《生物化学》课程教学资源（书籍文献）Biochemistry, EIGHTH EDITION 2015, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto, Jr. Lubert Stryer.pdf_P16-P20

xviii Contents All cellular RNA is synthesized by RNA polymerases 120 RNA polymerases take instructions from DNA templates 121 Transcription begins near promoter sites and ends at terminator sites 122 Transfer RNAs are the adaptor molecules in protein synthesis 123 4.6 Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point 124 Major features of the genetic code 125 Messenger RNA contains start and stop signals for protein synthesis 126 The genetic code is nearly universal 126 4.7 Most Eukaryotic Genes Are Mosaics of Introns and Exons 127 RNA processing generates mature RNA 127 Many exons encode protein domains 128 CHAPTER 5 Exploring Genes and Genomes 135 5.1 The Exploration of Genes Relies on Key Tools 136 Restriction enzymes split DNA into specific fragments 137 Restriction fragments can be separated by gel electrophoresis and visualized 137 DNA can be sequenced by controlled termination of replication 138 DNA probes and genes can be synthesized by automated solid-phase methods 139 Selected DNA sequences can be greatly amplified by the polymerase chain reaction 141 PCR is a powerful technique in medical diagnostics, forensics, and studies of molecular evolution 142 The tools for recombinant DNA technology have been used to identify disease-causing mutations 143 5.2 Recombinant DNA Technology Has Revolutionized All Aspects of Biology 143 Restriction enzymes and DNA ligase are key tools in forming recombinant DNA molecules 143 Plasmids and l phage are choice vectors for DNA cloning in bacteria 144 Bacterial and yeast artificial chromosomes 147 Specific genes can be cloned from digests of genomic DNA 147 Complementary DNA prepared from mRNA can be expressed in host cells 149 Proteins with new functions can be created through directed changes in DNA 150 Recombinant methods enable the exploration of the functional effects of disease-causing mutations 152 5.3 Complete Genomes Have Been Sequenced and Analyzed 152 The genomes of organisms ranging from bacteria to multicellular eukaryotes have been sequenced 153 The sequence of the human genome has been completed 154 Next-generation sequencing methods enable the rapid determination of a complete genome sequence 155 Comparative genomics has become a powerful research tool 156 5.4 Eukaryotic Genes Can Be Quantitated and Manipulated with Considerable Precision 157 Gene-expression levels can be comprehensively examined 157 New genes inserted into eukaryotic cells can be efficiently expressed 159 Transgenic animals harbor and express genes introduced into their germ lines 160 Gene disruption and genome editing provide clues to gene function and opportunities for new therapies 160 RNA interference provides an additional tool for disrupting gene expression 162 Tumor-inducing plasmids can be used to introduce new genes into plant cells 163 Human gene therapy holds great promise for medicine 164 CHAPTER 6 Exploring Evolution and Bioinformatics 169 6.1 Homologs Are Descended from a Common Ancestor 170 6.2 Statistical Analysis of Sequence Alignments Can Detect Homology 171 The statistical significance of alignments can be estimated by shuffling 173 Distant evolutionary relationships can be detected through the use of substitution matrices 174 Databases can be searched to identify homologous sequences 177 6.3 Examination of Three-Dimensional Structure Enhances Our Understanding of Evolutionary Relationships 177 Tertiary structure is more conserved than primary structure 178 Knowledge of three-dimensional structures can aid in the evaluation of sequence alignments 179 Repeated motifs can be detected by aligning sequences with themselves 180 Convergent evolution illustrates common solutions to biochemical challenges 181 Comparison of RNA sequences can be a source of insight into RNA secondary structures 182 6.4 Evolutionary Trees Can Be Constructed on the Basis of Sequence Information 183 Horizontal gene transfer events may explain unexpected branches of the evolutionary tree 184 6.5 Modern Techniques Make the Experimental Exploration of Evolution Possible 185 Ancient DNA can sometimes be amplified and sequenced 185 Molecular evolution can be examined experimentally 185 CHAPTER 5 Exploring Genes and Genomes 135 CHAPTER 6 Exploring Evolution and Bioinformatics 169

