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AMINO ACID STRUCTURES AND ABBREVIATIONS
Hydrophobic amino acids
COO⫺ COO⫺ CH3 COO⫺ COO⫺
H C CH3 H C CH H C CH2 H C CH2
NH⫹
3 NH⫹
3 CH3 NH⫹
3 NH⫹
3
N
H
Alanine (Ala, A) Valine (Val, V) Phenylalanine (Phe, F) Tryptophan (Trp, W)

COO⫺ CH3 COO⫺ CH3 COO⫺ COO⫺

CH2
H C CH2 CH H C CH CH2 CH3 H C CH2 CH2 S CH3 H C
CH2
NH⫹
3 CH3 NH⫹
3 NH⫹
3 H2N⫹
CH2
Leucine (Leu, L) Isoleucine (Ile, I) Methionine (Met, M) Proline (Pro, P)

Polar amino acids

COO⫺ COO⫺ CH3 COO⫺ COO⫺
H C CH2 OH H C CH OH H C CH2 OH H C CH2 SH
NH⫹
3 NH⫹
3 NH⫹
3 NH⫹
3

Serine (Ser, S) Threonine (Thr, T) Tyrosine (Tyr, Y) Cysteine (Cys, C)

COO⫺ O COO⫺ O COO⫺ COO⫺

N
H C CH2 C NH2 H C CH2 CH2 C NH2 H C CH2 H C H
NH⫹ NH⫹ N
3 3 NH⫹
3 H NH⫹
3

Asparagine (Asn, N) Glutamine (Gln, Q) Histidine (His, H) Glycine (Gly, G)

Charged amino acids

COO⫺ O COO⫺ O COO⫺ COO⫺ NH2
H C CH2 C O⫺ H C CH2 CH2 C O⫺ H C CH2 CH2 CH2 CH2 NH⫹
3 H C CH2 CH2 CH2 NH C NH⫹
2

NH⫹
3 NH⫹
3 NH⫹
3 NH⫹
3

Aspartate (Asp, D) Glutamate (Glu, E) Lysine (Lys, K) Arginine (Arg, R)

Essential Biochemistry
Fourth Edition

CHARLOT T E W. PRATT
Seattle Pacific University

KATHLEEN CORNELY
Providence College
VICE PRESIDENT, PUBLISHER Petra Recter
SPONSORING EDITOR Joan Kalkut
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SENIOR PRODUCTION EDITOR Elizabeth Swain

Cover image: The active site of RNA polymerase, based on a structure determined by Yuan He, Chunli
Yan, Jie Fang, Carla Inouye, Robert Tjian, Ivaylo Ivanov, and Eva Nogales (pdb 5IYD).

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10 9 8 7 6 5 4 3 2 1
 About the Authors
C H A R L O T T E PR AT T received a B.S. in biology from the University of Notre Dame
and a Ph.D. in biochemistry from Duke University. She is a protein chemist who has conducted
research in blood coagulation and inflammation at the University of North Carolina at
Chapel Hill. She is currently Associate Professor in the Biology Department at Seattle Pacific
University. Her interests include molecular evolution, enzyme action, and the relationship
between metabolic processes and disease. She has written numerous research and review
articles, has worked as a textbook editor, and is a co-author, with Donald Voet and Judith G. Voet,
of Fundamentals of Biochemistry, published by John Wiley & Sons, Inc.

K AT H L E E N COR N E LY holds a B.S. in chemistry from Bowling Green (Ohio) State

University, an M.S. in biochemistry from Indiana University, and a Ph.D. in nutritional
biochemistry from Cornell University. She currently serves as a Professor in the Department
of Chemistry and Biochemistry at Providence College where she has focused on expanding the
use of case studies and guided inquiry across a broad spectrum of classes. Her interest in active
pedagogy has led to her involvement in national programs including Project Kaleidoscope,
the POGIL Project, and the Howard Hughes Medical Institute SEA PHAGES program, which
has also fueled her current experimental research in phage genomics. She has been a member
of the editorial board of Biochemistry and Molecular Biology Education and has served for
several years as coordinator of the undergraduate poster competition at the annual meeting of
the American Society for Biochemistry and Molecular Biology.

iii
Brief Contents
PRE FAC E xi
Part 3 Metabolism
Part 1 Foundations 12 Metabolism and Bioenergetics 301

1 The Chemical Basis of Life 1 13 Glucose Metabolism 329

2 Aqueous Chemistry 24 14 The Citric Acid Cycle 362

15 Oxidative Phosphorylation 385

Part 2 Molecular Structure and
16 Photosynthesis 411
Function
17 Lipid Metabolism 432
3 From Genes to Proteins 52
18 Nitrogen Metabolism 464
4 Protein Structure 85
19 Regulation of Mammalian Fuel
5 Protein Function 119
Metabolism 497
6 How Enzymes Work 154

7 Enzyme Kinetics and Inhibition 183

Part 4 Genetic Information
8 Lipids and Membranes 215 20 DNA Replication and Repair 519

9 Membrane Transport 235 21 Transcription and RNA 551

10 Signaling 260 22 Protein Synthesis 580

11 Carbohydrates 283

iv
 Contents
PRE FAC E xi 3.2 Nucleic Acid Structure 56
DNA is a double helix 56
RNA is single-stranded 59
Part 1 Foundations Nucleic acids can be denatured and renatured 59
3.3 The Central Dogma 61
DNA must be decoded 62
1 The Chemical Basis of Life 1 A mutated gene can cause disease 63
3.4 Genomics 64
1.1 What Is Biochemistry? 1 Gene number is roughly correlated with organismal
1.2 Biological Molecules 3 complexity 65
Cells contain four major types of biomolecules 3 Genes are identified by comparing sequences 66
There are three major kinds of biological polymers 6 Genomic data reveal biological functions 67
Box 1.A Units Used in Biochemistry 7 3.5 Tools and Techniques: Manipulating DNA 68
1.3 Energy and Metabolism 10 Cutting and pasting generates recombinant DNA 69
Enthalpy and entropy are components of free energy 10 The polymerase chain reaction amplifies DNA 71
∆G is less than zero for a spontaneous process 11 Box 3.A Genetically Modified Organisms 72
Life is thermodynamically possible 12 Box 3.B DNA Fingerprinting 74
1.4 The Origin and Evolution of Life 14 DNA sequencing uses DNA polymerase to make a
The prebiotic world 14 complementary strand 74
Origins of modern cells 16 DNA can be altered 76
Box 1.B How Does Evolution Work? 17

2 Aqueous Chemistry 24
4 Protein Structure 85
2.1 Water Molecules and Hydrogen Bonds 24
Hydrogen bonds are one type of electrostatic force 26 4.1 Amino Acids, the Building Blocks of Proteins 86
Box 2.A Why Do Some Drugs Contain Fluorine? 28 The 20 amino acids have different chemical
Water dissolves many compounds 28 properties 87
2.2 The Hydrophobic Effect 29 Box 4.A Does Chirality Matter? 88
Amphiphilic molecules experience both hydrophilic Box 4.B Monosodium Glutamate 90
interactions and the hydrophobic effect 31 Peptide bonds link amino acids in proteins 90
The hydrophobic core of a lipid bilayer is a barrier The amino acid sequence is the first level of protein
to diffusion 31 structure 93
Box 2.B Sweat, Exercise, and Sports Drinks 32 4.2 Secondary Structure: The Conformation of the
2.3 Acid–Base Chemistry 33 Peptide Group 94
[H+] and [OH–] are inversely related 33 The α helix exhibits a twisted backbone
The pH of a solution can be altered 34 conformation 95
Box 2.C Atmospheric CO2 and Ocean Acidification 35 The β sheet contains multiple polypeptide strands 95
A pK value describes an acid’s tendency to ionize 36 Proteins also contain irregular secondary structure 96
The pH of a solution of acid is related to the pK 37 4.3 Tertiary Structure and Protein Stability 97
2.4 Tools and Techniques: Buffers 40 Proteins have hydrophobic cores 98
Protein structures are stabilized mainly by the
2.5 Clinical Connection: Acid–Base Balance
hydrophobic effect 99
in Humans 42 Other interactions help stabilize proteins 100
Protein folding begins with the formation of secondary
structures 101
Part 2 Molecular Structure and Some proteins have more than one conformation 102
Function 4.4 Quaternary Structure 104
4.5 Clinical Connection: Protein Misfolding and
3 From Genes to Proteins 52 Disease 105
4.6 Tools and Techniques: Analyzing Protein
3.1 Nucleotides 52 Structure 107
Nucleic acids are polymers of nucleotides 53 Chromatography takes advantage of a polypeptide’s
Some nucleotides have other functions 54 unique properties 107
v
vi CONTE NTS

Mass spectrometry reveals amino acid sequences 109 Chymotrypsin is activated by proteolysis 171
Protein structures are determined by X-ray Protease inhibitors limit protease activity 172
crystallography, electron crystallography, and 6.5 Clinical Connection: Blood Coagulation 173
NMR spectroscopy 110
Box 4.C Mass Spectrometry Applications 110
7 Enzyme Kinetics and
5 Protein Function 119
Inhibition 183

7.1 Introduction to Enzyme Kinetics 183

5.1 Myoglobin and Hemoglobin: Oxygen-Binding
7.2 Derivation and Meaning of the Michaelis–Menten
Proteins 120
Oxygen binding to myoglobin depends on the oxygen Equation 186
concentration 120 Rate equations describe chemical processes 186
Myoglobin and hemoglobin are related by The Michaelis–Menten equation is a rate equation for an
evolution 121 enzyme-catalyzed reaction 187
Oxygen binds cooperatively to hemoglobin 123 KM is the substrate concentration at which velocity is
A conformational shift explains hemoglobin’s cooperative half-maximal 189
behavior 124 The catalytic constant describes how quickly an enzyme
can act 190
Box 5.A Carbon Monoxide Poisoning 124
kcat /KM indicates catalytic efficiency 190
H+ ions and bisphosphoglycerate regulate oxygen binding
KM and Vmax are experimentally determined 191
to hemoglobin in vivo 126
Not all enzymes fit the simple Michaelis–Menten
5.2 Clinical Connection: Hemoglobin Variants 127 model 192
5.3 Structural Proteins 130 7.3 Enzyme Inhibition 194
Actin filaments are most abundant 130 Some inhibitors act irreversibly 195
Actin filaments continuously extend and retract 131 Competitive inhibition is the most common form of
Tubulin forms hollow microtubules 132 reversible enzyme inhibition 195
Some drugs affect microtubules 134 Transition state analogs inhibit enzymes 197
Keratin is an intermediate filament 135
Box 7.A Inhibitors of HIV Protease 198
Collagen is a triple helix 136
Other types of inhibitors affect Vmax 199
Box 5.B Vitamin C Deficiency Causes Scurvy 137 Allosteric enzyme regulation includes inhibition and
Collagen molecules are covalently cross-linked 139 activation 200
Box 5.C Bone and Collagen Defects 139 Several factors may influence enzyme activity 203
5.4 Motor Proteins 141 7.4 Clinical Connection: Drug Development 204
Myosin has two heads and a long tail 141
Myosin operates through a lever mechanism 142
Kinesin is a microtubule-associated motor protein 143 8 Lipids and Membranes 215
Box 5.D Myosin Mutations and Deafness 144
Kinesin is a processive motor 146 8.1 Lipids 215
Fatty acids contain long hydrocarbon chains 216
Box 8.A Omega-3 Fatty Acids 216
6 How Enzymes Work 154 Some lipids contain polar head groups 217
Lipids perform a variety of physiological functions 219
6.1 What Is an Enzyme? 154 Box 8.B The Lipid Vitamins A, D, E, and K 221
Enzymes are usually named after the reaction
8.2 The Lipid Bilayer 222
they catalyze 157
The bilayer is a fluid structure 223
6.2 Chemical Catalytic Mechanisms 158 Natural bilayers are asymmetric 224
A catalyst provides a reaction pathway with a lower
8.3 Membrane Proteins 225
activation energy barrier 159
Integral membrane proteins span the bilayer 225
Enzymes use chemical catalytic mechanisms 160
An α helix can cross the bilayer 226
Box 6.A Depicting Reaction Mechanisms 162 A transmembrane β sheet forms a barrel 226
The catalytic triad of chymotrypsin promotes peptide Lipid-linked proteins are anchored in the membrane 227
bond hydrolysis 164
8.4 The Fluid Mosaic Model 228
6.3 Unique Properties of Enzyme Catalysts 166 Membrane glycoproteins face the cell exterior 229
Enzymes stabilize the transition state 166
Efficient catalysis depends on proximity and orientation
effects 168 9 Membrane Transport 235
The active-site microenvironment promotes catalysis 168
6.4 Chymotrypsin in Context 169 9.1 The Thermodynamics of Membrane Transport 235
Not all serine proteases are related by evolution 170 Ion movements alter membrane potential 237
Enzymes with similar mechanisms exhibit different Membrane proteins mediate transmembrane ion
substrate specificity 170 movement 237
 CONTENTS vii

9.2 Passive Transport 240 Starch and glycogen are fuel-storage molecules 288
Porins are β barrel proteins 240 Cellulose and chitin provide structural support 289
Ion channels are highly selective 241 Box 11.A Cellulosic Biofuel 290
Box 9.A Pores Can Kill 242 Bacterial polysaccharides form a biofilm 291
Gated channels undergo conformational changes 242 11.3 Glycoproteins 291
Aquaporins are water-specific pores 243 Oligosaccharides are N-linked or O-linked 292
Some transport proteins alternate between Oligosaccharide groups are biological markers 293
conformations 244 Box 11.B The ABO Blood Group System 293
9.3 Active Transport 245 Proteoglycans contain long glycosaminoglycan
The Na,K-ATPase changes conformation as it pumps ions chains 294
across the membrane 246 Bacterial cell walls are made of peptidoglycan 295
ABC transporters mediate drug resistance 247
Secondary active transport exploits existing
gradients 247 Part 3 Metabolism
9.4 Membrane Fusion 248
Box 9.B Antidepressants Block Serotonin Transport 250
SNAREs link vesicle and plasma membranes 251
12 Metabolism and Bioenergetics 301
Endocytosis is the reverse of exocytosis 252
12.1 Food and Fuel 301
Box 9.C Exosomes 253 Cells take up the products of digestion 302
Box 12.A Dietary Guidelines 303
Monomers are stored as polymers 304
10 Signaling 260 Fuels are mobilized as needed 304
12.2 Metabolic Pathways 306
10.1 General Features of Signaling Pathways 260 Some major metabolic pathways share a few
A ligand binds to a receptor with a characteristic common intermediates 307
affinity 261 Many metabolic pathways include oxidation–
reduction reactions 308
Box 10.A Bacterial Quorum Sensing 262
Metabolic pathways are complex 310
Most signaling occurs through two types of receptors 263
The effects of signaling are limited 264 Box 12.B The Transcriptome, the Proteome, and
the Metabolome 311
10.2 G Protein Signaling Pathways 265 Human metabolism depends on vitamins 312
G protein–coupled receptors include seven
transmembrane helices 265 12.3 Free Energy Changes in Metabolic Reactions 314
The receptor activates a G protein 265 The free energy change depends on reactant
Adenylate cyclase generates the second messenger concentrations 314
cyclic AMP 266 Unfavorable reactions are coupled to favorable
Cyclic AMP activates protein kinase A 267 reactions 316
Signaling pathways are also switched off 267 Free energy can take different forms 318
The phosphoinositide signaling pathway generates two Box 12.C Powering Human Muscles 320
second messengers 269 Regulation occurs at the steps with the largest free energy
Calmodulin mediates some Ca2+ signals 270 changes 321
10.3 Receptor Tyrosine Kinases 270
The insulin receptor dimer binds one insulin 271
The receptor undergoes autophosphorylation 271 13 Glucose Metabolism 329
Box 10.B Cell Signaling and Cancer 273
13.1 Glycolysis 330
10.4 Lipid Hormone Signaling 274
Reactions 1–5 are the energy-investment phase
Eicosanoids are short-range signals 275
of glycolysis 330
Box 10.C Aspirin and Other Inhibitors of Cyclooxygenase 276 Reactions 6–10 are the energy-payoff phase
of glycolysis 336
Box 13.A Catabolism of Other Sugars 340
11 Carbohydrates 283 Pyruvate is converted to other substances 341
Box 13.B Alcohol Metabolism 342
11.1 Monosaccharides 283 13.2 Gluconeogenesis 344
Most carbohydrates are chiral compounds 284 Four gluconeogenic enzymes plus some glycolytic
Cyclization generates α and β anomers 285 enzymes convert pyruvate to glucose 345
Monosaccharides can be derivatized in many Gluconeogenesis is regulated at the fructose
different ways 286 bisphosphatase step 346
11.2 Polysaccharides 287 13.3 Glycogen Synthesis and Degradation 347
Lactose and sucrose are the most common Glycogen synthesis consumes the free energy of UTP 348
disaccharides 288 Glycogen phosphorylase catalyzes glycogenolysis 349
viii CONTE NTS

