INTERNATIONAL SEVENTH EDITION

I

Jeremy M. Berg

John L. Tymoczko

Lubert Stryer ,~-

with Gregory J. Gatto, Jr.

II W. H. Freeman and Company · New York palgrave macmitlan

I

. / THE MOLECULAR DESIGN OF LI FE mistry: An Evolving Science 1

Composition and Structure 25

•""'''n•·•no Proteins and Proteomes 67

RNA, and the Flow of Genetic Information 113

~:v..,••nr•na Genes and Genomes 145

~::vr••nr•no Evolution and Bioinformatics 181

< Hemoglobin: Portrait of a Protein in Action 203

· · Enzymes: Basic Concepts and Kinetics 227

Catalytic Strategies 261

Regulatory Strategies 299

Carbohydrates 329

Lipids and Cell Membranes 357

Membrane Channels and Pumps 383

Signal-Transduction Pathways 415

n TRANSDUCING AND STORING ENERGY Metabolism: Basic Concepts and Design 443

....... · Glycolysis and Gluconeogenesis 469

> 1 The Citric Acid Cycle 51 5

·••••••· 8 Oxidative Phosphorylation 543 ••••···19 The Light Reactions of Photosynthesis 585

• \ 20 The Calvin Cycle and the Pentose Phosphate · Pathway 609

Glycogen Metabolism 637

Fatty Acid Metabolism 663

Protein Turnover and Amino Acid Catabolism 697

Pari m SYNTHESIZING THE MOLECULES OF UFE 24 The Biosynthesis of Amino Acids 729

25 Nucleotide Biosynthesis 761

26 The Biosynthesis of Membrane Lipids and Steraids 787

27 The Integration of Metabolism 821

28 DNA Replication, Repair, and Recombination 849

RNA Synthesis and Processing 883

30 Protein Synthesis 921

31 The Control of Gene Expression in Prokaryotes 957

32 The Control of Gene Expression in Eukaryotes 973

Part IV RESPONDING TO ENVIRONMENTAL 33 Sensory Systems 995

34 The Immune System 1017

35 Molecular Motors 1 049

36 Drug Development 1 073

CONTENTS

P~re V

Part I THE MOlECULAR DESIGN OF UFE

Chapter 1 Biochemistry: An Evolving Science

1.1 Biochemical Unity Underlies Biologkai Diversity

1.2 DNA lllustrates the lnterplay Between Form and Function DNA is constructed from four building blocks

Two single strands ofDNA combine to form a double helix

DNA structure explains heredity and the storage of information

1.3 Concepts from Chemistry Explain the Properties of Biological Molecules The double helix can form from its component strands

Covalent and noncovalent bonds are important for the structure and stability of biological molecules

The double helix is an expression of the rules of chemistry

T4e laws of thermodynamics govern the behavior of biochemical systems

Heat is released in the formation of the double helix

Acid-base reactions are central in many biochemical processes

Acid-base reactions can disrupt the double helix

Buffers regulate pH in organisms and in the laboratory

1.4 The Genomic Revolution ls Transforming Biochemistry and Medicine The sequencing of the human genome is a landmark in human history

Genome sequences encode proteins and patterns of express10n

Individuality depends on the interplay between genes and environment

APPENDIX: Visualizing Molecular Structures I: Small Molecules

Chapter 2 Protein Composition and Structure

2.1 Proteins Are Built from a Repertoire of 20 Amino Acids

2.2 Primary Structure: Amino Acids Are Unked by Peptide Bonds to Form Polypeptide Chains Proteins have unique amino acid sequences specified by genes

Polypeptide chains are flexible yet conformationally restricted

4 4

5

5

6 6

7

10

11

12

13

14

15

17

17

18

19

21

25

27

33

35

36

xvi Contents

2.3 Secondary Structure: Polypeptide Chains Can 3.2 Amino Acid Sequences of Proteins Can Fold into Regular Structures Such As the Alpha Be Determined Experimentally 81 Helix, the Beta Sheet, and Turns and loops 38 Peptide sequences can be determined by automated The alpha helix is a coiled structure stabilized Edman degradation 82 by intrachain hydrogen bonds 38 Proteins c<m be specifically cleaved into small Beta sheets are stabilized by hydrogen bonding between peptides to facilitate analysis 84 polypeptide strands 40 Genomic and proteomic methods are complementary 86 Polypeptide chains can change direction by 3.3 lmmunology Provides lmportant Techniques making reverse turns and loops 42 with Which to lnvestigate Proteins 86 Fibrous proteins provide structural support for Antihoclies to specifi.c proteins can be generated 86 cells and tissues 43

Monoclonal antihoclies with virtually any 2.4 Tertiary Structure: Water-Soluble Proteins desired specificity can be readily prepared 88 Fold into Compact Structures with Proteins can be detected and quantified by using an Nonpolar Cores 45 enzyme-linked immunosorbent assay 90

2.5 Quaternary Structure: Polypeptide Chains Western blotting permits the detection of

Can Assemble into Multisubunit Structures 48 proteins separated by gel electrophoresis 91

2.6 The Amino Acid Sequence of a Protein Fluorescent markers make the visualization of

Determines lts Three-Dimensional Structure 49 proteins in the cell possible 92

Amino acids have different propensities for 3.4 Mass Spectrometry ls a Powerful Technique forming alpha helices, beta sheets, and beta turns 50 for the ldlentification of Peptides and Proteins 93

Protein folding is a highly cooperative process 52 The mass of a protein can be precisely determined

Proteins fold by progressive stabilization of by mass spectrometry 93

intermediates rather than by random search 52 Peptides can be sequenced by mass spectrometry 95

Prediction of three-dimensional structure from ·Individual proteins can be identified by

sequence remains a great challenge 54 mass spect:rometry 96

Some proteins are inherently unstructured and 3.5 Peptiides Can Be Synthesized by can exist in multiple conformations 54 Automated Solid-Phase Methods 97 Protein misfolding and aggregation are associated 3.6 Three-Dimensional Protein Structure with some neurological diseases 55

Can Be Determined by X-ray Crystallography Protein modification and cleavage confer and NMR Spectroscopy 100 new capabilities 57

X-ray crystallography reveals three-dimensional APPENDIX: Visualizing Molecular Structures II: Proteins 60 structure in atomic detail 100

Nuclear magnetic resonance spectroscopy can reveal the st:ructures of proteins in solution 103

Chapter 3 Exploring Proteins and Proteomes 67

The proteome is the functional representation of Chapter ~~ DNA, RNA, and the Flow of the genome 68 Information 113 3.1 The Purification of Proteins ls an Essential

4.1 A Nucleic Acid Consists of Four Kinds of First Step in Understanding Their Function 68

Bases Linked to a Sugar-Phosphate Backbone 114 The assay: How do we recognize the protein that we are looking for? 69 RNA and DNA differ in the sugar component and

one of the bases 114 Proteins must be released from the cell to be purifi.ed 69

Nucleotides are the monomeric units of nucleic acids 115 Proteins.can be purified according to solubility, size, charge, ~d binding affinity 70 DNA molecules are very long 117

Proteins can be separated by gel electrophoresis and 4.2 A Pair of Nucleic Acid Chains with displayed 73 Complementary Sequences Can Form a A protein purification scheme can be quantitatively Double-Helical Structure 117 evaluated 77 The double helix is stabilized by hydrogen bonds and

Ultracentrifugation is valuable for separating van der W aals interactions 117 biomolecules and determining their masses 78 DNA can assume a variety of structural forms 119 Protein purification can be made easier with the use Z-DNA is a left-handed double helix in which of recombinant DNA technology 80 backhone phosphates zigzag 120

Contents xvii

moleeules are eireular and supereoiled 121 5.2 Recombinant DNA Technology Has Revolutionized All Aspects of Biology 154

