Contents xvii Some DNA molecules are circular and supercoiled 117 5.2 Recombinant DNA Technology Has Single-stranded nucleic acids can adopt Revolutionized All Aspects of Biology 148 elaborate structures 117 Restriction enzymes and DNA ligase are key tools in 4.3 The Double Helix Facilitates the Accurate forming recombinant DNA molecules 148 Transmission of Hereditary Information 118 Plasmids and lambda phage are choice vectors for Differences in DNA density established the validity DNA cloning in bacteria 149 of the semiconservative-replication hypothesis 119 Bacterial and yeast artificial chromosomes 151 The double helix can be reversibly melted 120 Specific genes can be cloned from digests of 4.4 DNA Is Replicated by Polymerases genomic DNA 151 That Take Instructions from Templates 121 Complementary DNA prepared from mRNA can be expressed in host cells 154 DNA polymerase catalyzes phosphodiester-bridge Proteins with new functions can be created through formation 121 directed changes in DNA The genes of some viruses are made of RNA 122 Recombinant methods enable the exploration of the 4.5 Gene Expression Is the Transformation of functional effects of disease-causing mutations DNA Information into Functional Molecules 123 5.3 Complete Genomes Have Been Several kinds of RNA play key roles in gene expression 123 Sequenced and Analyzed 15 All cellular RNA is synthesized by RNA polymerases 124 The genomes of organisms ranging from bacteria to RNA polymerases take instructions from DNA templates 126 multicellular eukaryotes have been sequenced 158 Transcription begins near promoter sites and ends at The sequencing of the human genome has terminator sites 126 been finished 159 Transfer RNAs are the adaptor molecules in protein Next-generation sequencing methods enable the rapid synthesis 127 determination of a whole genome sequence 160 4.6 Amino Acids Are Encoded by Groups of Comparative genomics has become a powerful Three Bases Starting from a Fixed Point 128 research tool 160 Major features of the genetic code 129 5.4 Eukaryotic Genes Can Be Quantitated and Messenger RNA contains start and stop signals for Manipulated with Considerable Precision 16 protein synthesis 130 Gene-expression levels can be comprehensively The genetic code is nearly universal 131 examined 161 4.7 Most Eukaryotic Genes Are Mosaics of New genes inserted into eukaryotic cells can be Introns and Exons 131 efficiently expressed 163 RNA processing generates mature RNA 132 Transgenic animals harbor and express genes 133 introduced into their germ lines 164 Many exons encode protein domains Gene disruption provides clues to gene function 164 RNA interference provides an additional tool for disrupting gene expression 165 Chapter 5 Exploring Genes and Genomes 139 Tumor-inducing plasmids can be used to introduce 5.1 The Exploration of Genes Relies on new genes into plant cells 166 Key Tools 140 Human gene therapy holds great promise for medicine 167 Restriction enzymes split DNA into specific fragments 141 Restriction fragments can be separated by gel Chapter 6 Exploring Evolution and electrophoresis and visualized 141 Bioinformatics 173 DNA can be sequenced by controlled termination of 143 6.1 Homologs Are Descended from a replication Common Ancestor 174 DNA probes and genes can be synthesized by automated solid-phase methods 144 6.2 Statistical Analysis of Sequence Selected DNA sequences can be greatly amplified Alignments Can Detect Homology 175 by the polymerase chain reaction 145 The statistical significance of alignments can be PCR is a powerful technique in medical diagnostics. estimated by shuffling 17 forensics,and studies of molecular evolution 146 Distant evolutionary relationships can be detected The tools for recombinant DNA technology through the use of substitution matrices 178 have been used to identify disease-causing Databases can be searched to identify homologous mutations 147 sequences 181
Contents xvii Some DNA molecules are circular and supercoiled 117 Single-stranded nucleic acids can adopt elaborate structures 117 4.3 The Double Helix Facilitates the Accurate Transmission of Hereditary Information 118 Differences in DNA density established the validity of the semiconservative-replication hypothesis 119 The double helix can be reversibly melted 120 4.4 DNA Is Replicated by Polymerases That Take Instructions from Templates 121 DNA polymerase catalyzes phosphodiester-bridge formation 121 The genes of some viruses are made of RNA 122 4.5 Gene Expression Is the Transformation of DNA Information into Functional Molecules 123 Several kinds of RNA play key roles in gene expression 123 All cellular RNA is synthesized by RNA polymerases 124 RNA polymerases take instructions from DNA templates 126 Transcription begins near promoter sites and ends at terminator sites 126 Transfer RNAs are the adaptor molecules in protein synthesis 127 4.6 Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point 128 Major features of