Original PDF Biochemistry Canadian Edition by Reginald H Garrett PDF

(Original PDF) Biochemistry Canadian
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Contents in Brief
PART I: Building Blocks of the Cell 1

1. The Facts of Life: Chemistry Is the Logic of Biological Phenomena 1
2. Water: The Medium of Life 32
3. Thermodynamics of Biological Systems 53
4. Amino Acids 75
5. Proteins: Their Primary Structure and Biological Functions 98
6. Proteins: Secondary, Tertiary, and Quaternary Structure 140
7. Carbohydrates and the Glycoconjugates of Cell Surfaces 189
8. Lipids 228
9. Lipid Biosynthesis 252
10. Membranes and Membrane Transport 299
11. The Reception and Transmission of Extracellular Information 349
PART II: Protein Dynamics 403

12. Enzymes—Kinetics and Specificity 403
13. Mechanisms of Enzyme Action 442
14. Enzyme Regulation 477
15. Molecular Motors 505
PART III: Metabolism and Its Regulation 537

16. Nutrition and the Organization of Metabolism 537
17. Glycolysis 561
18. The Tricarboxylic Acid Cycle 591
19. Electron Transport and Oxidative Phosphorylation 621
20. Photosynthesis 659
21. Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway 693
22. Fatty Acid Catabolism 735
23. Nitrogen Acquisition and Amino Acid Metabolism 761
PART IV: Nucleic Acids 808

24. Nucleotides and Nucleic Acids 808
25. Structure of Nucleic Acids 833
26. Synthesis and Degradation of Nucleotides 871
27. Recombinant DNA: Cloning and Creation of Chimeric Genes 897
28. DNA Metabolism: Replication, Recombination, and Repair 926
PART V: Information Transfer 963

29. Transcription and the Regulation of Gene Expression 963
30. Protein Synthesis 1009
31. Post-transcriptional Regulation of Gene Expression: mRNA Turnover and Micro-RNA 1048
32. Completing the Protein Life Cycle: Folding, Processing, and Degradation 1086
33. Metabolic Integration and Organ Specialization 1109
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About the Authors iv Archaea and Bacteria Have a Relatively Simple

Preface xxix Structural Organization 19
The Structural Organization of Eukaryotic Cells Is More
Laboratory Techniques in Biochemistry xl Complex Than That of Prokaryotic Cells 21
1.6 What Are Viruses? 23
1.7 Do Biomolecules Ever Behave as Genetic Agents? 26
PART I Building Blocks of the Cell Prions and Viroids Can Act as Genetic Agents 26
SUMMARY 29
1 The Facts of Life: Chemistry Is the Logic of PROBLEMS 30
Biological Phenomena 1 FURTHER READING 31
1.1 What Are the Distinctive Properties of Living
Systems? 2 2 Water: The Medium of Life 32
1.2 What Kinds of Molecules Are Biomolecules? 5 2.1 What Are the Properties of Water? 33
Biomolecules Are Carbon Compounds 6 Water Has Unusual Properties 33
Hydrogen Bonding in Water Is Key to Its
1.3 What Is the Structural Organization of Complex
Properties 34
Biomolecules? 6
The Structure of Ice Is Based on H-Bond Formation 34
Metabolites Are Used to Form the Building Blocks
of Macromolecules 6 Molecular Interactions in Liquid Water Are Based on
H Bonds 35
Membranes Are Supramolecular Assemblies That
Define the Boundaries of Cells 10 The Solvent Properties of Water Derive from Its Polar
Nature 35
The Unit of Life Is the Cell 10
Water Can Ionize to Form Hⴙ and OHⴚ 39
1.4 How Do the Properties of Biomolecules Reflect
Their Fitness to the Living Condition? 10 2.2 What Is pH? 40
Biological Macromolecules and Their Building Blocks Strong Electrolytes Dissociate Completely in
Have a “Sense” or Directionality 11 Water 41
Biological Macromolecules Are Informational 11 Weak Electrolytes Are Substances That Dissociate Only
Slightly in Water 42
Biomolecules Have Characteristic Three-Dimensional
Architecture 12 The Henderson–Hasselbalch Equation Describes the
Dissociation of a Weak Acid in the Presence of Its
Weak Forces Maintain Biological Structure and
Conjugate Base 43
Determine Biomolecular Interactions 12
Titration Curves Illustrate the Progressive Dissociation
Hydrogen Bonds Are Important in Biomolecular
of a Weak Acid 44
Interactions 13
Phosphoric Acid Has Three Dissociable Hⴙ 45
The Defining Concept of Biochemistry Is
“Molecular Recognition Through Structural 2.3 What Are Buffers and What Do They Do? 46
Complementarity” 14 The Phosphate Buffer System Is a Major Intracellular
Biomolecular Recognition Is Mediated by Weak Buffering System 46
Chemical Forces 15 Dissociation of the Histidine–Imidazole Group Also
Weak Forces Restrict Organisms to a Narrow Range Serves as an Intracellular Buffering System 47
of Environmental Conditions 16 “Good” Buffers Are Buffers Useful within Physiological
Enzymes Catalyze Metabolic Reactions 17 pH Ranges 47
The Time Scale of Life 17 HUMAN BIOCHEMISTRY: The Bicarbonate Buffer
System of Blood Plasma 48
1.5 What Is the Organization and Structure of Cells? 17
HUMAN BIOCHEMISTRY: Blood pH and
The Evolution of Early Cells Gave Rise to Eubacteria,
Respiration 49
Archaea, and Eukaryotes 18
What Are Common Buffers Used in Biochemistry? 49
How Many Genes Does a Cell Need? 18
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2.4 What Properties of Water Give It a Unique Role There Are 20 Common Amino Acids 77
in the Environment? 50 Are There Other Ways to Classify Amino Acids? 80
SUMMARY 50 Amino Acids 21 and 22—and More? 81
PROBLEMS 51 Several Amino Acids Occur Only Rarely in Proteins 81
FURTHER READING 52 Amino Acid Derivatives 82
3 Thermodynamics of Biological Systems 53 4.2 What Are the Acid–Base Properties of Amino
Acids? 82
3.1 What Are the Basic Concepts of
Amino Acids Are Weak Polyprotic Acids 82
Thermodynamics? 54
The First Law: The Total Energy of an Isolated System Side Chains of Amino Acids Undergo Characteristic
Is Conserved 54 Ionizations 84
Enthalpy Is a More Useful Function for Biological Isoelectric Points of Amino Acids 85
Systems 55 4.3 What Are the Post-translational Modifications
The Second Law: Systems Tend Toward Disorder and of Amino Acids? 86
Randomness 57 4.4 What Are the Optical and Stereochemical
A DEEPER LOOK: Entropy, Information, and the Properties of Amino Acids? 86
Importance of “Negentropy” 58 Amino Acids Are Chiral Molecules 86
The Third Law: Why Is “Absolute Zero” So Important? 58 Chiral Molecules Are Described by the d,l and R,S
Free Energy Provides a Simple Criterion for Equilibrium 58 Naming Conventions 86
3.2 What Can Thermodynamic Parameters Tell CRITICAL DEVELOPMENTS IN BIOCHEMISTRY:
Us about Biochemical Events? 60 Green Fluorescent Protein—The “Light Fantastic” from
Jellyfish to Gene Expression 87
3.3 What Are the Characteristics of High-Energy
Biomolecules? 61 4.5 What Are the Spectroscopic Properties
ATP Is an Intermediate Energy-Shuttle Molecule 62 of Amino Acids? 87
Group Transfer Potentials Quantify the Reactivity CRITICAL DEVELOPMENTS IN BIOCHEMISTRY:
of Functional Groups 63 Discovery of Optically Active Molecules and
Determination of Absolute Configuration 88
The Hydrolysis of Phosphoric Acid Anhydrides
Is Highly Favourable 64 Phenylalanine, Tyrosine, and Tryptophan Absorb
Ultraviolet Light 88
The Hydrolysis ⌬G°’ of ATP and ADP Is Greater Than
That of AMP 66 Amino Acids Can Be Characterized by Nuclear
Magnetic Resonance 89
Acetyl Phosphate and 1,3-Bisphosphoglycerate
Are Phosphoric-Carboxylic Anhydrides 67 A DEEPER LOOK: The Murchison Meteorite—
Discovery of Extraterrestrial Handedness 90
Enol Phosphates Are Potent Phosphorylating Agents 67
CRITICAL DEVELOPMENTS IN BIOCHEMISTRY:
Guanidino Phosphates Are Energy Reserve
Rules for Description of Chiral Centres in the (R,S)
Compounds 68
System 91
3.4 What Are the Complex Equilibria Involved
4.6 What Is the Fundamental Structural Pattern
in ATP Hydrolysis? 69
in Proteins? 91
The ⌬G°’ of Hydrolysis for ATP Is pH Dependent 69
The Peptide Bond Has Partial Double-Bond
Metal Ions Affect the Free Energy of Hydrolysis of ATP 70 Character 92
Concentration Affects the Free Energy of Hydrolysis The Polypeptide Backbone Is Relatively Polar 92
of ATP 70
Peptides Can Be Classified According to How Many
3.5 Why Are Coupled Processes Important Amino Acids They Contain 94
to Living Things? 71 Proteins Are Composed of One or More Polypeptide
3.6 What Is the Daily Human Requirement for ATP? 71 Chains 94
A DEEPER LOOK: ATP Changes the Keq by a Factor of SUMMARY 95
108 72
PROBLEMS 96
SUMMARY 73
FURTHER READING 97
PROBLEMS 73
FURTHER READING 74 5 Proteins: Their Primary Structure and Biological
Functions 98
4 Amino Acids 75 5.1 What Architectural Arrangements Characterize
4.1 What Are the Structures and Properties Protein Structure? 99
of Amino Acids? 76 Protein Structure Is Described in Terms of Four Levels
Typical Amino Acids Contain a Central Tetrahedral of Organization 99
Carbon Atom 76 Non-covalent Forces Drive Formation of the Higher
Amino Acids Can Join via Peptide Bonds 76 Orders of Protein Structure 101
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Proteins Fall into Three Basic Classes According A Mutant Protein Is a Protein with a Slightly Different
to Shape and Solubility 101 Amino Acid Sequence 128
A Protein’s Conformation Can Be Described as Its A DEEPER LOOK: Bovine Spongiform Encephalopathy
Overall Three-Dimensional Structure 102 (BSE) and Its Effect on the Canadian Economy 130
5.2 How Are Proteins Isolated and Purified 5.7 Can Polypeptides Be Synthesized in the
from Cells? 102 Laboratory? 130
Dialysis and Ultrafiltration 103 Solid-Phase Methods Are Very Useful in Peptide
A Number of Protein Separation Methods Exploit Synthesis 130
Differences in Size and Charge 103 5.8 Do Proteins Have Chemical Groups Other Than
A Typical Protein Purification Scheme Uses a Series Amino Acids? 132
of Separation Methods 104 5.9 What Are the Many Biological Functions of
A DEEPER LOOK: Estimation of Protein Concentrations Proteins? 133
in Solutions of Biological Origin 104 SUMMARY 135
5.3 How Are Amino Acid Mixtures Separated? 105 PROBLEMS 136
Amino Acids Can Be Separated by FURTHER READING 138
Chromatography 105
Summary of the Types of Chromatographic 6 Proteins: Secondary, Tertiary, and Quaternary
Techniques 105 Structure 140
5.4 How Is the Amino Acid Analysis of Proteins 6.1 What Non-covalent Interactions Stabilize
Performed? 111 Protein Structure? 141
Acid Hydrolysis Liberates the Amino Acids of a Hydrogen Bonds Are Formed Whenever Possible 142
Protein 111
Hydrophobic Interactions Drive Protein Folding 142
Chromatographic Methods Are Used to Separate
Ionic Interactions Usually Occur on the Protein
the Amino Acids 111
Surface 142
The Amino Acid Compositions of Different Proteins
Van der Waals Interactions Are Ubiquitous 142
Are Different 111
6.2 What Role Does the Amino Acid Sequence Play
5.5 How Is the Primary Structure of a Protein
in Protein Structure? 143
Determined? 111
The Sequence of Amino Acids in a Protein Is 6.3 What Are the Elements of Secondary Structure
Distinctive 111 in Proteins, and How Are They Formed? 143
Sanger Was the First to Determine the Sequence All Protein Structure Is Based on the Amide Plane 143
of a Protein 112 The Alpha-Helix Is a Key Secondary Structure 145
Both Chemical and Enzymatic Methodologies A DEEPER LOOK: Knowing What the Right Hand and
Are Used in Protein Sequencing 112 Left Hand Are Doing 146
Step 1. Separation of Polypeptide Chains 112 The b-Pleated Sheet Is a Core Structure in
A DEEPER LOOK: The Virtually Limitless Number of Proteins 149
Different Amino Acid Sequences 113 CRITICAL DEVELOPMENTS IN BIOCHEMISTRY: In
Step 2. Cleavage of Disulfide Bridges 113 Bed with a Cold, Pauling Stumbles onto the a-Helix
and a Nobel Prize 150
Step 3. N- and C-Terminal Analysis 113
Helix–Sheet Composites in Spider Silk 151
Steps 4 and 5. Fragmentation of the Polypeptide
Chain 115 b-Turns Allow the Protein Strand to Change
Direction 152
Step 6. Reconstruction of the Overall Amino Acid
Sequence 118 6.4 How Do Polypeptides Fold into Three-Dimensional
Protein Structures? 152
The Amino Acid Sequence of a Protein Can Be
Determined by Mass Spectrometry 118 Fibrous Proteins Usually Play a Structural Role 153
Sequence Databases Contain the Amino Acid A DEEPER LOOK: The Coiled-Coil Motif in
Sequences of Millions of Different Proteins 122 Proteins 155
5.6 What Is the Nature of Amino Acid Sequences? 122 Globular Proteins Mediate Cellular Function 159
Homologous Proteins from Different Organisms Helices and Sheets Make Up the Core of Most
Have Homologous Amino Acid Sequences 122 Globular Proteins 159
Computer Programs Can Align Sequences and Waters on the Protein Surface Stabilize the
Discover Homology between Proteins 123 Structure 160
Related Proteins Share a Common Evolutionary Packing Considerations 160
Origin 125 HUMAN BIOCHEMISTRY: Collagen-Related
Apparently Different Proteins May Share a Common Diseases 162
Ancestry 128 Protein Domains Are Nature’s Modular Strategy
for Protein Design 162
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Classification Schemes for the Protein Universe Are Haworth Projections Are a Convenient Device
Based on Domains 164 for Drawing Sugars 195
Denaturation Leads to Loss of Protein Structure and Monosaccharides Can Be Converted to Several
Function 166 Derivative Forms 196
Anfinsen’s Classic Experiment Proved That Sequence A DEEPER LOOK: Honey: An Ancestral Carbohydrate
Determines Structure 168 Treat 199
Is There a Single Mechanism for Protein Folding? 169 7.3 What Is the Structure and Chemistry
What Is the Thermodynamic Driving Force for Folding of Oligosaccharides? 200
of Globular Proteins? 170 Disaccharides Are the Simplest Oligosaccharides 200
Marginal Stability of the Tertiary Structure Makes A DEEPER LOOK: Trehalose: A Natural Protectant for
Proteins Flexible 171 Bugs 202
Motion in Globular Proteins 172 A Variety of Higher Oligosaccharides Occur in
The Folding Tendencies and Patterns of Globular Nature 202
Proteins 172 7.4 What Is the Structure and Chemistry of
Most Globular Proteins Belong to One of Four Polysaccharides? 203
Structural Classes 174 Nomenclature for Polysaccharides Is Based
Molecular Chaperones Are Proteins That Help Other on Their Composition and Structure 203
Proteins to Fold 176 Polysaccharides Serve Energy Storage, Structure,
Some Proteins Are Intrinsically Unstructured 176 and Protection Functions 203
HUMAN BIOCHEMISTRY: A1-Antitrypsin: A Tale of Polysaccharides Provide Stores of Energy 204
Molecular Mousetraps and a Folding Disease 178 Polysaccharides Provide Physical Structure
HUMAN BIOCHEMISTRY: Diseases of Protein and Strength to Organisms 205
Folding 179 A DEEPER LOOK: A Complex Polysaccharide in Red
HUMAN BIOCHEMISTRY: Structural Genomics 179 Wine: The Strange Story of Rhamnogalacturonan II 208
6.5 How Do Protein Subunits Interact at the A DEEPER LOOK: Billiard Balls, Exploding Teeth, and
Quaternary Level of Protein Structure? 179 Dynamite: The Colourful History of Cellulose 210
There Is Symmetry in Quaternary Structures 181 Polysaccharides Provide Strength and Rigidity to
Quaternary Association Is Driven by Weak Forces 183 Bacterial Cell Walls 210
A DEEPER LOOK: Immunoglobulins: All the Features Peptidoglycan Is the Polysaccharide of Bacterial
of Protein Structure Brought Together 184 Cell Walls 210
Immunoglobulin-Based Techniques 184 Animals Display a Variety of Cell Surface
Polysaccharides 212
Open Quaternary Structures Can Polymerize 184
There Are Structural and Functional Advantages to 7.5 What Are Glycoproteins, and How Do They
Quaternary Association 184 Function in Cells? 213
HUMAN BIOCHEMISTRY: Faster-Acting Insulin: Polar Fish Depend on Antifreeze Glycoproteins 215
Genetic Engineering Solves a Quaternary Structure A DEEPER LOOK: Drug Research Finds a Sweet Spot 216
Problem 185 N-Linked Oligosaccharides Can Affect the Physical
CRITICAL DEVELOPMENTS IN BIOCHEMISTRY: Properties and Functions of a Protein 216
Banting and Best: The Great Canadian Discovery 185 Oligosaccharide Cleavage Can Serve as a Timing
SUMMARY 186 Device for Protein Degradation 216
PROBLEMS 187 A DEEPER LOOK: N-Linked Oligosaccharides Help
Proteins Fold 218
FURTHER READING 187
7.6 How Do Proteoglycans Modulate Processes in
7 Carbohydrates and the Glycoconjugates of Cell Cells and Organisms? 218
Surfaces 189 Functions of Proteoglycans Involve Binding to Other
Proteins 218
BIOCHEMISTRY: A CANADIAN CONTEXT: The
Proteoglycans May Modulate Cell Growth
Synthesis of Sucrose 190
Processes 220
7.1 What Are Carbohydrates, and How Are They
Proteoglycans Make Cartilage Flexible and
Named? 190
Resilient 221
7.2 What Is the Structure and Chemistry
7.7 Do Carbohydrates Provide a Structural Code? 222
of Monosaccharides? 191
Selectins, Rolling Leukocytes, and the Inflammatory
Monosaccharides Are Classified as Aldoses and
Response 222
Ketoses 191
Galectins: Mediators of Inflammation, Immunity, and
Stereochemistry Is a Prominent Feature of
Cancer 223
Monosaccharides 192
C-Reactive Protein: A Lectin That Limits Inflammation
Monosaccharides Exist in Cyclic and Anomeric Forms 193
Damage 224
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xii Detailed Contents
SUMMARY 225 Acetate Units Are Committed to Fatty Acid Synthesis