13.4 The Pentose Phosphate Pathway 350 Complex III transfers electrons from ubiquinol to
The oxidative reactions of the pentose phosphate cytochrome c 394
pathway produce NADPH 350 Complex IV oxidizes cytochrome c and reduces O2 397
Isomerization and interconversion reactions generate a Box 15.A Free Radicals and Aging 398
variety of monosaccharides 351 15.3 Chemiosmosis 399
A summary of glucose metabolism 352 Chemiosmosis links electron transport and oxidative
13.5 Clinical Connection: Disorders of Carbohydrate phosphorylation 400
Metabolism 353 The proton gradient is an electrochemical gradient 400
Glycogen storage diseases affect liver and muscle 354 15.4 ATP Synthase 401
ATP synthase rotates as it translocates protons 401
The binding change mechanism explains how
14 The Citric Acid Cycle 362 ATP is made 403
The P:O ratio describes the stoichiometry of oxidative
phosphorylation 403
14.1 The Pyruvate Dehydrogenase Reaction 362
Box 15.B Uncoupling Agents Prevent ATP Synthesis 404
The pyruvate dehydrogenase complex contains multiple
The rate of oxidative phosphorylation depends on the rate
copies of three different enzymes 363
of fuel catabolism 404
Pyruvate dehydrogenase converts pyruvate
to acetyl-CoA 363
14.2 The Eight Reactions of the Citric Acid Cycle 365
1. Citrate synthase adds an acetyl group 16 Photosynthesis 411
to oxaloacetate 366
2. Aconitase isomerizes citrate to isocitrate 368 16.1 Chloroplasts and Solar Energy 411
3. Isocitrate dehydrogenase releases the first CO2 369 Pigments absorb light of different wavelengths 412
4. α-Ketoglutarate dehydrogenase releases the Light-harvesting complexes transfer energy to the reaction
second CO2 369 center 414
5. Succinyl-CoA synthetase catalyzes substrate-level
16.2 The Light Reactions 415
phosphorylation 370
Photosystem II is a light-activated oxidation–
6. Succinate dehydrogenase generates ubiquinol 370
reduction enzyme 416
7. Fumarase catalyzes a hydration reaction 371
The oxygen-evolving complex of Photosystem II
8. Malate dehydrogenase regenerates oxaloacetate 371
oxidizes water 417
14.3 Thermodynamics of the Citric Acid Cycle 372 Cytochrome b6f links Photosystems I and II 418
The citric acid cycle is an energy-generating A second photooxidation occurs at Photosystem I 419
catalytic cycle 372 Chemiosmosis provides the free energy for ATP
The citric acid cycle is regulated at three steps 372 synthesis 421
The citric acid cycle probably evolved as a synthetic
16.3 Carbon Fixation 422
pathway 373
Rubisco catalyzes CO2 fixation 422
Box 14.A Mutations in Citric Acid Cycle Enzymes 373
Box 16.A The C4 Pathway 424
14.4 Anabolic and Catabolic Functions of the Citric The Calvin cycle rearranges sugar molecules 424
Acid Cycle 375 The availability of light regulates carbon fixation 426
Citric acid cycle intermediates are precursors of other Calvin cycle products are used to synthesize sucrose
molecules 375 and starch 426
Anaplerotic reactions replenish citric acid cycle
intermediates 376
Box 14.B The Glyoxylate Pathway 377
17 Lipid Metabolism 432

17.1 Lipid Transport 432

15 Oxidative Phosphorylation 385 17.2 Fatty Acid Oxidation 435
Fatty acids are activated before they are degraded 435
15.1 The Thermodynamics of Oxidation–Reduction Each round of β oxidation has four reactions 436
Reactions 385 Degradation of unsaturated fatty acids requires
Reduction potential indicates a substance’s tendency to isomerization and reduction 439
accept electrons 386 Oxidation of odd-chain fatty acids yields
The free energy change can be calculated from the change propionyl-CoA 440
in reduction potential 388 Some fatty acid oxidation occurs in peroxisomes 442
15.2 Mitochondrial Electron Transport 390 17.3 Fatty Acid Synthesis 443
Mitochondrial membranes define two compartments 390 Acetyl-CoA carboxylase catalyzes the first step
Complex I transfers electrons from NADH to of fatty acid synthesis 444
ubiquinone 392 Fatty acid synthase catalyzes seven reactions 445
Other oxidation reactions contribute to the ubiquinol Other enzymes elongate and desaturate newly synthesized
pool 394 fatty acids 447
 CONTENTS ix

Box 17.A Fats, Diet, and Heart Disease 448 Additional hormones influence fuel metabolism 505
Fatty acid synthesis can be activated and inhibited 449 AMP-dependent protein kinase acts as a fuel sensor 506
Box 17.B Inhibitors of Fatty Acid Synthesis 450 19.3 Disorders of Fuel Metabolism 507
Acetyl-CoA can be converted to ketone bodies 450 The body generates glucose and ketone bodies during
17.4 Synthesis of Other Lipids 452 starvation 507
Triacylglycerols and phospholipids are built from Box 19.B Marasmus and Kwashiorkor 507
acyl-CoA groups 452 Obesity has multiple causes 508
Cholesterol synthesis begins with acetyl-CoA 454 Diabetes is characterized by hyperglycemia 509
A summary of lipid metabolism 457 The metabolic syndrome links obesity and diabetes 511
19.4 Clinical Connection: Cancer Metabolism 511
Aerobic glycolysis supports biosynthesis 512
18 Nitrogen Metabolism 464 Cancer cells consume large amounts of glutamine 512

18.1 Nitrogen Fixation and Assimilation 464

Nitrogenase converts N2 to NH3 465 Part 4 Genetic Information
Ammonia is assimilated by glutamine synthetase and
glutamate synthase 466
Transamination moves amino groups between
20 DNA Replication and Repair 519
compounds 467
20.1 The DNA Replication Machinery 519
Box 18.A Transaminases in the Clinic 469 Replication occurs in factories 520
18.2 Amino Acid Biosynthesis 469 Helicases convert double-stranded DNA to
Several amino acids are easily synthesized from common single-stranded DNA 521
metabolites 470 DNA polymerase faces two problems 522
Amino acids with sulfur, branched chains, or aromatic DNA polymerases share a common structure and
groups are more difficult to synthesize 471 mechanism 523
Box 18.B Glyphosate, the Most Popular Herbicide 473 DNA polymerase proofreads newly synthesized DNA 525
Amino acids are the precursors of some signaling An RNase and a ligase are required to complete
molecules 475 the lagging strand 525
Box 18.C Nitric Oxide 476 20.2 Telomeres 528
18.3 Amino Acid Catabolism 476 Telomerase extends chromosomes 529
Amino acids are glucogenic, ketogenic, or both 477 Box 20.A HIV Reverse Transcriptase 530
Box 18.D Diseases of Amino Acid Metabolism 480 Is telomerase activity linked to cell immortality? 531
18.4 Nitrogen Disposal: The Urea Cycle 480 20.3 DNA Damage and Repair 531
Glutamate supplies nitrogen to the urea cycle 481 DNA damage is unavoidable 531
The urea cycle consists of four reactions 482 Repair enzymes restore some types of damaged DNA 533
18.5 Nucleotide Metabolism 485 Base excision repair corrects the most frequent
Purine nucleotide synthesis yields IMP and then DNA lesions 533
AMP and GMP 485 Nucleotide excision repair targets the second most
Pyrimidine nucleotide synthesis yields UTP and CTP 486 common form of DNA damage 535
Ribonucleotide reductase converts ribonucleotides to Double-strand breaks can be repaired by joining
deoxyribonucleotides 487 the ends 535
Thymidine nucleotides are produced by Recombination also restores broken DNA molecules 536
methylation 488 20.4 Clinical Connection: Cancer as a Genetic
Nucleotide degradation produces uric acid or amino Disease 538
acids 489 Tumor growth depends on multiple events 538
DNA repair pathways are closely linked to cancer 539
20.5 DNA Packaging 540
19 Regulation of Mammalian DNA is negatively supercoiled 541
Topoisomerases alter DNA supercoiling 541
Fuel Metabolism 497 Eukaryotic DNA is packaged in nucleosomes 543

19.1 Integration of Fuel Metabolism 498

Organs are specialized for different functions 498 21 Transcription and RNA 551
Metabolites travel between organs 499
Box 19.A The Intestinal Microbiome Contributes to 21.1 Initiating Transcription 552
Metabolism 500 What is a gene? 552
19.2 Hormonal Control of Fuel Metabolism 501 DNA packaging affects transcription 553
Insulin is released in response to glucose 502 DNA also undergoes covalent modification 555
Insulin promotes fuel use and storage 503 Transcription begins at promoters 555
Glucagon and epinephrine trigger fuel mobilization 504 Transcription factors recognize eukaryotic promoters 557
x CONTE NTS

Enhancers and silencers act at a distance from Some synthetases have proofreading activity 584
the promoter 558 tRNA anticodons pair with mRNA codons 584
Box 21.A DNA-Binding Proteins 558 Box 22.A The Genetic Code Expanded 585
Prokaryotic operons allow coordinated gene 22.2 Ribosome Structure 586
expression 560 The ribosome is mostly RNA 586
21.2 RNA Polymerase 562 Three tRNAs bind to the ribosome 587
RNA polymerases have a common structure 22.3 Translation 589
and mechanism 562 Initiation requires an initiator tRNA 589
RNA polymerase is a processive enzyme 564 The appropriate tRNAs are delivered to the ribosome
Transcription elongation requires a conformational during elongation 590
change in RNA polymerase 564 The peptidyl transferase active site catalyzes
Transcription is terminated in several ways 565 peptide bond formation 593
21.3 RNA Processing 567 Box 22.B Antibiotic Inhibitors of Protein Synthesis 594
Eukaryotic mRNAs receive a 5′ cap and Release factors mediate translation termination 595
a 3′ poly(A) tail 567 Translation is efficient in vivo 596
Splicing removes introns from eukaryotic RNA 567 22.4 Post-Translational Events 597
mRNA turnover and RNA interference limit gene Chaperones promote protein folding 597
expression 569 The signal recognition particle targets some proteins
rRNA and tRNA processing includes the addition, deletion, for membrane translocation 599
and modification of nucleotides 572 Many proteins undergo covalent modification 600
RNAs have extensive secondary structure 573

G LO SS A RY G-1
22 Protein Synthesis 580
ODD-NUMBERED SOLUTIONS S-1
22.1 tRNA and the Genetic Code 580
The genetic code is redundant 581
tRNAs have a common structure 581 INDE X I-1
tRNA aminoacylation consumes ATP 582
 Preface
Several years ago, we set out to write a short biochemistry With the same goal of making it easy for students to nav-
textbook that combined succinct, clear chapters with extensive igate complex topics, some material within sections has been
problem sets. We believed that students would benefit from a reorganized, and several new sections of text now focus on key
modern approach involving broad but not overwhelming cov- content areas: 14.3 Thermodynamics of the Citric Acid Cycle,
erage of biochemical facts, focusing on the chemistry behind 17.1 Lipid Transport, 18.5 Nucleotide Metabolism, 20.5 DNA
biology, and providing students with practical knowledge and Packaging, 21.1 Initiating Transcription, and 22.1 tRNA and
problem-solving opportunities. Our experience in the classroom the Genetic Code.
continues to remind us that effective learning also requires stu- Above all, the focus of the fourth edition is ease of use,
dents to become as fully engaged with the material as possible. particularly for students and instructors taking advantage of
To that end, we have embraced a strategy of posing questions new ways to assess student understanding. New Learning
and suggesting study activities throughout each chapter, so that Objectives at the start of every section are based on verbs,
students will not simply read and memorize but will explore giving students an indication of what they need to be able to
and discover on their own—a truer reflection of how biochem- do, not just know. Before You Go On study hints at end of each
ists approach their work in the laboratory or clinic. section reinforce the activities that support learning. The end-
As always, we view our textbook as a guidebook for stu- of-chapter problem sets have been refreshed, with a total of
dents, providing a solid foundation in biochemistry, presenting 1,624 problems (averaging 74 per chapter, an increase of 18%
complete, up-to-date information, and showing the practical over the previous edition). Problems are grouped by section and
aspects of biochemistry as it applies to human health, nutrition, offered in pairs, with the answers to odd-numbered problems
and disease. We hope that students will develop a sense of provided in an appendix.
familiarity and comfort as they encounter new material, explore
it, and test their understanding through problem solving.

Traditional Pedagogical
New to This Edition Strengths
Many details in the text and illustration program have been up- • “Do You Remember?” review questions start each chapter,
dated, with virtually no section left untouched. Some significant to help students tie new topics to what they have already
changes are worth mentioning: Chapter 3 includes an updated studied.
discussion of genomics and a completely new presentation of
• Figure Questions that accompany key tables and figures
DNA sequencing technologies and the use of CRISPR-Cas to
prompt students to inspect information more closely.
edit genes. Other new items include a discussion of archaeal
lipids, details on the GLUT membrane transport protein, a box • Key sentences summarizing main points are printed in
on exosomes, new illustrations of respiratory cilia and bac- italics to assist with quick visual identification.
terial peptidoglycan, new molecular graphics of mitochon- • Tools and Techniques Sections appear at the end of
drial respiratory complexes, an updated presentation of the Chapters 2, 3, and 4, to showcase practical aspects of
ribonucleotide reductase mechanism, and more information biochemistry and provide an overview of experimental
on the microbiome, cancer, and obesity. Descriptions of DNA techniques that students will encounter in their reading or
replication and transcription have been extensively modified, laboratory experience.
with numerous new diagrams to present a more realistic pic- • Metabolism overview figures introduced in Chapter 12
ture of these processes. The histone code and readers, writers, and revisited in subsequent chapters help students place in-
and erasers are explained. New details on RNA splicing and dividual metabolic pathways into a broader context.
protein translocation round out the revised text.
• Chapter Summaries, organized by major section headings,
Eight health-related topics that were previously confined
highlight important concepts to guide students to the most
to short boxes have been updated and expanded to Clinical
important points within each section.
Connection sections to give them the appropriate attention:
2.5 Acid–Base Balance in Humans, 4.5 Protein Misfolding and • Key terms are in boldface. Their definitions are also in-
Disease, 5.2 Hemoglobin Variants, 6.5 Blood Coagulation, 7.4 cluded in the Glossary.
Drug Development, 13.5 Disorders of Carbohydrate Metabo- • An annotated list of Selected Readings for each chapter in-
lism, 19.4 Cancer Metabolism, and 20.4 Cancer as a Genetic cludes recent short papers, mostly reviews, that students are
Disease. likely to find useful as sources of additional information.
xi
xii PRE FACE

phosphorylation (Chapter 15); the light and dark reactions of

Organization photosynthesis (Chapter 16); lipid catabolism and biosyn-
thesis (Chapter 17); and pathways involving nitrogen-containing
We have chosen to focus on aspects of biochemistry that tend compounds, including the synthesis and degradation of amino
to receive little coverage in other courses or present a chal- acids, the synthesis and degradation of nucleotides, and
lenge to many students. Thus, in this textbook, we devote pro- the nitrogen cycle (Chapter 18). The final chapter of Part 2
portionately more space to topics such as acid–base chemistry, explores the integration of mammalian metabolism, with
enzyme mechanisms, enzyme kinetics, oxidation–reduction extensive discussions of hormonal control of metabolic path-
reactions, oxidative phosphorylation, photosynthesis, and the ways, disorders of fuel metabolism, and cancer (Chapter 19).
enzymology of DNA replication, transcription, and transla- Part 4, the management of genetic information, includes
tion. At the same time, we appreciate that students can become three chapters, covering DNA replication and repair
overwhelmed with information. To counteract this tendency, (Chapter 20), transcription (Chapter 21), and protein
we have intentionally left out some details, particularly in the synthesis (Chapter 22). Because these topics are typically
chapters on metabolic pathways, in order to emphasize some also covered in other courses, Chapters 20–22 emphasize the
general themes, such as the stepwise nature of pathways, their relevant biochemical details, such as topoisomerase action,
evolution, and their regulation. nucleosome structure, mechanisms of polymerases and
The 22 chapters of Essential Biochemistry are relatively other enzymes, structures of accessory proteins, proofread-
short, so that students can spend less time reading and more ing strategies, and chaperone-assisted protein folding.
time extending their learning through active problem-solving.
Most of the problems require some analysis rather than
simple recall of facts. Many problems based on research data
provide students a glimpse of the “real world” of science and
medicine.
The WileyPLUS Advantage
Although each chapter of Essential Biochemistry, Fourth
Edition is designed to be self-contained so that it can be WileyPLUS is a research-based online environment for effective
covered at any point in the syllabus, the 22 chapters are organ- teaching and learning. WileyPLUS is packed with interactive
ized into four parts that span the major themes of biochemistry, study tools and resources, including the complete online text-
including some chemistry background, structure–function re- book.
lationships, the transformation of matter and energy, and how NEW Ten Guided Tours cover the major topics of the
genetic information is stored and made accessible. course. These multi-part tutorials explain biochemistry in time
Part 1 of the textbook includes an introductory chapter and and space. Interactive questions at the end of each tour rein-
a chapter on water. Students with extensive exposure to chem- force learning.
istry can use this material for review. For students with little NEW Assignable End-of-Chapter Questions, over 20 per
previous experience, these two chapters provide the chemistry chapter, can be assigned to students through WileyPLUS.
background they will need to appreciate the molecular struc- NEW Twenty-four Sample Calculation Videos walk
tures and metabolic reactions they will encounter later. students through each step of the sample calculations.
Part 2 begins with a chapter on the genetic basis of mac- NEW Brief Bioinformatics Exercises crafted by Rakesh
romolecular structure and function (Chapter 3, From Genes Mogul at California State Polytechnic University, Pomona,
to Proteins). This is followed by chapters on protein structure provide detailed instructions for novices to access and use
(Chapter 4) and protein function (Chapter 5), with coverage of bioinformatics databases and software tools. Each of the 57
myoglobin and hemoglobin, and cytoskeletal and motor pro- exercises includes multiple-choice questions to help students
teins. An explanation of how enzymes work (Chapter 6) pre- gauge their success in learning from these resources.
cedes a discussion of enzyme kinetics (Chapter 7), an arrange- NEW Do You Remember Practice Quizzes help students
ment that allows students to grasp the importance of enzymes prepare for new material by reinforcing relevant topics from
and to focus on the chemistry of enzyme-catalyzed reactions previous chapters.
before delving into the more quantitative aspects of enzyme NEW Concept Check Questions for each section allow
kinetics. A chapter on lipid chemistry (Chapter 8, Lipids and students to test their knowledge.
Membranes) is followed by two chapters that discuss critical NEW Discussion Questions are thought-provoking
biological functions of membranes (Chapter 9, Membrane questions that serve as a point of departure for student discus-
Transport, and Chapter 10, Signaling). The section ends with sion and engagement with content.
a chapter on carbohydrate chemistry (Chapter 11), completing NEW Twenty-three Animated Process Diagrams bring
the survey of molecular structure and function. multi-step figures to life.
Part 3 begins with an introduction to metabolism that NEW ORION Biology and Chemistry Refresher of-
provides an overview of fuel acquisition, storage, and mo- fers ORIONS’s diagnostics and adaptive practice for foun-
bilization as well as the thermodynamics of metabolic reac- dational topics, to support Biochemistry students who come
tions (Chapter 12). This is followed, in traditional fashion, by to the course with differing levels of background knowledge.
chapters on glucose and glycogen metabolism (Chapter 13); the UPDATED Bioinformatics Projects, written by Paul
citric acid cycle (Chapter 14); electron transport and oxidative Craig at Rochester Institute of Technology, provide guidance
 P REFAC E xiii

for 12 extended explorations of online databases, with ques- • Test Bank Questions by Scott Lefler, Arizona State University.
tions, many open-ended, for students to learn on their own. • Practice and Pre-Lecture Questions by Steven Vik, South-
ern Methodist University, and Mary Peek, Georgia Institute
Additional Instructor Resources of Technology.
• PowerPoint Lecture Slides with Answer Slides by Mary
in WileyPLUS Peek, Georgia Institute of Technology.
• PowerPoint Art Slides. • Personal Response System (“Clicker”) Questions by Gail
• Exercise Questions with immediate descriptive feedback Grabner, University of Texas at Austin, and Mary Peek,
updated for the fourth edition by Rachel Milner, University Georgia Institute of Technology.
of Alberta; Adrienne Wright, University of Alberta; and
Mary Peek, Georgia Institute of Technology.