121 Restrietion enzymes and DNA ligase are key tools in

Double Helix Facilitates the Aceurate forming reeombinant DNA moleeules 154

n of Hereditary Information 122 Plasmids and lambda phage are ehoiee veetors for

in DNA density established the validity DNA cloning in baeteria 155

hypothesis 123 Baeterial and yeast artifieial ehromosomes 157

helix ean be reversibly melted 124 Speeifie genes ean be cloned from digests of

ls Replicated by Polymerases genomieDNA 157

lnstructions from Templates 125 Complementary DNA prepared from mRNA ean be expressed in hast eells 160

eatalyzes phosphodiester-bridge 125

Proteins with new funetions ean be ereated through direeted ehanges in DNA 162

126 Reeombinant methods enable the exploration of the

Expression ls the Transformation of funetional effeets of disease-eausing mutations 163 ation into Functional Molecules 127 5.3 Complete Genomes Have Been

of RNA play key roles in gene expression 127 Sequenced and Analyzed 163 RNA is synthesized by RNA polymerases 128 The genomes of organisms ranging from baeteria to

take instruetions from DNA templates 130 multieellular eukaryotes have been sequeneed 164 begins near promoter sites and ends at The sequeneing of the human genome has

130 been finished 165

131 Next-generation sequeneing methods enable the rapid determination of a whole genome sequenee 166

Acids Are Encoded by Groups of C?mparative genomies has become a powerful

Bases Starting from a Fixed Point 132 researeh tool 166

133 5.4 Eukaryotic Genes Can Be Quantitated and Manipulated with Considerable Precision 167

134 Gene-expression levels ean be eomprehensively · eode is nearly universal 135 examined 167

Eukaryotic Genes Are Mosaics of New genes inserted into eukaryotie eells ean be

and Exons 135 effieiently expressed 169

136 Transgenie animals harbor and express genes

eneode protein domains 137 introdueed into their germ lines 170 Gene disruption provides clues to gene function 170 RNA interferenee provides an additional tool for disrupting gene expression 171

5 Exploring Genes and Genomes 145 Tumor-indueing plasmids ean be used to introduee

Exploration of Genes Relies on new genes into plant eells 172

146 Humangene therapy holds great promise for medieine 173

enzymes split DNA into speeifie fragments 147 fragments ean be separated by gel Chapter 6 Exploring Evolution and

and visualized 147 Bioinformatics 181

149 6.1 Homologs Are Descended from a

and genes ean be synthesized by Common Ancestor 182

solid-phase methods 150 6.2 Statistkai Analysis of Sequence DNA sequenees ean be greatly amplified Alignments Can Detect Homology 183

ehain reaetion 151 The statistieal signifieanee of alignments ean be

a powerful teehnique in medieal diagnosties, estimated by shuffling 185 and studies of moleeular evolution 152 Distant evolutionary relationships ean be detected

for reeombinant DNA teehnology through the use of substitution matriees 186 used to identify disease-eausing Databases ean be searehed to identify homologaus

153 sequenees 189

xviii Contents

6.3 Examination of Three-Dimensional Additional globins are encoded in the human genome 219 Structure Enhances Our Understanding of APPENDIX: Binding Models Can Be Formulated in Evolutionary Relationships 190 Quantitative Terms: the Hill Plot and the Cancerted Model 221

T ertiary structure is more conserved than primary structure 191 Chapter 8 Enzymes: Basic Concepts and Knowledge of three-dimensional structures can Kinetics 227 aid in the evaluation of sequence alignments 192 8.1 Enzymes Are Powerful and Highly Repeated motifs can be detected by aligning Specific Catalysts 228 sequences with themselves 192

Many enzymes require cofactors for activity 229 Convergent evolution illustrates common solutions

Enzymes can transform energy from one form to biochemical challenges 193

into another 229 Comparison of RNA sequences can be a source of

8.2 Free Energy ls a Useful Thermodynamic insight into RNA secondary structures 194

6.4 Evolutionary Trees Can Be Constructed Function for Understanding Enzymes 230 The free-energy change provides information about on the Basis of Sequence Information 195 the spontaneity but not the rate of a reaction 230

6.5 Modern Techniques Make the Experimental The standard free-energy change of a reaction is Exploration of Evolution Possible 196 related to the equilibrium constant 231 Ancient DNA can sometimes be amplified Enzymes alter only the reaction rate and not the and sequenced 196 reaction equilibrium 232 Molecular evolution can be examined experimentally 197 8.3 Enzymes Aceeierate Reactions by Facilitating

Chapter 7 Hemoglobin: Portrait of a the Formation of the Transition State 233 The formation of an enzyme-substrate complex is

Protein in Action 203 the first step in enzymatic catalysis 234

7.1 Myoglobin and Hemoglobin Bind Oxygen . The active sites of enzymes have some at lron Atoms in Heme 204 common features 235

Changes in heme electronic structure upon oxygen The binding energy between enzyme and substrate binding are the basis for functional imaging studies 205 is important for catalysis 237

The structure of myoglobin prevents the release of 8.4 The Michaelis-Menten Equation Describes reactive oxygen species 206 the Kinetic Properties of Many Enzymes 237 Human hemoglobin is an assembly of four Kinetics is the study of reaction rates 237 myoglobin-like subunits 207 The steady-state assumption facilitates a description 7.2 Hemoglobin Binds Oxygen Cooperatively 207 of enzyme kinetics 238

Oxygen binding markedly changes the quaternary Variations in KM can have physiological consequences 240 structure of hemoglobin 209 KM and V max values can be determined by Hemoglobin cooperativity can be potentially explained several means 240 by several models 210 KM and V max values are important enzyme Structural changes at the heme groups are characteristics 241 transmitted to the <Xtßt- <Xzßz interface 212 kcatiKM is a measure of catalytic efficiency 242 2,3-Bisphosphoglycerate in red cells is crucial in Most biochemical reactions include multiple substrates 243 determining the oxygen affinity ofhemoglobin 212 Allosteric enzymes do not obey Carbon monoxide can disrupt oxygen transport by Michaelis-Menten kinetics 245 hemoglobin 213

8.5 Enzymes Can Be lnhibited by Specific 7.3 Hydrogen Ionsand Carbon Dioxide Promote Molecules 246 the Release of Oxygen: The Bohr Effect 214 Reversible inhibitors are kinetically distinguishable 247 7.4 Mutations in Genes Encoding Hemoglobin Irreversible inhibitors can be used to map Subunits Can Result in Disease 216 the active site 249

Sickle-cell anemia results from the aggregation of Transition-state analogs arepotent inhibitors mutated deoxyhemoglobin molecules 217 ofenzymes 251

Thalassemia is caused by an imbalanced production of Catalytic antihoclies demonstrate the importance of selective hemoglobin chains 218 binding of the transition state to enzymatic activity 251

The accumulation of free alpha-hemoglobin Penicillin irreversibly inactivates a key enzyme in chains is prevented 219 bacterial cell-wall synthesis 252

Enzymes are Classified on the Basis of Reactions That They Catalyze

254

256

262

263 possesses a highly reactive serine residue 263

=nl'i=tiri>flt·rvr>~m action proceeds in two steps linked .· ) < bound intermediate 264

. < , is part of a catalytic triad that also includes p~~~~(lme and aspartate 265

·=·=ow=·•••"' triads are found in other hydrolytic enzymes 268

triad has been dissected by '''"'"'"''"'''rc•rrc•n mutagenesis 270

-.:v:».''"'···'""' aspartyl, and metalloproteases are other classes of peptide-cleaving enzymes 271

''"'"'""'"''" inhibitors are important drugs 272

274 :Y.i:!<t.u'-''1!1'- anhydrase contains abound zinc ion

tij'$:~~ntlal for catalytic activity 275

.,.,.,,<,<dl'VI>l" entails zinc activation of a water molecule 276

shuttle facilitates rapid regeneration of

:=:==~~!'ll"·"''-Ll''"'form of the enzyme 277 :rin'""'ro-Prlt evolution has generated zinc-based

sites in different carbonic anhydrases 279

., Restrietion Enzymes Catalyze Highly ~~~~P.eCITIC DNA-Cieavage Reactions .279

'"""""""'"' is by in -line displacement of 3' -oxygen phosphorus by magnesium-activated water 280

