to Constantinople at all, he had the probabilities of opening some
such negotiation in view. This was not his own account of the matter,
although, in weighing the motives for complying with the Dey’s
demands, it is not impossible he permitted such a consideration to
have some weight.
The visit of Clarke, the well known traveler, occurred while the
George Washington was at Constantinople. The former
accompanied Bainbridge to the Black Sea, in the frigate’s long-boat,
where the American ensign was displayed also, for the first time. It
appears that an officer was one of the party in the celebrated visit of
the traveler to the seraglio, Bainbridge confirming Dr. Clarke’s
account of the affair, with the exception that he, himself, looked upon
the danger as very trifling.
During the friendly intercourse which existed between Capt.
Bainbridge and the Capudan Pacha, the latter incidentally mentioned
that the governor of the castles was condemned to die for suffering
the George Washington to pass without a firman, and that the
warrant of execution only waited for his signature, in order to be
enforced. Shocked at discovering the terrible strait to which he had
unintentionally reduced a perfectly innocent man, Bainbridge frankly
admitted his own act, and said if any one had erred it was himself;
begging the life of the governor, and offering to meet the
consequences in his own person. This generous course was not