the genetic code 129 Messenger RNA contains start and stop signals for protein synthesis 130 The genetic code is nearly universal 131 4.7 Most Eukaryotic Genes Are Mosaics of Introns and Exons 131 RNA processing generates mature RNA 132 Many exons encode protein domains 133 Chapter 5 Exploring Genes and Genomes 139 5.1 The Exploration of Genes Relies on Key Tools 140 Restriction enzymes split DNA into specific fragments 141 Restriction fragments can be separated by gel electrophoresis and visualized 141 DNA can be sequenced by controlled termination of replication 143 DNA probes and genes can be synthesized by automated solid-phase methods 144 Selected DNA sequences can be greatly amplified by the polymerase chain reaction 145 PCR is a powerful technique in medical diagnostics, forensics, and studies of molecular evolution 146 The tools for recombinant DNA technology have been used to identify disease-causing mutations 147 5.2 Recombinant DNA Technology Has Revolutionized All Aspects of Biology 148 Restriction enzymes and DNA ligase are key tools in forming recombinant DNA molecules 148 Plasmids and lambda phage are choice vectors for DNA cloning in bacteria 149 Bacterial and yeast artificial chromosomes 151 Specific genes can be cloned from digests of genomic DNA 151 Complementary DNA prepared from mRNA can be expressed in host cells 154 Proteins with new functions can be created through directed changes in DNA 156 Recombinant methods enable the exploration of the functional effects of disease-causing mutations 157 5.3 Complete Genomes Have Been Sequenced and Analyzed 157 The genomes of organisms ranging from bacteria to multicellular eukaryotes have been sequenced 158 The sequencing of the human genome has been finished 159 Next-generation sequencing methods enable the rapid determination of a whole genome sequence 160 Comparative genomics has become a powerful research tool 160 5.4 Eukaryotic Genes Can Be Quantitated and Manipulated with Considerable Precision 161 Gene-expression levels can be comprehensively examined 161 New genes inserted into eukaryotic cells can be efficiently expressed 163 Transgenic animals harbor and express genes introduced into their germ lines 164 Gene disruption provides clues to gene function 164 RNA interference provides an additional tool for disrupting gene expression 165 Tumor-inducing plasmids can be used to introduce new genes into plant cells 166 Human gene therapy holds great promise for medicine 167 Chapter 6 Exploring Evolution and Bioinformatics 173 6.1 Homologs Are Descended from a Common Ancestor 174 6.2 Statistical Analysis of Sequence Alignments Can Detect Homology 175 The statistical significance of alignments can be estimated by shuffling 177 Distant evolutionary relationships can be detected through the use of substitution matrices 178 Databases can be searched to identify homologous sequences 181
xviii Contents 6.3 Examination of Three-Dimensional Additional globins are encoded in the human genome 211 Structure Enhances Our Understanding of APPENDIX:Binding Models Can Be Formulated in Evolutionary Relationships 182 Quantitative Terms:the Hill Plot and the Concerted Model 213 Tertiary structure is more conserved than primary structure 183 Chapter 8 Enzymes:Basic Concepts and Knowledge of three-dimensional structures can Kinetics 219 aid in the evaluation of sequence alignments 184 8.1 Enzymes Are Powerful and Highly Repeated motifs can be detected by aligning Specific Catalysts 220 sequences with themselves 184 Many enzymes require cofactors for activity 221 Convergent evolution illustrates common solutions to biochemical challenges 185 Enzymes can transform energy from one form into another 221 Comparison of RNA sequences can be a source of insight into RNA secondary structures 186 8.2 Free Energy Is a Useful Thermodynamic Function for Understanding Enzymes 222 6.4 Evolutionary Trees Can Be Constructed on the Basis of Sequence Information 187 The free-energy change provides information about the spontaneity but not the rate of a reaction 222 6.5 Modern Techniques Make the Experimental The standard free-energy change of a reaction is Exploration of Evolution Possible 188 related to the equilibrium constant 223 Ancient DNA can sometimes be amplified Enzymes alter only the reaction rate and not the and sequenced 188 reaction equilibrium 224 Molecular evolution can be examined experimentally 189 8.3 Enzymes Accelerate Reactions by Facilitating the Formation of the Transition State 225 Chapter 7 Hemoglobin:Portrait of a The formation of an enzyme-substrate complex is Protein in Action 195 the first step in enzymatic catalysis 226 7.1 Myoglobin and Hemoglobin Bind Oxygen The active sites of enzymes have some at lron Atoms in Heme 196 common features 227 Changes in heme electronic structure upon oxygen The binding energy between enzyme and substrate binding are the basis for functional imaging studies 197 is important for catalysis 229 The structure of