:=:==..:,::: enzymes require magnesium for ·····==:•=•.····==. activity 282

? complete catalytic apparatus is assembled · .·.·.·.··.·.·. complexes of cognate DNA molecules,

specificity 283

===~=~~~"·•-'-"'u DNA is protected by the addition of methyl to specific bases 285

n restriction enzymes have a catalytic core in gqi'l}rrlon and are probably related by horizontal

transfer 286

Myosins Harness Changes in Enzyme ·an to Couple ATP Hydrolysis to

'·'""''r""'"'Cal Work 287

of the transition state for A TP hydrolysis ~se:oci1ate:d with a substantial conformational change

287

288

Contents ::d X

The altered conformation of myosin persists for a substantial period of time

Myosinsare a family of enzymes containing P-loop structures

Chapter 10 Regulatory Strategies

Allosterically regulated enzymes do not follow

290

291

299

Michaelis-Menten kinetics 301

A TCase consists of separable catalytic and regulatory subunits 301

Allosteric interactions in A TCase are mediated by large changes in quaternary structure 302

Allosteric regulators modulate the T -to-R equilibrium 305

10.2 lsozymes Provide a Means of Regulation Specific to Distinct Tissues and Developmental Stages 306

1 0.3 Covalent Modification ls a Means of Regulating Enzyme Activity 307 Kinases and phosphatases control the extent of protein phosphorylation 308

Phosphorylation is a highly effective means of regulating the activities of target proteins 310

Cyclic AMP activates protein kinase A by altering the quaternary structure 311

A TP and the target protein bind to a deep cleft in the catalytic subunit of protein kinase A 312

1 0.4 Many Enzymes Are Activated by Specific Proteolytic Cleavage 312 Chymotrypsinogen is p.ctivated by specific cleavage of a single peptide bond 313

Proteolytic activation of chymotrypsinogen leads to the formation of a substrate-binding site 314

The generation of trypsin from trypsinogen leads to the activation of other zymogens 315

Some proteolytic enzymes have specific inhibitors 316

Blood clotting is accomplished by a cascade of zymogen activations 317

Fibrinogen is converted by thrombin into a fibrin clot 318

Prothrombin is readied for activation by a vitamin K-dependent modification 320

Hemophilia revealed an early step in clotting 321

The clotting process must be precisely regulated 321

Chapter 11 Carbohydrates 329

11.1 Monosaccharides Are the Simplest Carbohydrates 330 Many common sugars exist in cyclic forms

Pyranose and furanose rings can assume different conformations

332

334

XX Contents

Glucose is a reducing sugar 335 A membrane lipid is an amphipathic molecule

Monosaccharides are joined to alcohols and containing a hydrophilic and a hydrophobic moiety 363 amines through glycosidic bonds 336 12.3 Phospholipids and Glycolipids Readily Phosphorylated sugars are key intermediates in Form Bimolecular Sheets in Aqueous Media 364 energy generation and biosyntheses 336 Lipid vesicles can be formed from phospholipids 365 11 .2 Monosaccharides Are Linked to Form Lipid bilayers are highly impermeable to ions and Complex Carbohydrates 337 most polar molecules 366 Sucrose, lactose, and maltose are the common 12.4 Proteins Carry Out Most Membrane disaccharides 337 Processes 367 Glycogen and starch are storage forms of glucose 338 Proteins associate with the lipid bilayer in a Cellulose, a structural component of plants, is made variety of ways 367 of chains of glucose 338 Proteins interact with membranes in a variety 11.3 Carbohydrates Can Be Linked to Proteins ofways 368 to Form Glycoproteins 339 Some proteins associate with membranes through

Carbohydrates can be linked to proteins through covalently attached hydrophobic groups 371 asparagine (N-linked) or through serine or Transmembranehelices can be accurately threonine (0-linked) residues 340 predicted from amino acid sequences 371 The glycoprotein erythropoietin is a vital hormone 340 12.5 Lipids and Many Membrane Proteins Proteoglycans, composed of polysaccharides and Diffuse Rapidly in the Plane of the protein, have important structural roles 341 Membrane 373 Proteoglycans are important components of cartilage 342 The fluid mosaic model allows lateral movement Mucins are glycoprotein components of mucus 343 but not rotation through the membrane 374 Protein glycosylation takes place in the lumen of the Membrane fluidity is controlled by fatty acid endoplasmic reticulum and in the Golgi complex 343 _ composition and cholesterol content 374 Specific enzymes are responsible for oligosaccharide Lipid rafts are highly dynamic complexes formed assembly 345 between cholesterol and specific lipids 375 Blood groups are based on protein glycosylation All biological membranes are asymmetric 375 patterns 345 12.6 Eukaryotic Cells Contain Compartments Errors in glycosylation can result in pathological Bounded by Interna! Membranes 376 conditions 346 Oligosaccharides can be "sequenced" 346

11.4 Leetins Are Specific Carbohydrate-Binding Chapter 13 Membrane Channels and Pumps 383 Proteins 347

The expression of transporters largely defines the Leetins promote interactions between cells 348 metabolic activities of a given cell type 384 Leetins are organized into different classes 348

13.1 The Transport of Molecules Across a Influenza virus binds to sialic acid residues 349 Membrane May Be Active or Passive 384

Chapter 12 Lipids and Cell Membranes 357 Many molecules require protein transporters to cross membranes 384

Many common features underlie the diversity of Free energy stored in concentration gradients can be

biological membranes 358 quantified 385

'12.1 Fatty Acids Are Key Constituents of 13.2 Two Families of Membrane Proteins Lipids 358 Use ATP Hydrolysis to Pump Ions and

Fatty a~Jd names are based on their parent hydrocarbons 358 Molecules Across Membranes 386

F atty acids vary in chain length and degree of P~type ATPases couple phosphorylation and

unsaturation 359 conformational changes to pump calcium ions across membranes 386

12.2 There Are Three Common Types of Digitalis specifically inhibits the Na+ -K+ pump Membrane Lipids 360 by blocking its dephosphorylation 389 Phospholipids are the major dass of membrane lipids 360 P-type ATPases are evolutionarily conserved and Membranelipids can include carbohydrate moieties 361 play a wide range of roles 390 Cholesterol is a lipid based on a steroid nucleus 362 Multidrug resistance highlights a family of Archaeal membranes are built from ether lipids with membrane pumps with ATP-binding cassette branched chains 362 domains 390

Contents xxi

Permeas'e ls an Archetype of Insulinbinding results in the cross-phosphorylation

~ That Use One and activation of the insulin receptor 426

Gradient to Power the Formation The activated insulin-receptor kinase initiates a

392 kinase cascade 426

Channels Can Rapidly Transport Insulin signaling is terminated by the action of

Membranes 394 phosphatases 429

are mediated by transient changes 14.3 EGF Signaling: Signai-Transduction

K+ permeability 394 Pathways Are Poised to Respond 429 conductance rneasurements reveal EGF binding results in the dimerization of the

of single channels 395 EGF receptor 429

of a potassium ion channel is an The EGF receptor undergoes phosphorylation of

for many ion-channel structures 395 its carboxyl-terminal tail 431

of the potassium ion channel reveals EGF signaling leads to the activation of Ras, a

ion specificity 396 small G protein 431

of the potassium ion channel explains Activated Ras initiates a protein kinase cascade 432

of transport 399 EGF signaling is terminated by protein phosphatases

requires substantial conformational and the intrinsic GTPase activity of Ras 432

specific ion-channel domains 399 14.4 Many Elements Recur with Variation can be activated by occlusion of the pore: in Different Signai-Transduction

-chain model 400 Pathways 433 receptor is an archetype for 14.5 Defects in Signal-Transduction

ion channels 401 Pathways Can Lead to Cancer and Other

integrate the activities of several ion working in concert 402

Diseases 434

of ion channels by mutations or Monoclonal antihoclies can be used to inhibit

can be potentially life threatening 404 signal-transduction pathways activated in tumors 434

Junctions Allow Ions and Small Protein kinase inhibitors can be effective anticancer drugs 435

to Flow Betvveen Communicating Cells 405 Cholera and whooping cough are due to altered Channels lncrease the Permeability G-protein activity 435

