Essential Biochemistry

Preface xiv

Part 1 Foundations

1 The Chemical Basis of Life 1

1.1 What Is Biochemistry? 1

1.2 Biological Molecules 3

Cells contain four major types of biomolecules 3

There are three major kinds of biological polymers 6

Box 1.A Units Used in Biochemistry 7

1.3 Energy and Metabolism 10

Enthalpy and entropy are components of free energy 11

ΔG is less than zero for a spontaneous process 12

Life is thermodynamically possible 12

1.4 The Origin of Cells 14

Prebiotic evolution led to cells 15

Box 1.B How Does Evolution Work? 17

Eukaryotes are more complex than prokaryotes 17

The human body includes microorganisms 19

2 Aqueous Chemistry 27

2.1 Water Molecules and Hydrogen Bonds 27

Hydrogen bonds are one type of electrostatic force 29

Water dissolves many compounds 31

Box 2.A Why Do Some Drugs Contain Fluorine? 31

2.2 The Hydrophobic Effect 33

Amphiphilic molecules experience both hydrophilic interactions and the hydrophobic effect 35

The hydrophobic core of a lipid bilayer is a barrier to diffusion 35

Box 2.B Sweat, Exercise, and Sports Drinks 36

2.3 Acid–Base Chemistry 37

[H+] and [OH–] are inversely related 38

The pH of a solution can be altered 39

Box 2.C Atmospheric CO2 and Ocean Acidification 39

A pK value describes an acid’s tendency to ionize 40

The pH of a solution of acid is related to the pK 41

2.4 Tools and Techniques: Buffers 44

2.5 Clinical Connection: Acid–Base Balance in Humans 46

Part 2 Molecular Structure and Function

3 Nucleic Acid Structure and Function 57

3.1 Nucleotides 57

Nucleic acids are polymers of nucleotides 58

Some nucleotides have other functions 60

3.2 Nucleic Acid Structure 61

DNA is a double helix 62

RNA is single-stranded 64

Nucleic acids can be denatured and renatured 64

3.3 The Central Dogma 67

Box 3.A Replication, Mitosis, Meiosis, and Mendel’s Laws 67

DNA must be decoded 70

A mutated gene can cause disease 71

Genes can be altered 72

Box 3.B Genetically Modified Organisms 73

3.4 Genomics 74

The exact number of human genes is not known 75

Genome size varies 75

Genomics has practical applications 77

Box 3.C Viruses 78

4 Protein Structure 86

4.1 Amino Acids, the Building Blocks of Proteins 86

The 20 amino acids have different chemical properties 88

Box 4.A Does Chirality Matter? 89

Box 4.B Monosodium Glutamate 91

Peptide bonds link amino acids in proteins 91

The amino acid sequence is the first level of protein structure 94

4.2 Secondary Structure: The Conformation of the Peptide Group 95

The α helix exhibits a twisted backbone conformation 96

The β sheet contains multiple polypeptide strands 96

Proteins also contain irregular secondary structure 98

4.3 Tertiary Structure and Protein Stability 99

Proteins can be described in different ways 99

Globular proteins have a hydrophobic core 100

Protein structures are stabilized mainly by the hydrophobic effect 101

Box 4.C Thioester Bonds as Spring-Loaded Traps 103

Protein folding is a dynamic process 103

Box 4.D Baking and Gluten Denaturation 104

Disorder is a feature of many proteins 105

Protein functions may depend on disordered regions 106

4.4 Quaternary Structure 107

4.5 Clinical Connection: Protein Misfolding and Disease 109

4.6 Tools and Techniques: Analyzing Protein Structure 111

Chromatography takes advantage of a polypeptide’s unique properties 111

Mass spectrometry reveals amino acid sequences 114

Box 4.E Mass Spectrometry Applications 116

Protein structures are determined by NMR spectroscopy, X-ray crystallography, and cryo-electron microscopy 116