myoglobin prevents the release of 8.4 The Michaelis-Menten Equation Describes reactive oxygen species 198 the Kinetic Properties of Many Enzymes 229 Human hemoglobin is an assembly of four Kinetics is the study of reaction rates 229 myoglobin-like subunits 199 The steady-state assumption facilitates a description 7.2 Hemoglobin Binds Oxygen Cooperatively 199 of enzyme kinetics 230 Oxygen binding markedly changes the quaternary Variations in KM can have physiological consequences 232 structure of hemoglobin 201 KM and Vmax values can be determined by Hemoglobin cooperativity can be potentially explained several means 232 by several models 202 KM and Vmax values are important enzyme Structural changes at the heme groups are characteristics 233 transmitted to the oB-2B2 interface 204 kcat/KM is a measure of catalytic efficiency 234 2,3-Bisphosphoglycerate in red cells is crucial in Most biochemical reactions include multiple substrates 235 determining the oxygen affinity of hemoglobin 204 Allosteric enzymes do not obey Carbon monoxide can disrupt oxygen transport by Michaelis-Menten kinetics 237 hemoglobin 205 8.5 Enzymes Can Be Inhibited by Specific 7.3 Hydrogen lons and Carbon Dioxide Promote Molecules 238 the Release of Oxygen:The Bohr Effect 206 Reversible inhibitors are kinetically distinguishable 239 7.4 Mutations in Genes Encoding Hemoglobin Irreversible inhibitors can be used to map Subunits Can Result in Disease 208 the active site 241 Sickle-cell anemia results from the aggregation of Transition-state analogs are potent inhibitors mutated deoxyhemoglobin molecules 209 of enzymes 243 Thalassemia is caused by an imbalanced production of Catalytic antibodies demonstrate the importance of selective hemoglobin chains 210 binding of the transition state to enzymatic activity 243 The accumulation of free alpha-hemoglobin Penicillin irreversibly inactivates a key enzyme in chains is prevented 211 bacterial cell-wall synthesis 244
xviii Contents 6.3 Examination of Three-Dimensional Structure Enhances Our Understanding of Evolutionary Relationships 182 Tertiary structure is more conserved than primary structure 183 Knowledge of three-dimensional structures can aid in the evaluation of sequence alignments 184 Repeated motifs can be detected by aligning sequences with themselves 184 Convergent evolution illustrates common solutions to biochemical challenges 185 Comparison of RNA sequences can be a source of insight into RNA secondary structures 186 6.4 Evolutionary Trees Can Be Constructed on the Basis of Sequence Information 187 6.5 Modern Techniques Make the Experimental Exploration of Evolution Possible 188 Ancient DNA can sometimes be amplified and sequenced 188 Molecular evolution can be examined experimentally 189 Chapter 7 Hemoglobin: Portrait of a Protein in Action 195 7.1 Myoglobin and Hemoglobin Bind Oxygen at Iron Atoms in Heme 196 Changes in heme electronic structure upon oxygen binding are the basis for functional imaging studies 197 The structure of myoglobin prevents the release of reactive oxygen species 198 Human hemoglobin is an assembly of four myoglobin-like subunits 199 7.2 Hemoglobin Binds Oxygen Cooperatively 199 Oxygen binding markedly changes the quaternary structure of hemoglobin 201 Hemoglobin cooperativity can be potentially explained by several models 202 Structural changes at the heme groups are transmitted to the a1b1– a2b2 interface 204 2,3-Bisphosphoglycerate in red cells is crucial in determining the oxygen affinity of hemoglobin 204 Carbon monoxide can disrupt oxygen transport by hemoglobin 205 7.3 Hydrogen Ions and Carbon Dioxide Promote the Release of Oxygen: The Bohr Effect 206 7.4 Mutations in Genes Encoding Hemoglobin Subunits Can Result in Disease 208 Sickle-cell anemia results from the aggregation of mutated deoxyhemoglobin molecules 209 Thalassemia is caused by an imbalanced production of hemoglobin chains 210 The accumulation of free alpha-hemoglobin chains is prevented 211 Additional globins are encoded in the human genome 211 APPENDIX: Binding Models Can Be Formulated in Quantitative Terms: the Hill Plot and the Concerted Model 213 Chapter 8 Enzymes: Basic Concepts and Kinetics 219 8.1 Enzymes Are Powerful and Highly Specific Catalysts 220 Many enzymes require cofactors for activity 221 Enzymes can transform energy from one form into another 221 8.2 Free Energy Is a Useful Thermodynamic Function for Understanding Enzymes 222 The free-energy change provides information about the spontaneity but not the rate of a reaction 222 The standard free-energy change of a reaction is related to the equilibrium constant 223 Enzymes alter only the reaction rate and not the reaction equilibrium 224 8.3 Enzymes Accelerate Reactions by Facilitating the Formation of the Transition State 225 The formation of an enzyme–substrate complex is the first step in enzymatic catalysis 226 The active sites of enzymes have some common features 227 The binding energy between enzyme and