Acknowledgments
We would like to thank everyone who helped develop Essential Missouri
Biochemistry, Fourth Edition, including Biochemistry Editor Joan Nuran Ercal, Missouri University of Science and Technology
Kalkut, Product Designer Sean Hickey, Associate Development Nebraska
Editor Laura Rama, Senior Production Editor Elizabeth Swain, Jodi Kreiling, University of Nebraska, Omaha
Senior Designer Tom Nery, and Senior Photo Editor Billy Ray. New Jersey
We also thank all the reviewers who provided essential feedback on Bryan Speigelberg, Rider University
manuscript and media, corrected errors, and made valuable sugges- Yufeng Wei, Seton Hall University
tions for improvements that have been so important in the writing and New York
development of Essential Biochemistry, Fourth Edition. Sergio Abreu, Fordham University
Susan Rotenberg, Queens College of CUNY
Fourth Edition Reviews Oregon
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 CHAPTER 1
The Chemical Basis of Life
Astrid & Hanns-Frieder Michler /
Science Source Images

While no one has yet succeeded in reproducing all of a cell’s chemical reactions in a test tube, it is
possible to identify and quantify the thousands of molecules present in a cell, such as this amoeba.
Understanding the structures and functions of those molecules is key to understanding how cells live,
move, grow, and reproduce.

This first chapter offers a preview of the study of biochemistry, broken down into three sections
that reflect how topics in this book are organized. First come brief descriptions of the four
major types of small biological molecules and their polymeric forms. Next is a summary of
the thermodynamics that apply to metabolic reactions. Finally, there is a discussion of the
origin of self-replicating life-forms and their evolution into modern cells. These short dis-
cussions introduce some of the key players and major themes of biochemistry and provide a
foundation for the topics that will be encountered in subsequent chapters.

LEARNING OBJECTIVE
1.1 What Is Biochemistry?
Recognize the main themes
of biochemistry.
Biochemistry is the scientific discipline that seeks to explain life at the molecular level. It uses
the tools and terminology of chemistry to describe the various attributes of living organisms.
Biochemistry offers answers to such fundamental questions as “What are we made of?” and
“How do we work?” Biochemistry is also a practical science: It generates powerful techniques
that underlie advances in other fields, such as genetics, cell biology, and immunology; it offers
insights into the treatment of diseases such as cancer and diabetes; and it improves the effi-
ciency of industries such as wastewater treatment, food production, and drug manufacturing.
Some aspects of biochemistry can be approached by studying individual molecules iso-
lated from cells. A thorough understanding of each molecule’s physical structure and chem-
ical reactivity helps lead to an understanding of how molecules cooperate and combine to
form larger functional units and, ultimately, the intact organism (Fig. 1.1). But just as a clock
completely disassembled no longer resembles a clock, information about a multitude of bio-
logical molecules does not necessarily reveal how an organism lives. Biochemists therefore
investigate how organisms behave under different conditions or when a particular molecule
is modified or absent. In addition, they collect vast amounts of information about molecular
structures and functions—information that is stored and analyzed by computer, a field of study
known as bioinformatics. A biochemist’s laboratory is as likely to hold racks of test tubes as
flasks of bacteria or computers.
1
2 CH APTE R 1 The Chemical Basis of Life

Organism
Organ
Cell

Liver Organelle

Hepatocyte

Mitochondrion
Molecules
FIGURE 1.1 Levels of Human
organization in a living Citrate synthase
organism. Biochemistry focuses
on the structures and functions of
molecules. Interactions between
molecules give rise to higher-order
structures (for example, organelles),
DNA
which may themselves be Citrate
components of larger entities,
leading ultimately to the entire
organism. [Photodisc/Rubberball/ Ubiquinone
Getty Images]

Chapters 3 through 22 of this book are divided into three groups that roughly correspond
to three major themes of biochemistry:

1. Living organisms are made of macromolecules. Some molecules are responsible for the
physical shapes of cells. Others carry out various activities in the cell. (For convenience,
we often use cell interchangeably with organism since the simplest living entity is a
single cell.) In all cases, the structure of a molecule is intimately linked to its function.
Understanding a molecule’s structural characteristics is therefore an important key to
understanding its functional significance.
2. Organisms acquire, transform, store, and use energy. The ability of a cell to carry out
metabolic reactions—to synthesize its constituents and to move, grow, and reproduce—
requires the input of energy. A cell must extract this energy from the environment and
spend it or store it in a manageable form.
3. Biological information is transmitted from generation to generation. Modern human
beings look much like they did 100,000 years ago. Certain bacteria have persisted for
millions, if not billions, of years. In all organisms, the genetic information that specifies
a cell’s structural composition and functional capacity must be safely maintained and
transmitted each time the cell divides.
Several other themes run throughout biochemistry, and we will highlight these where
appropriate.
4. Cells maintain a state of homeostasis. Even within its own lifetime, a cell may dramatically
alter its shape or metabolic activities, but it does so within certain limits. And in order
to remain in a steady, non-equilibrium state—homeostasis—the cell must recognize
changing internal and external conditions and regulate its activities.
5. Organisms evolve. Over long periods of time, the genetic composition of a population
of organisms changes. Examining the molecular makeup of living organisms allows
biochemists to identify the genetic features that distinguish groups of organisms and to
trace their evolutionary history.
6. Diseases can be explained at the biochemical level. Identifying the molecular defects that
underlie human diseases, or investigating the pathways that allow one organism to infect
another, is the first step in diagnosing, treating, preventing, or curing a host of ailments.
 Biological Molecules 3

LEARNING OBJECTIVES
1.2 Biological Molecules
Identify the major classes of
Even the simplest organisms contain a staggering number of different molecules, yet this num- biological molecules.
ber represents only an infinitesimal portion of all the molecules that are chemically possible. • List the elements found in
For one thing, only a small subset of the known elements are found in living systems (Fig. 1.2). biological molecules.
The most abundant of these are C, N, O, and H, followed by Ca, P, K, S, Cl, Na, and Mg. • Draw and name the common
Certain trace elements are also present in very small quantities. functional groups in
Virtually all the molecules in a living organism contain carbon, so biochemistry can be biological molecules.
considered to be a branch of organic chemistry. In addition, biological molecules are construc- • Draw and name the common
ted from H, N, O, P, and S. Most of these molecules belong to one of a few structural classes, linkages in biological
which are described below. molecules.
Similarly, the chemical reactivity of biomolecules is limited relative to the reactivity of
all chemical compounds. A few of the functional groups and intramolecular linkages that are • Distinguish the main
common in biochemistry are listed in Table 1.1. Familiarity with these functional groups is structural features of
essential for understanding the behavior of the different types of biological molecules we will carbohydrates, amino acids,
encounter throughout this book. nucleotides, and lipids.
• Identify the monomers and
linkages in polysaccharides,
Cells contain four major types of biomolecules polypeptides, and nucleic
acids.
Most of the cell’s small molecules can be divided into four classes. Although each class • Summarize the biological
contains many members, they are united under a single structural or functional definition. functions of the major
Identifying a particular molecule’s class may help predict its chemical properties and possibly classes of biological
its role in the cell. molecules.

1. Amino Acids Among the simplest compounds are the amino acids, so named be-
cause they contain an amino group (NH2) and a carboxylic acid group (COOH). Under
physiological conditions, these groups are actually ionized to NH+3 and COO–. The com-
mon amino acid alanine—like other small molecules—can be depicted in different ways, for
example, by a structural formula, a ball-and-stick model, or a space-filling model (Fig. 1.3).
Other amino acids resemble alanine in basic structure, but instead of a methyl group (CH3),
they have another group—called a side chain or R group—that may also contain N, O, or S;
for example,

COO⫺ COO⫺
O
H C CH2 C H C CH2 SH
NH⫹ NH2 NH⫹
3 3
Asparagine Cysteine

1
H
5 6 7 8 9
B C N O F
11 12 13 14 15 16 17
Na Mg Al Si P S Cl
19 20 23 24 25 26 27 28 29 30 33 34 35
K Ca V Cr Mn Fe Co Ni Cu Zn As Se Br
42 48 53
Mo Cd I
74
W

FIGURE 1.2 Elements found in biological systems. The most abundant elements are most darkly
shaded; trace elements are most lightly shaded. Not every organism contains every trace element.
Biological molecules primarily contain H, C, N, O, P, and S.
4 CH APTE R 1 The Chemical Basis of Life

TA BLE 1 .1 Common Functional Groups and Linkages in Biochemistry

COMPOUND NAME STRUCTURE a FUNCTIONAL GROUP

Amineb RNH2 or RNH⫹3

⫹
R2NH or R2NH⫹ 2 N or N (amino group)
R3N or R3NH⫹
Alcohol ROH OH (hydroxyl group)
Thiol RSH SH (sulfhydryl group)
Ether ROR O (ether linkage)
O O O
Aldehyde R C H C (carbonyl group), R C (acyl group)

O O O
Ketone R C R C (carbonyl group), R C (acyl group)
O O
Carboxylic acidb R C OH or C OH (carboxyl group) or
(Carboxylate) O O
R C O⫺ C O⫺ (carboxylate group)
O O
Ester R C OR C O (ester linkage)
O
Amide R C NH2
O O
R C NHR C N (amido group)
O
R C NR2
Imineb R NH or R NH⫹
2 ⫹ H
R NR or R NHR⫹ C N or C N (imino group)

O O
Phosphoric acid R O P OH or O P O (phosphoester linkage)
esterb
OH OH
O O O
R O P O⫺ P OH or P O⫺ (phosphoryl group, Pi )
O⫺ OH O⫺
O O O O
Diphosphoric acid R O P O P OH or O P O P O (phosphoanhydride linkage)
esterb
OH OH OH OH
O O O O O O
R O P O P O⫺ P O P OH or P O P O⫺
O⫺ O⫺ OH OH O⫺ O⫺
(diphosphoryl group, pyrophosphoryl group, PPi )

a
R represents any carbon-containing group. In a molecule with more than one R group, the groups may be the same or different.
b
Under physiological conditions, these groups are ionized and hence bear a positive or negative charge.

Q Cover the Structure column and draw the structure for each compound listed on the left. Do the same for each functional group.
 Biological Molecules 5

COO⫺
H C CH3
NH⫹
3
(a)
In a structural formula, some
bonds, such as the C—O and (b) (c)
N—H bonds, are implied.
Around the central carbon, the The atoms are color-coded by convention: In a space-filling model, each atom is
horizontal bonds extend C gray, N blue, O red, and H white. A ball- presented as a sphere whose radius
slightly above the plane of the and-stick representation reveals the (the van der Waals radius)
page, and the vertical bonds identities of the atoms and their positions corresponds to the distance of
extend slightly behind it. in space. closest approach by another atom.

FIGURE 1.3 Representations of alanine. The structural formula accurately depicted in the ball-and-stick model (b), although the
(a) indicates all the atoms and the major bonds. Because the central relative sizes and electrical charges of atoms are not shown. A space-
carbon atom has tetrahedral geometry, its four bonds do not lie flat filling model (c) best represents the actual shape of the molecule but
in the plane of the paper. This tetrahedral arrangement is more may obscure some of its atoms and linkages.

2. Carbohydrates Simple carbohydrates (also called monosaccharides or just sug-

ars) have the formula (CH2O)n, where n is ≥ 3. Glucose, a monosaccharide with six carbon
atoms, has the formula C6H12O6. It is sometimes convenient to draw it as a ladder-like chain
(left); however, glucose forms a cyclic structure in solution (right):
O H
C
H C OH CH2OH
HO C H O
H H H
H C OH
OH H
H C OH HO OH

CH2OH H OH
Glucose

In the representation of the cyclic structure, the darker bonds project in front of the page
and the lighter bonds project behind it. In many monosaccharides, one or more hydroxyl
groups are replaced by other groups, but the ring structure and multiple OH groups of these
molecules allow them to be easily recognized as carbohydrates.

3. Nucleotides A five-carbon sugar, a nitrogen-containing ring, and one or more

phosphate groups are the components of nucleotides. For example, adenosine triphosphate
(ATP) contains the nitrogenous group adenine linked to the monosaccharide ribose, to which
a triphosphate group is also attached:
NH2
N
N Adenine
Triphosphate
O O O N N
⫺ O
O P O P O P O CH2
O⫺ O⫺ O⫺ H H Ribose
H H

OH OH
Adenosine triphosphate (ATP)
6 CH APTE R 1 The Chemical Basis of Life

The most common nucleotides are mono-, di-, and triphosphates containing the nitrogenous
ring compounds (or “bases”) adenine, cytosine, guanine, thymine, or uracil (abbreviated A,
C, G, T, and U).

4. Lipids The fourth major group of biomolecules consists of the lipids. These compounds
cannot be described by a single structural formula since they are a diverse collection of mole-
cules. However, they all tend to be poorly soluble in water because the bulk of their structure
is hydrocarbon-like. For example, palmitic acid consists of a highly insoluble chain of 15
carbons attached to a carboxylic acid group, which is ionized under physiological conditions.
The anionic lipid is therefore called palmitate.

O
CH2 CH2 CH2 CH2 CH2 CH2 CH2 C O⫺
H3C CH2 CH2 CH2 CH2 CH2 CH2 CH2
Palmitate

Cholesterol, although it differs significantly in structure from palmitate, is also poorly soluble
in water because of its hydrocarbon-like composition.

CH3 CH3
CH CH2 CH2 CH2 CH
CH3
CH3
CH3

HO
Cholesterol

Cells also contain a few other small molecules that cannot be easily classified into the groups
above or that are constructed from molecules belonging to more than one group.

There are three major kinds of biological polymers

In addition to small molecules consisting of relatively few atoms, organisms contain macro-
molecules that may consist of thousands of atoms. Such huge molecules are not synthesized
in one piece but are built from smaller units. This is a universal feature of nature: A few kinds
of building blocks can be combined in different ways to produce a wide variety of larger
structures. This is advantageous for a cell, which can get by with a limited array of raw mater-
ials. In addition, the very act of chemically linking individual units (monomers) into longer
strings (polymers) is a way of encoding information (the sequence of the monomeric units)
in a stable form. Biochemists use certain units of measure to describe both large and small
molecules (Box 1.A).
Amino acids, monosaccharides, and nucleotides each form polymeric structures with
widely varying properties. In most cases, the individual monomers become covalently linked
in head-to-tail fashion:

Residue

Monomers Polymer
 Biological Molecules 7

Box 1.A Units Used in Biochemistry

Biochemists follow certain conventions when quantifying objects mega (M) 106 nano (n) 10 –9
on a molecular scale. For example, the mass of a molecule can be kilo (k) 103 pico (p) 10 –12
expressed in atomic mass units; however, the masses of biolog- milli (m) 10 –3 femto (f) 10 –15
ical molecules—especially very large ones—are typically given micro (μ) 10–6
without units. Here it is understood that the mass is expressed
relative to one-twelfth the mass of an atom of the common car- For example, the concentration of the sugar glucose in human
bon isotope 12C (12.011 atomic mass units). Occasionally, units of blood is about 5 mM, but many intracellular molecules are present
daltons (D) are used (1 dalton = 1 atomic mass unit), often with at concentrations of μM or less.
the prefix kilo, k (kD). This is useful for macromolecules such as Distances are customarily expressed in angstroms, Å (1 Å =
proteins, many of which have masses in the range from 20,000 10–10 m) or in nanometers, nm (1 nm = 10–9 m). For example, the
(20 kD) to over 1,000,000 (1000 kD). distance between the centers of carbon atoms in a CC bond is
The standard metric prefixes are also necessary for expressing about 1.5 Å, and the diameter of a DNA molecule is about 20 Å.
the minute concentrations of biomolecules in living cells. Con-
centrations are usually given as moles per liter (mol ⋅ L–1 or M), Q The diameter of a typical spherical bacterial cell is about 1 μm.
with the appropriate prefix such as m, μ, or n: What is the cell’s volume?

The linkage between monomeric units is characteristic of each type of polymer. The monomers
are called residues after they have been incorporated into the polymer. Strictly speaking,
lipids do not form polymers, although they do tend to aggregate to form larger structures such
as cell membranes.

1. Proteins Polymers of amino acids are called polypeptides or proteins. Twenty different
amino acids serve as building blocks for proteins, which may contain many hundreds of amino
acid residues. The amino acid residues are linked to each other by amide bonds called peptide
bonds. A peptide bond (arrow) links the two residues in a dipeptide (the side chains of the
amino acids are represented by R1 and R2). (a)

R1 O R2 O
⫹
H3N C C N C C
H H H O⫺

Because the side chains of the 20 amino acids have different sizes, shapes, and chemical prop-
erties, the exact conformation (three-dimensional shape) of the polypeptide chain depends on
its amino acid composition and sequence. For example, the small polypeptide endothelin, with
21 residues, assumes a compact shape in which the polymer bends and folds to accommodate
the functional groups of its amino acid residues (Fig. 1.4).
The 20 different amino acids can be combined in almost any order and in almost any
proportion to produce myriad polypeptides, all of which have unique three-dimensional
shapes. This property makes proteins as a class the most structurally variable and therefore
the most functionally versatile of all the biopolymers. Accordingly, proteins perform a wide
variety of tasks in the cell, such as mediating chemical reactions and providing structural (b)
support. FIGURE 1.4 Structure of
human endothelin. The 21
amino acid residues of this
2. Nucleic Acids Polymers of nucleotides are termed polynucleotides or nucleic acids, polypeptide, shaded from blue to
better known as DNA and RNA. Unlike polypeptides, with 20 different amino acids available red, form a compact structure. In
for polymerization, each nucleic acid is made from just four different nucleotides. For exam- (a), each amino acid residue is
represented by a sphere. The
ple, the residues in RNA contain the bases adenine, cytosine, guanine, and uracil, whereas the
ball-and-stick model (b) shows all
residues in DNA contain adenine, cytosine, guanine, and thymine. Polymerization involves
the atoms except hydrogen.
the phosphate and sugar groups of the nucleotides, which become linked by phosphodiester [Structure (pdb 1EDN) determined by
bonds. B. A. Wallace and R. W. Jones.]
8 CH APTE R 1 The Chemical Basis of Life

O⫺
⫺
O P O
O
CH2 O Base
H H
H H

O H
Phosphodiester bond ⫺O P O
O
CH2 O Base
H H
H H

OH H

CGUACG In part because nucleotides are much less variable in structure and chemistry than amino
(a) acids, nucleic acids tend to have more regular structures than proteins. This is in keeping with
their primary role as carriers of genetic information, which is contained in their sequence
of nucleotide residues rather than in their three-dimensional shape (Fig. 1.5). Nevertheless,
many nucleic acids do bend and fold into compact globular shapes, as proteins do.

