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Titel:	Biochemistry
Von:	Jeremy M. Berg ; John L. Tymoczko ; Lubert Stryer
Person:	Berg, Jeremy M. 1958- Verfasser aut Tymoczko, John L. Stryer, Lubert 1948-2019 1938-2024
Hauptverfassende:	Berg, Jeremy M. 1958- (VerfasserIn), Tymoczko, John L. 1948-2019 (VerfasserIn), Stryer, Lubert 1938-2024 (VerfasserIn)
Format:	Buch
Sprache:	Englisch
Veröffentlicht:	New York Freeman [u.a.] 2012
Ausgabe:	Internat. 7. ed.
Notation:	WD 4000 WD 4010
Schlagwörter:	Biochemie Physiologische Chemie Einführung Lehrbuch
Medienzugang:	http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=021174175&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
Beschreibung:	Hier auch später erschienene, unveränderte Nachdrucke. - Erg. bildet: Student companion to accompany Biochemistry
Umfang:	Getr. Zählung zahlr. Ill., graph. Darst.
ISBN:	9781429276351 1429276355

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adam_text	BRIEF CONTENTS Part I THE MOLECULAR DESIGN OF LIFE 1 Biochemistry: An Evolving Science 1 2 Protein Composition and Structure 25 3 Exploring Proteins and Proteomes 67 4 DNA RNA and the Flow of Genetic Information 113 5 Exploring Genes and Genomes 145 6 Exploring Evolution and Bioinformatics 181 7 Hemoglobin: Portrait of a Protein in Action 203 8 Enzymes: Basic Concepts and Kinetics 227 9 Catalytic Strategies 261 10 Regulatory Strategies 299 11 Carbohydrates 329 12 Lipids and Cell Membranes 357 13 Membrane Channels and Pumps 383 14 Signal-Transduction Pathways 415 Part I! TRANSDUCING AND STORING ENERGY 15 Metabolism: Basic Concepts and Design 443 16 Glycolysis and Gluconeogenesis 469 17 The Citric Acid Cycle 515 18 Oxidative Phosphorylation 543 19 The Light Reactions of Photosynthesis 585 20 The Calvin Cycle and the Pentose Phosphate Pathway 609 21 Glycogen Metabolism 637 22 Fatty Acid Metabolism 663 23 Protein Turnover and Amino Acid Catabolism 697 Part I» SYNTHESIZING THE MOLECULES OF LIFE 24 The Biosynthesis of Amino Acids 729 25 Nucleotide Biosynthesis 761 26 The Biosynthesis of Membrane Lipids and Steroids 787 27 The Integration of Metabolism 821 28 DNA Replication, Repair, and Recombination 849 29 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 CHANGES 33 Sensory Systems 995 34 The Immune System 1017 35 Molecular Motors 1049 36 Drug Development 1073 CONTENTS Preface Part I THE MOLECULAR DESIGN OF LIFE Chapter l Biochemistry: An Evolving Science 1.1 Biochemical Unity Underlies Biological Diversity 1.2 DNA Illustrates the Interplay Between Form and Function DNA is constructed from four building blocks Two single strands of DNA combine to form a double helix DMA 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 The 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 Is Transforming Biochemistry and Medicine The sequencing of the human genome is a landmark in human history Genome sequences encode proteins and patterns of expression Individuality depends on the interplay between genes and environment APPENDIX: Visualizing Molecular Structures I: Small Molecules 4 4 6 6 10 11 12 1Л 14 15 17 17 18 19 21 Chapter 2 Protein Composition and Structure 25 2.1 Proteins Are Built from a Repertoire of 20 Amino Acids 27 2.2 Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains 33 Proteins have unique amino acid sequences specified by genes 35 Polypeptide chains are flexible yet conformationally restricted 36 xvi Contents 2.3 Secondary Structure: Polypeptide Chains Can Fold into Regular Structures Such As the Alpha Helix, the Beta Sheet, and Turns and Loops The alpha helix is a coiled structure stabilized by intrachain hydrogen bonds Beta sheets are stabilized by hydrogen bonding between polypeptide strands Polypeptide chains can change direction by making reverse turns and loops Fibrous proteins provide structural support for cells and tissues 2.4 Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures with Nonpolar Cores 2.5 Quaternary Structure: Polypeptide Chains Can Assemble into Multisubunit Structures 2.6 The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure Amino acids have different propensities for forming alpha helices, beta sheets, and beta turns Protein folding is a highly cooperative process Proteins fold by progressive stabilization of intermediates rather than by random search Prediction of three-dimensional structure from sequence remains a great challenge Some proteins are inherently unstructured and can exist in multiple