substrate is important for catalysis 229 8.4 The Michaelis–Menten Equation Describes the Kinetic Properties of Many Enzymes 229 Kinetics is the study of reaction rates 229 The steady-state assumption facilitates a description of enzyme kinetics 230 Variations in KM can have physiological consequences 232 KM and Vmax values can be determined by several means 232 KM and Vmax values are important enzyme characteristics 233 kcat/KM is a measure of catalytic efficiency 234 Most biochemical reactions include multiple substrates 235 Allosteric enzymes do not obey Michaelis–Menten kinetics 237 8.5 Enzymes Can Be Inhibited by Specific Molecules 238 Reversible inhibitors are kinetically distinguishable 239 Irreversible inhibitors can be used to map the active site 241 Transition-state analogs are potent inhibitors of enzymes 243 Catalytic antibodies demonstrate the importance of selective binding of the transition state to enzymatic activity 243 Penicillin irreversibly inactivates a key enzyme in bacterial cell-wall synthesis 244
Contents xix 8.6 Enzymes Can Be Studied One Molecule The altered conformation of myosin persists for a at a Time 246 substantial period of time 282 APPENDIX:Enzymes are Classified on the Basis Myosins are a family of enzymes containing P-loop of the Types of Reactions That They Catalyze 248 structures 283 Chapter 10 Regulatory Strategies 289 Chapter 9 Catalytic Strategies 253 10.1 Aspartate Transcarbamoylase Is Allosterically Inhibited by the End Product of Its Pathway 290 A few basic catalytic principles are used by many enzymes 254 Allosterically regulated enzymes do not follow Michaelis-Menten kinetics 291 9.1 Proteases Facilitate a Fundamentally ATCase consists of separable catalytic and regulatory Difficult Reaction 255 subunits 291 Chymotrypsin possesses a highly reactive serine residue 255 Allosteric interactions in ATCase are mediated by large Chymotrypsin action proceeds in two steps linked changes in quaternary structure 292 by a covalently bound intermediate 256 Allosteric regulators modulate the T-to-R equilibrium 295 Serine is part of a catalytic triad that also includes histidine and aspartate 257 10.2 Isozymes Provide a Means of Regulation Specific to Distinct Tissues and Developmental Catalytic triads are found in other hydrolytic enzymes 260 Stages 296 The catalytic triad has been dissected by site-directed mutagenesis 262 10.3 Covalent Modification Is a Means of Cysteine,aspartyl,and metalloproteases are other Regulating Enzyme Activity 297 major classes of peptide-cleaving enzymes 263 Kinases and phosphatases control the extent of protein Protease inhibitors are important drugs 264 phosphorylation 298 9.2 Carbonic Anhydrases Make a Fast Phosphorylation is a highly effective means of regulating the activities of target proteins 300 Reaction Faster 266 Cyclic AMP activates protein kinase A by altering the Carbonic anhydrase contains a bound zinc ion quaternary structure 301 essential for catalytic activity 267 ATP and the target protein bind to a deep cleft Catalysis entails zinc activation of a water molecule 268 in the catalytic subunit of protein kinase A 302 A proton shuttle facilitates rapid regeneration of the active form of the enzyme 269 10.4 Many Enzymes Are Activated by Specific Proteolytic Cleavage 302 Convergent evolution has generated zinc-based active sites in different carbonic anhydrases 271 Chymotrypsinogen is activated by specific cleavage of a single peptide bond 303 9.3 Restriction Enzymes Catalyze Highly Proteolytic activation of chymotrypsinogen leads Specific DNA-Cleavage Reactions 271 to the formation of a substrate-binding site 304 Cleavage is by in-line displacement of 3'-oxygen The generation of trypsin from trypsinogen leads from phosphorus by magnesium-activated water 272 to the activation of other zymogens 305 Restriction enzymes require magnesium for Some proteolytic enzymes have specific inhibitors 306 catalytic activity 274 Blood clotting is accomplished by a cascade of The complete catalytic apparatus is assembled zymogen activations 307 only within complexes of cognate DNA molecules, Fibrinogen is converted by thrombin into a ensuring specificity 275 fibrin clot 308 Host-cell DNA is protected by the addition of methyl groups to specific bases 277 Prothrombin is readied for activation by a vitamin K-dependent modification 310 Type II restriction enzymes have a catalytic core in common and are probably related by horizontal Hemophilia revealed an early step in clotting 311 gene transfer 278 The clotting process must be precisely regulated 311 9.4 Myosins Harness Changes in Enzyme 319 Conformation to Couple ATP Hydrolysis to Chapter 11 Carbohydrates Mechanical Work 279 11.1 Monosaccharides Are the Simplest ATP hydrolysis proceeds by the attack of water on Carbohydrates 320 the gamma-phosphoryl group 279 Many common sugars exist in cyclic forms 322 Formation of the transition state for ATP hydrolysis Pyranose and furanose rings can assume different is associated with a substantial conformational change 280 conformations 324