Membranes to Water 406

14 Signai-Transduction Pathways 415 Part U TRANSDUCING AND dependls on molecular circuits 416 STORING ENERGY

meric G Proteins Transmit Chapter 15 Metabolism: Basic Concepts and Reset Themselves 417 and Design 443

binding to 7TM receptors leads to the of heterotrimeric: G proteins 419 15.1 Metabolism ls Composed of Many G proteins transmit signals by binding Coupled, lnterconnecting Reactions 444

proteins 420 Metabolism consists of energy-yielding and stimulates the phosphorylation of many energy-requiring reactions 444

by activating protein kinase A 420 A thermodynamically unfavorable reaction can be driven by a favorable reaction 445

421 15.2 ATP ls the Universal Currency of Free

receptors activate the phosphoinositide cascade 422 Energy in Biologkai Systems 446 ion is a widely used second messenger 423 A TP hydrolysis is exergonic 446 ion often activates the regulatory protein A TP hydrolysis drives metabolism by shifting the

424 equilibrium of coupled reactions 447

lin Signaling: Phosphorylation The high phosphoryl potential of A TP results Are Central to Many from structural differences between ATP and its nsduction Processes 425 hydrolysis products 449

receptor is a dimer that closes around Phosphoryl-transfer potential is an important form insulin molecule 426 of cellular energy transformation 450

nii Contents

15.3 The Oxidation of Carbon Fuels ls an Many adults are intolerant of milk because they

lmportant Source of Cellular Energy 451 are deficient in lactase 487

Compounds with high phosphoryl-transfer potential Galactose is highly toxic if the transferase is missing 488

can couple carbon oxidation to A TP synthesis 4S2 16.2 The Glycolytic Pathway ls Tightly Ion gradients across membranes provide an Contralied 488 important form of cellular energy that can be Glycolysis in muscle is regulated to meet the need coupled to A TP synthesis 4S3 for ATP 489 Energy from foodstuffs is extracted in three stages 4S3 The regulation of glycolysis in the liver illustrates 15.4 Metabolie Patlhways Contain Many the biochemical versatility of the liver 490

Recurring Motifs 454 A family of transporters enables glucose to enter

Activated carriers exemplify the modular design and and leave animal cells 493

economy of metabolism 4S4 Cancer and exercise training affect glycolysis in a

Many activated carriers are derived from vitamins 4S7 similar fashion 494

Key reactions are reiterated throughout metabolism 4S9 16.3 Glucose Can Be Synthesized from Metabolie processes are regulated in three Nonearbehydrate Precursors 495 principal ways 461 Gluconeogenesis is not a reversal of glycolysis 497 Aspects of metabolism may have evolved from an The conversion of pyruvate into phosphoenolpyruvate RNAworld 463 begins with the formation of oxaloacetate 498

Oxaloacetate is shuttled into the cytoplasm and converted into phosphoenolpyruvate 499

Chapter 16 Glycolysis and Gluconeogenesis 469 The conversion of fructose 1, 6-bisphosphate into

Glucose is generated from dietary carbohydrates 470 fructose 6-phosphate and orthophosphate is an

Glucose is an important: fuel for most organisms 471 irreversible step soo

16.1 Glycoiysis ls an Energy-Conversion The generation of free glucose is an important control point soo

Pathway in Many Organisms 471 Six high-transfer-potential phosphoryl groups are Hexakinase traps glucose in the cell and begins spent in synthesizing glucose from pyruvate S01 glycolysis 471

16.4 Gluconeogenesis and Glycolysis Are Fructose 1,6-bisphosphate is generated from glucose Reciprocally Regulated 502 6-phosphate 473

The six-carbon sugar is cleaved into t:wo Energy charge determines whether glycolysis or

three-carbon fragments 474 gluconeogenesis will be most active S02

Mechanism: Triase phosphate isomerase salvages a The balance bet:ween glycolysis and gluconeogenesis

three-carbon fragment 47S in the liver is sensitive to blood-glucose concentration S03

The oxidation of an alde:hyde to an acid powers Substrate cycles amplify metabolic signals and

the formation of a compound with high produce heat SOS

phosphoryl-transfer potential 476 Lactate and alanine formed by contracting muscle

Mechanism: Phosphorylation is coupled to the are used by other organs SOS

oxidation of glyceraldehyde 3-phosphate by a Glycolysis and gluconeogenesis are evolutionarily

thioester intermediate 478 intertwined S07

A TP is formed by phosphoryl transfer from Chapter 17 The Citric Acid Cycle 515 1, 3-bisphosphoglycerate 479

Additional A TP is gene:rated with the formation of The citric acid cycle harvests high-energy electrons S16 pyruvate 480

Pyruvate Dehydrogenase Links Glycolysis Two ATP molecules are formed in the conversion 17.1

of glucdse into pyruvate 481 to the Citric Acid Cycle 517

NAD+ is regenerated from the metabolism Mechanism: The synthesis of acetyl coenzyme a from

ofpyruvate 482 pyruvate requires three enzymes and five Coenzymes S18

Fermentations provide usable energy in the absence Flexible linkages allow lipoamide to move bet:ween

ofoxygen 484 different active sites S20

The binding site for NAD+ is similar in many 17.2 The Citric Acid Cycle Oxidizes dehydrogenases 48S Two-Carbon Units 521 Fructoseand galactose are converted into glycolytic Citrate synthase forms citrate from oxaloacetate and intermediates 48S acetyl coenzyme A S22

. . ·.· . . · The mechanism of citrate synthase . . . . . undesirable reactions

isomerized into is:ocitrate

ll1ll~,!~~<'·"' is oxidized and decarboxylated to

~~<~~~';~'in"l coenzyme A is formed by the oxidative ii~c~t.bOX)Tlatlon of alpha-ketoglutarate