PROBLEMS 225 by Formation of Malonyl-CoA 255
FURTHER READING 227 Acetyl-CoA Carboxylase Is Biotin-Dependent and
Displays Ping-Pong Kinetics 255
8 Lipids 228 Acetyl-CoA Carboxylase in Animals Is a Multifunctional
Protein 255
8.1 What Are the Structures and Chemistry of Fatty
Acids? 229 Phosphorylation of ACC Modulates Activation by
Citrate and Inhibition by Palmitoyl-CoA 256
HUMAN BIOCHEMISTRY: Fast Foods in Canada 232
Acyl Carrier Proteins Carry the Intermediates
8.2 What Are the Structures and Chemistry
in Fatty Acid Synthesis 258
of Triacylglycerols? 232
In Some Organisms, Fatty Acid Synthesis Takes Place
A DEEPER LOOK: Polar Bears Prefer Non-polar
in Multi-enzyme Complexes 258
Food 233
A DEEPER LOOK: Choosing the Best Organism for the
8.3 What Are the Structures and Chemistry Experiment 258
of Glycerophospholipids? 233
Decarboxylation Drives the Condensation of
Glycerophospholipids Are the Most Common Acetyl-CoA and Malonyl-CoA 259
Phospholipids 235
Reduction of the b-Carbonyl Group Follows a Now
Ether Glycerophospholipids Include PAF and Familiar Route 260
Plasmalogens 236
Eukaryotes Build Fatty Acids on Megasynthase
HUMAN BIOCHEMISTRY: Platelet-Activating Factor: A Complexes 261
Potent Glyceroether Mediator 237
C16 Fatty Acids May Undergo Elongation and
8.4 What Are Sphingolipids, and How Are They Unsaturation 263
Important for Higher Animals? 237
Unsaturation Reactions Occur in Eukaryotes in the
A DEEPER LOOK: Moby Dick and Spermaceti: A Middle of an Aliphatic Chain 265
Valuable Wax from Whale Oil 239
The Unsaturation Reaction May Be Followed by Chain
8.5 What Are Waxes, and How Are They Used? 239 Elongation 265
8.6 What Are Terpenes, and What Is Their Relevance Mammals Cannot Synthesize Most Polyunsaturated
to Biological Systems? 240 Fatty Acids 265
A DEEPER LOOK: Why Do Plants Emit Isoprene? 241 Arachidonic Acid Is Synthesized from Linoleic Acid by
The Membranes of Archaea Are Rich in Isoprene- Mammals 266
Based Lipids 241 Regulatory Control of Fatty Acid Metabolism Is an
HUMAN BIOCHEMISTRY: Coumadin or Warfarin— Interplay of Allosteric Modifiers and Phosphorylation–
Agent of Life or Death 242 Dephosphorylation Cycles 266
8.7 What Are Steroids, and What Are Their HUMAN BIOCHEMISTRY: v3 and v6: Essential Fatty
Cellular Functions? 243 Acids with Many Functions 267
Cholesterol 243 Hormonal Signals Regulate ACC and Fatty Acid
Steroid Hormones Are Derived from Cholesterol 243 Biosynthesis 268
8.8 How Do Lipids and Their Metabolites Act 9.2 How Are Complex Lipids Synthesized? 269
as Biological Signals? 244 Glycerolipids Are Synthesized by Phosphorylation
A DEEPER LOOK: Glycerophospholipid Degradation: and Acylation of Glycerol 269
One of the Effects of Snake Venom 245 Eukaryotes Synthesize Glycerolipids from CDP-
HUMAN BIOCHEMISTRY: Plant Sterols and Stanols— Diacylglycerol or Diacylglycerol 269
Natural Cholesterol Fighters 247 Phosphatidylethanolamine Is Synthesized from
HUMAN BIOCHEMISTRY: 17b-Hydroxysteroid Diacylglycerol and CDP-Ethanolamine 270
Dehydrogenase 3 Deficiency 248 Exchange of Ethanolamine for Serine Converts
Phosphatidylethanolamine to Phosphatidylserine 272
SUMMARY 248
Eukaryotes Synthesize Other Phospholipids
PROBLEMS 249
via CDP-Diacylglycerol 272
FURTHER READING 250 Dihydroxyacetone Phosphate Is a Precursor to the
Plasmalogens 272
9 Lipid Biosynthesis 252
Platelet-Activating Factor Is Formed by Acetylation
9.1 How Are Fatty Acids Synthesized? 253 of 1-Alkyl-2-Lysophosphatidylcholine 275
Formation of Malonyl-CoA Activates Acetate Units Sphingolipid Biosynthesis Begins with Condensation
for Fatty Acid Synthesis 253 of Serine and Palmitoyl-CoA 275
Fatty Acid Biosynthesis Depends on the Reductive Ceramide Is the Precursor for Other Sphingolipids
Power of NADPH 253 and Cerebrosides 275
Cells Must Provide Cytosolic Acetyl-CoA and Reducing 9.3 How Are Eicosanoids Synthesized, and What
Power for Fatty Acid Synthesis 254 Are Their Functions? 278
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Eicosanoids Are Local Hormones 278 Lipids Form Ordered Structures Spontaneously in
Prostaglandins Are Formed from Arachidonate Water 302
by Oxidation and Cyclization 278 The Fluid Mosaic Model Describes Membrane
A Variety of Stimuli Trigger Arachidonate Release Dynamics 304
and Eicosanoid Synthesis 278 10.2 What Are the Structure and Chemistry
A DEEPER LOOK: The Discovery of Prostaglandins 278 of Membrane Proteins? 306
A DEEPER LOOK: The Molecular Basis for the Action Peripheral Membrane Proteins Associate Loosely
of Non-steroidal Anti-inflammatory Drugs 280 with the Membrane 306
“Take Two Aspirin and…” Inhibit Your Prostaglandin Integral Membrane Proteins Are Firmly Anchored
Synthesis 281 in the Membrane 307
9.4 How Is Cholesterol Synthesized? 282 Lipid-Anchored Membrane Proteins Are Switching
Mevalonate Is Synthesized from Acetyl-CoA via Devices 314
HMG-CoA Synthase 282 A DEEPER LOOK: Exterminator Proteins—Biological
A Thiolase Brainteaser Asks Why Thiolase Cannot Be Pest Control at the Membrane 315
Used in Fatty Acid Synthesis 283 HUMAN BIOCHEMISTRY: Prenylation Reactions as
Squalene Is Synthesized from Mevalonate 283 Possible Chemotherapy Targets 317
CRITICAL DEVELOPMENTS IN BIOCHEMISTRY: 10.3 How Are Biological Membranes Organized? 318
The Long Search for the Route of Cholesterol Membranes Are Asymmetric and Heterogeneous
Biosynthesis 285 Structures 318
HUMAN BIOCHEMISTRY: Statins Lower Serum 10.4 What Are the Dynamic Processes That Modulate
Cholesterol Levels 286 Membrane Function? 319
Conversion of Lanosterol to Cholesterol Requires Lipids and Proteins Undergo a Variety of Movements
Twenty Additional Steps 286 in Membranes 319
9.5 How Are Lipids Transported throughout the Body? 288 Membrane Lipids Can Be Ordered to Different
Lipoprotein Complexes Transport Triacylglycerols Extents 320
and Cholesterol Esters 288 10.5 How Does Transport Occur across Biological
Lipoproteins in Circulation Are Progressively Degraded Membranes? 327
by Lipoprotein Lipase 289 10.6 What Is Passive Diffusion? 328
The Structure of the LDL Receptor Involves Five Charged Species May Cross Membranes by Passive
Domains 289 Diffusion 329
The LDL Receptor ␤-Propeller Displaces LDL Particles 10.7 How Does Facilitated Diffusion Occur? 329
in Endosomes 291 Membrane Channel Proteins Facilitate
Defects in Lipoprotein Metabolism Can Lead to Diffusion 329
Elevated Serum Cholesterol 291 The Bacillus cereus NaK Channel Uses a Variation on
9.6 How Are Bile Acids Biosynthesized? 292 the K+ Selectivity Filter 333
HUMAN BIOCHEMISTRY: Steroid 5a-Reductase: CorA Is a Pentameric Mg2+ Channel 333
A Factor in Male Baldness, Prostatic Hyperplasia, and Chloride, Water, Glycerol, and Ammonia Flow
Prostate Cancer 293 through Single-Subunit Pores 334
9.7 How Are Steroid Hormones Synthesized and 10.8 How Does Energy Input Drive Active Transport
Utilized? 293 Processes? 335
Pregnenolone and Progesterone Are the Precursors All Active Transport Systems Are Energy-Coupling
of All Other Steroid Hormones 293 Devices 335
Steroid Hormones Modulate Transcription in the Many Active Transport Processes Are Driven by
Nucleus 294 ATP 335
Cortisol and Other Corticosteroids Regulate a Variety A DEEPER LOOK: Cardiac Glycosides: Potent Drugs
of Body Processes 295 from Ancient Times 340
Anabolic Steroids Have Been Used Illegally to ABC Transporters Use ATP to Drive Import and Export
Enhance Athletic Performance 295 Functions and Provide Multidrug Resistance 340
SUMMARY 295 10.9 How Are Certain Transport Processes Driven
PROBLEMS 296 by Light Energy? 341
FURTHER READING 297 Bacteriorhodopsin Uses Light Energy to Drive Proton
Transport 343
10 Membranes and Membrane Transport 299 10.10 How Is Secondary Active Transport Driven
10.1 What Are the Chemical and Physical Properties by Ion Gradients? 343
of Membranes 300 Na+ and H+ Drive Secondary Active Transport 343
The Composition of Membranes Suits Their AcrB Is a Secondary Active Transport System 343
Functions 301
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xiv Detailed Contents
SUMMARY 345 HUMAN BIOCHEMISTRY: Cancer, Oncogenes, and