Contents xix CHAPTER 7 Hemoglobin: Portrait of a Protein in Action 191 7.1 Myoglobin and Hemoglobin Bind Oxygen at Iron Atoms in Heme 192 Changes in heme electronic structure upon oxygen binding are the basis for functional imaging studies 193 The structure of myoglobin prevents the release of reactive oxygen species 194 Human hemoglobin is an assembly of four myoglobinlike subunits 195 7.2 Hemoglobin Binds Oxygen Cooperatively 195 Oxygen binding markedly changes the quaternary structure of hemoglobin 197 Hemoglobin cooperativity can be potentially explained by several models 198 Structural changes at the heme groups are transmitted to the a1b1–a2b2 interface 200 2,3-Bisphosphoglycerate in red cells is crucial in determining the oxygen affinity of hemoglobin 200 Carbon monoxide can disrupt oxygen transport by hemoglobin 201 7.3 Hydrogen Ions and Carbon Dioxide Promote the Release of Oxygen: The Bohr Effect 202 7.4 Mutations in Genes Encoding Hemoglobin Subunits Can Result in Disease 204 Sickle-cell anemia results from the aggregation of mutated deoxyhemoglobin molecules 205 Thalassemia is caused by an imbalanced production of hemoglobin chains 207 The accumulation of free alpha-hemoglobin chains is prevented 207 Additional globins are encoded in the human genome 208 APPENDIX: Binding Models Can Be Formulated in Quantitative Terms: The Hill Plot and the Concerted Model 210 CHAPTER 8 Enzymes: Basic Concepts and Kinetics 215 8.1 Enzymes are Powerful and Highly Specific Catalysts 216 Many enzymes require cofactors for activity 217 Enzymes can transform energy from one form into another 217 8.2 Gibbs Free Energy Is a Useful Thermodynamic Function for Understanding Enzymes 218 The free-energy change provides information about the spontaneity but not the rate of a reaction 218 The standard free-energy change of a reaction is related to the equilibrium constant 219 Enzymes alter only the reaction rate and not the reaction equilibrium 220 8.3 Enzymes Accelerate Reactions by Facilitating the Formation of the Transition State 221 The formation of an enzyme–substrate complex is the first step in enzymatic catalysis 222 The active sites of enzymes have some common features 223 The binding energy between enzyme and substrate is important for catalysis 225 8.4 The Michaelis–Menten Model Accounts for the Kinetic Properties of Many Enzymes 225 Kinetics is the study of reaction rates 225 The steady-state assumption facilitates a description of enzyme kinetics 226 Variations in KM can have physiological consequences 228 KM and Vmax values can be determined by several means 228 KM and Vmax values are important enzyme characteristics 229 kcat/KM is a measure of catalytic efficiency 230 Most biochemical reactions include multiple substrates 231 Allosteric enzymes do not obey Michaelis–Menten kinetics 233 8.5 Enzymes Can Be Inhibited by Specific Molecules 234 The different types of reversible inhibitors are kinetically distinguishable 235 Irreversible inhibitors can be used to map the active site 237 Penicillin irreversibly inactivates a key enzyme in bacterial cell-wall synthesis 239 Transition-state analogs are potent inhibitors of enzymes 240 Catalytic antibodies demonstrate the importance of selective binding of the transition state to enzymatic activity 241 8.6 Enzymes Can Be Studied One Molecule at a Time 242 APPENDIX: Enzymes are Classified on the Basis of the Types of Reactions That They Catalyze 245 CHAPTER 9 Catalytic Strategies 251 A few basic catalytic principles are used by many enzymes 252 9.1 Proteases Facilitate a Fundamentally Difficult Reaction 253 Chymotrypsin possesses a highly reactive serine residue 253 Chymotrypsin action proceeds in two steps linked by a covalently bound intermediate 254 Serine is part of a catalytic triad that also includes histidine and aspartate 255 Catalytic triads are found in other hydrolytic enzymes 258 The catalytic triad has been dissected by site-directed mutagenesis 260 Cysteine, aspartyl, and metalloproteases are other major classes of peptide-cleaving enzymes 260 Protease inhibitors are important drugs 263 CHAPTER 7 Hemoglobin: Portrait of a Protein in Action 191 CHAPTER 8 Enzymes: Basic Concepts and Kinetics 215 CHAPTER 9 Catalytic Strategies 251