5 Protein Function 125

5.1 Myoglobin and Hemoglobin: Oxygen-Binding Proteins 126

Oxygen binding to myoglobin depends on the oxygen concentration 127

Myoglobin and hemoglobin are related by evolution 128

Oxygen binds cooperatively to hemoglobin 129

A conformational shift explains hemoglobin’s cooperative behavior 130

Box 5.A Carbon Monoxide Poisoning 130

H+ ions and bisphosphoglycerate regulate oxygen binding to hemoglobin in vivo 132

5.2 Clinical Connection: Hemoglobin Variants 134

5.3 Structural Proteins 136

Actin filaments are most abundant 137

Actin filaments continuously extend and retract 138

Tubulin forms hollow microtubules 139

Keratin is an intermediate filament 142

Collagen is a triple helix 144

Box 5.B Vitamin C Deficiency Causes Scurvy 144

Collagen molecules are covalently cross-linked 145

Box 5.C Bone and Collagen Defects 147

5.4 Motor Proteins 148

Myosin has two heads and a long tail 148

Myosin operates through a lever mechanism 150

Kinesin is a microtubule-associated motor protein 151

Box 5.D Myosin Mutations and Deafness 151

Kinesin is a processive motor 152

5.5 Antibodies 154

Immunoglobulin G includes two antigen-binding sites 154

B lymphocytes produce diverse antibodies 156

Researchers take advantage of antibodies’ affinity and specificity 157

6 How Enzymes Work 167

6.1 What Is an Enzyme? 167

Enzymes are usually named after the reaction they catalyze 170

6.2 Chemical Catalytic Mechanisms 171

A catalyst provides a reaction pathway with a lower activation energy barrier 173

Enzymes use chemical catalytic mechanisms 173

Box 6.A Depicting Reaction Mechanisms 175

The catalytic triad of chymotrypsin promotes peptide bond hydrolysis 177

6.3 Unique Properties of Enzyme Catalysts 180

Enzymes stabilize the transition state 180

Efficient catalysis depends on proximity and orientation effects 181

The active-site microenvironment promotes catalysis 182

6.4 Chymotrypsin in Context 183

Not all serine proteases are related by evolution 183

Enzymes with similar mechanisms exhibit different substrate specificity 184

Chymotrypsin is activated by proteolysis 185

Protease inhibitors limit protease activity 186

6.5 Clinical Connection: Blood Coagulation 187

7 Enzyme Kinetics and Inhibition 198

7.1 Introduction to Enzyme Kinetics 198

7.2 Derivation and Meaning of the Michaelis–Menten Equation 201

Rate equations describe chemical processes 201

The Michaelis–Menten equation is a rate equation for an enzyme-catalyzed reaction 202

KM is the substrate concentration at which velocity is half-maximal 204

The catalytic constant describes how quickly an enzyme can act 204

kcat/KM indicates catalytic efficiency 205

KM and Vmax are experimentally determined 205

Not all enzymes fit the simple Michaelis–Menten model 207

7.3 Enzyme Inhibition 209

Some inhibitors act irreversibly 209

Competitive inhibition is the most common form of reversible enzyme inhibition 210