PROBLEMS 346 Tumour Suppressor Genes 371
FURTHER READING 347 Inositol Phospholipid Breakdown Yields
Inositol-1,4,5-Trisphosphate and Diacylglycerol 372
11 The Reception and Transmission of Extracellular Activation of Phospholipase C Is Mediated by G
Information 349 Proteins or by Tyrosine Kinases 372
Phosphatidylcholine, Sphingomyelin, and
BIOCHEMISTRY: A CANADIAN CONTEXT: Dr. Tony
Glycosphingolipids Also Generate Second
Pawson 351
Messengers 373
11.1 What Are Hormones? 351 Calcium Is a Second Messenger 373
Steroid Hormones Act in Two Ways 351 Intracellular Calcium-Binding Proteins Mediate
Polypeptide Hormones Share Similarities the Calcium Signal 374
of Synthesis and Processing 352 HUMAN BIOCHEMISTRY: PI Metabolism and the
11.2 What Is Signal Transduction? 352 Pharmacology of Li 375
Many Signalling Pathways Involve Enzyme Calmodulin Target Proteins Possess a Basic
Cascades 353 Amphiphilic Helix 375
Signalling Pathways Connect Membrane Interactions 11.5 How Do Effectors Convert the Signals to Actions
with Events in the Nucleus 353 in the Cell? 376
Signalling Pathways Depend on Multiple Molecular Protein Kinase A Is a Paradigm of Kinases 376
Interactions 353 A DEEPER LOOK: Mitogen-Activated Protein Kinases
11.3 How Do Signal-Transducing Receptors Respond and Phosphorelay Systems 377
to the Hormonal Message? 355 Protein Kinase C Is a Family of Isozymes 378
The G-Protein–Coupled Receptors Are 7-TMS Integral Protein Tyrosine Kinase pp60c-src Is Regulated
Membrane Proteins 357 by Phosphorylation/Dephosphorylation 378
The Single TMS Receptors Are Guanylyl Cyclases Protein Tyrosine Phosphatase SHP-2 Is a Non-receptor
or Tyrosine Kinases 357 Tyrosine Phosphatase 379
RTKs and RGCs Are Membrane-Associated Allosteric 11.6 How Are Signalling Pathways Organized
Enzymes 358 and Integrated? 379
EGF Receptor Is Activated by Ligand-Induced GPCRs Can Signal Through G-Protein–Independent
Dimerization 359 Pathways 380
EGF Receptor Activation Forms an Asymmetric G Protein Signalling Is Modulated by RGS/GAPs 380
Tyrosine Kinase Dimer 359
GPCR Desensitization Leads to New Signalling
The Insulin Receptor Mediates Several Signalling Pathways 383
Pathways 361
A DEEPER LOOK: Whimsical Names for Proteins and
The Insulin Receptor Adopts a Folded Dimeric Genes 384
Structure in the Membrane 362
Receptor Responses Can Be Coordinated by
Autophosphorylation of the Insulin Receptor Kinase Transactivation 384
Opens the Active Site 363
Signals from Multiple Pathways Can Be
Receptor Guanylyl Cyclases Mediate Effects Integrated 384
of Natriuretic Hormones 363
11.7 How Do Neurotransmission Pathways Control
A Symmetric Dimer Binds an Asymmetric Peptide
the Function of Sensory Systems? 386
Ligand 364
Nerve Impulses Are Carried by Neurons 386
Non-receptor Tyrosine Kinases Are Typified by
pp60src 365 Ion Gradients Are the Source of Electrical Potentials in
Neurons 387
Soluble Guanylyl Cyclases Are Receptors for Nitric
Oxide 366 Action Potentials Carry the Neural Message 387
A DEEPER LOOK: Nitric Oxide, Nitroglycerine, and The Action Potential Is Mediated by the Flow of Naⴙ
Alfred Nobel 366 and Kⴙ Ions 387
Neurons Communicate at the Synapse 389
11.4 How Are Receptor Signals Transduced? 367
Communication at Cholinergic Synapses Depends
GPCR Signals Are Transduced by G Proteins 367
upon Acetylcholine 390
Cyclic AMP Is a Second Messenger 368
There Are Two Classes of Acetylcholine Receptors 390
cAMP Activates Protein Kinase A 369
The Nicotinic Acetylcholine Receptor Is a Ligand-
Ras and Other Small GTP-Binding Proteins Gated Ion Channel 391
Are Proto-oncogene Products 369
Acetylcholinesterase Degrades Acetylcholine
G Proteins Are Universal Signal Transducers 370 in the Synaptic Cleft 392
Specific Phospholipases Release Second A DEEPER LOOK: Tetrodotoxin and Saxitoxin Are Na
Messengers 370 Channel Toxins 393
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Detailed Contents xv
Muscarinic Receptor Function Is Mediated by G The Michaelis Constant, Km, Is Defined as

Proteins 394 (k1k2)/k1 413
Other Neurotransmitters Can Act Within When [S] Km, v Vmax/2 413
Synaptic Junctions 395 Plots of v Versus [S] Illustrate the Relationships
Glutamate and Aspartate Are Excitatory Amino Acid between Vmax, Km, and Reaction Order 414
Neurotransmitters 395 Turnover Number Defines the Activity of One Enzyme
G-Aminobutyric Acid and Glycine Are Inhibitory Molecule 415
Neurotransmitters 395 The Ratio kcat/km Defines the Catalytic Efficiency of an
HUMAN BIOCHEMISTRY: The Biochemistry of Enzyme 415
Neurological Disorders 397 Linear Plots Can Be Derived from the Michaelis–
The Catecholamine Neurotransmitters Menten Equation 416
Are Derived from Tyrosine 398 Non-linear Lineweaver–Burk or Hanes–Woolf Plots
Various Peptides Also Act as Neurotransmitters 399 Are a Property of Regulatory Enzymes 418
SUMMARY 399 Enzymatic Activity Is Strongly Influenced by pH 418
PROBLEMS 400 A DEEPER LOOK: An Example of the Effect of Amino
Acid Substitutions on Km and kcat: Wild-Type
FURTHER READING 401
and Mutant Forms of Human Sulfite Oxidase 418
The Response of Enzymatic Activity to Temperature Is
Complex 419
PART II Protein Dynamics 12.4 What Can Be Learned from the Inhibition
of Enzyme Activity? 419
12 Enzymes—Kinetics and Specificity 403 Enzymes May Be Inhibited Reversibly or
Irreversibly 419
Enzymes Are the Agents of Metabolic Function 404
Reversible Inhibitors May Bind at the Active Site
12.1 What Characteristic Features Define Enzymes? 404 or at Some Other Site 419
BIOCHEMISTRY: A CANADIAN CONTEXT: The A DEEPER LOOK: The Equations of Competitive
Discovery of Ribozymes 404 Inhibition 421
Catalytic Power Is Defined as the Ratio of the Enzyme- Enzymes Can Also Be Inhibited in an Irreversible
Catalyzed Rate of a Reaction to the Uncatalyzed Manner 423
Rate 405
12.5 What Is the Kinetic Behaviour of Enzymes
Specificity Is the Term Used to Define the Selectivity of Catalyzing Bimolecular Reactions? 425
Enzymes for Their Substrates 405
HUMAN BIOCHEMISTRY: Viagra—An Unexpected
Regulation of Enzyme Activity Ensures That the Rate Outcome in a Program of Drug Design 426
of Metabolic Reactions Is Appropriate to Cellular
The Conversion of AEB to PEQ Is the Rate-Limiting
Requirements 405
Step in Random Single-Displacement Reactions 426
Enzyme Nomenclature Provides a Systematic Way of
In an Ordered Single-Displacement Reaction, the
Naming Metabolic Reactions 406
Leading Substrate Must Bind First 427
Coenzymes and Cofactors Are Non-protein
Double-Displacement (Ping-Pong) Reactions Proceed
Components Essential to Enzyme Activity 407
via Formation of a Covalently Modified Enzyme
12.2 Can the Rate of an Enzyme-Catalyzed Reaction Intermediate 428
Be Defined in a Mathematical Way? 408 Exchange Reactions Are One Way to Diagnose
Chemical Kinetics Provides a Foundation for Exploring Bisubstrate Mechanisms 429
Enzyme Kinetics 408 Multisubstrate Reactions Can Also Occur in Cells 430
Bimolecular Reactions Are Reactions Involving Two
12.6 How Can Enzymes Be So Specific? 431
Reactant Molecules 409
The “Lock and Key” Hypothesis Was the First
Catalysts Lower the Free Energy of Activation for a
Explanation for Specificity 431
Reaction 409
The “Induced Fit” Hypothesis Provides a More
Decreasing ΔG‡ Increases Reaction Rate 410
Accurate Description of Specificity 431
12.3 What Equations Define the Kinetics of “Induced Fit” Favours Formation of the Transition
Enzyme-Catalyzed Reactions? 411 State 432
The Substrate Binds at the Active Site of an Specificity and Reactivity 432
Enzyme 411
12.7 Are All Enzymes Proteins? 432
The Michaelis–Menten Equation Is the Fundamental
Equation of Enzyme Kinetics 411 RNA Molecules That Are Catalytic Have Been Termed
“Ribozymes” 432
Assume That [ES] Remains Constant During an
Enzymatic Reaction 412 Antibody Molecules Can Have Catalytic Activity 434
Assume That Velocity Measurements Are Made 12.8 Is It Possible to Design an Enzyme to Catalyze
Immediately After Adding S 412 Any Desired Reaction? 435
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CRITICAL DEVELOPMENTS IN BIOCHEMISTRY: As Product Accumulates, the Apparent Rate of the