:::;O<:W~~1p,Ju'·''"' with high phosphoryl-transfer potential !Ierteraxeu from succinyl coenzyme A

~~~:M~~J~arusrn: Succinyl coen:~yme A synthetase ~!Jti~psfor.ms types of biochemical energy

::,Q~i:il«)ac·eta·te is regenerated by the oxidation

acid cycle produces high-transfer-potential ete~::troJ:u;, ATP, and COz

Entry to the Citric Acid Cycle and Metaoonsm Through 11: Are Contralied

n"''"""r"' dehydrogenase complex is regulated :?all9.S1tencat.Ly and by reversible phosphorylation

···==··,, ·· disruption of pyruvate: metabolism is the cause · and poisoning by mercury and arsenic

The Glyoxylate Cycle Enables Plants · Bacteria to Grow on Acetate

18 Oxidative Phosphorylation

Eukaryotic Oxidaitive Phosphorylation Place in Mitochondria

ltO•Chc>ndlna are bounded by a double membrane

522 524

524

525

525

526

527

528

530

531 532

533

534

534

535

536

536

543

544 544

545

546

546

548

549

551

Contents xxiii

Ubiquinol is the entry point for electrons from F ADH2 of flavoproteins 553 Electrons flow from ubiquinol to cytochrome c through Q-cytochrome c oxidoreductase 553 The Q cycle funnels electrons from a two-electron carrier to a one-electron carrier and pumps protons 554 Cytochrome c oxidase catalyzes the reduction of molecular oxygen to water 555 Taxie derivatives of molecular oxygen such as superoxide radical are scavenged by protective enzymes 558 Electrons can be transferred between groups that are not in contact 560 The conformation of cytochrome c has remained essentially constant for more than a billion years 561

18.4 A Proton Gradient Powers the Synthesis of ATP 561 ATP synthase is composed of a proton-conducting unit and a catalytic unit 563 Proton flow through A TP synthase leads to the release of tightly bound A TP: The bindling-ehange mechanism 564 Rotational catalysis is the world' s smallest molecular motor 565 Proton flow araund the c ring powers A TP synthesis 566 A TP synthase and G proteins have several common features 568

18.5 Many Shuttles Allow Movement Across Mitochondrial Membranes 568 Electrons from cytoplasmic NADH enter mitochondria by shuttles 569 The entry of ADP into mitochondria is coupled to the exit of ATP by ATP-ADP translocase 570 Mitochondrial transporters for metabolites have a common tripartite structure 571

18.6 The Regulation of Cellular Respiration ls Governed Primarily by the Need for ATP 572 The complete oxidation of glucose yields about 30 molecules of A TP 572 The rate of oxidative phosphorylation is determined by the need for A TP 573 Regulated uncoupling leads to the generation ofheat 574 Oxidative phosphorylation can be inhibited at many stages 576 Mitochondrial diseases are being discovered 576 Mitochondria play a key role in apoptosis 577 Power transmission by proton gradients is a central motif of bioenergetics 577

Chapter 19 The Light Reactions of Photosynthesis 585

Photosynthesis converts light energy into chemical energy 586

19.1 Photosynthesis Takes Place in Chloroplasts 587 The primary events of photosynthesis take place in thylakoid membranes 587 Chloroplasts arose from an endosymbiotic event 588

xxiv Contents

19.2 Light Absorption by Chlorophyll lnduces 20.2 The Activity of the Calvin Cycle Depends Electron Transfer 588 on Environmental Conditions 617 A special pair of chlorophylls initiate charge separation 589 Rubisco is activated by light-driven changes in proton

Cyclic electron flow reduces the cytochrome of the and magnesium ion concentrations 618

reaction center 592 Thioredoxin plays a key role in regulating the

19.3 Two Photosystems Generate a Proton Calvin cycle 618

Gradient and NADPH in Oxygenic The C4 pathway of tropical plants accelerates

Photosynthesis 592 photosynthesis by concentrating carbon dioxide 619

Photosystem li transfers electrons from water to Crassulacean acid metabolism permits growth in

plastoquinone and generates a proton gradient 592 arid ecosystems 620

Cytochrome bflinks photosystem li to photosystem I 595 20.3 The Pentose Phosphate Pathway

Photosystem I uses light energy to generate reduced Generates NADPH and Synthesizes

ferredoxin, a powerful reductant 595 Five-Carbon Sugars 62"1

Ferredoxin-NADP+ reductase converts NADP+ Two molecules ofNADPH are generated in the

intoNADPH 596 conversio:n of glucose 6-phosphate into ribulose

19.4 A Proton Gradient Across the Thylakoid 5-phosphate 621

Membrane Drives ATP Synthesis 597 The pentose phosphate pathway and glycolysis are linked by transketolase and transaldolase 621

The A TP synthase of chloroplasts closely resembles Mechanism: Transketolase and transaldolase stabilize

those of mitochondria and prokaryotes 598 carbanionic intermediates by different mechanisms 624

Cyclic electron flow through photosystem I Ieads to 20.4 The Metabolism of Glucose 6-phosphate the production of A TP instead of NADPH 599

The absorption of eight photons yields one 02, two by the Pentose Phosphate Pathway ls

NADPH, and three A TP molecules 600 Coordinated wlth Glycolysis 626

19.5 Accessory Pigments Funnel Energy into The rate of the pentose phosphate pathway is controlled

Reaction Centers 601 . by the levd ofNADP+ 626

Resonance energy transfer allows energy to move The flow of glucose 6-phosphate depends on the

from the site of initial absorbance to the reaction need for NADPH, ribose 5-phosphate, and A TP 627

center 601 Through the looking-glass: The Calvin cycle and the

Light-harvesting complexes contain additional pentose phosphate pathway are mirror images 629

chlorophylls and carotinoids 602 20.5 Glucose 6-phosphate Dehydrogenase

The components of photosynthesis are highly organized 603 Plays a Key Role in Protection Against Reactive

Many herbicides inhibit the light reactions of Oxygen Species · 629

photosynthesis 604 Glucose 6-phosphate dehydrogenase defi.ciency causes

19.6 The Ability to Convert Light into Chemical a drug-induced hemolytic anemia 629

Energy is Ancient 604 A defi.ciency of glucose 6-phosphate dehydrogenase confers an evolutionary advantage in some circumstances 631

Chapter 20 The Calvin Cycle and Pentose Phosphate Pathway 609 Chapter 21 Glycogen Metabolism 637

20.1 The Calvin Cycle Synthesizes Hexeses Glycogen metabolism is the regulated release and

from Carbon Dioxide and Water 610 storage of glucose 638

Carbon dioxide reacts with ribulose 1,5-bisphosphate 21.1 Glycogen Breakdown Requires the to form two molecules of 3-phosphoglycerate 611 lnterplay of Several Enzymes 639 Rubisc6 activity depends on magnesium and Phosphorylase catalyzes the phosphorolytic cleavage carbamate 612 of glycogen torelease glucose 1-phosphate 639

Rubisco also catalyzes a wasteful oxygenase reaction: Mechanisrn: Pyridoxal phosphate participates in the Catalytic imperfection 613 phosphorolytic cleavage of glycogen 640

Hexosephosphatesare made from phosphoglycerate, A debranching enzyme also is needed for the and ribulose 1,5-bisphosphate is regenerated 614 breakdown of glycogen 641 Three A TP and two NADPH molecules are used to Phosphoglucomutase converts glucose 1-phosphate bring carbon dioxide to the Ievel of a hexose 617 into glucose 6-phosphate 642 Starch and sucrose are the major carbohydrate The liver c:ontains glucose 6-phosphatase, a stores in plants 617 hydrolytic enzyme absent from muscle 643

Contents XXV

ls Regulated by Allosteric The complete oxidation of palmitate yields

Reversible Phosphorylation 643 106 molecules of A TP 671

is regulated by the intracellular :22.3 Unsaturated and Odd-Chain Fatty Acids 643 Require Additional Steps for Degradation 672

produces glucose for use by other An isomerase and a reductase are required for 645 the oxidation of unsaturated fatty acids 672

Odd-chain fatty acids yield propionyl CoA in the 645 final thiolysis step 673

ne and Glucagon Signal the Vitamin B12 contains a corrin ring and a cobalt atom 674 Breakdown 646 Mechanism: Methylmalonyl CoA mutase catalyzes a

the signal for the initiation of rearrangement to form succinyl CoA 675 646 Fatty acidsarealso oxidized in peroxisomes 676

must be rapidly turned off Ketone hoclies are formed from acetyl CoA when 648 fat breakdown predominates 677

of glycogen phosphorylase became Ketone hoclies are a major fuel in some tissues 678 as the enzyme evolved 649 Animals cannot convert fatty acids into glucose 680

ls Synthesized and Degraded 22.4 Fatty Acids Are Synthesized by Fatty Pathways 649 Acid Synthase 680

649 F atty acids are synthesized and degraded by different pathways 680