conformations Protein misfolding and aggregation are associated with some neurological diseases Protein modification and cleavage confer new capabilities APPENDIX: Visualizing Molecular Structures II: Proteins 38 38 40 42 43 45 48 49 50 52 52 54 54 55 57 60 Chapter 3 Exploring Proteins and Proteomes 67 The proteome is the functional representation of the genome 68 3.1 The Purification of Proteins Is an Essential First Step in Understanding Their Function 68 The assay: How do we recognize the protein that we are looking for? 69 Proteins must be released from the cell to be purified 69 Proteins can be purified according to solubility, size, charge, and binding affinity 70 Proteins can be separated by gel electrophoresis and displayed 73 A protein purification scheme can be quantitatively evaluated 77 Ultracentrifugation is valuable for separating biomolecules and determining their masses 78 Protein purification can be made easier with the use of recombinam DX A tedhnoloçv 80 3.2 Amino Acid Sequences of Proteins Can Be Determined Experimentally Peptide sequences can be determined by automated Edman degradation Proteins can be specifically cleaved into small peptides to facilitate analysis Genomic and proteomic methods are complementary 3.3 Immunology Provides Important Techniques with Which to Investigate Proteins Antibodies to specific proteins can be generated Monoclonal antibodies with virtually any desired specificity can be readily prepared Proteins can be detected and quantified by using an enzyme-linked immunosorbent assay Western blotting permits the detection of proteins separated by gel electrophoresis Fluorescent markers make the visualization of proteins in the cell possible 3.4 Mass Spectrometry Is a Powerful Technique for the Identification of Peptides and Proteins The mass of a protein can be precisely determined by mass spectrometry Peptides can be sequenced by mass spectrometry Individual proteins can be identified by mass spectrometry 3.5 Peptides Can Be Synthesized by Automated Solid-Phase Methods 3.6 Three-Dimensional Protein Structure Can Be Determined by X-ray Crystallography and NMR Spectroscopy X-ray crystallography reveals three-dimensional structure in atomic detail Nuclear magnetic resonance spectroscopy can reveal the structures of proteins in solution 81 82 84 86 86 86 Chapter 4 DNA, RNA, and the Flow of Information 90 91 92 93 93 95 96 97 100 100 103 113 4.1 A Nucleic Acid Consists of Four Kinds of Bases Linked to a Sugar-Phosphate Backbone 114 RNA and DNA differ in the sugar component and one of the bases 114 Nucleotides are the monomeric units of nucleic acids 115 DNA molecules are very long 117 4.2 A Pair of Nucleic Acid Chains with Complementary Sequences Can Form a Double-Helical Structure 117 The double helix is stabilized by hydrogen bonds and van der Waals interactions 117 DNA can assume a variety of structural forms 119 Z-DNA is a left-handed double helix in which backbone phosphates zigzag 120 Contents xvii Some DNA molecules are circular and supercoiled Single-stranded nucleic acids can adopt elaborate structures 4.3 The Double Helix Facilitates the Accurate Transmission of Hereditary Information Differences in DNA density established the validity of the semiconservative-replication hypothesis The double helix can be reversibly melted 4.4 DNA Is Replicated by Polymerases That Take Instructions from Templates DNA polymerase catalyzes phosphodiester-bridge formation The genes of some viruses are made of RNA 4.5 Gene Expression Is the Transformation of DNA Information into Functional Molecules Several kinds of RNA play key roles in gene expression All cellular RNA is synthesized by RNA polymerases RNA polymerases take instructions from DNA templates Transcription begins near promoter sites and ends at terminator sites Transfer RNAs are the adaptor molecules in protein synthesis 4.6 Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point Major features of the genetic code Messenger RNA contains start and stop signals for protein synthesis The genetic code is nearly universal 4.7 Most Eukaryotic Genes Are Mosaics of Introns and Exons RNA processing generates mature RNA Many exons encode protein domains 121 121 122 123 124 125 125 126 127 127 128 130 130 131 132 1 ЗЛ 134 135 135 136 137 Chapter 5 Exploring Genes and Genomes 145 5.1 The Exploration of Genes Relies on Key Tools 146 Restriction enzymes split DNA into specific fragments 147 Restriction