Drug Discovery and Personalized Medicine 436 Enzymatic Reaction Decreases 478
SUMMARY 437 Genetic Regulation of Enzyme Synthesis and Decay
PROBLEMS 438 Determines the Amount of Enzyme Present at Any
Moment 478
FURTHER READING 440
Enzyme Activity Can Be Regulated Allosterically 478
13 Mechanisms of Enzyme Action 442 Allosteric Regulation of Phosphofructokinase 479
13.1 What Are the Magnitudes of Enzyme-Induced Enzyme Activity Can Be Regulated Through Covalent
Rate Accelerations? 442 Modification 480
13.2 What Role Does Transition-State Stabilization Regulation of Enzyme Activity Can Also Be
Play in Enzyme Catalysis? 444 Accomplished in Other Ways 480
13.3 How Does Destabilization of ES Affect Enzyme Zymogens Are Inactive Precursors of Enzymes 481
Catalysis? 445 Isozymes Are Enzymes with Slightly Different
13.4 How Tightly Do Transition-State Analogs Bind Subunits 481
to the Active Site? 447 14.2 What Are the General Features of Allosteric
A DEEPER LOOK: Transition-State Analogs Make Our Regulation? 483
World Better 448 Regulatory Enzymes Have Certain Exceptional
13.5 What Are the Mechanisms of Catalysis? 450 Properties 483
Enzymes Facilitate Formation of Near-Attack 14.3 Can Allosteric Regulation Be Explained
Conformations 450 by Conformational Changes in Proteins? 484
A DEEPER LOOK: How to Read and Write The Symmetry Model for Allosteric Regulation Is
Mechanisms 452 Based on 2 Conformational States for a Protein 484
Covalent Catalysis 453 Conformational Changes 485
General Acid–Base Catalysis 454 Changes in the Oligomeric State of a Protein Can Also
Result in Allosteric Behaviour 485
Low-Barrier Hydrogen Bonds 455
Metal Ion Catalysis 456 14.4 What Kinds of Covalent Modification Regulate
the Activity of Enzymes? 486
A DEEPER LOOK: How Do Active-Site Residues
Interact to Support Catalysis? 457 Covalent Modification Through Reversible
Phosphorylation 486
The Hydrolytic Mechanism of Lysozyme 457
Protein Kinases: Target Recognition and Intrasteric
13.6 What Can Be Learned from Typical Enzyme Control 487
Mechanisms? 459
Phosphorylation Is Not the Only Form of Covalent
Serine Proteases 459
Modification That Regulates Protein Function 488
The Digestive Serine Proteases 459
14.5 Is the Activity of Some Enzymes Controlled
The Chymotrypsin Mechanism in Detail: Kinetics 460 by Both Allosteric Regulation and Covalent
The Serine Protease Mechanism in Detail: Events at Modification? 489
the Active Site 460 The Pyruvate Dehydrogenase Reaction Links Glycolysis
The Aspartic Proteases 462 to the Citric Acid Cycle 489
A DEEPER LOOK: Transition-State Stabilization in the Pyruvate Dehydrogenase Activity Is Regulated Both
Serine Proteases 464 Allosterically and Covalently 489
The Mechanism of Action of Aspartic Proteases 465 14.6 Is There an Example in Nature of the Relationship
The AIDS Virus HIV-1 Protease Is an Aspartic Protease 465 between Quaternary Structure and the Emergence of
Chorismate Mutase: A Model for Understanding Allosteric Properties? Hemoglobin and Myoglobin—
Catalytic Power and Efficiency 466 Paradigms of Protein Structure and Function 490
HUMAN BIOCHEMISTRY: Protease Inhibitors Give The Comparative Biochemistry of Myoglobin and
Life to AIDS Patients 468 Hemoglobin Reveals Insights into Allostery 491
CRITICAL DEVELOPMENTS IN BIOCHEMISTRY: Myoglobin Is an Oxygen-Storage Protein 492
Caught in the Act! A High-Energy Intermediate in the O2 Binds to the Mb Heme Group 492
Phosphoglucomutase Reaction 470 O2 Binding Alters Mb Conformation 492
SUMMARY 472 Cooperative Binding of Oxygen by Hemoglobin Has
PROBLEMS 473 Important Physiological Significance 493
FURTHER READING 475 Hemoglobin Has an a2b2 Tetrameric Structure 493
Oxygenation Markedly Alters the Quaternary Structure
14 Enzyme Regulation 477 of Hb 493
14.1 What Factors Influence Enzymatic Activity? 478 Movement of the Heme Iron Ion by Less Than
The Availability of Substrates and Cofactors Usually 0.04 nm Induces the Conformational Change in
Determines How Fast the Reaction Goes 478 Hemoglobin 493
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A DEEPER LOOK: The Oxygen-Binding Curves of HUMAN BIOCHEMISTRY: Effectors of Microtubule

Myoglobin and Hemoglobin 494 Polymerization as Therapeutic Agents 519
A DEEPER LOOK: The Physiological Significance of the Dyneins Move Organelles in a Plus-to-Minus Direction;
Hb:O2 Interaction 496 Kinesins, in a Minus-to-Plus Direction—Mostly 520
The Oxy and Deoxy Forms of Hemoglobin Represent Cytoskeletal Motors Are Highly Processive 521
2 Different Conformational States 496 ATP Binding and Hydrolysis Drive Hand-over-Hand
The Allosteric Behaviour of Hemoglobin Has Both Movement of Kinesin 521
Symmetry (MWC) Model and Sequential (KNF) Model The Conformation Change That Leads to Movement Is
Components 496 Different in Myosins and Dyneins 522
H+ Promotes the Dissociation of Oxygen from 15.4 How Do Molecular Motors Unwind DNA? 522
Hemoglobin 497
Negative Cooperativity Facilitates Hand-over-Hand
CO2 Also Promotes the Dissociation of O2 from Movement 525
Hemoglobin 497
Papillomavirus E1 Helicase Moves along DNA on a
A DEEPER LOOK: Changes in the Heme Iron upon O2 Spiral Staircase 526
Binding 497
15.5 How Do Bacterial Flagella Use a Proton Gradient
2,3-Bisphosphoglycerate Is an Important Allosteric to Drive Rotation? 527
Effector for Hemoglobin 498
The Flagellar Rotor Is a Complex Structure 528
BPG Binding to Hb Has Important Physiological
Gradients of Hⴙ and Naⴙ Drive Flagellar Rotors 528
Significance 499
The Flagellar Rotor Self-Assembles in a Spontaneous
Fetal Hemoglobin Has a Higher Affinity for O2
Process 530
Because It Has a Lower Affinity for BPG 499
Flagellar Filaments Are Composed of Protofilaments
HUMAN BIOCHEMISTRY: Hemoglobin and Nitric
of Flagellin 531
Oxide 500
Motor Reversal Involves Conformational Switching of
Sickle-Cell Anemia Is Characterized by Abnormal Red
Motor and Filament Proteins 531
Blood Cells 501
Sickle-Cell Anemia Is a Molecular Disease 501 SUMMARY 533
SUMMARY 502 PROBLEMS 533
PROBLEMS 503 FURTHER READING 534
FURTHER READING 504
15 Molecular Motors 505 PART III Metabolism and Its Regulation