650 The formation of malonyl CoA is the committed step 651 in fatty acid synthesis 681

Intermediates in fatty acid synthesis are attached to 651 an· acyl carrier protein 681

is an efficient storage form of glucose 651 Fatty acid synthesis consists of a series of condensation,

Breakdown and Synthesis Are reduction, dehydration, and reduction reactions 682

Regulated 652 Fatty acids are synthesized by a multifunctional enzyme complex in animals 683

653 The synthesis of palmitate requires 8 molecules of acetyl

glycogen synthesis by inactivating CoA, 14 molecules ofNADPH, and 7 molecules of A TP 685

synthase kinase 654 Citrate carries acetyl gr~mps from mitochondria to the cytoplasm for fatty acid synthesis 686

655 Several sources supply NADPH for fatty acid synthesis 686

understanding of glycogen-storage Fatty acid synthase inhibitors may be useful drugs 687 is possible 656 22.5 The Elongation and Unsaturation of

22 Fatty Acid Metabolism 663 Fatty Acids Are Accomplished by Accessory Enzyme Systems 687

. •·.······· .. degradation and synthesis mirror each Membrane-bound enzymesgenerate unsaturated fatty acids 688

their chemical reactions 664 Eicosanoid hormones are derived from polyunsaturated

Are Highly Concentrated fatty acids 688

665 22.6 Acetyl CoA Carboxylase Plays a Key Role ........ .· lipids are digested by pancreatic lipases 665 in Controlling Fatty Acid Metabolism 690

· ? . lil'~ds are transported in chylomicrons 666 Acetyl CoA carboxylase is regulated by conditions in

Use of Fatty Acids As Fuel Requires the cell 690

Stages of Proces:sing 667 Acetyl CoA carboxylase is regulated by a variety of

are hydrolyzed by hormone-stimulated hormones 690

667 Chapter 23 Protein Turnever and Amino

are linked to coe:nzyme A before they Acid Catabolism 697 668

carries long-chain activated fatty acids 23.1 Proteins Are Degraded to Amino Acids 698 mitochondrial matrix 669 The digestion of dietary proteins begins in the

· ·••···. CoA, NADH, and FAD Hz are generated in stomach and is completed in the intestine 698

· ··•· round of fatty acid oxidation 670 Cellular proteins are degraded at different rates 699

xxvi Contents

23.2 Protein Turnever ls Tightly Regulated 699 Ubiquitin tags proteins for destruction 699

The proteasome digests the ubiquitin-tagged proteins 701

The ubiquitin pathway and the proteasome have prokaryotic Counterparts 701

Protein degradation can be used to regulate biological function 702

23.3 The First Step in Amino Acid Degradation ls the Removal of Nitrogen 704 Alpha-amino groups are converted into ammonium ions by the oxidative deamination of glutamate 704

Mechanism: Pyridoxal phosphate forms Schiff-base intermediates in aminotransferases 705

Aspartate aminotransferase is an archetypal pyridoxal-dependent transaminase 706

Pyridoxal phosphate enzymes catalyze a wide array of reactions 707

Serine and threonine can be directly deaminated 708

Peripheral tissues transport nitrogen to the liver

23.4 Ammonium Ion ls Converted into Urea in Most Terrestrial V,ertebrates The urea cycle begins w:ith the formation of carbamoyl phosphate

The urea cycle is linked to gluconeogenesis

Urea-cycle enzymes are evolutionarily related to enzymes in other metabolic pathways

lnherited defects of the urea cycle cause hyperammonemia and can lead to brain darnage

Ureais not the only means of disposing of excess nitrogen

23.5 Carbon Atoms of Degraded Amino Acids Emerge As Major Metabolie Intermediates Pyruvate is an entry point into metabolism for a number of amino acids

Oxaloacetate is an entry point into metabolism for aspartate and asparagine

Alpha-ketoglutarate is an entry point into metabolism for five-carbon amino acids

SuccinY,~ coenzyme A is a point of entry for several nonpolar amino acids

Methionine degradation requires the formation of a key methyl donor, S-adenosylmethionine

The branched-chain amino acids yield acetyl CoA, acetoacetate, or propionyl CoA

Oxygenases are required for the degradation of aromatic amino acids

23.6 lnborn Errors of Metabolism Can Disrupt Amino Acid Degradation

708

709

709

711

712

712

713

714

715

716

716

717

717

717

719

721

Part m SYNTHESIZ!NG THE MOlECUlES OF UFE

Chapter 24 The Biosynthesis of Amino Acids 729

Amino acid synthesis requires solutions to three key biochemical problems 730

24.1 Nitrogen Fixation: Microorganisms Use ATP and a Powerful Reductant to Reduce Atmospheric Nitrogen to Ammonia 730 The iron-molybdenum cofactor of nitrogenase binds and reduces atmospheric nitrogen 731

Ammonium ion is assimilated into an amino acid through glutamate and glutamine 733

24.2 Amino Acids Are Made from Intermediates of the Citric Acid Cycle and Other Major Pathways 735 Human beings can synthesize some amino acids but must obtain others from the diet 735

Aspartate, alanine, and glutamate are formed by the addition of an amino group to an alpha-ketoacid 736

A common step determines the chirality of all amino acids

. The formation of asparagine from aspartate requires an adenylated intermediate

Glutamate is the precursor of glutamine, proline, and arginine

3-Phosphoglycerate is the precursor of serine, cysteine, and glycine

Tetrahydrofolate carries activated one-carbon units at several oxidation Ievels

S-Adenosylmethioriine is the major donor of methyl groups

Cysteine is synthesized from serine and homocysteine

High homocysteine Ievels correlate with vascular disease

Shikimate and chorismate are intermediates in the biosynthesis of aromatic amino acids

Tryptophan synthase illustrates substrate channeling in enzymatic catalysis

24.3 Feedback Inhibition Regulates Amino Acid Biosynthesis Branched pathways require sophisticated regulation

An enzymatic cascade modulates the activity of glutamine synthetase

24.4 Amino Acids Are Precursors of Many Biomolecules Glutathione, a gamma-glutamyl peptide, serves as a sulfhydryl buffer and an antioxidant

Nitric oxide, a short-lived signal molecule, is formed from arginine

737

737

738

738

739

740

742

743

743

746

747

747

749

750

751

751

Contents xxvii

synthesized from glycine and succinyl The synthesis of purine nucleotides is controlled by 752 feedback inhibition at several sites 777

in some inherited disorders of The synthesis of deoxyribonucleotides is 754 controlled by the regulation of ribonucleotide

reductase 778

761 25.5 Disruptions in Nucleotide Metabolism Can Cause Pathological Conditions 778 The loss of adenosine deaminase activity results

762 in severe combined immunodeficiency 778

Pyrimidine Ring ls Assembled de Gout is induced by high serum levels of urate 779 < ·· by Salvage Pathways 763 Lesch-Nyhan syndrome is a dramatic consequence

of mutations in a salvage-pathway enzyme 780

763 F olic acid deficiency promotes birth defects such as spina bifida 781

763

763 Chapter 26 The Biosynthesis of Membrane

a ribose ring from PRPP to Lipids and Steroids 787 nucleotide and is converted 16.1 Phosphatidate ls a Common Intermediate

764 in the Synthesis of Phospholipids and Triacylglycerols 788

765 The synthesis of phospholipids requires an activated

765 intermediate 789 recycle pyrimidine bases 766 Sphingolipids are synthesized from ceramide 791

Bases Can Be Synthesized de Gangliosides are carbohydrate-rich sphingolipids Recycled by Salvage Pathways 766 that contain acidic sugars 792

ring system is assembled on ribose Sphingolipids confer diversity on lipid structure and 766 function 793

ring is assembled by successive steps of Respiratory distress syndrome and T ay-Sachs disease by phosphorylation followed by result from the disruption of lipid metabolism 793

767 Phosphatiditic acid phosphatase is a key regulatory 769 enzyme in lipid metabolism 794

770 26.2 Cholesterol ls Synthesized from Acetyl Coenzyme A in Three Stages 795

economize intracellular energy The synthesis of mevalonate, which is activated as 770 isopentenyl pyrophosphate, initiates the synthesis of

bonucleotides Are Synthesized cholesterol 795 of Ribonucleotides Through Squalene (C3o) is synthesized from six molecules of

Mechanism 771 isopentenyl pyrophosphate (Cs) 796

A tyrosyl radical is critical to the action Squalene cyclizes to form cholesterol 797 reductase 771 26.3 The Complex Regulation of

.. other than tyrosyl radical are Cholesterol Biosynthesis Takes Place at . ....

· by other ribonucleotide reductases 773 Several Levels 798 is formed by the methylation of Lipoproteins transport cholesterol and triacylglycerols