Transition state analogs inhibit enzymes 212

Other types of inhibitors affect Vmax 213

Box 7.A Inhibitors of HIV Protease 214

Allosteric enzyme regulation includes inhibition and activation 216

Several factors may influence enzyme activity 219

7.4 Clinical Connection: Drug Development 219

8 Lipids and Membranes 234

8.1 Lipids 234

Fatty acids contain long hydrocarbon chains 235

Box 8.A Omega-3 Fatty Acids 236

Some lipids contain polar head groups 237

Lipids perform a variety of physiological functions 239

Box 8.B The Lipid Vitamins A, D, E, and K 240

8.2 The Lipid Bilayer 241

The bilayer is a fluid structure 242

Natural bilayers are asymmetric 243

8.3 Membrane Proteins 244

Integral membrane proteins span the bilayer 245

An α helix can cross the bilayer 245

A transmembrane β sheet forms a barrel 246

Lipid-linked proteins are anchored in the membrane 246

8.4 The Fluid Mosaic Model 248

Membrane proteins have a fixed orientation 249

Lipid asymmetry is maintained by enzymes 250

9 Membrane Transport 258

9.1 The Thermodynamics of Membrane Transport 258

Ion movements alter membrane potential 259

Membrane proteins mediate transmembrane ion movement 260

9.2 Passive Transport 263

Porins are β barrel proteins 263

Ion channels are highly selective 264

Gated channels undergo conformational changes 265

Box 9.A Pores Can Kill 265

Aquaporins are water-specific pores 266

Some transport proteins alternate between conformations 268

9.3 Active Transport 269

The Na,K-ATPase changes conformation as it pumps ions across the membrane 269

ABC transporters mediate drug resistance 271

Secondary active transport exploits existing gradients 271

9.4 Membrane Fusion 272

SNAREs link vesicle and plasma membranes 273

Box 9.B Antidepressants Block Serotonin Transport 275

Endocytosis is the reverse of exocytosis 276

Autophagosomes enclose cell materials for degradation 277

Box 9.C Exosomes 278

10 Signaling 287

10.1 General Features of Signaling Pathways 287

A ligand binds to a receptor with a characteristic affinity 288

Most signaling occurs through two types of receptors 289

The effects of signaling are limited 290

10.2 G Protein Signaling Pathways 291

G protein–coupled receptors include seven transmembrane helices 292

The receptor activates a G protein 293

The second messenger cyclic AMP activates protein kinase A 294

Arrestin competes with G proteins 296

Signaling pathways must be switched off 296

The phosphoinositide signaling pathway generates two second messengers 297

Many sensory receptors are GPCRs 298

Box 10.A Opioids 299

10.3 Receptor Tyrosine Kinases 300

The insulin receptor dimer changes conformation 300

The receptor undergoes autophosphorylation 302

Box 10.B Cell Signaling and Cancer 303

10.4 Lipid Hormone Signaling 303

Eicosanoids are short-range signals 305

Box 10.C Inhibitors of Cyclooxygenase 306

11 Carbohydrates 315

11.1 Monosaccharides 315

Most carbohydrates are chiral compounds 316

Cyclization generates α and β anomers 317

Monosaccharides can be derivatized in many different ways 318

Box 11.A The Maillard Reaction 319

11.2 Polysaccharides 320

Lactose and sucrose are the most common disaccharides 321

Starch and glycogen are fuel-storage molecules 321

Cellulose and chitin provide structural support 322

Box 11.B Cellulosic Biofuel 323

Bacterial polysaccharides form a biofilm 324

11.3 Glycoproteins 325

Oligosaccharides are N-linked or O-linked 325

Oligosaccharide groups are biological markers 326

Box 11.C The ABO Blood Group System 327

Proteoglycans contain long glycosaminoglycan chains 327

Bacterial cell walls are made of peptidoglycan 328

Part 3 Metabolism

12 Metabolism and Bioenergetics 337

12.1 Food and Fuel 337

Cells take up the products of digestion 338

Monomers are stored as polymers 339

Fuels are mobilized as needed 340

12.2 Metabolic Pathways 343

Some major metabolic pathways share a few common intermediates 343

Many metabolic pathways include oxidation–reduction reactions 344

Metabolic pathways are complex 346

Human metabolism depends on vitamins 347

Box 12.A The Transcriptome, the Proteome, and the Metabolome 348

Box 12.B Iron Metabolism 351

12.3 Free Energy Changes in Metabolic Reactions 352

The free energy change depends on reactant concentrations 352

Unfavorable reactions are coupled to favourable reactions 354

Energy can take different forms 356

Regulation occurs at the steps with the largest free energy changes 357

13 Glucose Metabolism 366

13.1 Glycolysis 366

Energy is invested at the start of glycolysis 367

ATP is generated near the end of glycolysis 373

Box 13.A Catabolism of Other Sugars 378

Some cells convert pyruvate to lactate or ethanol 379

Box 13.B Alcohol Metabolism 380

Pyruvate is the precursor of other molecules 381

13.2 Gluconeogenesis 383

Four gluconeogenic enzymes plus some glycolytic enzymes convert pyruvate to glucose 383