15.1 What Is a Molecular Motor? 505
15.2 What Is the Molecular Mechanism of Muscle
Contraction? 506
16 Nutrition and the Organization of Metabolism 537
16.1 Is Metabolism Similar in Different Organisms? 538
Muscle Contraction Is Triggered by Ca2ⴙ Release
from Intracellular Stores 506 Living Things Exhibit Metabolic Diversity 538
The Molecular Structure of Skeletal Muscle Is Based Oxygen Is Essential to Life for Aerobes 538
on Actin and Myosin 506 A DEEPER LOOK: Calcium Carbonate—A Biological
HUMAN BIOCHEMISTRY: Smooth Muscle Effectors Sink for CO2 539
Are Useful Drugs 507 The Flow of Energy in the Biosphere and the Carbon
HUMAN BIOCHEMISTRY: The Molecular Defect in and Oxygen Cycles Are Intimately Related 539
Duchenne Muscular Dystrophy Involves an Actin- 16.2 What Can Be Learned from Metabolic Maps? 539
Anchoring Protein 510 The Metabolic Map Can Be Viewed as a Set of Dots
The Mechanism of Muscle Contraction Is Based on and Lines 539
Sliding Filaments 511 Alternative Models Can Provide New Insights into
A DEEPER LOOK: The P-Loop: A Common Motif Pathways 540
in Enzymes That Hydrolyze Nucleoside Multi-enzyme Systems May Take Different Forms 542
Triphosphates 512 16.3 How Do Anabolic and Catabolic Processes
CRITICAL DEVELOPMENTS IN BIOCHEMISTRY: Form the Core of Metabolic Pathways? 543
Molecular “Tweezers” of Light Take the Measure of a Anabolism Is Biosynthesis 543
Muscle Fibre’s Force 514
Anabolism and Catabolism Are Not Mutually
15.3 What Are the Molecular Motors That Orchestrate Exclusive 544
the Mechanochemistry of Microtubules? 515
The Pathways of Catabolism Converge to a Few End
Filaments of the Cytoskeleton Are Highways Products 544
That Move Cellular Cargo 515
Anabolic Pathways Diverge, Synthesizing an
Three Classes of Motor Proteins Move Intracellular Astounding Variety of Biomolecules from a Limited
Cargo 516 Set of Building Blocks 546
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xviii Detailed Contents
Amphibolic Intermediates Play Dual Roles 546 Reaction 7: Phosphoglycerate Kinase Is the Break-
Corresponding Pathways of Catabolism and Even Reaction 575
Anabolism Differ in Important Ways 546 Reaction 8: Phosphoglycerate Mutase Catalyzes
ATP Serves in a Cellular Energy Cycle 546 a Phosphoryl Transfer 576
NAD Collects Electrons Released in Catabolism 547 Reaction 9: Dehydration by Enolase Creates PEP 577
NADPH Provides the Reducing Power for Anabolic Reaction 10: Pyruvate Kinase Yields More ATP 577
Processes 548 17.5 What Are the Metabolic Fates of NADH and
Coenzymes and Vitamins Provide Unique Chemistry Pyruvate Produced in Glycolysis? 580
and Essential Nutrients to Pathways 549 Anaerobic Metabolism of Pyruvate Leads
16.4 What Experiments Can Be Used to Elucidate to Lactate or Ethanol 580
Metabolic Pathways? 550 Lactate Accumulates under Anaerobic Conditions
Mutations Create Specific Metabolic Blocks 551 in Animal Tissues 581
Isotopic Tracers Can Be Used as Metabolic Probes 551 17.6 How Do Cells Regulate Glycolysis? 581
NMR Spectroscopy Is a Non-invasive Metabolic 17.7 Are Substrates Other Than Glucose Used
Probe 552 in Glycolysis? 581
Metabolic Pathways Are Compartmentalized within HUMAN BIOCHEMISTRY: Tumour Diagnosis Using
Cells 553 Positron Emission Tomography (PET) 582
16.5 What Can the Metabolome Tell Us about Mannose Enters Glycolysis in Two Steps 583
a Biological System? 555 Galactose Enters Glycolysis via the Leloir Pathway 583
16.6 What Food Substances Form the Basis of Human An Enzyme Deficiency Causes Lactose Intolerance 585
Nutrition? 557 Glycerol Can Also Enter Glycolysis 585
Humans Require Protein 557 HUMAN BIOCHEMISTRY: Lactose—From Mother’s
Carbohydrates Provide Metabolic Energy 557 Milk to Yogurt—and Lactose Intolerance 585
A DEEPER LOOK: A Popular Fad Diet—Low 17.8 How Do Cells Respond to Hypoxic Stress? 586
Carbohydrates, High Protein, High Fat 557 SUMMARY 587
Lipids Are Essential, But in Moderation 558
PROBLEMS 588
Fibre May Be Soluble or Insoluble 558
FURTHER READING 589
SUMMARY 558
PROBLEMS 559 18 The Tricarboxylic Acid Cycle 591
FURTHER READING 559 18.1 What Is the Chemical Logic of the TCA
Cycle? 593
17 Glycolysis 561 The TCA Cycle Provides a Chemically Feasible Way of
17.1 What Are the Essential Features of Glycolysis? 562 Cleaving a 2-Carbon Compound 593
17.2 Why Are Coupled Reactions Important in 18.2 How Is Pyruvate Oxidatively Decarboxylated
Glycolysis? 563 to Acetyl-CoA? 595
17.3 What Are the Chemical Principles and Features A DEEPER LOOK: The Coenzymes of the Pyruvate
of the First Phase of Glycolysis? 564 Dehydrogenase Complex 597
Reaction 1: Glucose Is Phosphorylated by Hexokinase 18.3 How Are 2 CO2 Molecules Produced from
or Glucokinase—The First Priming Reaction 565 Acetyl-CoA? 600
Reaction 2: Phosphoglucoisomerase Catalyzes the The Citrate Synthase Reaction Initiates the TCA
Isomerization of Glucose-6-Phosphate 568 Cycle 600
Reaction 3: ATP Drives a Second Phosphorylation Isocitrate Dehydrogenase Catalyzes the First Oxidative
by Phosphofructokinase—The Second Priming Decarboxylation in the Cycle 602
Reaction 569 a-Ketoglutarate Dehydrogenase Catalyzes the Second
A DEEPER LOOK: Phosphoglucoisomerase: Oxidative Decarboxylation of the TCA Cycle 603
A Moonlighting Protein 570 18.4 How Is Oxaloacetate Regenerated to Complete
Reaction 4: Cleavage by Fructose Bisphosphate the TCA Cycle? 604
Aldolase Creates Two, Three-Carbon Succinyl-CoA Synthetase Catalyzes Substrate Level
Intermediates 571 Phosphorylation 604
Reaction 5: Triose Phosphate Isomerase Completes The First 5 Steps of the TCA Cycle Produce NADH,
the First Phase of Glycolysis 572 CO2, GTP (ATP), and Succinate 605
17.4 What Are the Chemical Principles and Features Succinate Dehydrogenase Is FAD Dependent 605
of the Second Phase of Glycolysis? 573 Fumarase Catalyzes the Trans-Hydration of Fumarate
Reaction 6: Glyceraldehyde-3-Phosphate to Form l-Malate 606
Dehydrogenase Creates a High-Energy Malate Dehydrogenase Completes the Cycle by
Intermediate 573 Oxidizing Malate to Oxaloacetate 606
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Detailed Contents xix
18.5 What Are the Energetic Consequences HUMAN BIOCHEMISTRY: Solving a Medical Mystery
of the TCA Cycle? 607 Revolutionized Our Treatment of Parkinson’s
The Carbon Atoms of Acetyl-CoA Have Different Fates Disease 631
in the TCA Cycle 607 Complex II Oxidizes Succinate and Reduces
A DEEPER LOOK: Steric Preferences in NAD- Coenzyme Q 631
Dependent Dehydrogenases 608 Complex III Mediates Electron Transport from
18.6 Can the TCA Cycle Provide Intermediates Coenzyme Q to Cytochrome c 633
for Biosynthesis? 610 Complex IV Transfers Electrons from
HUMAN BIOCHEMISTRY: Mitochondrial Diseases Cytochrome c to Reduce Oxygen on the Matrix
Are Rare 611 Side 635
18.7 What Are the Anaplerotic, or “Filling-Up,” Proton Transport across Cytochrome c Oxidase
Reactions? 611 Is Coupled to Oxygen Reduction 637
A DEEPER LOOK: Fool’s Gold and the Reductive Citric The Four Electron-Transport Complexes Are
Acid Cycle—The First Metabolic Pathway? 612 Independent 638
Electron Transfer Energy Stored in a Proton Gradient:
18.8 How Is the TCA Cycle Regulated? 613
The Mitchell Hypothesis 639
Pyruvate Dehydrogenase Is Regulated by
Phosphorylation/Dephosphorylation 613 19.4 What Are the Thermodynamic Implications
of Chemiosmotic Coupling? 640
Isocitrate Dehydrogenase Is Strongly Regulated 615
19.5 How Does a Proton Gradient Drive
18.9 Can Any Organisms Use Acetate as Their Sole the Synthesis of ATP? 641
Carbon Source? 615
ATP Synthase Is Composed of F1 and F0 641
The Glyoxylate Cycle Operates in Specialized
Organelles 616 The Catalytic Sites of ATP Synthase Adopt Three
Different Conformations 643
Isocitrate Lyase Short-Circuits the TCA Cycle by
Producing Glyoxylate and Succinate 616 Boyer’s 18O Exchange Experiment Identified
the Energy-Requiring Step 643
The Glyoxylate Cycle Helps Plants Grow in
the Dark 617 Boyer’s Binding Change Mechanism Describes
the Events of Rotational Catalysis 644
Glyoxysomes Must Borrow 3 Reactions from
Mitochondria 617 Proton Flow through F0 Drives Rotation of the Motor
and Synthesis of ATP 644
SUMMARY 618
Racker and Stoeckenius Confirmed the Mitchell Model
PROBLEMS 619 in a Reconstitution Experiment 646
FURTHER READING 620 Inhibitors of Oxidative Phosphorylation Reveal Insights
about the Mechanism 646
19 Electron Transport and Oxidative Uncouplers Disrupt the Coupling of Electron Transport
Phosphorylation 621 and ATP Synthase 647
19.1 Where in the Cell Do Electron Transport ATP–ADP Translocase Mediates the Movement
and Oxidative Phosphorylation Occur? 622 of ATP and ADP across the Mitochondrial
Mitochondrial Functions Are Localized in Specific Membrane 648
Compartments 622 HUMAN BIOCHEMISTRY: Endogenous
The Mitochondrial Matrix Contains the Enzymes of the Uncouplers Enable Organisms to Generate
TCA Cycle 623 Heat 649
19.2 What Are Reduction Potentials, and How Are 19.6 What Is the P/O Ratio for Mitochondrial Oxidative
They Used to Account for Free Energy Changes Phosphorylation? 649
in Redox Reactions? 623 19.7 How Are the Electrons of Cytosolic NADH Fed
Standard Reduction Potentials Are Measured into Electron Transport? 650
in Reaction Half-Cells 624 The Glycerophosphate Shuttle Ensures Efficient
e0’ Values Can Be Used to Predict the Direction Use of Cytosolic NADH 651
of Redox Reactions 625 The Malate–Aspartate Shuttle Is Reversible 651
e0’ Values Can Be Used to Analyze Energy Changes The Net Yield of ATP from Glucose Oxidation
in Redox Reactions 626 Depends on the Shuttle Used 652
The Reduction Potential Depends on 3.5 Billion Years of Evolution Have Resulted
Concentration 626 in a Very Efficient System 653
19.3 How Is the Electron-Transport Chain 19.8 How Do Mitochondria Mediate Apoptosis? 653
Organized? 627 Cytochrome c Triggers Apoptosome Assembly 654
The Electron-Transport Chain Can Be Isolated in
SUMMARY 655
Four Complexes 628
PROBLEMS 656
Complex I Oxidizes NADH and Reduces
Coenzyme Q 629 FURTHER READING 658
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xx Detailed Contents
20 Photosynthesis 659
Cyclic Photophosphorylation Generates ATP but Not
NADPH or O2 679
20.1 What Are the General Properties of
20.7 How Is Carbon Dioxide Used to Make Organic
Photosynthesis? 660
Molecules? 680
Photosynthesis Occurs in Membranes 660
Ribulose-1,5-Bisphosphate Is the CO2 Acceptor in CO2
Photosynthesis Consists of Both Light Reactions Fixation 680
and Dark Reactions 662
2-Carboxy-3-Keto-Arabinitol Is an Intermediate in the
Water Is the Ultimate e Donor for Photosynthetic Ribulose-1,5-Bisphosphate Carboxylase Reaction 681
NADP Reduction 663
Ribulose-1,5-Bisphosphate Carboxylase Exists in
20.2 How Is Solar Energy Captured by Chlorophyll? 663 Inactive and Active Forms 681
Chlorophylls and Accessory Light-Harvesting Pigments CO2 Fixation into Carbohydrate Proceeds
Absorb Light of Different Wavelengths 664 via the Calvin–Benson Cycle 682
The Light Energy Absorbed by Photosynthetic The Enzymes of the Calvin Cycle Serve 3 Metabolic
Pigments Has Several Possible Fates 665 Purposes 682
The Transduction of Light Energy into Chemical Energy The Calvin Cycle Reactions Can Account for Net
Involves Oxidation–Reduction 666 Hexose Synthesis 683
Photosynthetic Units Consist of Many Chlorophyll The Carbon Dioxide Fixation Pathway Is Indirectly
Molecules but Only a Single Reaction Centre 667 Activated by Light 683
20.3 What Kinds of Photosystems Are Used to Capture Light Induces Movement of Mg2 Ions from the
Light Energy? 667 Thylakoid Vesicles into the Stroma 686
Chlorophyll Exists in Plant Membranes in Association Protein–Protein Interactions Mediated by an
with Proteins 668 Intrinsically Unstructured Protein Also Regulate
PSI and PSII Participate in the Overall Process of Calvin–Benson Cycle Activity 686
Photosynthesis 668 20.8 How Does Photorespiration Limit CO2
The Pathway of Photosynthetic Electron Transfer Fixation? 686
Is Called the Z Scheme 668 Tropical Grasses Use the Hatch–Slack Pathway to
Oxygen Evolution Requires the Accumulation of 4 Capture Carbon Dioxide for CO2 Fixation 686
Oxidizing Equivalents in PSII 670 Cacti and Other Desert Plants Capture CO2 at
Electrons Are Taken from H2O to Replace Electrons Night 689
Lost from P680 670 SUMMARY 689
Electrons from PSII Are Transferred to PSI via the PROBLEMS 690
Cytochrome b6f Complex 670
FURTHER READING 691
Plastocyanin Transfers Electrons from the Cytochrome
b6f Complex to PSI 671
21 Gluconeogenesis, Glycogen Metabolism, and
20.4 What Is the Molecular Architecture of the Pentose Phosphate Pathway 693
Photosynthetic Reaction Centres? 671
21.1 What Is Gluconeogenesis, and How Does It
The R. viridis Photosynthetic Reaction Centre Is an
Operate? 694
Integral Membrane Protein 672
BIOCHEMISTRY: A CANADIAN CONTEXT:
Photosynthetic Electron Transfer by the R. viridis
Reaction Centre Leads to ATP Synthesis 672 Determining the Kinetic Mechanism of
Phosphoenolpyruvate Carboxykinase 694
The Molecular Architecture of PSII Resembles the
R. viridis Reaction Centre Architecture 673 The Substrates for Gluconeogenesis Include Pyruvate,
Lactate, and Amino Acids 695
How Does PSII Generate O2 from H2O? 674
Nearly All Gluconeogenesis Occurs in the Liver and
The Molecular Architecture of PSI Resembles the
Kidneys in Animals 695
R. viridis Reaction Centre and PSII Architecture 675
HUMAN BIOCHEMISTRY: The Chemistry of Glucose
How Do Green Plants Carry Out Photosynthesis? 675
Monitoring Devices 695
20.5 What Is the Quantum Yield of Photosynthesis? 677
Gluconeogenesis Is Not Merely the Reverse of
Calculation of the Photosynthetic Energy Glycolysis 696
Requirements for Hexose Synthesis Depends on
Gluconeogenesis: Something Borrowed, Something
H/hn and ATP/H Ratios 677
New 696
20.6 How Does Light Drive the Synthesis of ATP? 677 Four Reactions Are Unique to Gluconeogenesis 696
The Mechanism of Photophosphorylation Is HUMAN BIOCHEMISTRY: Gluconeogenesis Inhibitors
Chemiosmotic 678 and Other Diabetes Therapy Strategies 701
CF1CF0–ATP Synthase Is the Chloroplast Equivalent of
21.2 How Is Gluconeogenesis Regulated? 701
the Mitochondrial F1F0–ATP Synthase 678
CRITICAL DEVELOPMENTS IN BIOCHEMISTRY:
Photophosphorylation Can Occur in Either a
The Pioneering Studies of Carl and Gerty Cori 702
Non-cyclic or a Cyclic Mode 678
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Detailed Contents xxi
Gluconeogenesis Is Regulated by Allosteric and