774 throughout the organism 801 reductase catalyzes the regeneration The blood levels of certain lipoproteins can serve

a one-carbon carrier 775 diagnostic purposes 802 anticancer drugs block the synthesis Low-density lipoproteins play a central role in

775 cholesterol metabolism 803 The absence of the LDL receptor leads to

776 hypercholesterolemia and atherosclerosis 804 Mutations in the LDL receptor prevent LDL release

777 and result in receptor destruction 805

xxviii Contents

HDL appears to proteet against arteriosclerosis 806 Metabolie adaptations in prolonged starvation

The clinieal management of eholesterollevels ean be minimize protein degradation 838

understood at a bioehemieallevel 807 27.6 Ethanol Alters Energy Metabolism in 26.4 lmportant Derivatives of Cholesterol the Liver 840 lnclude Bile Salts and Steroid Hormones 807 Ethanol metabolism leads to an exeess ofNADH 840

Letters identify the steroid rings and numbers Exeess ethanol eonsumption disrupts vitamin identify the earbon atoms 809 metabolism 842

Stereidsare hydroxylated by-eytoehrome P450 monooxygenases that use NADPH and 02 809 Chapter 28 DNA Replication, Repair, and The eytoehrome P450 system is widespread and Recombination 849 performs a proteetive funetion 810 28.1 DNA Replication Proceeds by the Pregnenolone, a preeursor of many other steroids, is Polymerization of Deoxyribonucleoside formed from eholesterol by cleavage of its side ehain 811 Triphosphates Along a Template 850 Progesterene and eortieosteroids are synthesized from

DNA polymerases require a template and a primer 850 pregnenolone 811

Androgens and estrogens are synthesized from All DNA polymerases have struetural features in

pregnenolone 812 eommon 851

Vitamin D is derived from eholesterol by the Two bound metal ions partieipate in the

ring-splitting aetivity oflight 813 polymerase reaetion 851

The speeifieity of replieation is dietated by

Chapter 27 The Integration of Metabolism 821 eomplementarity of shape between bases 852

27.1 Caloric Homeostasis ls a Means of An RNA primer synthesized by primase enables DNA synthesis to begin 853

Regulating Body Weight 822 One strand ofDNA is made eontinuously, whereas 27.2 The Brain Plays a Key Role in Caloric the other strand is synthesized in fragments 853 Homeostasis 824 DNA ligase joins ends of DNA in duplex regions 854 Signals from the gastrointestinal traet induee feelings TheSeparation ofDNA Strands requires speeifie of satiety 824 helieases and A TP hydrolysis 854. Leptin and insulin regulate long-term eontrol 28.2 DNA Unwinding and Supercoiling Are over ealorie homeostasis 825 Controlled by Topoisomerases 855 Leptin is one of several hormones seereted by The linking number ofDNA, a topologieal property, adipose tissue 826 determines the de~ree of supereoiling 856 Leptin resistanee may be a eontributing faetor T opoisomerases prepare the double helix for to obesity 827 unwinding 858 Dieting is used to eombat obesity 827 Type I topoisomerases relax supereoiled struetures 858 27.3 Diabetes ls a Common Metabolie Disease Type li topoisomerases ean introduee negative Often Resulting from Obesity 828 supereoils through eoupling to A TP hydrolysis 859 Insulin initiates a eomplex signal-transduetion 28.3 DNA Replication ls Highly Coordinated 861 pathway in muscle 828

DNA replieation requires highly proeessive polymerases 861 Metabolie syndrome often preeedes type 2 diabetes 830

The leading and lagging strands are synthesized Exeess fatty aeids in muscle modify metabolism 830 in a eoordinated fashion 862 Insulin resistanee in muscle faeilitates panereatie failure 831 DNA replieation in Escherichia coli begins at a Metabolie derangements in type 1 diabetes result from unique site 864 insulin insuffieieney and glueagon excess 832 DNA synthesis in eukaryotes is initiated at multiple sites 865 'l7.1i Exercise Beneficially Alters the Telomeres are unique struetures at the ends of Biochemistry of Cells 833 linear chromosomes 866

Mitochondrial biogenesis is stimulated by museular aetivity 834 Telomeres are replicated by telomerase, a speeialized

Fuel choice during exercise is determined by the polymerase that earries its own RNA template 867

intensity and duration of aetivity 835 28.4 Many Types of DNA Darnage Can Be 27.5 Food lntake and Starvation lnduce Repaired 867 Metabolie Changes 836 Errors ean arise in DNA replication 867

The starved-fed cycle is the physiological response Bases can be damaged by oxidizing agents, alkylating to a fast 837 agents, and light 868

Contents xxix

can be deteclted and repaired by a Enhancer sequences can stimulate transcription at systems 869 start sites thousands ofbases away 900

of thymine instead of uracil in DNA 29.3 The Transcription Products of Eukaryotic repair of deaminated cytosine 871 Polymerases Are Processed 901

diseases are caused by the expansion RNA polymerase I produces three ribosomal RNAs 901 of three nucleotides 872

RNA polymerase Ill produces transfer RNA 902 are caused by the defective repair

The product of RNA polymerase II, the pre-mRNA 872

transcript, acquires a 5' cap and a 3' poly(A) tail 902

873 Small regulatory RNAs are cleaved from larger precursors 904

ONA Recombination Plays lmportant Roles RNA editing changes the proteins encoded by mRNA 904 Repair, and Other Processes 874 Sequences at the ends of introns specify splice sites

in mRNA precursors 905 874 Splicing consists of two sequential transesterification

reactions proceed through reactions 906 intermediates 875 Small nuclear RNAs in spliceosomes catalyze the

splicing of mRNA precursors 907

883 Transcription and processing of mRNA are coupled 909

Mutations that affect pre-mRNA splicing cause disease 909 comprises three stages: Initiation, Most human pre-mRNAS can be spliced in alternative

and termination 884 ways to yield different proteins 910

885 29.4 The Discovery of Catalytic RNA Was are formed de novo and grow in the Revealing in Regard to Both Mechanism and

· == ::

0 direction 886 Evolution 911 }\'< polymerases backtrack and correct errors 888

to initiate transcription 888 Chapter 30 Protein Synthesis 921 subunits of RNA polymerase recognize

30.1 Protein Synthesis Requires the Translation sites 889

of Nucleotide Sequences into Amino Acid polymerases must unwind the template

helix for transcription to take place 890 Sequences 922

takes place at tramscription bubbles The synthesis of long proteins requires a low error

along the DNA template 890 frequency 922

within the newly transcribed RNA signal Transfer RNA molecules have a common design 923

891 Some transfer RNA molecules recognize more than

messenger RNAs dire:ctly sense metabolite one codon because ofwobble in base-pairing 925

892 30.2 Aminoacyl Transfer RNA Synthetases protein helps to terminate the transcription Read the Genetic Code 927

892 Amino acids are first activated by adenylation 927

inhibit transcription 893 Aminoacyl-tRNA synthetases have highly discriminating

of transfer and ribosomal RNA are amino acid activation sites 928

Proofreading by aminoacyl-tRNA synthetases increases 895 the fidelity of protein synthesis 929

Synthetases recognize various features of transfer RNA

896 molecules 930

of RNA polymerase synthesize RNA in Aminoacyl-tRNA synthetases can be divided into two

cells 897 classes 931

30.3 The Ribosome ls the Site of Protein II promoter region 898 Synthesis 931 protein complex initiates the assembly of Ribosomal RNAs (SS, 16S, and 23S rRNA) play a central

transcription complex 899 role in protein synthesis 932

transcription factoJrs interact with eukaryotic Ribosomes have three tRNA-binding sites that bridge 900 the 30s and 50s subunits 934

:n:xx Contents

The start signal is usually AUG preceded by several 31.3 Regulatory Circuits Can Result in Switching bases that pair with 16S rRNA 934 Between Patterns of Gene Expression 964 Bacterial protein synthesis is initiated by Lambda repressor regulates its own expression 964 formylmethionyl transfer RNA 935 A circuit based on lambda repressor and Cro form Formylmethionyl-tRNAfis placed in the P site of a genetic switch 965 the ribosome in the formation of the 70S Many prokaryotic cells release chemical signals that initiation complex 936 regulate gene expression in other cells 965 Elongation factors deliver aminoacyl-tRNA to the Biofilms are complex communities of prokaryotes 966 ribosome 936

Peptidyl transferase catalyzes peptide-band 31.4 Gene Expression Can Be Contralied at