fragments can be separated by gel electrophoresis and visualized 147 DNA can be sequenced by controlled termination of replication 149 DNA probes and genes can be synthesized by automated solid-phase methods 150 Selected DNA sequences can be greatly amplified by the polymerase chain reaction 151 PCR is a powerful technique in medical diagnostics. forensics, and studies of molecuîar évolution 152 The tools for recombinant DNA technology have been used to identify disease-causing mutations 153 5.2 Recombinant DNA Technology Has Revolutionized All Aspects of Biology Restriction enzymes and DNA ligase are key tools in forming recombinant DNA molecules Plasmids and lambda phage are choice vectors for DNA cloning in bacteria Bacterial and yeast artificial chromosomes Specific genes can be cloned from digests of genomicDNA Complementary DNA prepared from mRNA can be expressed in host cells Proteins with new functions can be created through directed changes in DNA Recombinant methods enable the exploration of the functional effects of disease-causing mutations 5.3 Complete Genomes Have Been Sequenced and Analyzed The genomes of organisms ranging from bacteria to multicellular eukaryotes have been sequenced The sequencing of the human genome has been finished Next-generation sequencing methods enable the rapid determination of a whole genome sequence Comparative genomics has become a powerful research tool 5.4 Eukaryotic Genes Can Be Quantitated and Manipulated with Considerable Precision Gene-expression levels can be comprehensively examined New genes inserted into eukaryotic cells can be efficiently expressed Transgenic animals harbor and express genes introduced into their germ lines Gene disruption provides clues to gene function RNA interference provides an additional tool for disrupting gene expression Tumor-inducing plasmids can be used to introduce new genes into plant cells Human gene therapy holds great promise for medicine Chapter 6 Exploring Evolution and Bioinformatics 6.2 Statistical Analysis of Sequence Alignments Can Detect Homoiogy The statistical significance of alignments can be estimated by shuffling Distant evolutionär} relationships can be detected through the use of substitution matrices Databases can be searched to identify homologous sequences 154 154 155 157 157 160 162 163 163 164 165 166 166 167 167 169 170 170 171 172 173 181 6.1 Homologs Are Descended from a Common Ancestor 182 Î83 185 186 189 xvi і і Contents 6.3 Examination of Three-Dimensional Structure Enhances Our Understanding of Evolutionary Relationships 190 Tertiary structure is more conserved than primary structure 191 Knowledge of three-dimensional structures can aid in the evaluation of sequence alignments 192 Repeated motifs can be detected by aligning sequences with themselves 192 Convergent evolution illustrates common solutions to biochemical challenges 193 Comparison of RNA sequences can be a source of insight into RNA secondary structures 194 6.4 Evolutionary Trees Can Be Constructed on the Basis of Sequence Information 195 6.5 Modern Techniques Make the Experimental Exploration of Evolution Possible 196 Ancient DNA can sometimes be amplified and sequenced 196 Molecular evolution can be examined experimentally 197 Additional globins are encoded in the human genome 219 APPENDIX: Binding Models Can Be Formulated in Quantitative Terms: the Hill Plot and the Concerted Model 221 Chapter 7 Hemoglobin: Portrait of a Protein in Action 203 7.1 Myoglobin and Hemoglobin Bind Oxygen at Iron Atoms in Heme 204 Changes in heme electronic structure upon oxygen binding are the basis for functional imaging studies 205 The structure of myoglobin prevents the release of reactive oxygen species 206 Human hemoglobin is an assembly of four myoglobin-like subunits 207 7.2 Hemoglobin Binds Oxygen Cooperatively 207 Oxygen binding markedly changes the quaternary structure of hemoglobin 209 Hemoglobin cooperativity can be potentially explained by several models 210 Structural changes at the heme groups are transmitted to the otjßt- αιβι interface 212 2,3-Bisphosphoglycerate in red cells is crucial in determining the oxygen affinity of hemoglobin 212 Carbon monoxide can disrupt oxygen transport by hemoglobin 213 7.3 Hydrogen Ions and Carbon Dioxide Promote the Release of Oxygen: The Bohr Effect 214 7.4 Mutations in Genes Encoding Hemoglobin Subunits Can Result in Disease 216 Sickle-cell anemia results from the aggregation of mutated