3. Polysaccharides Polysaccharides usually contain only one or a few different types

of monosaccharide residues, so even though a cell may synthesize dozens of different kinds
of monosaccharides, most of its polysaccharides are homogeneous polymers. This tends to
limit their potential for carrying genetic information in the sequence of their residues (as nu-
cleic acids do) or for adopting a large variety of shapes and mediating chemical reactions (as
proteins do). On the other hand, polysaccharides perform essential cell functions by serving
as fuel-storage molecules and by providing structural support. For example, plants link the
monosaccharide glucose, which is a fuel for virtually all cells, into the polysaccharide starch
for long-term storage. The glucose residues are linked by glycosidic bonds (the bond is shown
in red in this disaccharide):

CH2OH CH2OH
(b) O O
H H H H H H
FIGURE 1.5 Structure of a
nucleic acid. (a) Sequence of HO OH H O OH H OH
nucleotide residues, using
one-letter abbreviations.
(b) Ball-and-stick model of the H OH H OH
polynucleotide, showing all atoms
except hydrogen (this structure is
Glucose monomers are also the building blocks for cellulose, the extended polymer that helps
a six-residue segment of RNA).
[Structure (pdb ARF0108) determined make plant cell walls rigid (Fig. 1.6). The starch and cellulose polymers differ in the arrange-
by R. Biswas, S. N. Mitra, and M. ment of the glycosidic bonds between glucose residues.
Sundaralingam.]
The brief descriptions of biological polymers given above are generalizations, meant to
convey some appreciation for the possible structures and functions of these macromolecules.
Exceptions to the generalizations abound. For example, some small polysaccharides encode
information that allows cells bearing the molecules on their surfaces to recognize each other.
Likewise, some nucleic acids perform structural roles, for example, by serving as scaffolding
in ribosomes, the small particles where protein synthesis takes place. Under certain conditions,
 Biological Molecules 9

Glucose

Starch

Cellulose

FIGURE 1.6 Glucose and its polymers. Both starch and cellulose are polysaccharides containing
glucose residues. They differ in the type of chemical linkage between the monosaccharide units. Starch
molecules have a loose helical conformation, whereas cellulose molecules are extended and relatively stiff.

proteins are called on as fuel-storage molecules. A summary of the major and minor functions
of proteins, polysaccharides, and nucleic acids is presented in Table 1.2.

BEFORE GOING ON

• List the six most abundant elements in biological molecules.

• Name the common functional groups and linkages shown in Table 1.1.
• Give the structural or functional definitions for amino acids, monosaccharides,
nucleotides, and lipids.
• Describe the advantage of building a polymer from monomers.
• Give the structural definitions and major functions of proteins, polysaccharides, and
nucleic acids.
• Name the linkage in each type of polymer.
• List the major functions of proteins, polysaccharides, and nucleic acids.

TA B L E 1.2 Functions of Biopolymers

CARRY OUT SUPPORT

ENCODE METABOLIC STORE CELLULAR
BIOPOLYMER INFORMATION REACTIONS ENERGY STRUCTURES

Proteins — ✔ ✓ ✔

Nucleic acids ✔ ✓ — ✓

Polysaccharides ✓ — ✔ ✔

✔ major function
✓ minor function
10 CH APTE R 1 The Chemical Basis of Life

L EARNING OBJECTIVES
1.3 Energy and Metabolism
Explain how enthalpy,
entropy, and free energy Assembling small molecules into polymeric macromolecules requires energy. And unless
apply to biological systems. the monomeric units are readily available, a cell must synthesize the monomers, which also
• Define enthalpy, entropy, requires energy. In fact, cells require energy for all the functions of living, growing, and
and free energy. reproducing.
• Write the equation that links It is useful to describe the energy in biological systems using the terminology of thermody-
changes in enthalpy, namics (the study of heat and power). An organism, like any chemical system, is subject to the
entropy, and free energy. laws of thermodynamics. According to the first law of thermodynamics, energy cannot be cre-
• Relate changes in enthalpy ated or destroyed. However, it can be transformed. For example, the energy of a river flowing
and entropy to the over a dam can be harnessed as electricity, which can then be used to produce heat or perform
spontaneity of a process. mechanical work. Cells can be considered to be very small machines that use chemical energy
to drive metabolic reactions, which may also produce heat or carry out mechanical work.
• Describe the energy flow
that makes living systems
thermodynamically
possible.
Enthalpy and entropy are components of free energy
The energy relevant to biochemical systems is called the Gibbs free energy (after the scien-
tist who defined it) or just free energy. It is abbreviated G and has units of joules per mol
(J ⋅ mol1). Free energy has two components: enthalpy and entropy. Enthalpy (abbreviated
H, with units of J ⋅ mol1) is taken to be equivalent to the heat content of the system. Entropy
(abbreviated S, with units of J ⋅ K1 ⋅ mol1) is a measure of how the energy is dispersed within
that system. Entropy can therefore be considered to be a measure of the system’s disorder or
randomness, because the more ways a system’s components can be arranged, the more dis-
persed its energy. For example, consider a pool table at the start of a game when all 15 balls
are arranged in one neat triangle (a state of high order or low entropy). After play has begun,
the balls are scattered across the table, which is now in a state of disorder and high entropy
(Fig. 1.7).
Free energy, enthalpy, and entropy are related by the equation
G = H  TS [1.1]

where T represents temperature in Kelvin (equivalent to degrees Celsius plus 273). Tempera-
ture is a coefficient of the entropy term because entropy varies with temperature; the entropy
of a substance increases when it is warmed because more thermal energy has been dispersed

(a) (b)
FIGURE 1.7 Illustration of entropy. Entropy is a measure of the dispersal of energy in a system, so
it reflects the system’s randomness or disorder. (a) Entropy is low when all the balls are arranged in a
single area of the pool table. (b) Entropy is high after the balls have been scattered, because there are
now a large number of different possible arrangements of the balls on the table.
Q Compare the entropy of a ball of yarn before and after a cat has played with it.
 Energy and Metabolism 11

within it. The enthalpy of a chemical system can be measured, although with some difficulty,
but it is next to impossible to measure a system’s entropy because this would require counting
all the possible arrangements of its components or all the ways its energy could be spread out
among them. Therefore, it is more practical to deal with changes in these quantities (change is
indicated by the Greek letter delta, ∆) so that
∆G = ∆H  T∆S [1.2]

Biochemists can measure how the free energy, enthalpy, and entropy of a system differ before
and after a chemical reaction. For example, exothermic reactions are accompanied by the
release of heat to the surroundings (Hfinal  Hinitial = ∆H < 0), whereas endothermic reactions
absorb heat from the surroundings (∆H > 0). Similarly, the entropy change, Sfinal  Sinitial = ∆S,
can be positive or negative. When ∆H and ∆S for a process are known, Equation 1.2 can be
used to calculate the value of ∆G at a given temperature (see Sample Calculation 1.1).

S A MPLE CALCULATIO N 1.1

Problem SEE SAMPLE

Use the information below to calculate the change in enthalpy and the change in entropy CALCULATION
for the reaction A → B. VIDEOS

Enthalpy (kJ · mol1) Entropy (J · K1 · mol1)

A 60 22
B 75 97

Solution
∆H = HB – HA ∆S = SB – SA
= 75 kJ ⋅ mol–1 – 60 kJ ⋅ mol–1 = 97 J ⋅ K–1 ⋅ mol–1
= 15 kJ ⋅ mol–1 – 22 J ⋅ K–1 ⋅ mol–1
= 15,000 J ⋅ mol–1 = 75 J ⋅ K–1 ⋅ mol–1

∆G is less than zero for a spontaneous process

A china cup dropped from a great height will break, but the pieces will never reassemble
themselves to restore the cup. The thermodynamic explanation is that the broken pieces have
less free energy than the intact cup. In order for a process to occur, the overall change in free
energy (∆G) must be negative. For a chemical reaction, this means that the free energy of the
products must be less than the free energy of the reactants:
∆G = Gproducts – Greactants < 0 [1.3]

When ∆G is less than zero, the reaction is said to be spontaneous or exergonic. A nonspon-
taneous or endergonic reaction has a free energy change greater than zero; in this case, the
reverse reaction is spontaneous.
A→B B→A
∆G > 0 ∆G < 0
Nonspontaneous Spontaneous
Note that thermodynamic spontaneity does not indicate how fast a reaction occurs, only whether
it will occur as written. (The rate of a reaction depends on other factors, such as the concentra-
tions of the reacting molecules, the temperature, and the presence of a catalyst.) When a reac-
tion, such as A → B, is at equilibrium, the rate of the forward reaction is equal to the rate of the
reverse reaction, so there is no net change in the system. In this situation, ∆G = 0.
12 CH APTE R 1 The Chemical Basis of Life

A quick examination of Equation 1.2 reveals that a reaction that occurs with a decrease
in enthalpy and an increase in entropy is spontaneous at all temperatures because ∆G is
always less than zero. These results are consistent with everyday experience. For example,
heat moves spontaneously from a hot object to a cool object, and items that are neatly arranged
tend to become disordered, never the other way around. (This is a manifestation of the second
law of thermodynamics, which states that energy tends to spread out.) Accordingly, reactions
in which the enthalpy increases and entropy decreases do not occur. If enthalpy and entropy
both increase or both decrease during a reaction, the value of ∆G then depends on the temper-
ature, which governs whether the T∆S term of Equation 1.2 is greater than or less than the ∆H
term. This means that a large increase in entropy can offset an unfavorable (positive) change
in enthalpy. Conversely, the release of a large amount of heat (∆H < 0) during a reaction can
offset an unfavorable decrease in entropy (see Sample Calculation 1.2).

SAMP LE CA LCU LAT I O N 1 . 2

SEE SAMPLE Problem

CALCULATION Use the information given in Sample Calculation 1.1 to determine whether the reaction
VIDEOS A → B is spontaneous at 25°C.

Solution
Substitute the values for ∆H and ∆S, calculated in Sample Calculation 1.1, into Equation 1.2.
To express the temperature in Kelvin, add 273 to the temperature in degrees Celsius: 273 +
25 = 298 K.
∆G = ∆H – T∆S
= 15,000 J ⋅ mol–1 – 298 K (75 J ⋅ K–1 ⋅ mol–1)
= 15,000 – 22,400 J ⋅ mol–1
= –7400 J ⋅ mol–1
= –7.4 kJ ⋅ mol–1
Because ∆G is less than zero, the reaction is spontaneous. Even though the change in
enthalpy is unfavorable, the large increase in entropy makes ∆G favorable.

Life is thermodynamically possible

In order to exist, life must be thermodynamically spontaneous. Does this hold at the molecular
level? When analyzed in a test tube (in vitro, literally “in glass”), many of a cell’s metabolic
reactions have free energy changes that are less than zero, but some reactions do not. Never-
theless, the nonspontaneous reactions are able to proceed in vivo (in a living organism) because
they occur in concert with other reactions that are thermodynamically favorable. Consider two
reactions in vitro, one nonspontaneous (∆G > 0) and one spontaneous (∆G < 0):
A→B ∆G = +15 kJ ⋅ mol1 (nonspontaneous)
B→C ∆G = –20 kJ ⋅ mol1 (spontaneous)

When the reactions are combined, their ∆G values are added, so the overall process has a
negative change in free energy:
A+B→B+C ∆G = (15 kJ ⋅ mol1) + (–20 kJ ⋅ mol1)
A→C ∆G = –5 kJ ⋅ mol1
This phenomenon is shown graphically in Figure 1.8. In effect, the unfavorable “uphill” reac-
tion A → B is pulled along by the more favorable “downhill” reaction B → C.
Cells couple unfavorable metabolic processes with favorable ones so that the net change in
free energy is negative. Note that it is permissible to add ∆G values because the free energy, G,
 Energy and Metabolism 13

B B

Free energy
(G)
A

Reaction coordinate TA B L E 1. 3 Oxidation States of Carbon

FIGURE 1.8 Free energy changes in coupled reactions. A nonspontaneous reaction, COMPOUND a FORMULA
such as A → B, which has a positive value of ∆G, can be coupled to another reaction,
B → C, which has a negative value of ∆G and is therefore spontaneous. The reactions are Carbon dioxide O C O
coupled because the product of the first reaction, B, is a reactant for the second reaction. most oxidized
(least reduced )
Q Which reaction occurs spontaneously in reverse: C → B, B → A, or C → A?
H
O
Acetic acid H C C
depends only on the initial and final states of the system, without regard to the spe-
OH
cific chemical or mechanical work that occurred in going from one state to the other. H
Most macroscopic life on earth today is sustained by the energy of the sun Carbon monoxide C O
(this was not always the case, nor is it true of all organisms). In photosynthetic
O
organisms, such as green plants, light energy excites certain molecules so that their
Formic acid H C
subsequent chemical reactions occur with a net negative change in free energy.
These thermodynamically favorable (spontaneous) reactions are coupled to the OH
unfavorable synthesis of monosaccharides from atmospheric CO2 (Fig. 1.9). In this O
H H
process, the carbon is reduced. Reduction, the gain of electrons, is accomplished
Acetone H C C C H
by the addition of hydrogen or the removal of oxygen (the oxidation states of
H H
carbon are reviewed in Table 1.3). The plant—or an animal that eats the plant—
can then break down the monosaccharide to use it as a fuel to power other meta- H
O
bolic activities. In the process, the carbon is oxidized—it loses electrons through Acetaldehyde H C C
the addition of oxygen or the removal of hydrogen—and ultimately becomes CO2.
H
The oxidation of carbon is thermodynamically favorable, so it can be coupled H
to energy-requiring processes such as the synthesis of building blocks and their H
polymerization to form macromolecules. Formaldehyde C O
Virtually all metabolic processes occur with the aid of catalysts called H
enzymes, most of which are proteins (a catalyst greatly increases the rate of a
reaction without itself undergoing any net change). For example, specific enzymes Acetylene H C C H
catalyze the formation of peptide, phosphodiester, and glycosidic linkages during H H
polymer synthesis. Other enzymes catalyze cleavage of these bonds to break the H C C OH
Ethanol
polymers into their monomeric units.
H H
H H
Ethene C C
Free H H
Light energy
energy H H
Ethane H C C H
O C O H C OH O C O
Reduction Oxidation H H
(unfavorable) (favorable)
Carbon of H
a monosaccharide
Methane H C H
FIGURE 1.9 Reduction and reoxidation of carbon compounds. The sun provides the least oxidized
free energy to convert CO2 to reduced compounds such as monosaccharides. The (most reduced ) H
reoxidation of these compounds to CO2 is thermodynamically spontaneous, so free energy
can be made available for other metabolic processes. Note that free energy is not actually a
Compounds are listed in order of decreasing oxidation state
a substance that is physically released from a molecule. of the red carbon atom.
14 CH APTE R 1 The Chemical Basis of Life

A living organism—with its high level of organization of atoms, molecules, and larger
structures—represents a state of low entropy relative to its surroundings. Yet the organism
can maintain this thermodynamically unfavorable state as long as it continually obtains free
energy from its food. Thus, living organisms do indeed obey the laws of thermodynamics.
When the organism ceases to obtain a source of free energy from its surroundings or exhausts
its stored food, the chemical reactions in its cells reach equilibrium (∆G = 0), which results
in death.

BEFORE GOING ON

• Make up values for ∆H and ∆S to generate ∆G values corresponding to a spontaneous

and a nonspontaneous reaction.
• Show how increasing temperature affects ∆G when ∆H and ∆S are constant.
• Explain how thermodynamically unfavorable reactions proceed in vivo.
• Explain why an organism must have a steady supply of food.
• Describe the cycle of carbon reduction and oxidation in photosynthesis and in the
breakdown of a compound such as a monosaccharide.

L EARNING OBJECTIVES
1.4 The Origin and Evolution of Life
Summarize the evolutionary
history of cells. Every living cell originates from the division of a parental cell. Thus, the ability to replicate
• List the events that must (make a replica or copy of itself) is one of the universal characteristics of living organ-
have occurred during isms. In order to leave descendants that closely resemble itself, a cell must contain a set of
prebiotic evolution. instructions—and the means for carrying them out—that can be transmitted from gen-
• Name the three domains eration to generation. Over time, the instructions change gradually, so that species also
of life. change, or evolve. By carefully examining an organism’s genetic information and the cel-
• Distinguish prokaryotic and lular machinery that supports it, biochemists can draw some conclusions about the organ-
eukaryotic cells. ism’s relationship to more ancient life-forms. The history of evolution is therefore contained
not just within the fossil record but also in the molecular makeup of all living cells. For
example, nucleic acids participate in the storage and transmission of genetic information
in all organisms, and the oxidation of glucose is an almost universal means for generating
metabolic free energy. Consequently, DNA, RNA, and glucose must have been present in
the ancestor of all cells.