synthesis 937 Posttranscriptional Levels 967

The formation of a peptide bond is followed by the Attenuation is a prokaryotic mechanism for regulating

GTP-driven translocation of tRNAs and mRNA 938 transcription through the modulation of nascent

Protein synthesis is terminated by release factors RNA secondary structure 967

that read stop codons 940

30.4 Eukaryotic Protein Synthesis Differs Chapter 32 The Control of Gene Expression

from Prokaryotic Protein Synthesis Primarily in Eukaryotes 973

in Translation Initiation 941 32.1 Eukaryotic DNA ls Organized into Mutations in initiation factor 2 cause a curious Chromatin 974 pathological condition 942 Nucleosomes are complexes of DNA and histones 975

30.5 A Variety of Antibiotics and Toxins Can DNA wraps araund histone octamers to form

lnhibit Protein Synthesis 943 nucleosomes 975

Some antibiotics inhibit protein synthesis 943 32.2 Transcription Factars Bind DNA and Diphtheria toxin blocks protein synthesis in eukaryotes Regulate Transcription Initiation 977 by inhibiting translocation 944 A range ofDNA-binding structures are employed

Ricin fatally modifies 28S ribosemal RNA 945 by eukaryotic DNA-binding proteins 977

30.6 Ribosomes Bound to the Endoplasmic Activation domains interact with other proteins 978

Reticulum Manufacture Secretory and Multiple transcription factors interact with eukaryotic

Membrane Proteins 945 regulatory regions 979

Signal sequences mark proteins for translocation across Enhancers can stimulate transcription in specific

the endoplasmic reticulum membrane 945 cell types 979

Transport vesicles carry cargo proteins to their final lnduced pluripotent stem cells can be generated by

destination 947 introducing four transcription factors into differentiated cells 980

32.3 The Control of Gene Expression Can Chapter 31 The Control of Gene Expression Require Chromatin Remedeling 980 in Prokaryotes 957 The methylation ofDNA can alter patterns of gene

31.1 Many DNA-Binding Proteins Recognize expression 981

Specific DNA Sequences 958 Steraids and related hydrophobic molecules pass

The helix-turn-helix motif is common to many through membranesandbind to DNA-binding receptors 982

prokaryotic DNA-binding proteins 959 Nuclear hormone receptors regulate transcription by

31.2 Prokaryotic DNA-Binding Proteins Bind recruiting coactivators to the transcription complex 982

Specifically to Regulatory Sites in Operans 959 Steroid-hormone receptors are targets for drugs 984

An OQeron consists of regulatory elements and Chromatin structure is modulated through covalent

protein-encoding genes 960 modifications of histone tails 985

The lac repressor protein in the absence of lactose Histone deacetylases contribute to transcriptional

binds to the operator and blocks transcription 961 repression 986

Ligand binding can induce structural changes in :n.4 Eukaryotic Gene Expression Can Be regulatory proteins 962 Contralied at Posttranscriptional Levels 987 The operon is a common regulatory unit in Genes associated with iron metabolism are prokaryotes 962 translationally regulated in animals 987

Transcription can be stimulated by proteins that Small RNAs regulate the expression of many contact RNA polymerase 963 eukaryotic genes 989

Contents xxxi

NDING TO 34.1 Antibodies Possess Distinct

NTAL CHANGES Antigen-Binding and Effector Units 1021

34.2 Antibodies Bind Specific Molecules Systems 995 Through Hypervariable Loops 1023

Variety of Organic Compounds The immunoglobulin fold consists of a beta-sandwich framewerk with hypervariable loops 1024

by Olfaction 996 X-ray analyses have revealed how antihoclies

by an enormaus family of bind antigens 1024 helix receptors 996

Large antigens bind antihoclies with numerous decoded by a combinatorial mechanism 998 interactions 1026 ls a Combination of Senses That 34.3 Diversity ls Generated by Gene Different Mechanisms 1000 Rearrangements 1027 the human genome led to the J (joining) genes and D (diversity) genes increase large family of 7TM bitter receptors 1001 antibody diversity 1027

7TM receptor responds to sweet More than 108 antihoclies can be formed by 1002 combinatorial association and somatic mutation 1028

of glutamate and aspartate, is The oligomerization of antihoclies expressed on the heterodimeric receptor related to surfaces of immature B cells triggers antibody secretion 1029

1003 Different classes of antihoclies are formed by

. • ·)· .•. detected primarily by the passage of the hopping of V H genes 1030 · ·••}0:::< through channels 1003

34.4 Major-Histocompatibility-Complex from the effects of hydrogen Proteins Present Peptide Antigens on Cell 1003 Surfaces for Recognition by T-Cell Receptors 1031

Molecules in the Eye Peptides presented by MHC proteins occupy a deep

1004 groove flanked by alpha helices 1032

1004 T -cell receptors are antibody-like proteins cantairring variable and constant regions 1034

1005 CD8 on cytotoxic T cells acts in concert with T -cell receptors 1034

1006 Helper T cells stimulate cells that display foreign

recovery peptides bound to dass II MHC proteins 1036 is mediated by three cone receptors Helper T cells rely on the T -cell receptor and CD4 to

of rhodopsin 1007 recognize foreign peptides on antigen -presenting cells 1036 in the genes for the green and MHC proteins are highly diverse 1038

lead to "color blindness" 1008 Human immunodeficiency viruses subvert the

ring Depends on the Speedy immune system by destroying helper T cells 1039 of Mechanical Stimuli 1009 34.5 The Immune System Contributes to the

.· ·····.· use a connected bundle of stereocilia to Prevention and the Development of Human

motions 1009 Diseases 1040

channels have been identified in T cells are subjected to positive and negative

1010 selection in the thymus 1040

lncludes the Sensing of Pressure, Autoimmune diseases result from the generation and Other Factars 1011 of immune responses agairrst self-antigens 1041

reveal a receptor for sensing The immune system plays a role in cancer prevention 1041 and other painful stimuli 1011 Vaccines are a powerful means to prevent and

1012 eradicate disease 1042

1017 Chapter 35 Molecular Motors 1049

is an evolutionarily ancient 35.1 Most Molecular-Motor Proteins Are 1018 Members of the P-loop NTPase Superfamily 1050

immune system responds by using Molecular motors are generally oligomeric proteins of evolution 1019 with an A TPase core and an extended structure 1050

xxxH Contents

A TP binding and hydrolysis induce changes in the 36.2 D1rug Candidates Can Be Discovered conformation and binding affinity of motor proteins 1052 by Serendipity, Screening, or Design 1081 35.2 Myosins Move Along Actin Filaments 1054 Serendipitous observations can drive drug

Actin is apolar, self-assembling, dynamic polymer 1054 development 1081

Myosin head domains bind to actin filaments 1056 Screening libraries of compounds can yield drugs

Motions of single motor proteins can be directly or drug l1~ads 1083

observed 1056 Drugs can be designed on the basis of

Phosphate release triggers the myosin power strake 1057 three-dimensional structural information

Muscle is a complex of myosin and actin 1057 about their targets 1086

The length of the lever arm determines motor 36.3 Analyses of Genomes Hold Great velocity 1060 Promis~3 for Drug Discovery 1089

35.3 Kinesin and Dynein Move Along Potential targets can be identified in the human

Microtubules 1060 proteom1~ 1089

Microtubules are hollow cylindrical polymers 1060 Animal models can be developed to test the validity of potential drug targets 1090

Kinesin motion is highly processive 1062 Potentiall targets can be identified in the genomes 35.4 A Rotary Motor Drives Bacterial Motion 1064 of pathogens 1090 Bacteria swim by rotating their flagella 1064 Genetic differences influence individual responses

Proton flow drives bacterial flagellar rotation 1064 to drugs 1091

Bacterial chemotaxis depends on reversal of the 36.4 The Development of Drugs Proceeds direction of flagellar rotation 1066 Through Several Stages 1092

Clinical trials are time consuming and expensive 1092 Chapter 36 Drug Development 1073 The evollution of drug resistance can limit

36.1 The Development of Drugs Presents the utility of drugs for infectious agents

Huge Challenges 1074 and canc:er 1094

Drug candidates must be potent modulators of Answers to Problems At their targets 1074

Drugs must have suitable properties to reach their Index Bl targets 1075 Taxicity can limit drug effectiveness 1080