deoxyhemoglobin molecules 217 Thalassemia is caused by an imbalanced production of hemoglobin chains 218 The accumulation of free alpha-hemoglobin chains is prevented 219 Chapter 8 Enzymes: Basic Concepts and Kinetics 227 8.1 Enzymes Are Powerful and Highly Specific Catalysts 228 Many enzymes require cofactors for activity 229 Enzymes can transform energy from one form into another 229 8.2 Free Energy Is a Useful Thermodynamic Function for Understanding Enzymes 230 The free-energy change provides information about the spontaneity but not the rate of a reaction 230 The standard free-energy change of a reaction is related to the equilibrium constant 231 Enzymes alter only the reaction rate and not the reaction equilibrium 232 8.3 Enzymes Accelerate Reactions by Facilitating the Formation of the Transition State 233 The formation of an enzyme—substrate complex is the first step in enzymatic catalysis 234 The active sites of enzymes have some common features 235 The binding energy between enzyme and substrate is important for catalysis 237 8.4 The Michaelis-Menten Equation Describes the Kinetic Properties of Many Enzymes 237 Kinetics is the study of reaction rates 237 The steady-state assumption facilitates a description of enzyme kinetics 238 Variations in Км can have physiological consequences 240 Km and Vmax values can be determined by several means 240 Км and Vmax values are important enzyme characteristics 241 ^cat/^M is a measure of catalytic efficiency 242 Most biochemical reactions include multiple substrates 243 Allosteric enzymes do not obey Michaelis-Menten kinetics 245 8.5 Enzymes Can Be Inhibited by Specific Molecules 246 Reversible inhibitors are kinetically distinguishable 247 Irreversible inhibitors can be used to map the active site 249 Transition-state analogs are potent inhibitors of enzymes 251 Catalytic antibodies demonstrate the importance of selective binding of the transition state to enzymatic activity 251 Penicillin irreversibly inactivates a key enzyme in bacterial cell-wall synthesis 252 Contents χ ι χ 8.6 Enzymes Can Be Studied One Molecule at a Time APPENDIX: Enzymes are Classified on the Basis of the Types of Reactions That They Catalyze 254 256 The altered conformation of myosin persists for a substantial period of time 290 Myosins are a family of enzymes containing P-loop structures 291 Chapter 9 Catalytic Strategies A few basic catalytic principles are used by many enzymes 262 9.1 Proteases Facilitate a Fundamentally Difficult Reaction 263 Chymotrypsin possesses a highly reactive serine residue 263 Chymotrypsin action proceeds in two steps linked by a covalently bound intermediate 264 Serine is part of a catalytic triad that also includes histidine and aspartate 265 Catalytic triads are found in other hydrolytic enzymes 268 The catalytic triad has been dissected by site-directed mutagenesis 270 Cysteine, aspartyl, and metalloproteases are other major classes of peptide-cleaving enzymes 271 Protease inhibitors are important drugs 272 9.2 Carbonic Anhydrases Make a Fast Reaction Faster 274 Carbonic anhydrase contains a bound zinc ion essential for catalytic activity 275 Catalysis entails zinc activation of a water molecule 276 A proton shuttle facilitates rapid regeneration of the active form of the enzyme 277 Convergent evolution has generated zinc-based active sites in different carbonic anhydrases 279 9.3 Restriction Enzymes Catalyze Highly Specific DNA-Cleavage Reactions 279 Cleavage is by in-line displacement of 3 -oxygen from phosphorus by magnesium-activated water 280 Restriction enzymes require magnesium for catalytic activity 282 The complete catalytic apparatus is assembled only within complexes of cognate DNA molecules, ensuring specificity 283 Host-cell DNA is protected by the addition of methyl groups to specific bases 285 Type II restriction enzymes have a catalytic core in common and are probably related by horizontal gene transfer 286 9.4 Myosins Harness Changes in Enzyme Conformation to Couple ATP Hydrolysis to Mechanical Work 287 ATP hydrolysis proceeds by the attack of water on the gamma-phosphoryl group 287 Formation of the transition state for ATP hydrolysis is associated with a substantial conformational change 288 Chapter 10 Regulatory Strategies 299 261 ЮЛ Aspartate Transcarbamoylase Is Allosterically Inhibited by the End Product of Its Pathway Allosterically regulated enzymes do not follow Michaelis-Menten kinetics ATCase consists of separable