Gluconeogenesis is regulated at the fructose bisphosphatase step 385

13.3 Glycogen Synthesis and Degradation 386

Glycogen synthesis consumes the energy of UTP 386

Glycogen phosphorylase catalyzes glycogenolysis 388

13.4 The Pentose Phosphate Pathway 389

The oxidative reactions of the pentose phosphate pathway produce NADPH 389

Isomerization and interconversion reactions generate a variety of monosaccharides 390

A summary of glucose metabolism 392

13.5 Clinical Connection: Disorders of Carbohydrate Metabolism 393

Glycogen storage diseases affect liver and muscle 394

14 The Citric Acid Cycle 403

14.1 The Pyruvate Dehydrogenase Reaction 403

The pyruvate dehydrogenase complex contains multiple copies of three different enzymes 404

Pyruvate dehydrogenase converts pyruvate to acetyl-CoA 404

14.2 The Eight Reactions of the Citric Acid Cycle 406

1. Citrate synthase adds an acetyl group to oxaloacetate 407

2. Aconitase isomerizes citrate to isocitrate 409

3. Isocitrate dehydrogenase releases the first CO2 410

4. α-Ketoglutarate dehydrogenase releases the second CO2 410

5. Succinyl-CoA synthetase catalyzes substrate-level phosphorylation 411

6. Succinate dehydrogenase generates ubiquinol 412

7. Fumarase catalyzes a hydration reaction 412

8. Malate dehydrogenase regenerates oxaloacetate 412

14.3 Thermodynamics of the Citric Acid Cycle 413

The citric acid cycle is an energy-generating catalytic cycle 413

The citric acid cycle is regulated at three steps 414

Box 14.A Mutations in Citric Acid Cycle Enzymes 415

The citric acid cycle probably evolved as a synthetic pathway 415

14.4 Anabolic and Catabolic Functions of the Citric Acid Cycle 416

Citric acid cycle intermediates are precursors of other molecules 416

Anaplerotic reactions replenish citric acid cycle intermediates 418

Box 14.B The Glyoxylate Pathway 419

15 Oxidative Phosphorylation 428

15.1 The Thermodynamics of Oxidation–Reduction Reactions 428

Reduction potential indicates a substance’s tendency to accept electrons 429

The free energy change can be calculated from the change in reduction potential 431