xx Contents 9.2 Carbonic Anhydrases Make a Fast Reaction Faster 264 Carbonic anhydrase contains a bound zinc ion essential for catalytic activity 265 Catalysis entails zinc activation of a water molecule 265 A proton shuttle facilitates rapid regeneration of the active form of the enzyme 267 9.3 Restriction Enzymes Catalyze Highly Specific DNA-Cleavage Reactions 269 Cleavage is by in-line displacement of 39-oxygen from phosphorus by magnesium-activated water 269 Restriction enzymes require magnesium for catalytic activity 271 The complete catalytic apparatus is assembled only within complexes of cognate DNA molecules, ensuring specificity 272 Host-cell DNA is protected by the addition of methyl groups to specific bases 274 Type II restriction enzymes have a catalytic core in common and are probably related by horizontal gene transfer 275 9.4 Myosins Harness Changes in Enzyme Conformation to Couple ATP Hydrolysis to Mechanical Work 275 ATP hydrolysis proceeds by the attack of water on the gamma-phosphoryl group 276 Formation of the transition state for ATP hydrolysis is associated with a substantial conformational change 277 The altered conformation of myosin persists for a substantial period of time 278 Scientists can watch single molecules of myosin move 279 Myosins are a family of enzymes containing P-loop structures 280 CHAPTER 10 Regulatory Strategies 285 10.1 Aspartate Transcarbamoylase Is Allosterically Inhibited by the End Product of Its Pathway 286 Allosterically regulated enzymes do not follow Michaelis–Menten kinetics 287 ATCase consists of separable catalytic and regulatory subunits 287 Allosteric interactions in ATCase are mediated by large changes in quaternary structure 288 Allosteric regulators modulate the T-to-R equilibrium 291 10.2 Isozymes Provide a Means of Regulation Specific to Distinct Tissues and Developmental Stages 292 10.3 Covalent Modification Is a Means of Regulating Enzyme Activity 293 Kinases and phosphatases control the extent of protein phosphorylation 294 Phosphorylation is a highly effective means of regulating the activities of target proteins 296 Cyclic AMP activates protein kinase A by altering the quaternary structure 297 ATP and the target protein bind to a deep cleft in the catalytic subunit of protein kinase A 298 10.4 Many Enzymes Are Activated by Specific Proteolytic Cleavage 299 Chymotrypsinogen is activated by specific cleavage of a single peptide bond 299 Proteolytic activation of chymotrypsinogen leads to the formation of a substrate-binding site 300 The generation of trypsin from trypsinogen leads to the activation of other zymogens 301 Some proteolytic enzymes have specific inhibitors 302 Blood clotting is accomplished by a cascade of zymogen activations 303 Prothrombin requires a vitamin K-dependent modification for activation 304 Fibrinogen is converted by thrombin into a fibrin clot 304 Vitamin K is required for the formation of g-carboxyglutamate 306 The clotting process must be precisely regulated 307 Hemophilia revealed an early step in clotting 308 CHAPTER 11 Carbohydrates 315 11.1 Monosaccharides Are the Simplest Carbohydrates 316 Many common sugars exist in cyclic forms 318 Pyranose and furanose rings can assume different conformations 320 Glucose is a reducing sugar 321 Monosaccharides are joined to alcohols and amines through glycosidic bonds 322 Phosphorylated sugars are key intermediates in energy generation and biosyntheses 322 11.2 Monosaccharides Are Linked to Form Complex Carbohydrates 323 Sucrose, lactose, and maltose are the common disaccharides 323 Glycogen and starch are storage forms of glucose 324 Cellulose, a structural component of plants, is made of chains of glucose 324 11.3 Carbohydrates Can Be Linked to Proteins to Form Glycoproteins 325 Carbohydrates can be linked to proteins through asparagine (N-linked) or through serine or threonine (O-linked) residues 326 The glycoprotein erythropoietin is a vital hormone 327 Glycosylation functions in nutrient sensing 327 Proteoglycans, composed of polysaccharides and protein, have important structural roles 327 Proteoglycans are important components of cartilage 328 Mucins are glycoprotein components of mucus 329 Protein glycosylation takes place in the lumen of the endoplasmic reticulum and in the Golgi complex 330 CHAPTER 10 Regulatory Strategies 285 CHAPTER 11 Carbohydrates 315