Substrate-Level Control Mechanisms 703
22 Fatty Acid Catabolism 735
Substrate Cycles Provide Metabolic Control 22.1 How Are Fats Mobilized from Dietary Intake
Mechanisms 705 and Adipose Tissue? 736
Modern Diets Are Often High in Fat 736
21.3 How Are Glycogen and Starch Catabolized
in Animals? 705 Triacylglycerols Are a Major Form of Stored Energy in
Animals 736
Dietary Starch Breakdown Provides Metabolic
Energy 705 Hormones Trigger the Release of Fatty Acids from
Adipose Tissue 736
Metabolism of Tissue Glycogen Is Regulated 706
Degradation of Dietary Fatty Acids Occurs Primarily
21.4 How Is Glycogen Synthesized? 708 in the Duodenum 737
Glucose Units Are Activated for Transfer by Formation
22.2 How Are Fatty Acids Broken Down? 739
of Sugar Nucleotides 708
Knoop Elucidated the Essential Feature of
UDP–Glucose Synthesis Is Driven by Pyrophosphate
b-Oxidation 739
Hydrolysis 708
Glycogen Synthase Catalyzes Formation of a(1→4) Coenzyme A Activates Fatty Acids for Degradation 740
Glycosidic Bonds in Glycogen 709 Carnitine Carries Fatty Acyl Groups Across the Inner
HUMAN BIOCHEMISTRY: Advanced Glycation End Mitochondrial Membrane 741
Products: A Serious Complication of Diabetes 710 b-Oxidation Involves a Repeated Sequence of 4
Glycogen Branching Occurs by Transfer of Terminal Reactions 741
Chain Segments 710 HUMAN BIOCHEMISTRY: Carnitine Deficiency 742
21.5 How Is Glycogen Metabolism Controlled? 711 Repetition of the b-Oxidation Cycle Yields a
Glycogen Metabolism Is Highly Regulated 711 Succession of Acetate Units 746
Glycogen Synthase Is Regulated by Covalent Complete b-Oxidation of 1 Palmitic Acid Yields 106
Modification 711 Molecules of ATP 746
The Glycogen Phosphorylase Reaction Converts Migratory Birds Travel Long Distances on Energy from
Glycogen into Readily Usable Fuel in the Form of Fatty Acid Oxidation 747
Glucose-1-Phosphate 712 HUMAN BIOCHEMISTRY: Exercise Can Reverse the
Glycogen Phosphorylase Is a Homodimer 713 Consequences of Metabolic Syndrome 748
Glycogen Phosphorylase Activity Is Regulated Fatty Acid Oxidation Is an Important Source of
Allosterically 713 Metabolic Water for Some Animals 748
Covalent Modification of Glycogen Phosphorylase 22.3 How Are Odd-Carbon Fatty Acids Oxidized? 749
Trumps Allosteric Regulation 716 b-Oxidation of Odd-Carbon Fatty Acids Yields
Enzyme Cascades Regulate Glycogen Phosphorylase Propionyl-CoA 749
Covalent Modification 716 A B12-Catalyzed Rearrangement Yields Succinyl-CoA
Hormones Regulate Glycogen Synthesis and from l-Methylmalonyl-CoA 750
Degradation 717 Net Oxidation of Succinyl-CoA Requires Conversion
A DEEPER LOOK: Carbohydrate Utilization in to Acetyl-CoA 750
Exercise 718 A DEEPER LOOK: The Activation of Vitamin B12 751
HUMAN BIOCHEMISTRY: Von Gierke’s Disease: A 22.4 How Are Unsaturated Fatty Acids Oxidized? 752
Glycogen-Storage Disease 719
An Isomerase and a Reductase Facilitate the
21.6 Can Glucose Provide Electrons for b-Oxidation of Unsaturated Fatty Acids 752
Biosynthesis? 722 A DEEPER LOOK: Can Natural Antioxidants in Certain
The Pentose Phosphate Pathway Operates Mainly in Foods Improve Fat Metabolism? 752
Liver and Adipose Cells 722 Degradation of Polyunsaturated Fatty Acids Requires
The Pentose Phosphate Pathway Begins with Two 2,4-Dienoyl-CoA Reductase 753
Oxidative Steps 722
22.5 Are There Other Ways to Oxidize Fatty Acids? 753
There Are Four Non-oxidative Reactions in the
Peroxisomal b-Oxidation Requires FAD-Dependent
Pentose Phosphate Pathway 722
Acyl-CoA Oxidase 753
HUMAN BIOCHEMISTRY: Aldose Reductase and
Branched-Chain Fatty Acids Are Degraded via
Diabetic Cataract Formation 725
a-Oxidation 753
Utilization of Glucose-6-P Depends on the Cell’s Need
v-Oxidation of Fatty Acids Yields Small Amounts
for ATP, NADPH, and Ribose-5-P 728
of Dicarboxylic Acids 753
Xylulose-5-Phosphate Is a Metabolic Regulator 730
HUMAN BIOCHEMISTRY: Refsum’s Disease Is a
SUMMARY 731 Result of Defects in a-Oxidation 755
PROBLEMS 731 22.6 What Are Ketone Bodies, and What Role Do
FURTHER READING 733 They Play in Metabolism? 756
NEL
xxii Detailed Contents
Ketone Bodies Are a Significant Source of Fuel and A DEEPER LOOK: Amino Acid Biosynthesis Inhibitors
Energy for Certain Tissues 756 as Herbicides 795
HUMAN BIOCHEMISTRY: Large Amounts of Ketone A DEEPER LOOK: Intramolecular Tunnels Connect
Bodies Are Produced in Diabetes Mellitus 757 Distant Active Sites in Some Enzymes 796
SUMMARY 757 Histidine Biosynthesis and Purine Biosynthesis Are
PROBLEMS 758 Connected by Common Intermediates 796
FURTHER READING 759 23.5 How Does Amino Acid Catabolism Lead into
Pathways of Energy Production? 798
23 Nitrogen Acquisition and Amino Acid The Twenty Common Amino Acids Are Degraded
Metabolism 761 by Twenty Different Pathways That Converge to Just
Seven Metabolic Intermediates 798
23.1 Which Metabolic Pathways Allow Organisms
A DEEPER LOOK: Histidine—A Clue to Understanding
to Live on Inorganic Forms of Nitrogen? 762
Early Evolution? 800
Nitrogen Is Cycled between Organisms
A DEEPER LOOK: The Serine Dehydratase Reaction:
and the Inanimate Environment 762
A b-Elimination 801
Nitrate Assimilation Is the Principal Pathway
HUMAN BIOCHEMISTRY: Hereditary Defects
for Ammonium Biosynthesis 763
in Phe Catabolism Underlie Alkaptonuria and
Nitrate Reductase Contains Cytochrome b557 and Phenylketonuria 804
Molybdenum Cofactor 763
Animals Differ in the Form of Nitrogen That They
Organisms Gain Access to Atmospheric N2 via the Excrete 804
Pathway of Nitrogen Fixation 764
SUMMARY 804
23.2 What Is the Metabolic Fate of Ammonium? 768
PROBLEMS 805
The Major Pathways of Ammonium Assimilation Lead
to Glutamine Synthesis 769 FURTHER READING 806
23.3 What Regulatory Mechanisms Act on Escherichia
coli Glutamine Synthetase? 770
Glutamine Synthetase Is Allosterically Regulated 771 PART IV Nucleic Acids
Glutamine Synthetase Is Regulated by Covalent
Modification 771
Glutamine Synthetase Is Regulated through Gene
24 Nucleotides and Nucleic Acids 808
Expression 773 24.1 What Are the Structure and Chemistry
of Nitrogenous Bases? 809
23.4 How Do Organisms Synthesize Amino Acids? 773
Three Pyrimidines and 2 Purines are Commonly
HUMAN BIOCHEMISTRY: Human Dietary
Found in Cells 810
Requirements for Amino Acids 775
The Properties of Pyrimidines and Purines Can Be
Amino Acids Are Formed from a-Keto Acids by
Traced to Their Electron-Rich Nature 810
Transamination 775
24.2 What Are Nucleosides? 811
A DEEPER LOOK: The Mechanism of the
Aminotransferase (Transamination) Reaction 776 HUMAN BIOCHEMISTRY: Adenosine: A Nucleoside
with Physiological Activity 812
The Pathways of Amino Acid Biosynthesis Can Be
Organized into Families 776 24.3 What Are the Structure and Chemistry
The a-Ketoglutarate Family of Amino Acids Includes of Nucleotides? 813
Glu, Gln, Pro, Arg, and Lys 777 Cyclic Nucleotides Are Cyclic Phosphodiesters 813
The Urea Cycle Acts to Excrete Excess N Through Arg Nucleoside Diphosphates and Triphosphates Are
Breakdown 778 Nucleotides with 2 or 3 Phosphate Groups 813
A DEEPER LOOK: The Urea Cycle as Both an NDPs and NTPs Are Polyprotic Acids 814
Ammonium and a Bicarbonate Disposal Mechanism 782 Nucleoside 5-Triphosphates Are Carriers of Chemical
The Aspartate Family of Amino Acids Includes Asp, Energy 814
Asn, Lys, Met, Thr, and Ile 782 24.4 What Are Nucleic Acids? 815
HUMAN BIOCHEMISTRY: Asparagine and The Base Sequence of a Nucleic Acid Is Its Distinctive
Leukemia 783 Characteristic 815
The Pyruvate Family of Amino Acids Includes Ala, Val, 24.5 What Are the Different Classes of Nucleic
and Leu 785 Acids? 816
The 3-Phosphoglycerate Family of Amino Acids The Fundamental Structure of DNA Is a Double
Includes Ser, Gly, and Cys 788 Helix 817
The Aromatic Amino Acids Are Synthesized from Various Forms of RNA Serve Different Roles in
Chorismate 790 Cells 819
HUMAN BIOCHEMISTRY: Phenylketonuria and A DEEPER LOOK: Do the Properties of DNA Invite
Aspartame 793 Practical Applications? 820
NEL
Detailed Contents xxiii
A DEEPER LOOK: The RNA World and Early Single-Stranded DNA Can Renature to Form DNA
Evolution 823 Duplexes 849
The Chemical Differences between DNA and RNA The Rate of DNA Renaturation Is an Index of DNA
Have Biological Significance 824 Sequence Complexity 849
24.6 Are Nucleic Acids Susceptible to Hydrolysis? 825 A DEEPER LOOK: The Buoyant Density of DNA 849
RNA Is Susceptible to Hydrolysis by Base, but DNA Is Nucleic Acid Hybridization: Different DNA Strands of
Not 826 Similar Sequence Can Form Hybrid Duplexes 850
The Enzymes That Hydrolyze Nucleic Acids Are 25.4 Can DNA Adopt Structures of Higher
Phosphodiesterases 826 Complexity? 850
Nucleases Differ in Their Specificity for Different Forms Supercoils Are One Kind of Structural Complexity in
of Nucleic Acid 827 DNA 851
Restriction Enzymes Are Nucleases That Cleave 25.5 What Is the Structure of Eukaryotic
Double-Stranded DNA Molecules 827 Chromosomes? 853
Type II Restriction Endonucleases Are Useful Nucleosomes Are the Fundamental Structural Unit in
for Manipulating DNA in the Lab 827 Chromatin 853
Restriction Endonucleases Can Be Used to Map Higher-Order Structural Organization of Chromatin
the Structure of a DNA Fragment 828 Gives Rise to Chromosomes 854
SUMMARY 831 SMC Proteins Establish Chromosome Organization
PROBLEMS 831 and Mediate Chromosome Dynamics 855
FURTHER READING 832 25.6 Can Nucleic Acids Be Synthesized Chemically? 856
HUMAN BIOCHEMISTRY: Telomeres and
25 Structure of Nucleic Acids 833 Tumours 857
25.1 How Do Scientists Determine the Primary Phosphoramidite Chemistry Is Used to Form
Structure of Nucleic Acids? 834 Oligonucleotides from Nucleotides 857
The Nucleotide Sequence of DNA Can Be Determined Genes Can Be Synthesized Chemically 858
from the Electrophoretic Migration of a Defined 25.7 What Are the Secondary and Tertiary Structures
Set of Polynucleotide Fragments 834 of RNA? 858
Sanger’s Chain Termination, or Dideoxy, Method Transfer RNA Adopts Higher-Order Structure through
Uses DNA Replication to Generate a Defined Set of Intrastrand Base Pairing 861
Polynucleotide Fragments 834 Ribosomal RNA Also Adopts Higher-Order Structure
High-Throughput DNA Sequencing by the Light of through Intrastrand Base Pairing 863
Fireflies 836 Aptamers Are Oligonucleotides Specifically Selected
25.2 What Sorts of Secondary Structures Can Double- for Their Ligand-Binding Ability 865
Stranded DNA Molecules Adopt? 837 SUMMARY 867
Conformational Variation in Polynucleotide PROBLEMS 868
Strands 837
FURTHER READING 869
DNA Usually Occurs in the Form of Double-Stranded
Molecules 838
26 Synthesis and Degradation of Nucleotides 871
Watson–Crick Base Pairs Have Virtually Identical
26.1 Can Cells Synthesize Nucleotides? 872
Dimensions 838
The DNA Double Helix Is a Stable Structure 839 26.2 How Do Cells Synthesize Purines? 872
Double-Helical Structures Can Adopt a Number of IMP Is the Immediate Precursor to GMP and
Stable Conformations 839 AMP 872
A-Form DNA Is an Alternative Form of Right-Handed A DEEPER LOOK: Tetrahydrofolate and 1-Carbon
DNA 841 Units 875
Z-DNA Is a Conformational Variation in the Form AMP and GMP Are Synthesized from IMP 876
of a Left-Handed Double Helix 841 HUMAN BIOCHEMISTRY: Folate Analogs as
The Double Helix Is a Very Dynamic Structure 843 Antimicrobial and Anticancer Agents 877
Alternative Hydrogen-Bonding Interactions Give Rise The Purine Biosynthetic Pathway Is Regulated at
to Novel DNA Structures: Cruciforms, Triplexes, and Several Steps 877
Quadruplexes 845 ATP-Dependent Kinases Form Nucleoside
Diphosphates and Triphosphates from the Nucleoside
25.3 Can the Secondary Structure of DNA Be Denatured
Monophosphates 878
and Renatured? 847
Thermal Denaturation of DNA Can Be Observed by 26.3 Can Cells Salvage Purines? 879
Changes in UV Absorbance 847 26.4 How Are Purines Degraded? 880
pH Extremes or Strong H-Bonding Solutes Also The Major Pathways of Purine Catabolism Lead to Uric
Denature DNA Duplexes 847 Acid 880
NEL
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Although Palæolithic man worked so much in stone, he did not
build in it. Hence our knowledge of the kinds of shelters he made for
himself is almost nil. There are Upper Palæolithic “tectiform”
paintings which look as if they might be attempts to depict houses. It
is clear, moreover, that in this period the general development of the
mechanical arts was sufficiently advanced to allow of the
construction of some sort of rude edifices.
It is conceivable that as far back as the Lower Palæolithic simple
shelters of branches were constructed, or that skins may have been
hung over a few poles to keep off wind and rain. On account of the
perishable nature of the materials involved, it happens that there is
no proof either for or against such a supposition. It is possible that in
time, when patient excavations shall have revealed some particularly
well preserved site, the holes may yet be found in which the posts of
a Palæolithic hut were once set. In case of a fire, the carbonized
stumps might prove to have been preserved in place; or the butts of
the posts might have gradually rotted away and the space once
occupied by them have become filled with an earthy material of
different color and consistency from the surrounding soil. In this
lucky event, even the size and shape of the house might be
reconstructed from the relative positions of the post holes. From
evidence of just this sort some interesting ideas have actually been
obtained as to the houses and village plan of Neolithic European
peoples. Of course, the chances are much less that remains of this
sort would be preserved from the Palæolithic. But the method would
be equally applicable if favorable conditions offered; and it is in some
such way that we may hope in the future to learn a little about the
earliest habitations that mankind constructed. In any event the
example serves to illustrate the indirect and delicate means of which
the student of prehistory must consistently avail himself in his
reconstructions of the past; and gives reason to believe that all that
has been learned about early man in the last fifty years is very little
in comparison with what the ensuing generation and century will
bring to light.
79. Religion
It has already been said that knowledge of religion, a non-material
thing, can be preserved from the remote past only by the most
roundabout means. It is conceivable that the people of the Upper
Palæolithic spent at least as much time in ceremonial observances
as in working flint. Analogy with modern uncivilized tribes would
make us think that this is quite likely. But the stone tools have
remained lying in the earth, while the religious customs went out of
use thousands of years ago and the beliefs were forgotten. Yet this
is known: As far back as the Mousterian, thirty thousand years ago,
certain practices were being observed by the Neandertal race of
western Europe which modern savages observe in obedience to the
dictates of their religion. When these people of the Mousterian laid
away their dead, they put some of their belongings with them. When
existing nations do this, it is invariably in connection with a belief in
the continued existence of the soul after death. We may reasonably
conclude therefore that even in this long distant period human
beings had arrived at a crude recognition of the difference between
flesh and spirit; in short, religion had come into being. Even to say
that Neandertal man did not know whether his dead were dead,
implies his recognition of something different from life in the body, for
he recognized of course that the body had become different.
Whether the Neandertal race already held to the existence of spirits
distinct from man or superior to him, it is impossible to say.
The Upper Palæolithic Cro-Magnon peoples laid out the bodies of
their dead and sometimes folded them. They also sometimes
painted the bodies, and buried flint implements and food in the
graves. That is, funerary practices were becoming established. We
may assume that hand in hand with this development of
observances there went a growth of ritual and belief.
80. Palæolithic Art