The prebiotic world

A combination of theory and experimental data leads to several plausible scenarios for the
emergence of life from nonbiological (prebiotic) materials on the early earth. In one scenario,
inorganic compounds such as H2, H2O, NH3, and CH4—which may have been present in the
early atmosphere—could have given rise to simple biomolecules, such as amino acids, when
sparked by lightning. Laboratory experiments with the same raw materials and electrical dis-
charges to simulate lightning do in fact yield these molecules (Fig. 1.10). Other experiments
suggest that hydrogen cyanide (HCN), formaldehyde (HCOH), and phosphate could have
been converted to nucleotides with a similarly modest input of energy.
Over time, simple molecular building blocks could have accumulated and formed larger
structures, particularly in shallow waters where evaporation would have had a concentrating
effect. Eventually, conditions would have been ripe for the assembly of functional, living cells.
Charles Darwin proposed that life might have arisen in some “warm little pond”; however,
the early earth was probably a much more violent place, with frequent meteorite impacts and
volcanic activity.
 The Origin and Evolution of Life 15

Electrodes

Mixture
of gases

Condenser

Water

Heat
source
Stopcock
for removing
samples

FIGURE 1.10 Laboratory synthesis of biological molecules. A mixture of gases—H2, H2O, NH3,
and CH4—is subject to an electrical discharge. Newly formed compounds, such as amino acids,
accumulate in the aqueous phase as water vapor condenses. Samples of the reaction products can be
removed via the stopcock.

In an alternative scenario, supported by studies of the metabolism of some modern bac-

teria, the first cells could have developed at deep-sea hydrothermal vents, some of which are
characterized by temperatures as high as 350°C and clouds of gaseous H2S and metal sulfides
(giving them the name “black smokers”; Fig. 1.11). In the laboratory, incubating a few small
molecules in the presence of iron sulfide and nickel sulfide at 100°C yields acetic acid, an
organic compound with a newly formed CC bond:
FeS, NiS
CH3SH + CO + H2O ⏤⏤⟶ CH3COOH + H2S
Methyl Carbon Acetic acid
thiol monoxide

Under similar conditions, amino acids spontaneously form short polypeptides. Although
the high temperatures that are necessary for their synthesis also tend to break them down,
these compounds would have been stable in the cooler water next to the hydrothermal vent.
Regardless of how they formed, the first biological building blocks would have had to
polymerize. This process might have been stimulated when the organic molecules—often
bearing anionic (negatively charged) groups—aligned themselves on a cationic (positively
charged) mineral surface.

− Monomers
− Polymer
−
− − − − −
− − − −
FIGURE 1.11 A hydrothermal
+ + + + + + + + + + + +
vent. Life may have originated at
Clay these “black smokers,” where
high temperatures, H2S, and metal
sulfides might have stimulated
In fact, in the laboratory, common clay promotes the polymerization of nucleotides into RNA.
the formation of biological
Primitive polymers would have had to gain the capacity for self-replication. Otherwise, no molecules. [B. Murton/Southhampton
matter how stable or chemically versatile, such molecules would never have given rise to any- Oceanography Centre/Science Photo
thing larger or more complicated: The probability of assembling a fully functional cell from Library/Photo Researchers.]
16 CH APTE R 1 The Chemical Basis of Life

A a solution of thousands of separate small molecules is practically nil.

A Because RNA in modern cells represents a form of genetic informa-
A tion and participates in all aspects of expressing that information, it
A may be similar to the first self-replicating biopolymer. It might have
A made a copy of itself by first making a complement, a sort of mirror
Original image, that could then make a complement of itself, which would be
U 1. The polyA molecule serves
U U identical to the original molecule (Fig. 1.12).
U as a template for the
U synthesis of a polymer
containing uracil nucleotides,
A U
U, which are complementary Origins of modern cells
to adenine nucleotides (in
A U modern RNA, A pairs with U). A replicating molecule’s chances of increasing in number depend on
A U
A
natural selection, the phenomenon whereby the entities best suited
U
A U
to the prevailing conditions are the likeliest to survive and multiply
(Box 1.B). This would have favored a replicator that was chemically
2. The two polymer chains stable and had a ready supply of building blocks and free energy for
separate.
making copies of itself. Accordingly, it would have been advanta-
A U
geous to become enclosed in some sort of membrane that could pre-
A U vent valuable small molecules from diffusing away. Natural selection
A + U would also have favored replicating systems that developed the means
A U for synthesizing their own building blocks and for more efficiently
A U harnessing sources of free energy.
Original Complement The first cells were probably able to “fix” CO2 —that is, convert
3. The polyU molecule serves it to reduced organic compounds—using the free energy released in
A
A as a template for the the oxidation of readily available inorganic compounds such as H2S
A A synthesis of a new or Fe2+. Vestiges of these processes can be seen in modern metabolic
A complementary polyA chain. reactions that involve sulfur and iron.
Later, photosynthetic organisms similar to present-day cyanobac-
A U A
A U A teria (also called blue-green algae) used the sun’s energy to fix CO2:
A + U A
A U A CO2 + H2O → (CH2O) + O2
A U A

U 4. The chains again separate The concomitant oxidation of H2O to O2 dramatically increased the
U and the polyU polymer is concentration of atmospheric O2, about 2.4 billion years ago, and made
U discarded, leaving the it possible for aerobic (oxygen-using) organisms to take advantage of
U this powerful oxidizing agent. The anaerobic origins of life are still
original polyA molecule and
U
its exact copy. visible in the most basic metabolic reactions of modern organisms;
A A these reactions proceed in the absence of oxygen. Now that the earth’s
A A atmosphere contains about 18% oxygen, anaerobic organisms have not disappeared, but they
A + A have been restricted to microenvironments where O2 is scarce, such as the digestive systems
A A of animals or underwater sediments.
A A The earth’s present-day life-forms are of two types, which are distinguished by their cel-
Original Copy lular architecture:

FIGURE 1.12 Possible 1. Prokaryotes are small unicellular organisms that lack a discrete nucleus and usually
mechanism for the self- contain no internal membrane systems. This group comprises two subgroups that are
replication of a primitive RNA
remarkably different metabolically, although they are similar in appearance: the eubacteria
molecule. For simplicity, the RNA
molecule is shown as a polymer
(usually just called bacteria), exemplified by E. coli, and the archaea (or archaebacteria),
of adenine nucleotides, A. best known as organisms that inhabit extreme environments, although they are actually
found almost everywhere (Fig. 1.13).
Q Draw a diagram showing
how polyU would be replicated.
2. Eukaryotic cells are usually larger than prokaryotic cells and contain a nucleus and
other membrane-bounded cellular compartments (such as mitochondria, chloroplasts,
and endoplasmic reticulum). Eukaryotes may be unicellular or multicellular. This group
(also called the eukarya) includes microscopic organisms as well as familiar macroscopic
plants and animals (Fig. 1.14).

By analyzing the sequences of nucleotides in certain genes that are present in all species,
it is possible to construct a diagram that indicates how the bacteria, archaea, and eukarya are
 The Origin and Evolution of Life 17

Box 1.B How Does Evolution Work?

Documenting evolutionary change is relatively straightforward, wing did not suddenly appear in the offspring of a wingless parent
but the mechanisms whereby evolution occurs are prone to misun- but most likely developed bit by bit, over many generations, by
derstanding. Populations change over time, and new species arise modification of a gill or heat-exchange appendage. Each step of
as a result of natural selection. Selection operates on individuals, the wing’s development would have been subject to natural se-
but its effects can be seen in a population only over a period of lection, eventually making an individual that bore the appendage
time. Most populations are collections of individuals that share more likely to survive, perhaps by being able to first glide and then
an overall genetic makeup but also exhibit small variations due actually fly in pursuit of food or to evade predators.
to random alterations (mutations) in their genetic material as it is Although we tend to think of evolution as an imperceptibly
passed from parent to offspring. In general, the survival of an indi- slow process, occurring on a geological time scale, it is ongoing
vidual depends on how well suited it is to the particular conditions and accessible to observation in the laboratory. For example, un-
under which it lives. der optimal conditions, the bacterium Escherichia coli requires
Individuals whose genetic makeup grants them the greatest only about 20 minutes to produce a new generation. In the labo-
rate of survival have more opportunities to leave offspring with ratory, a culture of E. coli cells can progress through about 2500
the same genetic makeup. Consequently, their characteristics be- generations in a year (in contrast, 2500 human generations would
come widespread in a population, and, over time, the population require about 60,000 years). Hence, it is possible to subject a pop-
appears to adapt to its environment. A species that is well suited ulation of cultured bacterial cells to some “artificial” selection—
to its environment tends to persist; a poorly adapted species fails for example, by making an essential nutrient scarce—and observe
to reproduce and therefore dies out. how the genetic composition of the population changes over time
Because evolution is the result of random variations and as it adapts to the new conditions.
changing probabilities for successful reproduction, it is inherently
random and unpredictable. Furthermore, natural selection acts
on the raw materials at hand. It cannot create something out of Q Why can’t acquired (rather than genetic) characteristics
nothing but must operate in increments. For example, the insect serve as the raw material for evolution?

related. The number of sequence differences between two groups of organisms indicates how
long ago they diverged from a common ancestor: Species with similar sequences have a longer
shared evolutionary history than species with dissimilar sequences. This sort of analysis has
produced the evolutionary tree shown in Figure 1.15.
The evolutionary history of eukaryotes is complicated by the fact that eukaryotic cells
exhibit characteristics of both bacteria and archaea. Eukaryotic cells also contain organelles
that are almost certainly the descendants of free-living prokaryotic cells. Specifically, the
chloroplasts of plant cells, which carry out photosynthesis, closely resemble the photo-
synthetic cyanobacteria. The mitochondria of plant and animal cells, which are the site of

FIGURE 1.14 A eukaryotic cell. The

paramecium, a one-celled organism,
contains a nucleus and other membrane-
bounded compartments. [Dr. David Patterson/
Science Photo Library/Photo Researchers.]
FIGURE 1.13 Prokaryotic cells. These
single-celled Escherichia coli bacteria lack Q Describe the visible differences
a nucleus and internal membrane systems. between prokaryotic and eukaryotic
[E. Gray/Science Photo Library/Photo Researchers.] cells (Figures 1.13 and 1.14).
18 CH APTE R 1 The Chemical Basis of Life

Prokaryotes Eukaryotes
Animals
Eukarya
Archaea Fungi
Bacteria Plants Nucleus

DNA Organelles

FIGURE 1.15 Evolutionary tree based on nucleotide sequences. FIGURE 1.16 Possible origin of eukaryotic cells. The close
This diagram reveals that the ancestors of archaea and bacteria association of different kinds of free-living cells gradually led to the
separated before the eukarya emerged from an archaea-like ancestor. modern eukaryotic cell, which appears to be a mosaic of bacterial
Note that the closely spaced fungi, plants, and animals are actually and archaeal features and contains organelles that resemble whole
more similar to each other than are many groups of prokaryotes. bacterial cells.
[After Wheelis, M. L., Kandler, O., and Woese, C. R., Proc. Natl. Acad. Sci. USA, 89,
2930–2934 (1992).]

much of the eukaryotic cell’s aerobic metabolism, resemble certain bacteria. In fact, both
chloroplasts and mitochondria contain their own genetic material and protein-synthesizing
machinery.
It is likely that an early eukaryotic cell developed gradually from a mixed population
of prokaryotic cells. Over many generations of living in close proximity and sharing each
other’s metabolic products, some of these cells became incorporated within a single larger
cell. This arrangement would account for the mosaic-like character of modern eukaryotic cells
(Fig. 1.16).
At some point, cells in dense populations might have traded their individual existence for
a colonial lifestyle. This would have allowed for a division of labor as cells became specialized
and would have eventually produced multicellular organisms.
The earth currently sustains about 9 million different species (although estimates vary
widely). Perhaps some 500 million species have appeared and vanished over the course of
evolutionary history. It is unlikely that the earth harbors more than a few mammals that have
yet to be discovered, but new microbial species are routinely described. And although the
number of known prokaryotes (about 10,000) is much less than the number of known eukar-
yotes (for example, there are about 900,000 known species of insects), prokaryotic metabolic
strategies are amazingly varied. Nevertheless, by documenting characteristics that are com-
mon to all species, we can derive far-reaching conclusions about what life is made of, what
sustains it, and how it has developed over the eons.

BEFORE GOING ON

• Describe how simple prebiotic compounds could give rise to biological monomers and
polymers.
• Explain why anaerobic organisms arose before aerobic organisms.
• Describe the differences between prokaryotes and eukaryotes.
• Explain why eukaryotic cells appear to be mosaics.

Summary
1.2 Biological Molecules • The major classes of small molecules in cells are amino acids,
monosaccharides, nucleotides, and lipids. The major types of biological
• The most abundant elements in biological molecules are H, C, N, polymers are proteins, nucleic acids, and polysaccharides.
O, P, and S, but a variety of other elements are also present in living
systems.
 Problems 19

1.3 Energy and Metabolism 1.4 The Origin and Evolution of Life
• Free energy has two components: enthalpy (heat content) and entropy • The earliest cells may have evolved in concentrated solutions of
(disorder). Free energy decreases in a spontaneous process. molecules or near hydrothermal vents.
• Life is thermodynamically possible because unfavorable endergonic • Eukaryotic cells contain membrane-bounded organelles. Prokar-
processes are coupled to favorable exergonic processes. yotic cells, which are smaller and simpler, include the bacteria and
the archaea.

Key Terms
bioinformatics protein endothermic reaction evolution
homeostasis peptide bond ∆G complement
trace element conformation spontaneous process natural selection
amino acid polynucleotide exergonic reaction aerobic
carbohydrate nucleic acid nonspontaneous process anaerobic
monosaccharide phosphodiester bond endergonic reaction prokaryote
nucleotide polysaccharide in vitro bacteria
lipid glycosidic bond in vivo archaea
monomer free energy (G) reduction eukaryote
polymer enthalpy (H) oxidation eukarya
residue entropy (S) enzyme
polypeptide exothermic reaction replication

Bioinformatics
Brief Bioinformatics Exercises 1.2 Organic Functional Groups and the Three-Dimensional Structure
1.1 The Periodic Table of the Elements and Domains of Life of Vitamin C

Problems
1.2 Biological Molecules 2. Use Table 1.1 to assign the appropriate compound name to each
molecule.
1. Use Table 1.1 to assign the appropriate compound name to each
molecule. a. H3C O CH3
O OH
a. H3C (CH2)14 C OH b. H3C O P O CH3

b. H3C CH2 NH2 O

c. H3C CH2 SH
O
O
c. H3C C O CH2 CH3
d. H3C C CH3
d. H3C CH2 OH
20 CH APTE R 1 The Chemical Basis of Life

3. Investigators synthesized a series of compounds that showed 7. The nutritive quality of food can be analyzed by measuring the
promise as drugs for the treatment of Alzheimer’s disease. The struc- amounts of the chemical elements it contains. Most foods are mix-
ture of one of the compounds is shown below. Identify the functional tures of the three major types of molecules: a. fats (lipids), b. carbo-
groups in this compound. hydrates, and c. proteins. What elements are present in each of these
types of molecules?
OH
8. A compound present in many foods has the formula C44H86O8NP.
To which class of molecules does this compound belong? Explain
N your answer.
CH3 9. A healthy diet must include some protein. Assuming you had a way to
O
measure the amount of each element in a sample of food, which element
4. The structures of several molecules are shown below. Identify the would you measure in order to tell whether the food contained protein?
functional groups in each structure. 10. The structures of three compounds are shown below. Based on
O your answer to Problem 9, which of the three compounds would you
OH add to a food sample so that it would appear to contain more protein?
O C Which of the three compounds would already be present in a food
O C CH2OH OH sample that actually did contain protein? Explain.
O
H
HO OH N ⫹H N
3 CH C O⫺
Vitamin C Nicotinic acid (niacin) O H NH2
C CH2
O N N
H C OH CH2
H3CO CH3
CH3 CH2OPO32⫺ H2N N NH2 C O
H3CO (CH2 CH C CH2)10H O⫺
O A B C
Coenzyme Q
11. The structure of the compound urea is shown. Urea is a waste
5. Name the four types of small biological molecules. Which three product of metabolism excreted by the kidneys into the urine. Why do
are capable of forming polymeric structures? What are the names of doctors tell patients with kidney damage that they should consume a
the polymeric structures that are formed? low-protein diet?
6. To which of the four classes of biomolecules do the following O
compounds belong?
H2N C NH2
a. CH2OH Urea
O
H OH 12. The structures of the amino acids asparagine (Asn) and cysteine
H (Cys) are shown in Section 1.2. What functional group does Asn have that
OH H Cys does not? What functional group does Cys have that Asn does not?
HO H
13. The “straight-chain” structure of glucose is shown in Section 1.2.
H NH C CH3 What functional groups are present in the glucose molecule?