Contents xxi Specific enzymes are responsible for oligosaccharide assembly 331 Blood groups are based on protein glycosylation patterns 331 Errors in glycosylation can result in pathological conditions 332 Oligosaccharides can be “sequenced” 332 11.4 Lectins Are Specific Carbohydrate-Binding Proteins 333 Lectins promote interactions between cells 334 Lectins are organized into different classes 334 Influenza virus binds to sialic acid residues 335 CHAPTER 12 Lipids and Cell Membranes 341 Many common features underlie the diversity of biological membranes 342 12.1 Fatty Acids Are Key Constituents of Lipids 342 Fatty acid names are based on their parent hydrocarbons 342 Fatty acids vary in chain length and degree of unsaturation 343 12.2 There Are Three Common Types of Membrane Lipids 344 Phospholipids are the major class of membrane lipids 344 Membrane lipids can include carbohydrate moieties 345 Cholesterol is a lipid based on a steroid nucleus 346 Archaeal membranes are built from ether lipids with branched chains 346 A membrane lipid is an amphipathic molecule containing a hydrophilic and a hydrophobic moiety 347 12.3 Phospholipids and Glycolipids Readily Form Bimolecular Sheets in Aqueous Media 348 Lipid vesicles can be formed from phospholipids 348 Lipid bilayers are highly impermeable to ions and most polar molecules 349 12.4 Proteins Carry Out Most Membrane Processes 350 Proteins associate with the lipid bilayer in a variety of ways 351 Proteins interact with membranes in a variety of ways 351 Some proteins associate with membranes through covalently attached hydrophobic groups 354 Transmembrane helices can be accurately predicted from amino acid sequences 354 12.5 Lipids and Many Membrane Proteins Diffuse Rapidly in the Plane of the Membrane 356 The fluid mosaic model allows lateral movement but not rotation through the membrane 357 Membrane fluidity is controlled by fatty acid composition and cholesterol content 357 Lipid rafts are highly dynamic complexes formed between cholesterol and specific lipids 358 All biological membranes are asymmetric 358 12.6 Eukaryotic Cells Contain Compartments Bounded by Internal Membranes 359 CHAPTER 13 Membrane Channels and Pumps 367 The expression of transporters largely defines the metabolic activities of a given cell type 368 13.1 The Transport of Molecules Across a Membrane May Be Active or Passive 368 Many molecules require protein transporters to cross membranes 368 Free energy stored in concentration gradients can be quantified 369 13.2 Two Families of Membrane Proteins Use ATP Hydrolysis to Pump Ions and Molecules Across Membranes 370 P-type ATPases couple phosphorylation and conformational changes to pump calcium ions across membranes 370 Digitalis specifically inhibits the Na1–K1 pump by blocking its dephosphorylation 373 P-type ATPases are evolutionarily conserved and play a wide range of roles 374 Multidrug resistance highlights a family of membrane pumps with ATP-binding cassette domains 374 13.3 Lactose Permease Is an Archetype of Secondary Transporters That Use One Concentration Gradient to Power the Formation of Another 376 13.4 Specific Channels Can Rapidly Transport Ions Across Membranes 378 Action potentials are mediated by transient changes in Na1 and K1 permeability 378 Patch-clamp conductance measurements reveal the activities of single channels 379 The structure of a potassium ion channel is an archetype for many ion-channel structures 379 The structure of the potassium ion channel reveals the basis of ion specificity 380 The structure of the potassium ion channel explains its rapid rate of transport 383 Voltage gating requires substantial conformational changes in specific ion-channel domains 383 A channel can be inactivated by occlusion of the pore: the ball-and-chain model 384 The acetylcholine receptor is an archetype for ligand-gated ion channels 385 Action potentials integrate the activities of several ion channels working in concert 387 Disruption of ion channels by mutations or chemicals can be potentially life-threatening 388 13.5 Gap Junctions Allow Ions and Small Molecules to Flow Between Communicating Cells 389 13.6 Specific Channels Increase the Permeability of Some Membranes to Water 390 CHAPTER 12 Lipids and Cell Membranes 341 CHAPTER 13 Membrane Channels and Pumps 367