The highest achievement of the men of the Old Stone Age is their
art. The perfection to which they carried this art is simply astounding
in view of the comparative meagerness of their civilization otherwise.
It is also remarkable how full-fledged this achievement sprang into
existence. The Lower Palæolithic seems to have been without a
trace of art. With the Aurignacian, simple carving and painting
appear; and while the acme of accomplishment was not reached
until the Magdalenian, the essential foundations of a graphic art of
high order were laid in the late Aurignacian.
The Upper Palæolithic people carved in ivory, bone, and horn;
they incised or engraved on flattened and rounded surfaces of the
same material; and they carved and painted the walls of caves. They
modeled at times in clay and perhaps in other soft materials, and
may have drawn or painted pictures on skins and on exposed rock
surfaces, for all we know; we can judge only by the remains that
have actually come down to us. This art is not a child-like, struggling
attempt to represent objects in the rough, nor is it a mere decorative
playing with geometric figures. These first human artists set boldly to
work to depict; and while their technique was simple, it was carried
to a remarkably high degree of perfection. A few bold strokes gave
the outlines of an animal, but they gave it with such fidelity that the
species can often be recognized at a glance. The Cro-Magnon
people must have developed a high power of mental concentration
to be able to observe and reproduce so closely. The most gifted
individuals perhaps practised assiduously to attain their facility.
Palæolithic art is very different from that of most modern savages.
The latter often work out decorative patterns of some complexity,
richness, and æsthetic value, but when they attempt to depict nature,
they usually fail conspicuously. The lines are crude and wavering.
Any head, body, and tail with four legs stands for almost any animal.
It is a reasonable representation of an abstraction that they
accomplish, not the delineation of what is characteristic in the visible
form. Both observer and painter, among most living savages, are
supposed to know beforehand that the drawing represents a fox and
not a bear. At most, some symbols are added, such as a bushy tail
for a fox or a fin for a whale. It is only in rare cases that any but
advanced nations break away from these primitive tendencies and
learn to draw things as they really appear. The ancient Egyptians
developed such a faculty, and among savages the Bushmen are
remarkably gifted, but, on the whole, successful realistic art is an
accomplishment of high civilization. It is therefore something of a
mystery how the Cro-Magnon men of the Aurignacian brought
themselves to do so well.
Fig. 20. Limestone statuette from

Willendorf, Austria. Characteristic
of Aurignacian treatment of the
female figure: the face and limbs
are abbreviated or only indicated;
the parts concerned with
reproduction are exaggerated.
In sculpture their first efforts were directed upon figurines. These

mostly represent the human female. The head, hands, and feet are
either absent or much abbreviated. In the body, those parts having to
do with reproduction and fecundity are usually heavily exaggerated,
but at the same time given with considerable skill (Fig. 20). It is likely
that these statuettes served some religious cult. At any rate, the
carvings in three dimensions often represent the human figure,
whereas two-dimensional drawings, etchings, and paintings mostly
represent animals and are much more successful than the human
outlines. In the Magdalenian, miniature sculpture of animals was
added to that of the human figure (Fig. 21).
Success in seizing the salient outline was the earliest
characteristic of the paintings and drawings. The first Aurignacian
engravings are invariably in profile and usually show only the two
legs on the immediately visible side. In time the artists also learned
to suggest typical positions and movements—the motion of a
reindeer lowering its head to browse, the way an angry bull switches
his tail or paws the ground, the curl of the end of an elephant’s trunk
(Figs. 22, 24). In the Magdalenian, all four legs are usually depicted,
and the profile, although remaining most frequent, as it is most
characteristic, is no longer the only aspect. There are occasional
pictures of animals from before or behind, or of a reindeer with its
head turned backward.
Fig. 21. Horse carved in mammoth ivory. From Lourdes, France. The spirited
portrayal of the neck, ears, eyes, and mouth parts is characteristic of
Magdalenian sculpture.
There are also some devices which look like the beginnings of
attempts at composition. The effect of a row of reindeer is produced
by drawing out the first few in some detail, and then suggesting the
others by sketching in their horns (Fig. 23). Artists were no longer
content, in the Magdalenian, always to do each animal as a solitary,
static unit. They were trying, with some measure of success, to
represent the animals as they moved in life and perhaps to combine
several of them into one coherent picture or to suggest a setting.
By this time they had also acquired considerable ability in handling
colors. The Aurignacian and Solutrean artists restricted themselves
to monochrome effects. They engraved or painted outlines and
sometimes accentuated these by filling them in with pigment. But the
best of the later painters in the Magdalenian—those, for instance,
who left their frescoes on the walls of the famous cave of Altamira in
Spain—used three or four colors at once and blended these into
transition tones.
Fig. 22. Engraving of a charging mammoth. On a fragment of ivory tusk found at

La Madeleine, France. While the artist’s strokes were crude, he was able to
depict the animal’s action with remarkable vigor. Note the roll of the eye, the
flapping ears, the raised tail expressive of anger.
While animals constitute the subjects of probably four-fifths of the

specimens of Palæolithic art, and human beings most of the
remainder, representations of plants and unrealistic decorative
designs are known. The latter seem to have begun to be specially
prevalent in the latest Magdalenian, as if in preparation of the
conventionalized, non-naturalistic art of the transitional Azilian and
Neolithic.
81. Summary of Advance in the Palæolithic

The history of civilization has herewith been outlined from its first
dim beginnings to about twelve thousand years ago—say to the
neighborhood of 10,000 B.C., as the historian would put it. Progress
is immensely slow at the outset, but gradually speeds up. The
tabulation in Figure 25 summarizes some of the principal features of
this evolution. This diagram does not pretend to be complete; it does
try to include some of the most important and representative
inventions, arts, and accomplishments of the Old Stone Age.
Fig. 23. Magdalenian engraving of a herd of reindeer, found in the grotto of La

Mairie, France. The impressionistic manner enabled the artist to suggest
rather effectively a large herd while drawing out only four animals.
Thus it appears that the Chellean and Acheulean periods are

characterized essentially by a single art, that of chipping implements
on a core of flint, plus perhaps the use of fire. The Mousterian
evinces progress: stone tools are now made from the flake as well
as the core, possibly are sometimes hafted, bone is occasionally
utilized, and there are the first indications of budding religion; four or
five entries are required to represent these culture traits.
The greatest advance comes from the Mousterian to the
Aurignacian; in other words, between the Lower and the Upper
Palæolithic. Three times as many accomplishments are listed as in
the Mousterian, and whole series of new inventions are now first met
with: body ornaments, bone implements, æsthetic products. This
sudden leap in the figures goes far to signalize the importance of the
division between the Upper and the Lower Palæolithic. In the
Solutrean and Magdalenian still further inventions or refinements
appear, until, when the Old Stone Age comes to a close,[12] the stock
of human civilization may be described as perhaps twenty times as
rich as at the beginning. These figures are not to be taken too
literally. The tabulation could easily have been compiled on a more
elaborate basis. But even then the relative proportion of culture
features in each period would remain approximately as here given.
And as regards the general fact of accumulation of civilization, and
its range and nature, the diagram may be accepted as substantially
representative of what happened.
Fig. 24. Magdalenian engraving, perhaps a composition: browsing reindeer among

grass, reeds, and water. Note the naturalistic movement suggested by the
legs and position of the head. Engraved so as to encircle a piece of antler.
Found at Kesslerloch, Switzerland.
Fig. 25. Growth of civilization during the Palæolithic.
The end of the Palæolithic thus sees man in possession of a

number of mechanical arts which enable him to produce a
considerable variety of tools in several materials: sees him
controlling fire; cooking food; wearing clothes, and living in definite
habitations; probably possessing some sort of social grouping, order,
and ideas of law and justice; clearly under the influence of some kind
of religion; highly advanced in the plastic arts; and presumably
already narrating legends and singing songs. In short, many
fundamental elements of civilization were established. It is true that
the sum total of knowledge and accomplishments was still pitifully
small. The most advanced of the Old Stone Age men perhaps knew
and could do about one thing for every hundred that we know and
can do. A whole array of fundamental inventions—the bow and
arrow, pottery, domestication of animals and plants—had not yet
been attempted, and they do not appear on the scene until the
Neolithic. But in spite of the enormous gaps remaining to be filled in
the Neolithic and in the historic period, it does seem fair to say that
many of the outlines of what civilization was ultimately to be had
been substantially blocked out during the Upper Palæolithic. Most of
the framework was there, even though but a small fraction of its
content had yet been entered.
CHAPTER VII
HEREDITY, CLIMATE, AND CIVILIZATION
82. Heredity.—83. Geographical environment.—84. Diet.—85. Agriculture.

—86. Cultural factors.—87. Cultural distribution.—88. Historical
induction.
82. Heredity
The first of the several factors through which it is logically possible
to explain the life and conduct and customs of any people is race or
heredity: in other words, the inborn tendencies, bodily and mental, of
the people that carry these customs. At first sight it may seem that
this element of race might be quite influential. Since peoples differ in
inherited characteristics of body—complexion, features, hair, eye
color, head form, and the like—these bodily inherited peculiarities
ought to be accompanied by mentally inherited traits, such as
greater or less inclination to courage, energy, power of abstract
thought, mechanical ingenuity, musical or æsthetic proclivities, swift
reactions, ability to concentrate, gift of expression. Such racial
mental traits, again, might conceivably be expressed in the conduct
and culture of each people. Races born to a greater activity of the
mechanical faculties would achieve more or higher inventions, those
innately gifted in the direction of music would develop more subtly
melodious songs, and so on.
Yet in every particular case it is difficult or impossible to establish
by incontrovertible evidence that heredity is the specific cause of this
accomplishment, of this point of view, or of this mode of life; that it is
the determining factor to such and such degree of such and such
customs. This is not a denial of the probability that inborn racial
differences exist. It is an affirmation of the difficulty, discussed in
Chapters I, IV, and V, of knowing what is inborn; and more
specifically, of the difficulty of tracing particular customary activities
back to particular racial qualities. The problem of connecting specific
race traits with specific phenomena of culture or group conduct, such
as settled life, architecture in stone, religious symbolism, and the
like,—of determining how much of this type of architecture or
symbolism is instinctive in the race and how much of it is the result of
traditional or social influences,—remains unsolved.
For example, should one try to apply to the explanation of the
mode of life or culture of the Indians of the Southwestern United
States biological facts, such as their head form, one would be
confronted by the difficulty that long heads are characteristic of some
of the town-building tribes, or Pueblos, and also of some of the tribes
living in brush huts. Broad heads are also found among both the
settled and nomadic tribes. The Pueblo Taos and non-Pueblo Pima
are narrow-headed, the Pueblo Zuñi and non-Pueblo Apache broad-
headed. So with the pulse rate, which has been already mentioned
(§ 70) as unusually slow among the Southwestern Indians. It is the
same for the nomadic Apache who lived by fighting, and for the Hopi
and Zuñi who are famous for their timidity and gentleness. Similar
cases might be cited almost endlessly. It is evident that they are of a
kind with the lack of correspondence between race and speech, or
race and nationality, among the European peoples.
83. Geographical Environment