15.2 Mitochondrial Electron Transport 432

Mitochondrial membranes define two compartments 433

Complex I transfers electrons from NADH to ubiquinone 434

Other oxidation reactions contribute to the ubiquinol pool 436

Complex III transfers electrons from ubiquinol to cytochrome c 437

Complex IV oxidizes cytochrome c and reduces O2 439

Respiratory complexes associate with each other 441

Box 15.A Reactive Oxygen Species 442

15.3 Chemiosmosis 443

Chemiosmosis links electron transport and oxidative phosphorylation 443

The proton gradient is an electrochemical gradient 443

15.4 ATP Synthase 445

Proton translocation rotates the c ring of ATP synthase 445

The binding change mechanism explains how ATP is made 447

The P:O ratio describes the stoichiometry of oxidative phosphorylation 447

Box 15.B Uncoupling Agents Prevent ATP Synthesis 448

The rate of oxidative phosphorylation reflects the need for ATP 448

Box 15.C Powering Human Muscles 449

16 Photosynthesis 458

16.1 Chloroplasts and Solar Energy 458

Pigments absorb light of different wavelengths 459

Light-harvesting complexes transfer energy to the reaction center 461

16.2 The Light Reactions 463

Photosystem II is a light-activated oxidation–reduction enzyme 463

The oxygen-evolving complex of Photosystem II oxidizes water 464

Cytochrome b6f links Photosystems I and II 466

A second photooxidation occurs at Photosystem I 467

Chemiosmosis provides the free energy for ATP synthesis 469

16.3 Carbon Fixation 471

Rubisco catalyzes CO2 fixation 471

The Calvin cycle rearranges sugar molecules 472

Box 16.A The C4 Pathway 473

The availability of light regulates carbon fixation 475

Calvin cycle products are used to synthesize sucrose and starch 476

17 Lipid Metabolism 483

17.1 Lipid Transport 483

17.2 Fatty Acid Oxidation 486

Fatty acids are activated before they are degraded 487

Each round of β oxidation has four reactions 488

Degradation of unsaturated fatty acids requires isomerization and reduction 491

Oxidation of odd-chain fatty acids yields propionyl-CoA 492

Some fatty acid oxidation occurs in peroxisomes 494

17.3 Fatty Acid Synthesis 495

Acetyl-CoA carboxylase catalyzes the first step of fatty acid synthesis 496

Fatty acid synthase catalyzes seven reactions 497

Other enzymes elongate and desaturate newly synthesized fatty acids 500

Box 17.A Fats, Diet, and Heart Disease 500

Fatty acid synthesis can be activated and inhibited 501

Box 17.B Inhibitors of Fatty Acid Synthesis 502

Acetyl-CoA can be converted to ketone bodies 503

17.4 Synthesis of Other Lipids 505

Triacylglycerols and phospholipids are built from acyl-CoA groups 505

Cholesterol synthesis begins with acetyl-CoA 508

A summary of lipid metabolism 510

18 Nitrogen Metabolism 518

18.1 Nitrogen Fixation and Assimilation 518

Nitrogenase converts N2 to NH3 519

Ammonia is assimilated by glutamine synthetase and glutamate synthase 519

Transamination moves amino groups between compounds 521

Box 18.A Transaminases in the Clinic 523

18.2 Amino Acid Biosynthesis 523

Several amino acids are easily synthesized from common metabolites 524

Amino acids with sulfur, branched chains, or aromatic groups are more difficult to synthesize 526

