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PART 1 THE FACTS OF LIFE
Chapter 1: Why: Biology by the Numbers 3
Chapter 2: What and Where: Construction Plans for Cells and Organisms 29
Chapter 3: When: Stopwatches at Many Scales 75
Chapter 4: Who: “Bless the Little Beasties” 119
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DETAILED CONTENTS
Chapter 1 Why: Biology by the Numbers 3
1.1 PHYSICAL BIOLOGY OF THE CELL 3
Model Building Requires a Substrate of Biological Facts and Physical (or Chemical) Principles 4
1.2 THE STUFF OF LIFE 4
Organisms Are Constructed from Four Great Classes of Macromolecules 5
Nucleic Acids and Proteins Are Polymer Languages with Different Alphabets 6
1.3 MODEL BUILDING IN BIOLOGY 9
1.3.1 Models as Idealizations 9
Biological Stuff Can Be Idealized Using Many Different Physical Models 10
1.3.2 Cartoons and Models 15
Biological Cartoons Select Those Features of the Problem Thought to be Essential 1 5
Quantitative Models Can Be Built by Mathematicizing the Cartoons 18
1.4 QUANTITATIVE MODELS AND THE POWER OF IDEALIZATION 1 9
1.4.1 On the Springiness of Stuff 19
1.4.2 The Toolbox of Fundamental Physical Models 20
1.4.3 The Role of Estimates 22
1.4.4 On Being Wrong 23
1.4.5 Rules of Thumb: Biology by the Numbers 25
1.5 SUMMARY AND CONCLUSIONS 25
1.6 FURTHER READING 27
1.7 REFERENCES 27
Chapter 2 What and Where: Construction Plans for Cells and Organisms 29
2.1 AN ODE TO E. COLI 29
2.1.1 The Bacterial Standard Ruler 30
The Bacterium £. coli Will Serve as Our Standard Ruler 30
2.1.2 Taking the Molecular Census 32
The Cellular Interior Is Highly Crowded with Mean Spacings Between Molecules That Are Comparable to Molecular Dimensions 36
2.1.3 Looking Inside Cells 37
2.1.4 Where Does E. coli Fit? 39
Biological Structures Exist Over a Huge Range of Scales 39
2.2 CELLS AND STRUCTURES WITHIN THEM 40
2.2.1 Cells: A Rogue's Gallery 40
Cells Come in a Wide Variety of Shapes and Sizes and with a Huge Range of Functions 41
Cells from Humans Have a Huge Diversity of Structure and Function 45
2.2.2 The Cellular Interior: Organelles 47
2.2.3 Macromolecular Assemblies: The Whole is Greater than the Sum of the Parts 51
Macromolecules Come Together to Form Assemblies 51
Helical Motifs are Seen Repeatedly in Molecular Assemblies 51
Macromolecular Assemblies Are Arranged in Superstructures 53
2.2.4 Viruses as Assemblies 53
2.2.5 The Molecular Architecture of Cells: From Protein Data Bank (PDB) Files to Ribbon Diagrams 57
Macromolecular Structure Is Characterized Fundamentally by Atomic Coordinates 57
Chemical Groups Allow Us to Classify Parts of the Structure of Macromolecules 58
2.3 TELESCOPING UP IN SCALE: CELLS DON’T GO IT ALONE 60
2.3.1 Multicellularity as One of Evolution’s Great Inventions 61
Bacteria Interact to Form Colonies such as Biofilms 61
Teaming Up in a Crisis: Lifestyle of Dictyostelium discoideum 62
Multicellular Organisms Have Many Distinct Communities of Cells 64
2.3.2 Cellular Structures from Tissues to Nerve Networks 65
One Class of Multicellular Structures is the Epithelial Sheets 65
Tissues Are Collections of Cells and Extracellular Matrix 66
Nerve Cells Form Complex, Multicellular Complexes 66
2.3.3 Multicellular Organisms 67
Cells Differentiate During Development Leading to Entire Organisms 68
The Cells of the Nematode Worm Caenorhabditis elegans Have Been Charted Yielding a Cell-by-Cell Picture of the Organism 69
Higher-Level Structures Exist as Colonies of Organisms 71
2.4 SUMMARY AND CONCLUSIONS 71
2.5 PROBLEMS 72
2.6 FURTHER READING 73
2.7 REFERENCES 73
Chapter 3 When: Stopwatches at Many Scales 75
3.1 THE HIERARCHY OF TEMPORAL SCALES 75
3.1.1 The Pageant of Biological Processes 77
Biological Processes Are Characterized by a Huge
Diversity of Time Scales 77
3.1.2 The Evolutionary Stopwatch 83
3.1.3 The Cell Cycle and the Standard Clock 87
The E. coli Cell Cycle Will Serve as Our Standard Stopwatch 8.7
3.1.4 Three Views of Time in Biology 89
3.2 PROCEDURAL TIME 90
3.2.1 The Machines (or Processes) of the Central Dogma 90
The Central Dogma Describes the Processes
Whereby the Genetic Information Is Expressed Chemically 90
The Processes of the Central Dogma Are Carried Out by Sophisticated Molecular Machines 91
3.2.2 Clocks and Oscillators 93
Developing Embryos Divide on a Regular Schedule
Dictated by an Internal Clock 94
Diurnal Clocks Allow Cells and Organisms to Be on Time Everyday 94
3.3 RELATIVE TIME 97
3.3.1 Checkpoints and the Cell Cycle 98
The Eukaryotic Cell Cycle Consists of Four Phases
Involving Molecular Synthesis and Organization 98
3.3.2 Measuring Relative Time 100