When it comes to the second factor by which culture might
theoretically be explained—physical environment or geography—
similar difficulties are encountered.
It is of course plain that a primitive tribe under the equator would
never invent the ice box, and that the Eskimo will not keep their food
and water in buckets of bamboo, although it is possible that if the
Eskimo had had bamboo carried to them by ocean currents, they
would have been both glad and able to use it. The materials and
opportunities provided by nature may be made use of by each
people, while other materials not being provided, other arts or
customs can therefore not be developed. But evidently this
correspondence is mainly negative. Not performing an act because
one lacks the opportunity by no means proves that the opportunity
will necessarily lead to the performance. Two nations will live where
there is ice to store and one will invent and the other fail to invent the
ice chest. Whole series of peoples possess bamboo and clay, and
yet some of them draw water in bamboo joints and others in pots.
Obviously, natural environment does impose certain limiting
conditions on human life; but equally obviously, it does not cause
inventions or institutions.
The native Australians have wood and cord and flint but do not
make bows and arrows. Their civilization had not advanced to the
point where they were able to devise an efficient bow, and the
requisite idea failed to be carried to them from elsewhere as it was to
other peoples who also did not invent the weapon. The Polynesians,
on the other hand, seem once to have had the weapon, as
evidenced by their retaining it as a toy, but to have disused it,
perhaps because they specialized on fighting with spears and clubs.
Modern civilized people fight at long range, but have let bows go out
of use, except for sport, because their knowledge of metallurgy and
chemistry centuries ago progressed to the point where they could
produce firearms. Development or lack of development or
specialization of other cultural activities—social causes—thus
determine more directly than other factors whether or not a people
employ the bow and arrow. Of those mentioned, the Australians are
the only ones with whom a factor of natural environment might be
alleged to enter: namely, their isolation, which cut them off from
communications and the opportunity to learn from other races. Yet
such isolation is as much a matter of inability to traverse space as it
is a matter of physical distance. A developed art of navigation would
have abolished the Australian isolation. Thus, this seemingly
environmental cause of a cultural fact depends for its effectiveness
on a co-existing cultural cause. It is the latter which is the most
immediate or specific cause.
In general, then, it may be concluded that the directly determining
factors of cultural phenomena are not nature which gives or
withholds materials, but the general state of knowledge and
technology and advancement of the group; in short, historical or
cultural influences.
84. Diet
The greater part of the Southwest is arid. Fish are scarce. The
result is that most of the tribes get little opportunity to fish. Most of
these Southwestern Indians will not eat fish; in fact, think them
poisonous. This circumstance might lead to the following inference:
nature does not furnish fish in abundance; therefore the Indians got
out of the habit of eating them, and finally came to believe them
poisonous. At first blush this may seem a sufficient explanation. But
it is well to note that the explanation has two parts and that only one
of them has to do with nature: the habit of not eating fish because
they are too scarce to make it worth while. As soon as one proceeds
to the second step, that the disuse led to aversion and then to a false
belief of poisonousness, one has gone on to a different matter.
Disuse, aversion, and belief lie wholly within the field of human
conduct. To derive a psychological phenomenon, such as a belief,
from another psychological phenomenon such as a particular disuse,
because this disuse is founded on a geographical factor, would of
course be a logical fallacy. It can also be shown not to hold, since we
prize caviar and oysters and venison in proportion to their rarity.
Scarcity in this case thus leads to the contrary psychological attitude,
and either fails to establish beliefs or establishes favorable ones.
Again, either through a change in climate or through the
improvement of trade, a food that was scarce may become plentiful.
Or a people may remove to a new habitat, different from that in
which their customs of eating were formed. If environment alone
were the dominating cause of their customs, these customs should
then immediately alter. As a fact, a group sometimes adheres to its
old customs. The immediate cause of such conservatism is habit or
inertia or inclination toward superstition or fear of taboo, all of which
are mental reactions expressed in folkways or social customs. Thus
environment remains at most a partial and indirectly operating
cause.
A case in point is that of the Jews. It is often said that the Jew’s
prohibition against eating pork and oysters and lobsters originated in
hygienic considerations; that these were climatically unsafe foods for
him in Palestine. This explanation is more simple than true. Ancient
Palestine was an arid country in which hogs could not be raised with
economic profit, and so they were not raised; and the Philistine and
Phœnician kept the Jew from the coast along which he might have
obtained shellfish. Eating neither food, he happened to acquire a
distrust of them; having the distrust, he rationalized it by saying that
it was foreign and wicked and irreligious to act counter to his habits
—just like the Pueblo Indian; and in the end had the Lord issue the
prohibition for him. Yet this outcome is a long way from the starting
point of natural environment. The environment may indeed be said to
have furnished the first occasion, but the determining causes of the
taboos in the Mosaic law are of an entirely different kind—distrust,
custom, rationalization, psychological or cultural factors. If doubt
remains, it is dispelled by the orthodox Jew of to-day, whose
environment thrusts some of his forbidden foods at him as
economically and hygienically satisfactory, whereas he still shudders
at the thought of tasting them.
If this sort of cultural crystallizing of custom and subsequent
rationalizing or ritual sanctioning takes place among civilized and
intelligent people, the like must occur among uncivilized tribes.
85. Agriculture
Attempts have been made to derive the invention of agriculture
from climatic factors. The first theory was that farming took its rise in
the tropics, where agriculture came naturally, almost without effort,
under a bounteous sky. Only after people had acquired the habit of
farming and had moved into other less favorably endowed countries,
did they take their agriculture seriously in order to survive. But a
second, equally plausible, and quite contradictory theory has been
advanced, which looks toward the duress rather than the easy favors
of nature. On the basis of conditions among the modern Papago
Indians and the ancient inhabitants of the Southwest, it has been
argued that it must have been the peoples of arid countries who
invented agriculture, necessity driving them to it through shortage of
wild supplies.
Between such flat opposites, the choice is merely one of
unscientific guessing. In this particular case of the Southwest it is
certain that both guesses are wrong. Agriculture did not come to the
natives of this area because nature was favorable or because it was
unfavorable. It came because through increase of knowledge and
change of attitude, some people in the region of Southern Mexico or
Guatemala or beyond first turned agriculturists, and from them the
art was gradually carried, through nation after nation, to the
Southwestern tribes, and finally even to the Indians of the North
Atlantic coast.
The reasons for acceptance of this explanation are several. First is
the distribution of native agriculture, whose practice was about
equally spread in the two American continents with its middle in or
near Central America. If a geographical diffusion of the art from a
center took place, its radiation or extension would probably be about
equal to the north and south. Then, the middle portions of the new
world held the greatest concentration of native population, such as
would have tended to produce a pressure in the direction of the
establishment of agriculture and would also normally be a
consequence of the continued custom of farming, as opposed to
unsettled life. Again, the Southwestern tribes planted only maize,
beans, and squashes; the Mexicans grew in addition tomatoes, chili
peppers, cacao, and sweet potatoes. It looks as if they had carried
their agriculture farther through having been at it longer. Then,
pottery has evidently spread out from the same center, and the two
arts seem to go hand in hand. Other evidence might be adduced,
such as archæological excavations and the botanical fact that the
home of the nearest wild relatives of the plants cultivated in the
Southwest is the central or middle American area (§ 183).
In short, the Southwestern Indians did not farm because nature
induced them to make the invention. They did not make the invention
at all. A far away people made it, and from them it was transmitted to
the Southwest through a series of successive tribal contacts. These
contacts, which then are the specific cause of Southwestern
agriculture, constitute a human social factor; a cultural or
civilizational factor. Climatic or physical environment did not enter
into the matter at all, except to render agriculture somewhat difficult
in the arid Southwest, though not difficult enough to prevent it. Had
the Southwest been thoroughly desert, agriculture could not have got
a foot-hold there. But this would be only a limiting condition; the
active or positive causes that brought about the Southwestern
agriculture are its invention farther South, the spread of the invention
to the North, and its acceptance there.
Of course this conclusion sheds no light on the causes of the first
invention in the middle American region. The ultimate origin of the
phenomenon has not been penetrated. But the prevalence of
agriculture in the aboriginal Southwest for several thousand years
past has been pretty certainly accounted for, and by an explanation
in terms of culture or civilization, or the activity of societies of human
beings.
86. Cultural Factors

Such cultural causes constitute the third set or kind of factors by
which civilization is explainable. If the example just discussed is
representative, it is clear that cultural factors ordinarily interpret more
phenomena of civilization, and interpret them more fully, than factors
either of racial heredity or physical environment.
It is different in zoölogy and botany. The forms and behavior of
animals and plants are explainable in terms of heredity and
environment because animals and plants have no culture. It is true
that the forms and behavior are determined also by other animals
and plants, their characteristics, habits, and abundance, but these
factors are in a larger sense part of the environment. They are at any
rate sub-cultural. But since anthropology deals with beings whose
distinctive trait in social relations is the possession of the thing that
we call culture, the factors which biology employs are insufficient. It
is not that heredity and natural environment fail to apply to man, but
that they apply only indirectly and remotely to his civilization. This
fundamental fact has often been overlooked, especially in modern
times, because the biological sciences having achieved successful
increases of knowledge and understanding, the temptation was great
to borrow their method outright and apply it without serious
modification to the human material of anthropology. This procedure
simplified the situation, but yielded inadequate and illusory results.
For a very long time the idea that man possessed and animals
lacked a soul influenced people’s thought to such a degree that they
scarcely thought of human beings in terms of biological causality, of
heredity and environment. Then when a reaction began to set in,
less than two centuries ago, and it became more generally
recognized that man was an animal, the pendulum swung to the
other extreme and the tendency grew of seeing in him only the
animal, the cultureless being, and of either ignoring his culture or
thinking that it could be explained away by resolving it into the
factors familiar from biology. The just and wise course lies between.
The biological aspects of man must be interpreted in terms of
biological causation, his cultural aspects in terms first of all of cultural
causation. After they have been thus resolved, the cultural causes
may reduce to ultimate factors of heredity and natural environment.
87. Cultural Distribution

The Southwest also provides an example of how cultural
phenomena can be seen to be arranged geographically so as to
yield a meaning or to outline their history, without reference to
climate or natural influences. Near the center of the area, in northern
New Mexico and Arizona, live four groups of Pueblo or town building
Indians—the Hopi, Zuñi, Keres, and Tewa or Tano—who represent a
sort of élite of the native culture. They farm, make pottery,
accumulate wealth in turquoise, are governed by priests, worship
under a remarkably complex set of rituals, which involve altars,
masks, symbols of all sorts, and a rude sort of philosophy.
As one goes from the Pueblo center to the less settled tribes, one
encounters first the Navaho, who are earth hut builders and farm but
little, yet share much of the Pueblo elaborateness of ritual, including
altars, masks, and symbols. A little farther out, among the Apache
and Pima, the cults have perceptibly diminished in intricacy and
symbolic value: altars and masks are lacking.
The simplification increases among the more remote Mohave,
whose cults are based on dreams instead of priestly tradition. Still
farther, on the shores of the Pacific among the Luiseño and
Gabrielino, some Pueblo traits can still be found; cult altars and
pottery, for instance. But agriculture, homes of stone, turquoise,
priests, and the majority of Pueblo institutions are unknown. Finally,
still farther away in central California, the Yokuts now and then show
a culture trait reminiscent of the Pueblos: grooved arrow
straighteners, perhaps, or occasional rudely made pottery vessels.
These are suggestive bits; fragments that have been whittled away
or toned down. Pueblo culture as a whole has vanished at this
distance. In its place the Yokuts possess quite different arts and
institutions and beliefs.
What is the significance of this gradual fading away of one type of
civilization and its replacement by others? Evidently that certain
influences have radiated out from the higher Pueblo center, and that
the effect of these has diminished in proportion to the number of
tribes they have passed through. The Pueblos have succeeded in
handing over the largest share of their civilization to the adjacent
Navaho—and no doubt also received most from them. The Apache
being more remote, were less affected; and so on to the farthest
limits of the influences.
It is also clear that a time element is involved. A people receiving
an art from another obviously acquires this later than the inventors.
Most traits which the central Pueblos share with peripheral tribes
may be assumed to have existed longer among the Pueblos, simply
because they possess more traits in their culture and the flow has
prevailingly been out from them. Thus they make uncolored, two-
colored, and three-colored pottery; the tribes on the margin of the
Southwest, uncolored pottery only; those beyond the range of
immediate Southwestern influence, no pottery at all. Unless
therefore there should be special reasons suggestive of a
degenerative loss of the art among the marginal tribes—and no such
reasons are known—the conclusion is forced that Southwestern
pottery was first made by the ancestors of the Pueblos or their
predecessors in the central part of the area, presumably as plain
ware, and that thence knowledge of the art was gradually carried
outward. However while simple pottery making was thus being taken
up by the tribes nearest to the Pueblo district, the Pueblos were
going ahead and learning to ornament vessels with painted designs.
In time this added art also spread to the neighbors, but meanwhile
these had passed knowledge of the first stage on to the tribes still
farther out than themselves; and meanwhile also the Pueblos had
perhaps gone on to a third stage, that of combining colors in their
decoration.
In this way, if nothing interrupted the even regularity of the
process, the focal people, with their lead in creating or inventing or
improving, might pass through half a dozen successive stages of the
art, or of many arts, while the outermost peoples were just beginning
to receive the rudiments. The intermediate tribes would show
attainment of a less or greater number of stages in proportion to their
distance from the center. In this event the main facts concerning the
pottery art of the Southwest could be represented by a diagram of a
step pyramid, each level or step picturing a new increment to the
basic art. The Pueblos would be at the peak of the pyramid, five or
six steps high, the near-by tribes a step or two lower; and so on to
the outermost, who remain at, or have only recently attained to, the
first or lowest level; while beyond these would be the non-pottery-
making tribes wholly outside the Pueblo sphere of influence.
Of course on the actual map the distribution of the various forms
or stages of pottery made does not work out with the perfect
regularity of our schematic diagram. Here and there a tribe has
migrated from its habitat and disturbed the symmetry of
arrangement; or the population of a district has been so thin that it
could live on wild products without resorting to agriculture, so that it
remained more or less nomadic and had no use for fragile pottery; or
a third group of tribes developed basket making to a pitch which
yielded excellent vessels, with the result that they were satisfied and
failed to take up pottery, or took it up half-heartedly, so that the art

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PART I: Building Blocks of the Cell 1

PART II: Protein Dynamics 403

PART III: Metabolism and Its Regulation 537

PART IV: Nucleic Acids 808

PART V: Information Transfer 963

About the Authors iv Archaea and Bacteria Have a Relatively Simple

SUMMARY 225 Acetate Units Are Committed to Fatty Acid Synthesis

SUMMARY 345 HUMAN BIOCHEMISTRY: Cancer, Oncogenes, and

Muscarinic Receptor Function Is Mediated by G The Michaelis Constant, Km, Is Defined as

CRITICAL DEVELOPMENTS IN BIOCHEMISTRY: As Product Accumulates, the Apparent Rate of the

A DEEPER LOOK: The Oxygen-Binding Curves of HUMAN BIOCHEMISTRY: Effectors of Microtubule

SUMMARY 502 PROBLEMS 533

PROBLEMS 503 FURTHER READING 534

FURTHER READING 504

15 Molecular Motors 505 PART III Metabolism and Its Regulation

Gluconeogenesis Is Regulated by Allosteric and

80. Palæolithic Art

Fig. 20. Limestone statuette from

In sculpture their first efforts were directed upon figurines. These

Fig. 22. Engraving of a charging mammoth. On a fragment of ivory tusk found at

While animals constitute the subjects of probably four-fifths of the

81. Summary of Advance in the Palæolithic

Fig. 23. Magdalenian engraving of a herd of reindeer, found in the grotto of La

Thus it appears that the Chellean and Acheulean periods are

Fig. 24. Magdalenian engraving, perhaps a composition: browsing reindeer among

The end of the Palæolithic thus sees man in possession of a

82. Heredity.—83. Geographical environment.—84. Diet.—85. Agriculture.

83. Geographical Environment

86. Cultural Factors

87. Cultural Distribution

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