Contents xix 8.6 Enzymes Can Be Studied One Molecule at a Time 246 APPENDIX: Enzymes are Classified on the Basis of the Types of Reactions That They Catalyze 248 Chapter 9 Catalytic Strategies 253 A few basic catalytic principles are used by many enzymes 254 9.1 Proteases Facilitate a Fundamentally Difficult Reaction 255 Chymotrypsin possesses a highly reactive serine residue 255 Chymotrypsin action proceeds in two steps linked by a covalently bound intermediate 256 Serine is part of a catalytic triad that also includes histidine and aspartate 257 Catalytic triads are found in other hydrolytic enzymes 260 The catalytic triad has been dissected by site-directed mutagenesis 262 Cysteine, aspartyl, and metalloproteases are other major classes of peptide-cleaving enzymes 263 Protease inhibitors are important drugs 264 9.2 Carbonic Anhydrases Make a Fast Reaction Faster 266 Carbonic anhydrase contains a bound zinc ion essential for catalytic activity 267 Catalysis entails zinc activation of a water molecule 268 A proton shuttle facilitates rapid regeneration of the active form of the enzyme 269 Convergent evolution has generated zinc-based active sites in different carbonic anhydrases 271 9.3 Restriction Enzymes Catalyze Highly Specific DNA-Cleavage Reactions 271 Cleavage is by in-line displacement of 39-oxygen from phosphorus by magnesium-activated water 272 Restriction enzymes require magnesium for catalytic activity 274 The complete catalytic apparatus is assembled only within complexes of cognate DNA molecules, ensuring specificity 275 Host-cell DNA is protected by the addition of methyl groups to specific bases 277 Type II restriction enzymes have a catalytic core in common and are probably related by horizontal gene transfer 278 9.4 Myosins Harness Changes in Enzyme Conformation to Couple ATP Hydrolysis to Mechanical Work 279 ATP hydrolysis proceeds by the attack of water on the gamma-phosphoryl group 279 Formation of the transition state for ATP hydrolysis is associated with a substantial conformational change 280 The altered conformation of myosin persists for a substantial period of time 282 Myosins are a family of enzymes containing P-loop structures 283 Chapter 10 Regulatory Strategies 289 10.1 Aspartate Transcarbamoylase Is Allosterically Inhibited by the End Product of Its Pathway 290 Allosterically regulated enzymes do not follow Michaelis–Menten kinetics 291 ATCase consists of separable catalytic and regulatory subunits 291 Allosteric interactions in ATCase are mediated by large changes in quaternary structure 292 Allosteric regulators modulate the T-to-R equilibrium 295 10.2 Isozymes Provide a Means of Regulation Specific to Distinct Tissues and Developmental Stages 296 10.3 Covalent Modification Is a Means of Regulating Enzyme Activity 297 Kinases and phosphatases control the extent of protein phosphorylation 298 Phosphorylation is a highly effective means of regulating the activities of target proteins 300 Cyclic AMP activates protein kinase A by altering the quaternary structure 301 ATP and the target protein bind to a deep cleft in the catalytic subunit of protein kinase A 302 10.4 Many Enzymes Are Activated by Specific Proteolytic Cleavage 302 Chymotrypsinogen is activated by specific cleavage of a single peptide bond 303 Proteolytic activation of chymotrypsinogen leads to the formation of a substrate-binding site 304 The generation of trypsin from trypsinogen leads to the activation of other zymogens 305 Some proteolytic enzymes have specific inhibitors 306 Blood clotting is accomplished by a cascade of zymogen activations 307 Fibrinogen is converted by thrombin into a fibrin clot 308 Prothrombin is readied for activation by a vitamin K-dependent modification 310 Hemophilia revealed an early step in clotting 311 The clotting process must be precisely regulated 311 Chapter 11 Carbohydrates 319 11.1 Monosaccharides Are the Simplest Carbohydrates 320 Many common sugars exist in cyclic forms 322 Pyranose and furanose rings can assume different conformations 324
XX Contents Glucose is a reducing sugar 325 A membrane lipid is an amphipathic molecule Monosaccharides are joined to alcohols and containing a hydrophilic and a hydrophobic moiety 351 amines through glycosidic bonds 326 12.3 Phospholipids and Glycolipids Readily Phosphorylated sugars are key intermediates in Form Bimolecular Sheets in Aqueous Media 352 energy generation and biosyntheses 326 Lipid vesicles can be formed from phospholipids 353 11.2 Monosaccharides Are Linked to Form Lipid bilayers are highly impermeable to ions and Complex Carbohydrates 327 most polar molecules 354 Sucrose,lactose,and maltose are the common 12.4 Proteins Carry Out Most Membrane disaccharides 327 Processes 355 Glycogen and starch are storage forms of glucose 328 Proteins associate with the lipid bilayer in a Cellulose,a structural component of plants,is