O 14. Consider the monosaccharide fructose. a. How does its molecular

formula differ from that of glucose? b. How does its structure differ
b. NH2 from the structure of glucose?
N CH2OH

O C O
O N
⫺O P O CH2 O HO C H

O⫺ H H H C OH
H H
H C OH
OH OH
CH2OH
c. HS CH2 CH2 CH COO⫺ Fructose

NH⫹ 15. The structures of the nitrogenous bases uracil and cytosine are
3
shown below. How do their functional groups differ?
d.
O NH2

HN N

O O N O N
H H
R C O Uracil Cytosine
 Problems 21

16. What are the structural components of the biological molecules 28. Campers carry hot packs with them, especially when camping
called nucleotides? during the winter months or at high altitudes. The design is similar to
17. Compare the solubilities in water of alanine, glucose, palmitate, that described in Problem 27, except that calcium chloride is used in
and cholesterol, and explain your reasoning. place of the ammonium nitrate. The equation for the dissolution of
calcium chloride in water is shown below. How does the hot pack
18. Cell membranes are largely hydrophobic structures. Which
work?
compound will pass through a membrane more easily, glucose or
2,4-dinitrophenol? Explain. H2O
CaCl2 (s) ⏤⟶ Ca2+ (aq) + 2 Cl– (aq) ΔH = –81 kJ ⋅ mol–1

OH 29. Urea (NH2CONH2) dissolves readily in water; i.e., this is a spon-

NO2 taneous process. The beaker containing the dissolved compound is
cold to the touch. What conclusions can you make about the sign of
the a. enthalpy change and b. entropy change for this process?
30. For the reaction in which reactant A is converted to product B,
NO2 tell whether this process is favorable at a. 4°C and b. 37°C.
2,4-Dinitrophenol
H (kJ · mol–1) S (J · K–1 · mol–1)
19. What polymeric molecule forms a more regular structure, DNA
A 54 22
or protein? Explain this observation in terms of the cellular roles of
B 60 43
the two different molecules.
20. What are the two major biological roles of polysaccharides? 31. For a given reaction, the value of ∆H is 15 kJ ⋅ mol–1 and the
21. Pancreatic amylase digests the glycosidic bonds that link glucose value of ∆S is 51 J ⋅ K–1 ⋅ mol–1. Above what temperature will this
residues together in starch. Would you expect this enzyme to digest reaction be spontaneous?
the glycosidic bonds in cellulose as well? Explain why or why not. 32. Which of the following processes are spontaneous? a. A reaction
22. The complete digestion of starch in mammals yields 4 kilocalories that occurs with any size decrease in enthalpy and any size increase in
per gram (see Problem 21). What is the energy yield for cellulose? entropy. b. A reaction that occurs with a small increase in enthalpy
and a large increase in entropy. c. A reaction that occurs with a large
decrease in enthalpy and a small decrease in entropy. d. A reaction
1.3 Energy and Metabolism that occurs with any size increase in enthalpy and any size decrease in
entropy.
23. What is the sign of the entropy change for each of the following
33. The hydrolysis of pyrophosphate at 25°C is spontaneous. The en-
processes? a. Water freezes. b. Water evaporates. c. Dry ice sublimes.
thalpy change for this reaction is −14.3 kJ ⋅ mol–1. What is the sign
d. Sodium chloride dissolves in water. e. Several different types of
and the magnitude of ∆S for this reaction?
lipid molecules assemble to form a membrane.
34. Phosphoenolpyruvate donates a phosphate group to ADP to
24. Does entropy increase or decrease in the following reactions in
produce pyruvate and ATP. The ∆G value for this reaction at 25°C is
aqueous solution?
−63 kJ ⋅ mol–1 and the value of ∆S is 190 J ⋅ K–1 ⋅ mol–1. What is the
a. COO⫺ COO⫺ value of ∆H? Is heat absorbed from or released to the surroundings?
C O ⫹ CO2(g) C O 35. A monoclonal antibody binds to the protein cytochrome c.
The ∆H value for binding at 25°C is −87.9 kJ ⋅ mol–1 and the ∆S is
CH3 CH2 −118 J ⋅ K–1 ⋅ mol–1. a. Does entropy increase or decrease when the
antibody binds to the protein? b. Calculate ∆G for the formation of
COO⫺
the antibody−protein complex. Does the complex form spontaneously?
b. COO⫺ H c. The ∆G value for the binding of a second monoclonal antibody to
cytochrome c is −58.2 kJ ⋅ mol–1. Which antibody binds more readily
C O ⫹ H⫹ C O ⫹ CO2(g) to the protein?

CH3 CH3 36. Phosphofructokinase catalyzes the transfer of a phosphate

group (from ATP) to fructose-6-phosphate to produce fructose-1,
25. Which has the greater entropy, a polymeric molecule or a mixture 6-bisphosphate at 37°C. The ∆H value for this reaction is
of its constituent monomers? −9.5 kJ ⋅ mol–1 and the ∆G is −17.2 kJ ⋅ mol–1. a. Is heat absorbed
from or released to the surroundings? b. What is the value of ∆S for
26. How does the entropy change when glucose undergoes combustion?
the reaction? Does this reaction proceed with an increase or decrease
C6H12O6 + 6 O2 → 6 CO2 + 6 H2O in entropy? c. Which component makes a greater contribution to the free
energy change: the ∆H or ∆S value? Comment on the significance of
27. A soccer coach keeps a couple of instant cold packs in her bag in
this observation.
case one of her players suffers a muscle injury. Instant cold packs are
composed of a plastic bag containing a smaller water bag and solid am- 37. Glucose can be converted to glucose-6-phosphate:
monium nitrate. In order to activate the cold pack, the bag is kneaded glucose + phosphate → glucose-6-phosphate + H2O
until the smaller water bag breaks, which allows the released water to ∆G = 13.8 kJ ⋅ mol–1
dissolve the ammonium nitrate. The equation for the dissolution of am-
monium nitrate in water is shown below. How does the cold pack work? a. Is this reaction favorable? Explain.
b. Suppose the synthesis of glucose-6-phosphate is coupled with
H2O
NH4NO3 (s) ⏤⟶ NH+4 (aq) + NO3– (aq) the hydrolysis of ATP. Write the overall equation for the coupled
ΔH = 26.4 kJ ⋅ mol–1 process and calculate the ∆G for the coupled reaction. Is the
22 CH APTE R 1 The Chemical Basis of Life

conversion of glucose to glucose-6-phosphate favorable under 42. For each of the reactions in Problem 41, tell whether an
these conditions? Explain. oxidizing agent or a reducing agent is needed to accomplish the
reaction.
ATP + H2O → ADP + phosphate ΔG = –30.5 kJ ⋅ mol–1
43. In some cells, lipids such as palmitate (shown in Section 1.2),
38. Glyceraldehyde-3-phosphate (GAP) is converted to 1,3-bisphos-
rather than monosaccharides, serve as the primary metabolic fuel.
phoglycerate (1,3BPG) as shown.
a. Consider the oxidation state of palmitate’s carbon atoms and
GAP + Pi + NAD+ → 1,3BPG + NADH ΔG = +6.7 kJ ⋅ mol–1 explain how it fits into a scheme such as the one shown in Fig. 1.9.
b. On a per-carbon basis, which would make more free energy available
a. Is this reaction spontaneous? for metabolic reactions: palmitate or glucose?
b. The reaction shown above is coupled to the following reaction
in which 1,3BPG is converted to 3-phosphoglycerate (3PG): 44. Which yields more free energy when completely oxidized, stea-
rate or α-linolenate?
1,3BPG + ADP → 3PG + ATP ΔG = –18.8 kJ ⋅ mol–1
Write the equation for the overall conversion of GAP to 3PG. Is
the coupled reaction favorable? H3C (CH2)16 COO⫺
Stearate
39. Place these molecules in order from the most oxidized to the
most reduced.
H3 C CH2 (CH CHCH2)3 (CH2)6 COO⫺
O H ␣-Linolenate

H C OH H C H O C O
H
A B C 1.4 The Origin and Evolution of Life
45. Why is molecular information so important for classifying and
40. Identify the process described in the following statements as an tracing the evolutionary relatedness of bacterial species but less im-
oxidation or reduction process. a. Monosaccharides are synthesized portant for vertebrate species?
from carbon dioxide by plants during photosynthesis. b. An animal
46. The first theories to explain the similarities between bacteria and
eats the plant and breaks down the monosaccharide in order to obtain
mitochondria or chloroplasts suggested that an early eukaryotic cell
energy for cellular processes.
actually engulfed but failed to fully digest a free-living prokaryotic
41. Given the following reactions, tell whether the reactant is being cell. Why is such an event unlikely to account for the origin of mito-
oxidized or reduced. Reactions may not be balanced. chondria or chloroplasts?
O O 47. Draw a simple evolutionary tree that shows the relationships
between species A, B, and C based on the DNA sequences given here.
a. CH3 (CH2)14 C O⫺ 8 CH3 C S CoA

b. COO⫺ COO⫺ Species A TCGTCGAGTC

Species B TGGACTAGCC
CH2 CH2
Species C TGGACCAGCC
CH OH C O
COO⫺ COO⫺ 48. A portion of the evolutionary tree for a flu virus is shown here.
Different strains are identified by an H followed by a number.
c. COO⫺ COO⫺ a. Identify two pairs of closely related flu strains. b. Which strain(s)
CH CH2 is(are) most closely related to strain H3?

CH CH OH
H15
COO⫺ COO⫺
d. O H7
⫹H N CH C O⫺ H10
3

CH2 H3
O
S H4
⫹ H2 2 ⫹H3N CH C O⫺
S
CH2 H14
CH2
SH
⫺O C CH NH⫹
3

O
 Selected Readings 23

Selected Readings
Koonin, E. V., The origin and early evolution of eukaryotes in the Nee, S., More than meets the eye, Nature 429, 804–805 (2004). [A
light of phylogenomics, Genome Biol. 11, 209 (2010). [Discusses brief commentary about appreciating the metabolic diversity of mi-
several models for the origin of eukaryotic cells.] crobial life.]
Koshland, D. E., Jr., The seven pillars of life, Science 295, 2215–2216 Nisbet, E. G., and Sleep, N. H., The habitat and nature of early life,
(2002). [Describes some of the essential attributes of all organisms, Nature 409, 1083–1091 (2001). [Explains some of the hypotheses
including a DNA program, ability to mutate, compartmentalization, regarding the early earth and the origin of life, including the possib-
need for energy, ability to regenerate, adaptability, and seclusion.] ility that life originated at hydrothermal vents.]
Mora, C., Tittensor, D. P., Adl, S., Simpson, A. G. B., and Worm, B., Tinoco, I., Jr., Sauer, K., Wang, J. C., Puglisi, J. C., Harbison, G., and
How many species are there on earth and in the ocean? PLoS Biol Rovnyak, D., Physical Chemistry. Principles and Applications in
9(8): e1001127. doi:10.1371/journal.pbio.1001127 (2011). [Shows Biological Sciences (5th ed.), Chapters 2–4, Prentice-Hall (2014).
how statistical analysis of databases can be used to estimate the total [This and other physical chemistry textbooks present the basic
number of known and not-yet-described species.] equations of thermodynamics.]
CHAPTER 2
Aqueous Chemistry
Lisa Collins/robertharding/Getty Images, Inc.

Plotosus japonicus, a species of catfish, locates food by detecting the subtle change in pH caused by
the release of carbon dioxide from hidden prey organisms.

DO YOU REMEMBER?
• Organisms maintain a state of homeostasis (Section 1.1)
• Biological molecules are composed of a subset of all possible elements and functional groups
(Section 1.2).
• The free energy of a system is determined by its enthalpy and entropy (Section 1.3).

Water is a fundamental requirement for life, so it is important to understand the structural and
chemical properties of water. Not only are most biological molecules surrounded by water, but
their molecular structure is in part governed by how their component groups interact with water.
And water plays a role in how these molecules assemble to form larger structures or undergo
chemical transformation. In fact, water itself— or its H+ and OH− constituents—participates
directly in many biochemical processes. Therefore, an examination of water is a logical prelude
to exploring the structures and functions of biomolecules in the following chapters.

L EARNING OBJECTIVES
2.1 Water Molecules and Hydrogen Bonds
Explain water’s properties
in term of its ability to form What is the nature of the substance that accounts for about 70% of the mass of most organisms?
hydrogen bonds. The human body, for example, is about 60% by weight water, most of it in the extracellular
• Describe the electronic fluid (the fluid surrounding cells) and inside cells:
structure of a water molecule.
• Identify hydrogen bond
donor and acceptor groups. Intracellular Non-water (40%)
• List the other types of weak water (40%)
noncovalent forces that af-
fect biological molecules.
• Describe how water interacts
with polar and charged
solutes.

Extracellular water Water in circulatory

(15%) system (5%)
24
 Water Molecules and Hydrogen Bonds 25

In an individual H2O molecule, the central oxygen atom forms covalent bonds with two
H
hydrogen atoms, leaving two unshared pairs of electrons. The molecule therefore has ap-
proximately tetrahedral geometry, with the oxygen atom at the center of the tetrahedron, the
hydrogen atoms at two of the four corners, and electrons at the other two corners (Fig. 2.1).
As a result of this electronic arrangement, the water molecule is polar; that is, it has an
uneven distribution of charge. The oxygen atom bears a partial negative charge (indicated by the
symbol δ−), and each hydrogen atom bears a partial positive charge (indicated by the symbol δ+): O

δ+ δ+

FIGURE 2.1 Electronic

structure of the water molecule.
δ−
Four electron orbitals, in an
approximately tetrahedral
This polarity is the key to many of water’s unique physical properties.
arrangement, surround the central
Neighboring water molecules tend to orient themselves so that each partially positive oxygen. Two orbitals participate
hydrogen is aligned with a partially negative oxygen: in bonding to hydrogen (gray),
and two contain unshared
electron pairs.
δ−

δ+

This interaction, shaded yellow here, is known as a hydrogen bond. This weak electrostatic
attraction between oppositely charged particles actually has some covalent character. In addi-
tion, the bond has directionality, or a preferred orientation.
Each water molecule can potentially participate in four hydrogen bonds, since it has two
hydrogen atoms to “donate” to a hydrogen bond and two pairs of unshared electrons that can
“accept” a hydrogen bond. In ice, a crystalline form of water, each water molecule does indeed
form hydrogen bonds with four other water molecules (Fig. 2.2). This regular, lattice-like
structure breaks down when the ice melts.
In liquid water, each molecule can potentially form hydrogen bonds
with up to four other water molecules, but each bond has a lifetime of
only about 10−12 s. As a result, the structure of water is continually
flickering as water molecules rotate, bend, and reorient themselves.
Theoretical calculations and spectroscopic data suggest that water
molecules participate in only two strong hydrogen bonds, one as a
donor and one as an acceptor, generating transient hydrogen-bonded
clusters such as the six-membered ring shown here:

FIGURE 2.2 Structure of ice.

Each water molecule acts as a
donor for two hydrogen bonds
and an acceptor for two hydrogen
bonds, thereby interacting with
four other water molecules in the
crystal. (Only two layers of water
Because of its ability to form hydrogen bonds, water is highly cohesive. This accounts molecules are shown here.)
for its high surface tension, which allows certain insects to walk on water (Fig. 2.3). The co- Q Identify a hydrogen bond
hesiveness of water molecules also explains why water remains a liquid, whereas molecules donor and acceptor in this
of similar size, such as CH4 and H2S, are gases at room temperature (25ºC). At the same time, structure.
26 CH APTE R 2 Aqueous Chemistry

water is less dense than other liquids because hydrogen bonding demands that individual
molecules not just approach each other but interact with a certain orientation. This geometrical
constraint also explains why ice floats; for other materials, the solid is denser than the liquid.

Hydrogen bonds are one type of electrostatic force

Powerful covalent bonds define basic molecular constitutions, but much weaker noncovalent
FIGURE 2.3 A water strider
bonds, including hydrogen bonds, govern the final three-dimensional shapes of molecules and
supported by the surface how they interact with each other. For example, about 460 kJ · mol−1 (110 kcal · mol−1) of en-
tension of water. [Hermann ergy is required to break a covalent OH bond. But a hydrogen bond in water has a strength
Eisenbeiss/Photo Research, Inc.] of only about 20 kJ · mol−1 (4.8 kcal · mol−1). Other noncovalent interactions are weaker still.
Among the noncovalent interactions that occur in biological molecules are electrostatic
interactions between charged groups such as carboxylate (COO−) and amino (NH+3 )
groups. These ionic interactions are intermediate in strength to covalent bonds and hydrogen
bonds (Fig. 2.4).
Hydrogen bonds, despite their partial covalent nature, are classified as a type of electrostatic
interaction. At about 1.8 Å, they are longer and hence weaker than a covalent OH bond
(which is about 1 Å long). However, a completely noninteracting O and H would approach no
closer than about 2.7 Å, which is the sum of their van der Waals radii (the van der Waals
radius of an isolated atom is the distance from its nucleus to its effective electronic surface).

(a)

O H Covalent bond

1Å

(b)

O H Hydrogen bond

1.8 Å

(c)

O H No bond

2.7 Å

400 Hydrogen bonds usually involve NH and O H groups as hydrogen donors and the
electronegative N and O and occasionally S atoms as hydrogen acceptors (electronegativity is
350 a measure of an atom’s affinity for electrons; Table 2.1). Water, therefore, can form hydrogen
bonds not just with other water molecules but with a wide variety of other compounds that
Bond strength (kJ . mol−1)

300
bear N- and O-containing functional groups.
250

200 TA B L E 2. 1 Electronegativities of Some Elements

150 ELEMENT ELECTRONEGATIVITY

100 C 2.55

50 F 3.98

0 H 2.20
Covalent Ionic Hydrogen van der
bond interaction bond Waals N 3.04
interaction
O 3.44
FIGURE 2.4 Relative strengths of bonds in biological
S 2.58
molecules.
 Water Molecules and Hydrogen Bonds 27

H H H R
O H O O H N
R H R
Water–alcohol Water–amine

Likewise, these functional groups can form hydrogen bonds among themselves. For example,
the complementarity of bases in DNA and RNA is determined by their ability to form hydrogen
bonds with each other. Here, three NH groups are hydrogen bond donors, and N and O
atoms are acceptors:

Guanine

Cytosine

Other electrostatic interactions occur between particles that are polar but not actually
charged, for example, two carbonyl groups:

δ− δ+
C O C O

These forces, called van der Waals interactions, are usually weaker than hydrogen
bonds. The interaction between two strongly polar groups is known as a dipole–dipole
interaction and has a strength of about 9 kJ · mol−1. Very weak
van der Waals interactions, called London dispersion forces,
occur between nonpolar molecules as a result of small fluctu-
ations in their distribution of electrons that create a temporary
separation of charge. Nonpolar groups such as methyl groups
can therefore experience a small-attractive force, in this case
about 0.3 kJ · mol−1:


H 
H 
   
C H H C
H H

Not surprisingly, these forces act only when the groups are very
close, and their strength quickly falls off as the groups draw FIGURE 2.5 The cumulative
apart. If the groups approach too closely, however, their van der Waals radii collide and a effect of small forces. Just as
strong repulsive force overcomes the attractive force. the fictional giant Gulliver was
Although hydrogen bonds and van der Waals interactions are individually weak, biological restrained by many small tethers
at the hands of the tiny
molecules usually contain multiple groups capable of participating in these intermolecular
Lilliputians, the structures of
interactions, so their cumulative effect can be significant (Fig. 2.5). These weak forces also macromolecules are constrained
determine how biological moleucles can “recognize” or bind noncovalently to each other. by the effects of many weak
Drug molecules are typically designed to optimize the weak interactions that govern their noncovalent interactions. [Hulton
therapeutic activity (Box 2.A). Archive/Getty Images.]
28 CH APTE R 2 Aqueous Chemistry

Box 2.A Why Do Some Drugs Contain Fluorine?