catalytic and regulatory subunits Allosteric interactions in ATCase are mediated by large changes in quaternary structure Allosteric regulators modulate the Τ -to- R equilibrium 10.2 Isozymes Provide a Means of Regulation Specific to Distinct Tissues and Developmental Stages 10.3 Covalent Modification Is a Means of Regulating Enzyme Activity Kinases and phosphatases control the extent of protein phosphorylation Phosphorylation is a highly effective means of regulating the activities of target proteins Cyclic AMP activates protein kinase A by altering the quaternary structure ATP and the target protein bind to a deep cleft in the catalytic subunit of protein kinase A 10.4 Many Enzymes Are Activated by Specific Proteolytic Cleavage Chymotrypsinogen is activated by specific cleavage of a single peptide bond Proteolytic activation of chymotrypsinogen leads to the formation of a substrate-binding site The generation of trypsin from trypsinogen leads to the activation of other zymogens Some proteolytic enzymes have specific inhibitors Blood clotting is accomplished by a cascade of zymogen activations Fibrinogen is converted by thrombin into a fibrin clot Prothrombin is readied for activation by a vitamin K-dependent modification Hemophilia revealed an early step in clotting The clotting process must be precisely regulated Chapter 11 Carbohydrates 11.1 Monosaccharides Are the Simplest Carbohydrates Many common sugars exist in cyclic forms Pyranose and furanose rings can assume different conformations 300 301 301 302 305 306 307 308 310 311 312 312 313 314 315 316 317 318 320 321 321 329 330 332 334 xx Contents Glucose is a reducing sugar Monosaccharides are joined to alcohols and amines through glycosidic bonds Phosphorylated sugars are key intermediates in energy generation and biosyntheses 11.2 Monosaccharides Are Linked to Form Complex Carbohydrates Sucrose, lactose, and maltose are the common disaccharides Glycogen and starch are storage forms of glucose Cellulose, a structural component of plants, is made of chains of glucose 11.3 Carbohydrates Can Be Linked to Proteins to Form Glycoproteins Carbohydrates can be linked to proteins through asparagine (N-linked) or through serine or threonine (O-linked) residues The glycoprotein erythropoietin is a vital hormone Proteoglycans, composed of polysaccharides and protein, have important structural roles Proteoglycans are important components of cartilage Mucins are glycoprotein components of mucus Protein glycosylation takes place in the lumen of the endoplasmic reticulum and in the Golgi complex Specific enzymes are responsible for oligosaccharide assembly Blood groups are based on protein glycosylation patterns Errors in glycosylation can result in pathological conditions Oligosaccharides can be sequenced 11.4 Lectins Are Specific Carbohydrate-Binding Proteins Lectins promote interactions between cells Lectins are organized into different classes Influenza virus binds to sialic acid residues Chapter 12 Lipids and Cell Membranes 335 336 336 337 337 338 338 339 340 340 341 342 343 343 345 345 346 346 347 348 348 349 357 Many common features underlie the diversity of biological membranes 12.1 Fatty Acids Are Key Constituents of Lipids Fatty acid names are based on their parent hydrocarbons Fatty acids vary in chain length and degree of unsaturation 12.2 There Are Three Common Types of Membrane Lipids Phospholipids are the major class of membrane lipids Membrane lipids can include carbohydrate moieties Cholesterol is a lipid based on a steroid nucleus Archaeal membranes are built from ether lipids with branched chains 358 358 358 359 360 360 361 362 362 A membrane lipid is an amphipathic molecule containing a hydrophilic and a hydrophobic moiety 12.3 Phospholipids and Glycolipids Readily Form Bimolecular Sheets in Aqueous Media Lipid vesicles can be formed from phospholipids Lipid bilayers are highly impermeable to ions and most polar molecules 12.4 Proteins Carry Out Most Membrane Processes Proteins associate with the lipid bilayer in a variety of ways Proteins interact with membranes in a variety of ways Some proteins associate with membranes through covalently attached hydrophobic groups Transmembrane helices can be accurately predicted from amino acid sequences 12.5 Lipids and Many Membrane Proteins Diffuse Rapidly in the Plane of the Membrane The fluid mosaic model allows lateral movement but not rotation through the membrane Membrane fluidity