made variety of ways 355 of chains of glucose 328 Proteins interact with membranes in a variety 11.3 Carbohydrates Can Be Linked to Proteins of ways 356 to Form Glycoproteins 329 Some proteins associate with membranes through Carbohydrates can be linked to proteins through covalently attached hydrophobic groups 359 asparagine(N-linked)or through serine or Transmembrane helices can be accurately threonine(O-linked)residues 330 predicted from amino acid sequences 359 The glycoprotein erythropoietin is a vital hormone 330 12.5 Lipids and Many Membrane Proteins Proteoglycans,composed of polysaccharides and Diffuse Rapidly in the Plane of the protein,have important structural roles 331 Membrane 361 Proteoglycans are important components of cartilage 332 The fluid mosaic model allows lateral movement Mucins are glycoprotein components of mucus 333 but not rotation through the membrane 362 Protein glycosylation takes place in the lumen of the Membrane fluidity is controlled by fatty acid endoplasmic reticulum and in the Golgi complex 333 composition and cholesterol content 362 Specific enzymes are responsible for oligosaccharide Lipid rafts are highly dynamic complexes formed assembly 335 between cholesterol and specific lipids 363 Blood groups are based on protein glycosylation All biological membranes are asymmetric 363 patterns 335 12.6 Eukaryotic Cells Contain Compartments Errors in glycosylation can result in pathological Bounded by Internal Membranes 364 conditions 336 Oligosaccharides can be "sequenced" 336 11.4 Lectins Are Specific Carbohydrate-Binding Chapter 13 Membrane Channels and Pumps 371 Proteins 337 The expression of transporters largely defines the Lectins promote interactions between cells 338 metabolic activities of a given cell type 372 Lectins are organized into different classes 338 13.1 The Transport of Molecules Across a Influenza virus binds to sialic acid residues 339 Membrane May Be Active or Passive 372 Chapter 12 Lipids and Cell Membranes 345 Many molecules require protein transporters to cross membranes 372 Many common features underlie the diversity of Free energy stored in concentration gradients can be biological membranes 346 quantified 373 12.1 Fatty Acids Are Key Constituents of 13.2 Two Families of Membrane Proteins Lipids 346 Use ATP Hydrolysis to Pump lons and Fatty acid names are based on their parent hydrocarbons 346 Molecules Across Membranes 374 Fatty acids vary in chain length and degree of P-type ATPases couple phosphorylation and unsaturation 347 conformational changes to pump calcium ions across membranes 374 12.2 There Are Three Common Types of Membrane Lipids 348 Digitalis specifically inhibits the Na-K pump by blocking its dephosphorylation 377 Phospholipids are the major class of membrane lipids 348 P-type ATPases are evolutionarily conserved and Membrane lipids can include carbohydrate moieties 349 play a wide range of roles 378 Cholesterol is a lipid based on a steroid nucleus 350 Multidrug resistance highlights a family of Archaeal membranes are built from ether lipids with membrane pumps with ATP-binding cassette branched chains 350 domains 378
xx Contents Glucose is a reducing sugar 325 Monosaccharides are joined to alcohols and amines through glycosidic bonds 326 Phosphorylated sugars are key intermediates in energy generation and biosyntheses 326 11.2 Monosaccharides Are Linked to Form Complex Carbohydrates 327 Sucrose, lactose, and maltose are the common disaccharides 327 Glycogen and starch are storage forms of glucose 328 Cellulose, a structural component of plants, is made of chains of glucose 328 11.3 Carbohydrates Can Be Linked to Proteins to Form Glycoproteins 329 Carbohydrates can be linked to proteins through asparagine (N-linked) or through serine or threonine (O-linked) residues 330 The glycoprotein erythropoietin is a vital hormone 330 Proteoglycans, composed of polysaccharides and protein, have important structural roles 331 Proteoglycans are important components of cartilage 332 Mucins are glycoprotein components of mucus 333 Protein glycosylation takes place in the lumen of the endoplasmic reticulum and in the Golgi complex 333 Specific enzymes are responsible for oligosaccharide assembly 335 Blood groups are based on protein glycosylation patterns 335 Errors in glycosylation can result in pathological conditions 336 Oligosaccharides can be “sequenced” 336 11.4 Lectins Are Specific Carbohydrate-Binding Proteins 337 Lectins promote interactions between cells 338 Lectins are organized into different classes 338 Influenza virus binds to sialic acid residues 339 Chapter 12 Lipids and Cell Membranes 345 Many common features underlie the diversity of biological membranes 346 12.1 Fatty Acids Are Key Constituents of Lipids 346 Fatty acid names are based on their parent hydrocarbons 346 Fatty acids vary in chain length and degree of unsaturation 347 12.2 There Are Three Common Types of Membrane Lipids 348 Phospholipids are the major class