As mentioned in Section 1.2, the most abundant elements in biological properties without significantly altering its shape. The
biological molecules are H, C, N, O, P, and S. Fluorine only rarely small fluorine can take the place of hydrogen in a chemical struc-
appears in naturally occurring organic compounds. Why, then, do ture, but with its high electronegativity (see Table 2.1), F behaves
about one-quarter of all drug molecules, including the widely pre- much more like O than H. Consequently, transforming a relatively
scribed Prozac (fluoxetine, an antidepressant; Box 9.B), fluorouracil inert CH group into an electron-withdrawing CF group can
(an anticancer agent; Section 7.3), and Ciprofloxacin (an antibac- decrease the basicity of nearby amino groups (see Section 2.3).
terial agent; Section 20.5), contain F? Fewer positive charges in a drug allow it to more easily pass through
membranes to enter cells and exert its biological effect.
H In addition, the polar CF bond can participate in hydro-
O N gen bonding (CF · · · H C) or other dipole–dipole interac-
CH3 tions (such as CF · · · C  O), potentially augmenting the inter-
molecular attraction between a drug and its target molecule in the
F3C body. Better binding usually means that the drug will be effective
at lower concentrations and will have fewer side effects.
Prozac (Fluoxetine)

In designing an effective drug, pharmaceutical scientists often

Q Identify the hydrogen-bonding groups in Prozac.
intentionally introduce F in order to alter the drug’s chemical or

Water dissolves many compounds

Unlike most other solvent molecules, water molecules are able to form hydrogen bonds and
participate in other electrostatic interactions with a wide variety of compounds. Water has a
relatively high dielectric constant, which is a measure of a solvent’s ability to diminish the
electrostatic attractions between dissolved ions (Table 2.2). The higher the dielectric constant
of the solvent, the less able the ions are to associate with each other. The polar water molecules
surround ions (for example, the Na+ and Cl− ions from the salt NaCl) by aligning their partial
charges with the oppositely charged ions. Because the interactions between the polar water
Na+
molecules and the ions are stronger than the attractive forces between the Na+ and Cl− ions,
the salt dissolves (the dissolved particle is called a solute). Each solute ion surrounded by
water molecules (shown here) is said to be solvated (or hydrated, to indicate that the solvent
is water).
Biological molecules that bear polar or ionic functional groups are also readily solubil-
ized, in this case because the groups can form hydrogen bonds with the solvent water mol-
ecules. Glucose, for example, with its six hydrogen-bonding oxygens, is highly soluble in
Cl– water:

Note that when we describe the behavior of a single molecule, such as glucose in this example,
we are really describing the average behavior of a huge number of molecules. (Most biochem-
ical techniques cannot assess the activity of an individual molecule.)
The concentration of glucose in human blood is about 5 mM. In a solution of 5 mM glucose
in water, there are about 10,000 water molecules for every glucose molecule (the water
molecules are present at a concentration of about 55.5 M). However, biological molecules are
never found alone in such dilute conditions in vivo, because a large number of small molecules,
 The Hydrophobic Effect 29

TAB L E 2. 2 Dielectric Constants for Some Solvents at Room Temperature

SOLVENT DIELECTRIC CONSTANT

Formamide (HCONH2) 109

Water 80
Methanol (CH3OH) 33
Ethanol (CH3CH2OH) 25
1-Propanol (CH3CH2CH2OH) 20
1-Butanol (CH3CH2CH2CH2OH) 18
Benzene (C6H6) 2

Q Compare the hydrogen-bonding ability of these solvents.

FIGURE 2.6 Portion of a
large polymers, and macromolecular aggregates collectively form a solution that is more like Dictyostelium cell visualized by
a hearty stew than a thin, watery soup (Fig. 2.6). cryoelectron tomography. In
this technique, the cells are rapidly
Inside a cell, the spaces between molecules may be only a few Å wide, enough room for
frozen so that they retain their fine
only two water molecules to fit. This allows solute molecules, each with a coating of properly
structure, and two-dimensional
oriented water molecules, to slide past each other. This thin coating, or shell, of water may be electron micrographs taken from
enough to keep molecules from coming into van der Waals contact (van der Waals interactions different angles are merged to
are weak but attractive), thereby helping maintain the cell’s contents in a crowded but fluid state. re-create a three-dimensional
image. The red structures are
filaments of the protein actin,
BEFORE GOING ON ribosomes and other macromolec-
ular complexes are colored green,
• Explain why a water molecule is polar. and membranes are blue. Small
• Draw three hydrogen-bonded water molecules. molecules (not visible) fill the
spaces between these larger cell
• Describe the structure of liquid water.
components. [Courtesy Wolfgang
• Compare the strengths of covalent bonds, hydrogen bonds, ionic interactions, and van Baumeister, Max Planck Institute for
der Waals interactions. Biochemistry.]

• Describe what happens when an ionic substance dissolves in water.

• Explain why water is a more effective solvent than ammonia or methanol.

LEARNING OBJECTIVES
2.2 The Hydrophobic Effect
Relate the solubility of
substances to the
Glucose and other readily hydrated substances are said to be hydrophilic (water-loving). In
hydrophobic effect.
contrast, a compound such as dodecane (a C12 alkane),
• Explain the hydrophobic
effect in terms of water’s
entropy.
• Predict the water solubility
of hydrophobic and
hydrophilic substances.
• Describe how amphiphilic
which lacks polar groups, is relatively insoluble in water and is said to be hydrophobic
substances behave in water.
(water-fearing). Although pure hydrocarbons are rare in biological systems, many biological
molecules contain hydrocarbon-like portions that are insoluble in water. • Explain why a lipid bilayer
When a nonpolar substance such as vegetable oil (which consists of hydrocarbon-like is a barrier to diffusion.
molecules) is added to water, it does not dissolve but forms a separate phase. In order for the
water and oil to mix, free energy must be added to the system (for example, by stirring vigor-
ously or applying heat). Why is it thermodynamically unfavorable to dissolve a hydrophobic
substance in water? One possibility is that enthalpy is required to break the hydrogen bonds
among solvent water molecules in order to create a “hole” into which a nonpolar molecule can fit.
30 CH APTE R 2 Aqueous Chemistry

Nonpolar molecule

Layer of
constrained
Water water
molecules

FIGURE 2.7 Hydration of a nonpolar molecule. When a nonpolar substance (green) is added to
water, the system loses entropy because the water molecules surrounding the nonpolar solute (orange)
lose their freedom to form hydrogen bonds. The loss of entropy is a property of the entire system, not
just the water molecules nearest the solute, because these molecules are continually changing places
with water molecules from the rest of the solution. The loss of entropy presents a thermodynamic
barrier to the hydration of a nonpolar solute.

Experimental measurements, however, show that the free energy barrier (ΔG) to the solvation
process depends much more on the entropy term (ΔS) than on the enthalpy term (ΔH; recall
from Chapter 1 that ΔG = ΔH − TΔS; Equation 1.2). This is because when a hydrophobic
molecule is hydrated, it becomes surrounded by a layer of water molecules that cannot parti-
cipate in normal hydrogen bonding with each other but instead must align themselves so that
their polar ends are not oriented toward the nonpolar solute. This constraint on the structure
of water represents a loss of entropy in the system, because now the highly mobile water
molecules have lost some of their freedom to rapidly form, break, and re-form hydrogen bonds
with other water molecules (Fig. 2.7). But note that the loss of entropy is not due to the forma-
tion of a frozen “cage” of water molecules around the nonpolar solute, as commonly pictured,
because in liquid water, the solvent molecules are in constant motion.
When a large number of nonpolar molecules are introduced into a sample of water, they do
not disperse and become individually hydrated, each surrounded by a layer of water molecules.
Instead, the nonpolar molecules tend to clump together, removing themselves from contact
with water molecules. (This explains why small oil droplets coalesce into one large oily phase.)
Although the entropy of the nonpolar molecules is thereby reduced, this thermodynamically
unfavorable event is more than offset by the increase in the entropy of the water molecules,
which regain their ability to interact freely with other water molecules (Fig. 2.8).
The exclusion of nonpolar substances from an aqueous solution is known as the hydrophobic
effect. It is a powerful force in biochemical systems, even though it is not a bond or an attractive
interaction in the conventional sense. The nonpolar molecules do not experience any additional
attractive force among themselves; they aggregate only because they are driven out of the

(a) (b)

FIGURE 2.8 Aggregation of nonpolar molecules in water. (a) The individual hydration of dispersed
nonpolar molecules (green) decreases the entropy of the system because the hydrating water molecules
(orange) are not as free to form hydrogen bonds. (b) Aggregation of the nonpolar molecules increases
the entropy of the system, since the number of water molecules required to hydrate the aggregated
solutes is less than the number of water molecules required to hydrate the dispersed solute molecules.
This increase in entropy accounts for the spontaneous aggregation of nonpolar substances in water.
Q Explain why it is incorrect to describe the behavior shown in part (b) in terms of “hydrophobic
bonds.”
 The Hydrophobic Effect 31

aqueous phase by the unfavorable entropy cost of individually hydrating them. The hydrophobic Polar head group
effect governs the structures and functions of many biological molecules. For example, each
Nonpolar tail
polypeptide chain of a protein folds into a globular mass so that its hydrophobic groups are
in the interior, away from the solvent, and its polar groups are on the exterior, where they can
interact with water. Similarly, the structure of the lipid membrane that surrounds all cells is
maintained by the hydrophobic effect acting on the lipids.

Amphiphilic molecules experience both hydrophilic

interactions and the hydrophobic effect
Consider a molecule such as the fatty acid palmitate:
FIGURE 2.9 Cross section of a
micelle formed by amphiphilic
molecules. The hydrophobic tails
of the molecules aggregate, out of
contact with water, due to the
hydrophobic effect. The polar
The hydrocarbon “tail” of the molecule (on the right) is nonpolar, while its carboxylate “head” head groups are exposed to and
(on the left) is strongly polar. Molecules such as this one, which have both hydrophobic and can interact with the solvent water
molecules.
hydrophilic portions, are said to be amphiphilic or amphipathic. What happens when am-
phiphilic molecules are added to water? In general, the polar groups of amphiphiles orient
themselves toward the solvent molecules and are therefore hydrated, while the nonpolar
groups tend to aggregate due to the hydrophobic effect. As a result, the amphiphiles may form
a spherical micelle, a particle with a solvated surface and a hydrophobic core (Fig. 2.9).
Depending in part on the relative sizes of the hydrophilic and hydrophobic portions of
the amphiphiles, the molecules may form a sheet rather than a spherical micelle. The am-
phiphilic lipids that provide the structural basis of biological membranes form two-layered
sheets called bilayers, in which a hydrophobic layer is sandwiched between hydrated polar Polar head group
surfaces (Fig. 2.10). The structures of biological membranes are discussed in more detail in
Chapter 8. The formation of micelles or bilayers is thermodynamically favored because the Nonpolar tails

hydrogen-bonding capacity of the polar head groups is satisfied through interactions with
solvent water molecules, and the nonpolar tails are sequestered from the solvent.

The hydrophobic core of a lipid bilayer is

a barrier to diffusion
To eliminate its solvent-exposed edges, a lipid bilayer tends to close up to form a vesicle,
shown cut in half:
FIGURE 2.10 A lipid bilayer.
The amphiphilic lipid molecules
form two layers so that their polar
head groups are exposed to the
solvent while their hydrophobic
tails are sequestered in the interior
of the bilayer, away from water.
The likelihood of amphiphilic
molecules forming a bilayer
rather than a micelle depends in
part on the sizes and nature of the
hydrophobic and hydrophilic
groups. One-tailed lipids tend to
Many of the subcellular compartments (organelles) in eukaryotic cells have a similar structure. form micelles (see Fig. 2.9), and
When the vesicle forms, it traps a volume of the aqueous solution. Polar solutes in the two-tailed lipids tend to form
enclosed compartment tend to remain there because they cannot easily pass through the bilayers.
hydrophobic interior of the bilayer. The energetic cost of transferring a hydrated polar group Q Indicate where a sodium ion
through the nonpolar lipid tails is too great. (In contrast, small nonpolar molecules such as O2 and a benzene molecule would
can pass through the bilayer relatively easily.) be located.
32 CH APTE R 2 Aqueous Chemistry

INTRACELLULAR EXTRACELLULAR
160 160

Concentration (mM)

Concentration (mM)
120 120

80 80

(a) (b)
40 40
FIGURE 2.11 A bilayer
prevents the diffusion of polar 0 0
substances. (a) Solutes Na+ K+ Cl− Na+ K+ Cl−
spontaneously diffuse from a
region of high concentration to FIGURE 2.12 Ionic composition of intracellular and extracellular fluid. Human cells contain
a region of low concentration. much higher concentrations of potassium than of sodium or chloride; the opposite is true of the fluid
(b) A lipid barrier, which presents outside the cell. The cell membrane helps maintain the concentration differences.
a thermodynamic barrier to the
passage of polar substances, Normally, substances that are present at high concentrations tend to diffuse to regions of
prevents the diffusion of polar lower concentration. (This movement “down” a concentration gradient is a spontaneous process
substances out of the inner driven by the increase in entropy of the solute molecules.) A barrier such as a bilayer can prevent
compartment (it also prevents this diffusion (Fig. 2.11). This helps explain why cells, which are universally enclosed by a mem-
the inward diffusion of polar brane, can maintain their specific concentrations of ions, small molecules, and biopolymers even
substances from the external when the external concentrations of these substances are quite different (Fig. 2.12). The solute
solution). composition of intracellular compartments and other biological fluids is carefully regulated. Not
surprisingly, organisms spend a considerable amount of metabolic energy to maintain the proper
concentrations of water and salts, and losses of one or the other must be compensated (Box 2.B).

Box 2.B Sweat, Exercise, and Sports Drinks

Animals, including humans, generate heat, even at rest, due to exhaustion” in humans is usually due to dehydration rather than an
their metabolic activity. Some of this heat is lost to the environ- actual increase in body temperature.
ment by radiation, convection, conduction, and—in terrestrial Numerous studies have concluded that athletes seldom drink
animals—the vaporization of water. Evaporation has a significant enough before or during exercise. Ideally, fluid intake should
cooling effect because about 2.5 kJ of heat is given up for every match the losses due to sweat, and the rate of intake should keep
gram (mL) of water lost. In humans and certain other animals, an pace with the rate of sweating. So what should the conscientious
increase in skin temperature triggers the activity of sweat glands, athlete drink? For activities lasting less than about 90 minutes,
which secrete a solution containing (in humans) about 50 mM especially when periods of high intensity alternate with brief peri-
Na+, 5 mM K+, and 45 mM Cl−. The body is cooled as the sweat ods of rest, water alone is sufficient. Commercial sports drinks
evaporates from its surface. containing carbohydrates can replace the water lost as sweat and
The evaporation of water accounts for a small portion of a also provide a source of energy. However, this carbohydrate boost
resting body’s heat loss, but sweating is the main mechanism for may be an advantage only during prolonged sustained activity,
dissipating heat generated when the body is highly active. During such as during a marathon, when the body’s own carbohydrate
vigorous exercise or exertion at high ambient temperatures, the stores are depleted. A marathon runner or a manual laborer in the
body may experience a fluid loss of up to 2 L per hour. Athletic hot sun might benefit from the salt found in sports drinks, but most
training not only improves the performance of the muscles and athletes don’t need the supplemental salt (although it does make
cardiopulmonary system, it also increases the capacity for sweat- the carbohydrate solution more palatable). A normal diet usually
ing so that the athlete begins to sweat at a lower skin temperature contains enough Na+ and Cl− to offset the losses in sweat.
and loses less salt in the secretions of the sweat glands. But re-
gardless of training, a fluid loss representing more than 2% of the Q Compare the ion concentrations of sweat and extracellular
body’s weight may impair cardiovascular function. In fact, “heat fluid.