is controlled by fatty acid composition and cholesterol content Lipid rafts are highly dynamic complexes formed between cholesterol and specific lipids All biological membranes are asymmetric 12.6 Eukaryotic Cells Contain Compartments Bounded by Internal Membranes 363 364 365 366 367 367 368 371 371 373 374 374 375 375 376 Chapter 13 Membrane Channels and Pumps 383 The expression of transporters largely defines the metabolic activities of a given cell type 384 13.1 The Transport of Molecules Across a Membrane May Be Active or Passive 384 Many molecules require protein transporters to cross membranes 384 Free energy stored in concentration gradients can be quantified 385 13.2 Two Families of Membrane Proteins Use ATP Hydrolysis to Pump Ions and Molecules Across Membranes 386 P-type ATPases couple phosphorylation and conformational changes to pump calcium ions across membranes 386 Digitalis specifically inhibits the Na+-K+ pump by blocking its dephosphorylation 389 P-type ATPases are evolutionarily conserved and play a wide range of roles 390 Multidrug resistance highlights a family of membrane pumps with ATP-binding cassette domains 390 Contents xxi 13.3 Lactose Permease Is an Archetype of Secondary Transporters That Use One Concentration Gradient to Power the Formation of Another 392 13.4 Specific Channels Can Rapidly Transport Ions Across Membranes 394 Action potentials are mediated by transient changes in Na+ and K+ permeability 394 Patch-clamp conductance measurements reveal the activities of single channels 395 The structure of a potassium ion channel is an archetype for many ion-channel structures 395 The structure of the potassium ion channel reveals the basis of ion specificity 396 The structure of the potassium ion channel explains its rapid rate of transport 399 Voltage gating requires substantial conformational changes in specific ion-channel domains 399 A channel can be activated by occlusion of the pore: the ball-and-chain model 400 The acetylcholine receptor is an archetype for ligand-gated ion channels 401 Action potentials integrate the activities of several ion channels working in concert 402 Disruption of ion channels by mutations or chemicals can be potentially life threatening 404 13.5 Gap Junctions Allow Ions and Small Molecules to Flow Between Communicating Cells 405 13.6 Specific Channels Increase the Permeability of Some Membranes to Water 406 Insulin binding results in the cross-phosphorylation and activation of the insulin receptor 426 The activated insulin-receptor kinase initiates a kinase cascade 426 Insulin signaling is terminated by the action of phosphatases 429 14.3 EGF Signaling: Signal-Transduction Pathways Are Poised to Respond 429 EGF binding results in the dimerization of the EGF receptor 429 The EGF receptor undergoes phosphorylation of its carboxyl-terminal tail 431 EGF signaling leads to the activation of Ras, a small G protein 431 Activated Ras initiates a protein kinase cascade 432 EGF signaling is terminated by protein phosphatases and the intrinsic GTPase activity of Ras 432 14.4 Many Elements Recur with Variation in Different Signal-Transduction Pathways 433 14.5 Defects in Signal-Transduction Pathways Can Lead to Cancer and Other Diseases 434 Monoclonal antibodies can be used to inhibit signal-transduction pathways activated in tumors 434 Protein kinase inhibitors can be effective anticancer drugs 435 Cholera and whooping cough are due to altered G -protein activity 435 Chapter 14 Signal-Transduction Pathways 415 Signal transduction depends on molecular circuits 416 14.1 Heterotrimeric G Proteins Transmit Signals and Reset Themselves 417 Ligand binding to 7TM receptors leads to the activation of heterotrimeric G proteins 419 Activated G proteins transmit signals by binding to other proteins 420 Cyclic AMP stimulates the phosphorylation of many target proteins by activating protein kinase A 420 G proteins spontaneously reset themselves through GTP hydrolysis 421 Some 7T f receptors activate the phosphoinositide cascade 422 Calcium ion is a widely used second messenger 423 Calcium ion often activates the regulatory protein calmodulin 424 14.2 Insulin Signaling: Phosphorylation Cascades Are Central to Many Signal-Transduction Processes 425 The insulin receptor is a dimer that closes around a bound insulin molecule 426 Part И TRANSDUCING AND STORING ENERGY Chapter 15 Metabolism: Basic Concepts and Design 443 15.1 Metabolism Is Composed of Many