Genetic Networks Are Collections of Genes Whose
Expression Is Interrelated 100
The Formation of the Bacterial Flagellum Is
Intricately Organized in Space and Time 101
3.3.3 Killing the Cell: The Life Cycles of Viruses 102
Viral Life Cycles Include a Series of Self-Assembly Processes 102
3.3.4 The Process of Development 104
3.4 MANIPULATED TIME 106
3.4.1 Chemical Kinetics and Enzyme Turnover 107
3.4.2 Beating the Diffusive Speed Limit 108
Diffusion Is the Random Motion of Microscopic
Particles in Solution 109
Diffusion Times Depend upon the Length Scale 109
Molecular Motors Move Cargo over Large
Distances in a Directed Way 110
Membrane Bound Proteins Transport Molecules
from One Side of a Membrane to the Other 112
3.4.3 Beating the Replication Limit 113
3.4.4 Eggs and Spores: Planning for the Next Generation 114
3.5 SUMMARY AND CONCLUSIONS 115
3.6 PROBLEMS 115
3.7 FURTHER READING 117
3.8 REFERENCES 117
Chapter 4 Who: “ Bless the Little Beasties” 119
4.1 CHOOSING A GRAIN OF SAND 119
Modern Genetics Began with the Use of Peas as a Model System 120
4.1.1 Biochemistry and Genetics 120
4.2 HEMOGLOBIN AS A MODEL PROTEIN 124
4.2.1 Hemoglobin, Receptor—Ligand Binding, and the Other Bohr 125
The Binding of Oxygen to Hemoglobin Has Served as a Model System for Ligand—Receptor Interactions More Generally 125
Quantitative Analysis of Hemoglobin Is Based upon Measuring the Fractional Occupancy of the Oxygen Binding Sites as a Function of Oxygen Pressure 125
4.2.2 Hemoglobin and the Origins of Structural Biology 126
The Study of the Mass of Hemoglobin Was Central
in the Development of Centrifugation 127
Structural Biology Has Its Roots in the
Determination of the Structure of Hemoglobin 127
4.2.3 Hemoglobin and Molecular Models of Disease 127
4.2.4 The Rise of Allostery and Cooperativity 128
4.3 BACTERIOPHAGE AND MOLECULAR BIOLOGY 129
4.3.1 Bacteriophage and the Origins of Molecular Biology 129
Bacteriophage Have Sometimes Been Called the “Hydrogen Atoms of Biology” 129
Experiments on Phage and Their Bacterial Hosts Demonstrated That Natural Selection Is Operative in Microscopic Organisms 130
The Hershey—Chase Experiment Both Confirmed the Nature of Genetic Material and Elucidated One of the Mechanisms of Viral DNA Entry into Cells 1 30
Experiments on Phage T4 Demonstrated the Sequence Hypothesis of Collinearity of DNA and Proteins 131
The Triplet Nature of the Genetic Code and DNA Sequencing were Carried Out on Phage Systems 132
Phage Were Instrumental in Elucidating the Existence of mRNA 133
General Ideas about Gene Regulation Were Learned
from the Study of Viruses as a Model System 1 33
4.3.2 Bacteriophage and Modern Biophysics 134
Many Single-Molecule Studies of Molecular Motors
Have Been Performed on Motors from Bacteriophage 134
4.4 A TALE OF TWO CELLS: E. COLI AS A MODEL SYSTEM 136
4.4.1 Bacteria and Molecular Biology 136
4.4.2 E. coli and the Central Dogma 136
The Hypothesis of Conservative Replication Has Falsifiable Consequences 136
Extracts from E coli Were Used to Perform In Vitro Synthesis of DNA, mRNA, and Proteins 1 38
4.4.3 The lac Operon as the “Hydrogen Atom” of Genetic Circuits 138
Gene Regulation in E coli Serves as a Model for Genetic Circuits in General 138
The lac Operon is a Genetic Network Which Controls the Production of the Enzymes Responsible for Digesting the Sugar Lactose 139
4.4.4 Signaling and Motility: The Case of Bacterial Chemotaxis 140
E coli Has Served as a Model System for the Analysis of Cell Motility 140
4.5 YEAST: FROM BIOCHEMISTRY TO THE CELL CYCLE 1 42
Yeast Has Served as a Model System Leading to Insights in Contexts Ranging from Vitalism to the Functioning of Enzymes to Eukaryotic Gene Regulation 142
4.5.1 Yeast and the Rise of Biochemistry 143
4.5.2 Dissecting the Cell Cycle 144
4.5.3 Deciding Which Way Is Up: Yeast and Polarity 145
4.5.4 Dissecting Membrane Traffic 147
4.5.5 Genomics and Proteomics 148
4.6 FLIES AND MODERN BIOLOGY 151
4.6.1 Flies and the Rise of Modern Genetics 151
Drosophila melanogaster Has Served as a Model System for Studies Ranging from Genetics to Development to the Functioning of the Brain and Even Behavior 151
4.6.2 How the Fly Got His Stripes 152
4.7 OF MICE AND MEN 154
4.8 THE CASE FOR EXOTICA 155
4.8.1 Specialists and Experts 155
4.8.2 The Squid Giant Axon and Biological Electricity 157
There Is a Steady-State Potential Difference Across the Membrane of Nerve Cells 157
Nerve Cells Propagate Electrical Signals and Use Them to Communicate with Each Other 1 59
4.8.3 Exotica Toolkit 159
4.9 SUMMARY AND CONCLUSIONS 160
4.10 PROBLEMS 161
4.11 FURTHER READING 162
4.12 REFERENCES 164