of membrane lipids 348 Membrane lipids can include carbohydrate moieties 349 Cholesterol is a lipid based on a steroid nucleus 350 Archaeal membranes are built from ether lipids with branched chains 350 A membrane lipid is an amphipathic molecule containing a hydrophilic and a hydrophobic moiety 351 12.3 Phospholipids and Glycolipids Readily Form Bimolecular Sheets in Aqueous Media 352 Lipid vesicles can be formed from phospholipids 353 Lipid bilayers are highly impermeable to ions and most polar molecules 354 12.4 Proteins Carry Out Most Membrane Processes 355 Proteins associate with the lipid bilayer in a variety of ways 355 Proteins interact with membranes in a variety of ways 356 Some proteins associate with membranes through covalently attached hydrophobic groups 359 Transmembrane helices can be accurately predicted from amino acid sequences 359 12.5 Lipids and Many Membrane Proteins Diffuse Rapidly in the Plane of the Membrane 361 The fluid mosaic model allows lateral movement but not rotation through the membrane 362 Membrane fluidity is controlled by fatty acid composition and cholesterol content 362 Lipid rafts are highly dynamic complexes formed between cholesterol and specific lipids 363 All biological membranes are asymmetric 363 12.6 Eukaryotic Cells Contain Compartments Bounded by Internal Membranes 364 Chapter 13 Membrane Channels and Pumps 371 The expression of transporters largely defines the metabolic activities of a given cell type 372 13.1 The Transport of Molecules Across a Membrane May Be Active or Passive 372 Many molecules require protein transporters to cross membranes 372 Free energy stored in concentration gradients can be quantified 373 13.2 Two Families of Membrane Proteins Use ATP Hydrolysis to Pump Ions and Molecules Across Membranes 374 P-type ATPases couple phosphorylation and conformational changes to pump calcium ions across membranes 374 Digitalis specifically inhibits the Na1–K1 pump by blocking its dephosphorylation 377 P-type ATPases are evolutionarily conserved and play a wide range of roles 378 Multidrug resistance highlights a family of membrane pumps with ATP-binding cassette domains 378
Contents xxi 13.3 Lactose Permease Is an Archetype of Insulin binding results in the cross-phosphorylation Secondary Transporters That Use One and activation of the insulin receptor 412 Concentration Gradient to Power the Formation The activated insulin-receptor kinase initiates a of Another 380 kinase cascade 412 13.4 Specific Channels Can Rapidly Transport Insulin signaling is terminated by the action of lons Across Membranes 382 phosphatases 415 Action potentials are mediated by transient changes 14.3 EGF Signaling:Signal-Transduction in Na*and K*permeability 382 Pathways Are Poised to Respond 41 Patch-clamp conductance measurements reveal EGF binding results in the dimerization of the the activities of single channels 383 EGF receptor 415 The structure of a potassium ion channel is an The EGF receptor undergoes phosphorylation of archetype for many ion-channel structures 383 its carboxyl-terminal tail 417 The structure of the potassium ion channel reveals EGF signaling leads to the activation of Ras,a the basis of ion specificity 384 small G protein 417 The structure of the potassium ion channel explains Activated Ras initiates a protein kinase cascade 418 its rapid rate of transport 387 EGF signaling is terminated by protein phosphatases Voltage gating requires substantial conformational and the intrinsic GTPase activity of Ras 418 changes in specific ion-channel domains 387 14.4 Many Elements Recur with Variation A channel can be activated by occlusion of the pore: in Different Signal-Transduction the ball-and-chain model 388 Pathways 419 The acetylcholine receptor is an archetype for ligand-gated ion channels 389 14.5 Defects in Signal-Transduction Pathways Can Lead to Cancer and Other Action potentials integrate the activities of several ion Diseases 420 channels working in concert 391 Disruption of ion channels by mutations or Monoclonal antibodies can be used to inhibit chemicals can be potentially life threatening 392 signal-transduction pathways activated in tumors 420 Protein kinase inhibitors can be effective anticancer 13.5 Gap Junctions Allow lons and Small drugs 421 Molecules to Flow Between Communicating Cells 393 Cholera and whooping cough are due to altered 13.6 Specific Channels Increase the Permeability G-protein activity 421 of Some Membranes to Water 394 Chapter 14 Signal-Transduction Pathways 401 Part II TRANSDUCING AND Signal transduction depends on molecular circuits 402 STORING ENERGY 14.1 Heterotrimeric G Proteins Transmit Chapter 15 Metabolism:Basic Concepts Signals and Reset Themselves 403 and Design 427 Ligand binding to 7TM receptors leads to the activation of heterotrimeric G proteins 405 15.1 Metabolism Is Composed of Many Activated G proteins transmit signals by binding Coupled,Interconnecting Reactions 428 to other proteins 406 