Box 18.B Homocysteine, Methionine, and One-Carbon Chemistry 527

Box 18.C Glyphosate, the Most Popular Herbicide 528

Amino acids are the precursors of some signaling molecules 530

Box 18.D Nitric Oxide 531

18.3 Amino Acid Catabolism 532

Amino acids are glucogenic, ketogenic, or both 532

Box 18.E Diseases of Amino Acid Metabolism 535

18.4 Nitrogen Disposal: The Urea Cycle 536

Glutamate supplies nitrogen to the urea cycle 537

The urea cycle consists of four reactions 538

18.5 Nucleotide Metabolism 540

Purine nucleotide synthesis yields IMP and then AMP and GMP 541

Pyrimidine nucleotide synthesis yields UTP and CTP 542

Ribonucleotide reductase converts ribonucleotides to deoxyribonucleotides 543

Thymidine nucleotides are produced by methylation 544

Nucleotide degradation produces urate or amino acids 545

19 Regulation of Mammalian Fuel Metabolism 555

19.1 Integration of Fuel Metabolism 555

Organs are specialized for different functions 556

Metabolites travel between organs 557

Box 19.A The Intestinal Microbiota Contribute to Metabolism 558

19.2 Hormonal Control of Fuel Metabolism 560

Insulin is released in response to glucose 560

Insulin promotes fuel use and storage 561

mTOR responds to insulin signaling 563

Glucagon and epinephrine trigger fuel mobilization 564

Additional hormones influence fuel metabolism 565

AMP-dependent protein kinase acts as a fuel sensor 566

Fuel metabolism is also controlled by redox balance and oxygen 566

19.3 Disorders of Fuel Metabolism 568

The body generates glucose and ketone bodies during starvation 568

Box 19.B Marasmus and Kwashiorkor 568

Obesity has multiple causes 569

Diabetes is characterized by hyperglycemia 570

Obesity, diabetes, and cardiovascular disease are linked 572

19.4 Clinical Connection: Cancer Metabolism 573

Aerobic glycolysis supports biosynthesis 573

Cancer cells consume large amounts of glutamine 574

Part 4 Genetic Information

20 DNA Replication and Repair 582

20.1 The DNA Replication Machinery 582

Replication occurs in factories 583

Helicases convert double-stranded DNA to single-stranded DNA 584

DNA polymerase faces two problems 585

DNA polymerases share a common structure and mechanism 587

DNA polymerase proofreads newly synthesized DNA 589

An RNase and a ligase are required to complete the lagging strand 590

20.2 Telomeres 593

Telomerase extends chromosomes 594

Box 20.A HIV Reverse Transcriptase 595

Is telomerase activity linked to cell immortality? 596

20.3 DNA Damage and Repair 596

DNA damage is unavoidable 597

Repair enzymes restore some types of damaged DNA 598

Base excision repair corrects the most frequent DNA lesions 598

Nucleotide excision repair targets the second most common form of DNA damage 599

Double-strand breaks can be repaired by joining the ends 601

Recombination also restores broken DNA molecules 601

Box 20.B Gene Editing with CRISPR 602

20.4 Clinical Connection: Cancer as a Genetic Disease 604

Tumor growth depends on multiple events 605

DNA repair pathways are closely linked to cancer 605

20.5 DNA Packaging 607

DNA is negatively supercoiled 607

Topoisomerases alter DNA supercoiling 608

Eukaryotic DNA is packaged in nucleosomes 610

20.6 Tools and Techniques: Manipulating DNA 611

Cutting and pasting generates recombinant DNA 612

The polymerase chain reaction amplifies DNA 614

DNA sequencing uses DNA polymerase to make a complementary strand 615

21 Transcription and RNA 627

21.1 Initiating Transcription 627

What is a gene? 628

DNA packaging affects transcription 628

DNA also undergoes covalent modification 631

Transcription begins at promoters 631

Transcription factors recognize eukaryotic promoters 633

Mediator integrates multiple regulatory signals 634

Box 21.A DNA-Binding Proteins 635

Prokaryotic operons allow coordinated gene expression 636

21.2 RNA Polymerase 638

RNA polymerases have a common structure and mechanism 639

Box 21.B RNA-Dependent RNA Polymerase 640

RNA polymerase is a processive enzyme 641

Transcription elongation requires changes in RNA polymerase 642

Transcription is terminated in several ways 644

21.3 RNA Processing 645

Eukaryotic mRNAs receive a 5′ cap and a 3′ poly(A) tail 645

Splicing removes introns from eukaryotic RNA 646

mRNA turnover and RNA interference limit gene expression 649

Box 21.C The Nuclear Pore Complex 649

rRNA and tRNA processing includes the addition, deletion, and modification of nucleotides 652

RNAs have extensive secondary structure 653

22 Protein Synthesis 663

22.1 tRNA and the Genetic Code 663

The genetic code is redundant 664

tRNAs have a common structure 665

tRNA aminoacylation consumes ATP 666

Editing increases the accuracy of aminoacylation 667

tRNA anticodons pair with mRNA codons 668

Box 22.A The Genetic Code Expanded 669

22.2 Ribosome Structure 669

The ribosome is mostly RNA 670

Three tRNAs and one mRNA bind to the ribosome 671

22.3 Translation 673

Initiation requires an initiator tRNA 673

The appropriate tRNAs are delivered to the ribosome during elongation 675

The peptidyl transferase active site catalyzes peptide bond formation 677

Box 22.B Antibiotic Inhibitors of Protein Synthesis 679

Release factors mediate translation termination 680

Translation is efficient and dynamic 681

22.4 Post-Translational Events 683

Chaperones promote protein folding 684

The signal recognition particle targets some proteins for membrane translocation 685

Many proteins undergo covalent modification 687

Glossary G-1

Odd-Numbered Solutions S-1

Index i-1