xxii Contents CHAPTER 14 Signal-Transduction Pathways 397 Signal transduction depends on molecular circuits 398 14.1 Heterotrimeric G Proteins Transmit Signals and Reset Themselves 399 Ligand binding to 7TM receptors leads to the activation of heterotrimeric G proteins 400 Activated G proteins transmit signals by binding to other proteins 402 Cyclic AMP stimulates the phosphorylation of many target proteins by activating protein kinase A 403 G proteins spontaneously reset themselves through GTP hydrolysis 403 Some 7TM receptors activate the phosphoinositide cascade 404 Calcium ion is a widely used second messenger 405 Calcium ion often activates the regulatory protein calmodulin 407 14.2 Insulin Signaling: Phosphorylation Cascades Are Central to Many Signal-Transduction Processes 407 The insulin receptor is a dimer that closes around a bound insulin molecule 408 Insulin binding results in the cross-phosphorylation and activation of the insulin receptor 408 The activated insulin-receptor kinase initiates a kinase cascade 409 Insulin signaling is terminated by the action of phosphatases 411 14.3 EGF Signaling: Signal-Transduction Pathways Are Poised to Respond 411 EGF binding results in the dimerization of the EGF receptor 411 The EGF receptor undergoes phosphorylation of its carboxyl-terminal tail 413 EGF signaling leads to the activation of Ras, a small G protein 413 Activated Ras initiates a protein kinase cascade 414 EGF signaling is terminated by protein phosphatases and the intrinsic GTPase activity of Ras 414 14.4 Many Elements Recur with Variation in Different Signal-Transduction Pathways 415 14.5 Defects in Signal-Transduction Pathways Can Lead to Cancer and Other Diseases 416 Monoclonal antibodies can be used to inhibit signaltransduction pathways activated in tumors 416 Protein kinase inhibitors can be effective anticancer drugs 417 Cholera and whooping cough are the result of altered G-protein activity 417 Part II TRANSDUCING AND STORING ENERGY CHAPTER 15 Metabolism: Basic Concepts and Design 423 15.1 Metabolism Is Composed of Many Coupled, Interconnecting Reactions 424 Metabolism consists of energy-yielding and energyrequiring reactions 424 A thermodynamically unfavorable reaction can be driven by a favorable reaction 425 15.2 ATP Is the Universal Currency of Free Energy in Biological Systems 426 ATP hydrolysis is exergonic 426 ATP hydrolysis drives metabolism by shifting the equilibrium of coupled reactions 427 The high phosphoryl potential of ATP results from structural differences between ATP and its hydrolysis products 429 Phosphoryl-transfer potential is an important form of cellular energy transformation 430 15.3 The Oxidation of Carbon Fuels Is an Important Source of Cellular Energy 432 Compounds with high phosphoryl-transfer potential can couple carbon oxidation to ATP synthesis 432 Ion gradients across membranes provide an important form of cellular energy that can be coupled to ATP synthesis 433 Phosphates play a prominent role in biochemical processes 434 Energy from foodstuffs is extracted in three stages 434 15.4 Metabolic Pathways Contain Many Recurring Motifs 435 Activated carriers exemplify the modular design and economy of metabolism 435 Many activated carriers are derived from vitamins 438 Key reactions are reiterated throughout metabolism 440 Metabolic processes are regulated in three principal ways 442 Aspects of metabolism may have evolved from an RNA world 444 CHAPTER 16 Glycolysis and Gluconeogenesis 449 Glucose is generated from dietary carbohydrates 450 Glucose is an important fuel for most organisms 451 16.1 Glycolysis Is an Energy-Conversion Pathway in Many Organisms 451 Hexokinase traps glucose in the cell and begins glycolysis 451 Fructose 1,6-bisphosphate is generated from glucose 6-phosphate 453 The six-carbon sugar is cleaved into two three-carbon fragments 454 Mechanism: Triose phosphate isomerase salvages a three-carbon fragment 455 The oxidation of an aldehyde to an acid powers the formation of a compound with high phosphoryl-transfer potential 457 Mechanism: Phosphorylation is coupled to the oxidation of glyceraldehyde 3-phosphate by a thioester intermediate 458 ATP is formed by phosphoryl transfer from 1,3-bisphosphoglycerate 459 Additional ATP is generated with the formation of pyruvate 460 Two ATP molecules are formed in the conversion of glucose into pyruvate 461 CHAPTER 14 Si l T d i P h Signal-Transduction Pathways 397 CHAPTER 15 Metabolism: Basic Concepts and Design 423 CHAPTER 16 Glycolysis and Gluconeogenesis 449