Metabolism consists of energy-yielding and Cyclic AMP stimulates the phosphorylation of many energy-requiring reactions 428 target proteins by activating protein kinase A 406 A thermodynamically unfavorable reaction can be G proteins spontaneously reset themselves through driven by a favorable reaction 429 GTP hydrolysis 407 15.2 ATP Is the Universal Currency of Free Some 7TM receptors activate the phosphoinositide cascade 408 Energy in Biological Systems 430 Calcium ion is a widely used second messenger 409 ATP hydrolysis is exergonic 430 Calcium ion often activates the regulatory protein calmodulin 410 ATP hydrolysis drives metabolism by shifting the equilibrium of coupled reactions 431 14.2 Insulin Signaling:Phosphorylation The high phosphoryl potential of ATP results Cascades Are Central to Many from structural differences between ATP and its Signal-Transduction Processes 411 hydrolysis products 433 The insulin receptor is a dimer that closes around Phosphoryl-transfer potential is an important form a bound insulin molecule 412 of cellular energy transformation 434
Contents xxi 13.3 Lactose Permease Is an Archetype of Secondary Transporters That Use One Concentration Gradient to Power the Formation of Another 380 13.4 Specific Channels Can Rapidly Transport Ions Across Membranes 382 Action potentials are mediated by transient changes in Na1 and K1 permeability 382 Patch-clamp conductance measurements reveal the activities of single channels 383 The structure of a potassium ion channel is an archetype for many ion-channel structures 383 The structure of the potassium ion channel reveals the basis of ion specificity 384 The structure of the potassium ion channel explains its rapid rate of transport 387 Voltage gating requires substantial conformational changes in specific ion-channel domains 387 A channel can be activated by occlusion of the pore: the ball-and-chain model 388 The acetylcholine receptor is an archetype for ligand-gated ion channels 389 Action potentials integrate the activities of several ion channels working in concert 391 Disruption of ion channels by mutations or chemicals can be potentially life threatening 392 13.5 Gap Junctions Allow Ions and Small Molecules to Flow Between Communicating Cells 393 13.6 Specific Channels Increase the Permeability of Some Membranes to Water 394 Chapter 14 Signal-Transduction Pathways 401 Signal transduction depends on molecular circuits 402 14.1 Heterotrimeric G Proteins Transmit Signals and Reset Themselves 403 Ligand binding to 7TM receptors leads to the activation of heterotrimeric G proteins 405 Activated G proteins transmit signals by binding to other proteins 406 Cyclic AMP stimulates the phosphorylation of many target proteins by activating protein kinase A 406 G proteins spontaneously reset themselves through GTP hydrolysis 407 Some 7TM receptors activate the phosphoinositide cascade 408 Calcium ion is a widely used second messenger 409 Calcium ion often activates the regulatory protein calmodulin 410 14.2 Insulin Signaling: Phosphorylation Cascades Are Central to Many Signal-Transduction Processes 411 The insulin receptor is a dimer that closes around a bound insulin molecule 412 Insulin binding results in the cross-phosphorylation and activation of the insulin receptor 412 The activated insulin-receptor kinase initiates a kinase cascade 412 Insulin signaling is terminated by the action of phosphatases 415 14.3 EGF Signaling: Signal-Transduction Pathways Are Poised to Respond 415 EGF binding results in the dimerization of the EGF receptor 415 The EGF receptor undergoes phosphorylation of its carboxyl-terminal tail 417 EGF signaling leads to the activation of Ras, a small G protein 417 Activated Ras initiates a protein kinase cascade 418 EGF signaling is terminated by protein phosphatases and the intrinsic GTPase activity of Ras 418 14.4 Many Elements Recur with Variation in Different Signal-Transduction Pathways 419 14.5 Defects in Signal-Transduction Pathways Can Lead to Cancer and Other Diseases 420 Monoclonal antibodies can be used to inhibit signal-transduction pathways activated in tumors 420 Protein kinase inhibitors can be effective anticancer drugs 421 Cholera and whooping cough are due to altered G-protein activity 421 Part II TRANSDUCING AND STORING ENERGY Chapter 15 Metabolism: Basic Concepts and Design 427 15.1 Metabolism Is Composed of Many Coupled, Interconnecting Reactions 428 Metabolism consists of energy-yielding and energy-requiring reactions 428 A thermodynamically unfavorable reaction can be driven by a favorable reaction 429 15.2 ATP Is the Universal Currency of Free Energy in Biological Systems 430 ATP hydrolysis is exergonic 430 ATP hydrolysis drives metabolism by shifting the equilibrium of coupled reactions 431 The high phosphoryl potential of ATP results from structural differences between ATP and its hydrolysis products 433 Phosphoryl-transfer potential is an important form of cellular energy transformation 434