Coupled, Interconnecting Reactions 444 Metabolism consists of energy-yielding and energy-requiring reactions 444 A thermodynamicaily unfavorable reaction can be driven by a favorable reaction 445 15.2 ATP is the Universal Currency of Free Energy in Biological Systems 446 ATP hydrolysis is exergonic 446 ATP hydrolysis drives metabolism by shifting the equilibrium of coupled reactions 447 The high phosphoryl potential of ATP results from structural differences between ATP and its hydrolysis products 449 Phosphoryl-transfer potential is an important form of cellular energy transformation 450 xxii Contents 15.3 The Oxidation of Carbon Fuels Is an Important Source of Cellular Energy Compounds with high phosphoryl-transfer potential can couple carbon oxidation to ATP synthesis Ion gradients across membranes provide an important form of cellular energy that can be coupled to ATP synthesis Energy from foodstuffs is extracted in three stages 15.4 Metabolic Pathways Contain Many Recurring Motifs Activated carriers exemplify the modular design and economy of metabolism Many activated carriers are derived from vitamins Key reactions are reiterated throughout metabolism Metabolic processes are regulated in three principal ways Aspects of metabolism may have evolved from an RNA world 451 452 453 453 454 454 457 459 461 463 Chapter 16 Glycolysis and Gluconeogenesis 469 Glucose is generated from dietary carbohydrates 470 Glucose is an important fuel for most organisms 471 Î6.Ï Glycolysis Is an Energy-Conversion Pathway in Many Organisms 471 Hcxokinase traps glucose in the cell and begins glycolysis 471 Fructose 1,6-bisphosphate is generated from glucose 6-phosphate 473 The six-carbon sugar is cleaved into two three-carbon fragments 474 Mechanism: Triose phosphate isomerase salvages a three-carbon fragment 475 The oxidation of an aldehyde to an acid powers the formation of a compound with high phosphoryl-transfer potential 476 Mechanism: Phosphorylation is coupled to the oxidation of glyceraldehyde 3-phosphate by a thioester intermediate 478 ATP is formed by phosphoryl transfer from l^-bisphosphoglycerate 479 Additional ATP is generated with the formation of pyruvate 480 Two ATP molecules are formed in the conversion of glucose into pyruvate 481 NAD* is regenerated from the metabolism of pyruvate 482 Fermentations provide usable energy in the absence ofoxygen 484 The binding site for NAD* is similar in many dehydrogenases 485 Fructose and galactose are converted into glycolytic intermediates 485 Many adults are intolerant of milk because they are deficient in lactase Galactose is highly toxic if the transferase is missing 16.2 The Glycolytic Pathway Is Tightly Controlled Glycolysis in muscle is regulated to meet the need for ATP The regulation of glycolysis in the liver illustrates the biochemical versatility of the liver A family of transporters enables glucose to enter and leave animal cells Cancer and exercise training affect glycolysis in a similar fashion 16.3 Glucose Can Be Synthesized from Noncarbohydrate Precursors Gluconeogenesis is not a reversal of glycolysis The conversion of pyruvate into phosphoenolpyruvate begins with the formation of oxaloacetate Oxaloacetate is shuttled into the cytoplasm and converted into phosphoenolpyruvate The conversion of fructose 1,6-bisphosphate into fructose 6-phosphate and orthophosphate is an irreversible step The generation of free glucose is an important control point Six high-transfer-potential phosphoryl groups are spent in synthesizing glucose from pyruvate 16.4 Gluconeogenesis and Glycolysis Are Reciprocally Regulated Energy charge determines whether glycolysis or gluconeogenesis will be most active The balance between glycolysis and gluconeogenesis in the liver is sensitive to blood-glucose concentration Substrate cycles amplify metabolic signals and produce heat Lactate and alaninę formed by contracting muscle are used by other organs Glycolysis and gluconeogenesis are evolutionarily intertwined Chapter 17 The Citric Acid Cycle 487 488 488 489 490 493 494 495 497 498 499 500 500 501 502 502 503 505 505 507 515 The citric acid cycle harvests high-energy electrons 516 17.1 Pyruvate Dehydrogenase Links Glycolysis to the Citric Acid Cycle 517 Mechanism: The synthesis of acetyl coenzyme a from pyruvate requires three enzymes and five coenzymes 518 Flexible linkages allow lipoamide to move between different active sites 520 17.2 The Citric Acid Cycle Oxidizes Two-Carbon