BEFORE GOING ON

• Describe the changes in entropy that occur when nonpolar substances are added to water.
• Explain how you can distinguish hydrophobic and hydrophilic substances.
• Explain why polar molecules dissolve more easily than nonpolar substances in water.
• Explain how a molecule can be both hydrophilic and hydrophobic. Give an example.
• Explain why a lipid bilayer is a barrier to the diffusion of polar molecules.
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not to be told until you reached the age of twenty-one. Sung-tchun
was anxious that you should not be exposed to the advances of
mere fortune-hunters until you were old enough to have had a
reasonable experience of the world.
“Now if the will had contained nothing else there would have been
no difficulty: you would have been perfectly safe. Unfortunately
Sung-tchun added a codicil which was, as events proved, to bring
you into terrible peril.
“That codicil provided that if you died childless the vast bulk of
Sung-tchun’s wealth should devolve upon a Chinese named Chi-ho
who was living in New York. Now here is a crucial fact. Chi-ho was
hopelessly in the power of Hartley Humphreys.
“Humphreys learned of the provisions of Sung-tchun’s will. He had
lived in China; he knew the country well and he was very wealthy.
By the treachery of an official of the Thu-tseng he learned of that
fatal codicil. It was an amazing instance of leakage of information for
which the history of the Thu-tseng knows no parallel and the
offender has expiated his crime by the forfeit of his life.
“Chi-ho probably never realized the vastness of the sum to which he
would be entitled if Thelma died childless. Humphreys, no doubt,
only told him part of the truth. Chi-ho, in consideration of getting his
freedom from Humphreys made over to the latter, in strictly legal
form, all his interests under the will of Sung-tchun. That document
was found among Humphreys’ papers after his death, of which
Thelma has already told you.
“Very soon after that document was signed Chi-ho died—stabbed to
death in what was said to be a tong feud in the Chinatown district of
New York. I cannot say with certainty that the whole thing was
arranged by Hartley Humphreys but Chi-ho’s death was very
convenient to him.
“Now you have this interesting position: only Thelma’s life stood
between Hartley Humphreys and the Sung-tchun fortune.
“All these facts came to me by cable—in code, of course, from
Canton. I did not think it necessary or desirable to tell you and of
course I had no permission to reveal the fact that Thelma was a
great heiress. But I was keenly on the watch. My Canton
correspondent warned me very specifically to beware of Hartley
Humphreys, whose secret record in China—outwardly he was of the
highest respectability—was appalling. And the Thu-tseng knew all
there was to know about him.
“That will explain to you, Yelverton, Humphreys’ alarm when he saw
the Crystal Claw. He knew it might mean anything—for instance that
Thelma was being watched over and guarded by the agents of the
most powerful secret society in the world. If that were the case, he
knew, a single false step would mean his certain ruin—perhaps even
his death.”
“You didn’t seem much concerned about his alarm when I told you,”
I interrupted.
“No,” said the doctor with a smile, “it wasn’t necessary. I should not
have been surprised if the sight of the Crystal Claw had frightened
him off his scheme. But his avarice was evidently so unbounded that
he was willing to run any risk for the sake of money.
“Now comes a curious part of the story that I think Mrs. Audley had
better tell herself.” He turned to Thelma. “Please tell Mr. Yelverton
about your marriage,” he said.
“Well,” said Thelma, hesitatingly. “I was introduced to Stanley Audley
at a dance at Harrogate. He was an electrical engineer and was
apparently also possessed of considerable means. We met
frequently. Twice I had tea at his rooms in London and one day at
the Savoy he introduced me to Harold Ruthen who, I understood,
was a newly formed acquaintance of his.
“Mother rather liked Stanley, who always spoke enthusiastically of
his firm, Messrs. Gordon & Austin, the great electrical supply
company, and of his eagerness for advancement. When we became
engaged mother raised no objection, for he was so keen and
enthusiastic in everything. One day he motored me down to a place
called ‘Crowmarsh,’ near Wallingford, where I found he possessed a
fine old-world house, where we were to live when we married. I was
charmed with it and we both spent a glorious day there. Three
weeks later we were, as you know, quietly married at St. James’
church in Piccadilly, and went at once out to Switzerland for our
honeymoon, where we met you both.
“Then one morning Stanley received a telegram. When he read it he
became both confused and alarmed. He did not show me the
message, but told me that it was imperative that he should return to
London at once. I now recollect that we were in the hall of the
Kürhaus when the concierge handed him the message, and seated
in his invalid chair, near the big stove on the right, was old Mr.
Humphreys, whom I did not then know, but who was no doubt
watching us intently.”
“He had followed you to Mürren with a very definite object,” Feng
went on. “He must have been watching you for some months
beforehand, and I have no doubt your sudden marriage was a
severe blow to his plans.
“I had serious difficulty in making friends with him. Of course he
knew I was a Chinese and I really believe that he suspected at first
that I was an agent of the Thu-tseng. It was only when he found
that I had been at Mürren some time before Thelma and Audley
arrived—and therefore, he thought, could not be specially interested
in them—that I succeeded in getting inside his guard. Of course, by
posing as his friend, I was able much more easily to keep track of
his movements.
“Do you remember your escape from the avalanche?”
“Rather!” said Thelma and I simultaneously.
“Perhaps you will be surprised to learn that that avalanche was not
the unaided work of Nature,” said the doctor. “You did not notice a
man some hundreds of feet above you?”
“No,” I said, “but what do you mean?”
“It’s a very easy thing to start an avalanche,” said Feng with a smile.
“There was a man above you that day and the avalanche was
started deliberately. Your guide John found out the truth afterwards.
But the would-be assassin—I have no doubt he was in the pay of
Humphreys—was never traced and the matter was hushed up. It
would not have done to let Humphreys know that the truth was
suspected. As a matter of fact I did suspect it and implored John to
investigate.
“But with regard to Stanley Audley I confess I was completely
misled. When he received that telegram recalling him to London I
believed that the story he had told you about his profession as
electrical engineer, was a true one. Only when it was proved to be
without foundation did I see that I, like yourself, had been cleverly
bamboozled. Until then I had believed Audley to be what he
represented himself to be. I never dreamed of the truth. Hartley
Humphreys, a crook to his finger tips, possessed a master-mind,
obsessed by criminality, and having no idea of my actual purpose he
acted with such amazing cunning and forethought that he must be
placed among the list of the master-criminals of the world.”
“Of course I had no suspicion,” said Thelma. “I didn’t even know
that I was an heiress.”
“And I was fool enough to think that Humphreys was my friend and
you were my enemy, Doctor,” I said with some shame as I thought
of how completely I had been deceived.
“Well,” laughed Feng, “that’s all over now. But I’m glad I was able to
deceive you because it helped me to deceive Humphreys. He was
quite aware of your feeling towards me. You are fairly transparent,
Yelverton, if you don’t mind my saying so!”
“The position was very extraordinary. Humphreys got Audley out of
the way—I will explain that later—and that, he thought, would leave
Thelma unprotected. But he never expected your interest in the
bride. You became a very unwelcome bit of grit in a very well-oiled
machine. You were constantly with Thelma, she was never left alone
for a moment—and you were in the way.”
And the shrewd old man smiled mysteriously.
 CHAPTER XXII
THE SECRET DISCLOSED

“But what was the mystery of Audley’s disappearance?” I asked

Feng, in breathless eagerness, now that the enigma was in course of
solution.
“Well, Humphreys at first did his level best to prevent the marriage,
but finding that impossible he went very cleverly to work. Audley,
who was a young man of means—though he pretended that his
profession was that of electrical engineer—had, Humphreys
discovered, fallen into the hands of a man named Graydon, a friend
of his, who lived in the same house as Audley and who was one of a
gang of note forgers.
“By clever means this gang had used Audley for their own purposes,
even to the extent of sometimes inducing him to assume Graydon’s
identity. Harold Ruthen was one of Graydon’s accomplices in passing
spurious notes, hence old Humphreys knew of Audley’s connection
with the forgers. After Thelma’s marriage which he had tried in vain
to prevent, it was highly necessary for the furtherance of
Humphreys’ sinister plan, to get her husband away. He therefore
caused to be sent to him at Mürren a veiled message that the police
were making inquiries in London and that he had better at once
efface himself, even from his wife. This he did, leaving Thelma in
your care.”
“But was Stanley really a forger?” I asked.
“At first I thought so, but later I found that the poor fellow had acted
in all innocence. He was being blackmailed by the gang and thus
forced to assist them, until he received that warning and fled,”
replied Feng. “I was all the time watching the very deep game
played by the wily old crook who posed as an invalid. With Audley
out of the way he expected that it would be easy to complete his
plans. Instead, to his great chagrin, you came forward as the bride’s
companion and protector. It was then that he determined, if you still
continued to watch over the girl, from whose husband he had
contrived to part her, that your activities should be suppressed. It
then became my active duty to keep guard over both of you, which I
did to the best of my ability.
“It was, of course, a difficult task. Had he been in New York you
would both have been watched night and day by men of the Thu-
tseng. The Chinese make the finest ‘shadowers’ in the world and in
New York they are so very numerous that I could employ them with
impunity. In London they are too conspicuous. It was really through
this that Humphreys nearly beat me at the finish.
“But I will give you an instance of how narrowly you escaped. Do
you remember one night when we all had supper with Humphreys at
a Chinese restaurant near Piccadilly Circus?”
“Yes,” I nodded.
“And you remember that I signalled to you not to eat the cold soup
that was served?”
“Yes,” I replied. “I thought you meant it was something I should not
like.”
“You would have been dead in five days if you had eaten it,” said
Feng grimly. “It was by a miracle of luck that I saw Humphreys drop
into it a tiny pellet as he reached his hand out for some bread. The
Chinese waiter took your soup away. Humphreys did not notice the
Chinese remark I made to the waiter, but that soup was preserved
and analyzed. It contained a virulent culture of the germs of typhoid
fever. The Chinese waiter, of course, was an agent of the Thu-tseng.
I daresay you will meet him some day. He happens to be a doctor
and a great friend of mine. He analyzed the soup for me. If you had
taken a spoonful of it while Humphreys was telling the funny stories
at which you were laughing, you would have been dead in five days
—of perfectly natural causes.”
“But, Thelma. Did you know anything of all this?” I asked turning to
her, astounded and muddled.
“Some of the facts I knew, but not all,” she replied. “I hope you will
forgive me, but I acted all along upon Doctor Feng’s instructions. At
Mürren I knew nothing, and was entirely unsuspicious of the plot
against us both.”
“Humphreys had degenerated into perhaps the cleverest financial
crook in Eastern Europe,” said Feng. “The way in which he held
Audley aloof from his wife while his friends Graydon and Ruthen
were at the same time terrorizing him and compelling him to assist
in passing their spurious notes, was a most remarkable feature of
the case. He acted with such caution and pre-arranged things so
cunningly, that I confess I was more than once misled and
befogged.
“It was he who sent you those warnings from Hammersmith and
North London in an endeavor to frighten you off. He certainly had a
sort of superstitious fear of you. My chief fear for Thelma was that
she might be secretly poisoned in a similar manner to the attempt
upon yourself. Therefore I insisted that she should never take her
meals in a restaurant alone.”
“And I was in ignorance,” I exclaimed.
“I deemed it best. I did not wish to alarm either of you, and indeed
it is only since the narrow escape you both had at Heathermoor
Gardens that I revealed to Thelma the motive of the plot. I did not
suspect that terrible death-trap, but as soon as Thelma was missing
I naturally felt that she must have fallen into the hands of one or
other of the gang. Judge my surprise when I discovered that she
surreptitiously, at Audley’s request, rejoined him in hiding at a small
private hotel in Gloucester Road, Kensington. Audley was in constant
dread of the police, an apprehension kept alive by Ruthen and
Graydon, and for that reason he destroyed his clothes and some
false notes before escaping from the room at Lancaster Gate. He
turned the key from the outside, in order further to mystify those
whom he believed to be his pursuers.”
“I was his pursuer,” I remarked.
“True. But he was avoiding you, as well as the police,” Feng said.
“He was told that you were making inquiries concerning him on his
wife’s behalf and would, if you gained the truth, reveal it to her.
Naturally, he had no desire that Thelma should know that the police
were wanting him upon grave charges of forgery.”
“But why did he not openly defy those men into whose hands he fell
before his marriage?” I asked. “Surely, he could have cleared himself
and have given information to the police.”
“Ah! Humphreys, the criminal with the master-mind took very good
care that he was so deeply implicated that he dare not utter a word,”
my friend pointed out. “Recollect his determination was that Thelma,
alone and without friends except her mother, should meet with an
untimely end in order that the Sung-tchun fortune should pass to
him.
“First, however, she married unexpectedly, and, secondly, you came
upon the scene as her protector. It was for that reason an attempt
was first made to poison you, and then that clever plot at Stamford
whereby you were drugged by that final cigarette given you by the
supposed commercial traveler, who afterwards entered your room,
forced against your lips a bottle containing a deadly drug, and made
it appear as though you had committed suicide. Humphreys believed
that you knew too much, so he intended that you should die before
the girl over whom you were so carefully watching. He had no idea,
however, of the part I was playing—until the police went to arrest
him.”
“But could you not have told me the truth long ago—and given me
warning?” I asked.
“That was impossible,” he replied. “Remember I warned you
repeatedly. You would only have laughed had I told you Humphreys
was your enemy: you were already deeply prejudiced against me.
Thelma, too, tried to induce you to give the whole thing up, but you
refused. Had Humphreys known that you suspected him he would
have had you both murdered out of hand and chanced detection.
But as things were he elected to wait until he could devise a plot
that would be absolutely safe. So long as Stanley Audley was out of
the way there was no need for him to do anything rash. And by his
patience he nearly won in the end.”
“But he very nearly lost,” I said. “Suppose Thelma and I had been
burnt to death. We could never have been identified and Humphreys
could not have proved Thelma’s death. That meant he could not
have inherited her fortune at any rate until sufficient time had
elapsed for the Courts to presume her death.”
“You are a lawyer, Yelverton, and of course that point would occur to
you. But it also occurred to Humphreys—another instance of his
amazing foresight—and he took steps accordingly. Thelma, show Mr.
Yelverton your locket.”
With a smile Thelma took from her pocket a heavy locket attached
to a chain and handed it to me. I was astonished at its massiveness
and weight, until I saw both locket and chain were of platinum. On
the front of the locket was deeply engraved the inscription, “Thelma
Audley—from Stanley.”
“Platinum; you see, Yelverton!” said old Feng.
I gasped in astonishment at the realization of Humphreys’
cleverness.
“Of course,” I said, “it would resist the fire, the locket would be
found in the débris and Thelma’s disappearance would be explained,
in part at any rate.”
“Yes,” rejoined Feng, “the locket would account for Thelma and what
more natural than the conclusion that the remains of the man found
with her were those of her husband?”
“But what has become of Stanley?” I asked, wondering why Thelma
was here without him.
“Stanley Audley is dead,” said Feng very gently, and I noticed the
slow tears begin to trickle down Thelma’s face. “He died like a hero.
It was he who rescued Thelma from the blazing room. By some
extraordinary chance the fire seems to have spread mainly in your
direction and Thelma escaped with the loss of most of her clothing
and her hair which was almost burnt off. But poor Stanley was so
terribly burned that he died three days later in the hospital. There is
no doubt he loved Thelma deeply and utterly regretted the trouble
he had brought upon her.”
Stanley Audley dead! I held my breath! Then Thelma was free! Such
was my involuntary reflection.
Thelma was weeping softly. I hardly dared look at her. But I put out
my hand and clasped hers. She turned her head away and gazed in
silence at the golden glow in the west across the sea. But she did
not withdraw her hand and a great wave of joy flooded through me.
“But how did we escape?” I asked Feng.
“We were only in the nick of time,” he replied. “When Thelma
disappeared from her husband in Gloucester Road I felt certain that
she had been decoyed away. She was—by a message purporting to
come from her husband asking her to call at Heathermoor Gardens.
She did so and fell into the hands of the man who intended she
should die. Yet so clever was old Humphreys, that, though I kept
him under close observation, I could not discern that he was acting
at all suspiciously. I did not know of course, of his plot to burn you
alive. But we were watching him very closely. That night Stanley and
I tracked him to the house at Hampstead. We saw you arrive later,
but we little dreamed that Thelma was held there a drugged and
helpless prisoner. She screamed twice, apparently, and you heard
her, but some accomplice of Humphreys’ gave her a hypodermic
injection—we found the mark afterwards on her arm.
“We watched until the first man-servant came out and later
Humphreys himself left the place and walking in some distance away
concealed himself in full view of the house. Then I knew you were
left in there, and I became seriously alarmed.
“Fortunately a constable was near, and unseen by the old villain I
approached him, told him of my suspicions, and we all three
approached the house together. To our rings and knocks there was
no answer, therefore we forced the door and rushed in. As we
opened the door of the room where you were, we saw the air-ball
burst and in a second the room was a furnace.
“Then came a desperate fight for life. Audley dashed to Thelma and
succeeded in getting her out into the street at the cost of his own
life, while I and the constable cut the rope which secured your
wrists, and carried you out terribly burned and insensible. Both the
constable and I were also burned, but not very seriously. Before the
fire brigade arrived the house had been seriously damaged: but for
our early warning it must have been utterly destroyed, as
Humphreys intended.
“Meanwhile, Humphreys, who had seen the failure of his plot, made
himself scarce and it was not until three days later that Inspector
Cayley of Scotland Yard, with two sergeants traced him to a room in
Earl’s Court Road, where he was hiding. But the old criminal had
locked himself in and before they could break open the door he had
put a bullet through his brain. A week ago both Ruthen and Graydon
were arrested at the Pavilion Hotel in Boulogne on charges of
passing spurious notes in various towns in France. They will, no
doubt, go to hard labor for some years.”
“Well, Yelverton,” the old man concluded, “I think you know
everything now. You have both had a very narrow escape from a
terrible fate. Only a devil in human form could have devised such an
atrocity. But now I’ll leave you alone for a bit: you will have plenty to
talk about.”
And with a cheery smile and a loving look at Thelma, the sturdy,
bearded old man, to whose watchfulness we both owed our lives,
turned on his heel and left the room.
The calm Riviera sunset had deepened into twilight, swiftly as it
always does, and the night clouds rising over the pine-clad Esterels
cast their long grey shadows across the calm sea. Beneath our
window twinkling lights shone and from among the orange graves
below came voices and merry laughter.
I had been speaking earnestly to Thelma—pleading with her all the
fervor of the love I had so long held in restraint but which, now she
was free, poured out with violence that overwhelmed me. She heard
me without comment or response. But she made no protest, she
allowed me to hold her hand, even when I pressed it tenderly to my
lips she did not withdraw it.
The hope that had never quite died rose again in my heart. I felt
Thelma trembling; a beautiful warmth that I had never seen before
glowed upon her cheeks, her eyes were lustrous with the brilliancy
of tears which welled up into them but did not fall. She stood looking
out across the broad Mediterranean towards the African coast which
the colors of the sunset paled into the faint splendor of the
afterglow.
The light was nearly gone, and still she made no sign. But presently
words failed me and I simply stood and held out my arms in a last
despairing appeal.
Then my darling came to me, slowly and sweetly, her great grey
eyes aflame with a light I had never seen before. And our lips met at
last.

We were married in October and spent our honeymoon in Seville

and Malaga. Christmas found us at the Hotel Regina at Wengen, a
little below Mürren, where we both went skiing daily. We visited
Mürren, of course, hallowed to us for all time as the place of that
strange first meeting from which all our troubles and all our
happiness had sprung.
We are rich, of course, Sung-tchun’s fortune was enormous. But we
live very quietly in my old home—my father’s quaint, old-world
cottage on the Salisbury road a few miles from Andover. Most of our
income, apart from our own modest wants, goes to help the slum
children of London. Thelma never tires of them and every summer
forms a big camp to which hundreds come down for a few days’
glorious holiday. They all seem to worship her and over even the
roughest of them she seems to exercise a magical fascination.
Old Doctor Feng, to whom we owe so much, is our chief friend. He
comes and goes as he pleases. There is a room reserved for him and
always ready. Devoted to Thelma, he spends much of his time with
us. He never tires of talking of the Crystal Claw, the magic talisman
that saved us for each other. And every now and again, with his
inimitable chuckle, he croaks out, “Yelverton, I told you the arm of
the Thu-tseng was long!”
It was long indeed. It stretched half across the world to give us—
two tiny units caught in a cruel trap—a helping hand in our dire
distress. We owe our wealth, our radiant happiness, our very lives to
the magical influence of the Crystal Claw.
THE END
 TRANSCRIBER’S NOTES:
Obvious typographical errors have been corrected.
Inconsistencies in hyphenation have been
standardized.
Archaic or variant spelling has been retained.
*** END OF THE PROJECT GUTENBERG EBOOK THE CRYSTAL CLAW
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