Units 521 Citrate synthase forms citrate from oxaloacetate and acetyl coenzyme A 522 Contents xxiii Mechanism: The mechanism of citrate synthase prevents undesirable reactions 522 Citrate is isomerized into isocitrate 524 Isocitrate is oxidized and decarboxylated to alpha-ketoglutarate 524 Succinyl coenzyme A is formed by the oxidative decarboxylation of alpha-ketoglutarate 525 A compound with high phosphoryl-transfer potential is generated from succinyl coenzyme A 525 Mechanism: Succinyl coenzyme A synthetase transforms types of biochemical energy 526 Oxaloacetate is regenerated by the oxidation of succinate 527 The citric acid cycle produces high-transfer-potential electrons, ATP, and CCb 528 17.3 Entry to the Citric Acid Cycle and Metabolism Through It Are Controlled 530 The pyruvate dehydrogenase complex is regulated allosterically and by reversible phosphoryiation 531 The citric acid cycle is controlled at several points 532 Defects in the citric acid cycle contribute to the development of cancer 533 Τ 7.4 The Citric Acid Cycle Is a Source of Biosynthetic Precursors 534 The citric acid cycle must be capable of being rapidly replenished 534 The disruption of pyruvate metabolism is the cause of beriberi and poisoning by mercury and arsenic 535 The citric acid cycle may have evolved from preexisting pathways 536 17.5 The Glyoxylate Cycle Enables Plants and Bacteria to Grow on Acetate 536 543 Chapter 18 Oxidative Phosphoryiation 18.1 Eukaryotic Oxidative Phosphoryiation Takes Place in Mitochondria 544 Mitochondria are bounded by a double membrane 544 Mitochondria are the result of an endosymbiotic event 545 18.2 Oxidative Phosphoryiation Depends on Electron Transfer 546 The electron-transfer potential of an electron is measured as redox potential 546 A 1.14-volt potential difference between XADH and molecular oxygen drives electron transport through the chain and favors the formation of a proton gradient 548 18.3 The Respiratory Chain Consists of Four Complexes: Three Proton Pumps and a Physical Link to the Citric Acid Cycle 549 The high-potential electrons of XADH enter the respiratory chain at XADH-Qoxidoreductase 551 Ubiquinol is the entry point for electrons from FADH? of flavoproteins Electrons flow from ubiquinol to cytochrome с through Q- cytochrome с oxidoreductase The Qcycle funnels electrons from a two-electron carrier to a one-electron carrier and pumps protons Gytochrome с oxidase catalyzes the reduction of molecular oxygen to water Toxic derivatives of molecular oxygen such as superoxide radical are scavenged by protective enzymes Electrons can be transferred between groups that are not in contact The conformation of cytochrome с has remained essentially constant for more than a billion years 18.4 A Proton Gradient Powers the Synthesis of ATP ATP synthase is composed of a proton-conducting unit and a catalytic unit Proton flow through ATP synthase leads to the release of tightly bound ATP: The binding-change mechanism Rotational catalysis is the world s smallest molecular motor Proton flow around the с ring powers ATP synthesis ATP synthase and G proteins have several common features 18.5 Many Shuttles Allow Movement Across Mitochondrial Membranes Electrons from cytoplasmic KADH enter mitochondria by shuttles The entry of AL) P into mitochondria is coupled to the exit of ATP by ATP-ADP translocase Mitochondrial transporters for metabolites have a common tripartite structure 18.6 The Regulation of Cellular Respiration Is Governed Primarily by the Need for ATP The complete oxidation of glucose yields about 30 molecules of ATP The rate of oxidative phosphoryiation is determined by the need for ATP Regulated uncoupling leads to the generation of heat Oxidative phosphoryiation can be inhibited at many stages Mitochondrial diseases are being discovered Mitochondria play a key role in apoptosis Power transmission by proton gradients is a central motif of bioenergetics Chapter 19 The Light Reactions of Photosynthesis 553 553 554 555 558 560 561 561 563 564 565 566 568 568 569 570 571 572 572 573 574 576 576 577 585 Photosynthesis converts light energy into chemical energy 586 19.1 Photosynthesis Takes Place in Chforoplasts 587 The primary events of photosynthesis take place in thylakoid membranes 587 Chloroplaste arose from an endosymbiotic event 588 xxiv Contents 19.2 Light Absorption by Chlorophyll Induces Electron Transfer A special pair of chlorophylls initiate charge separation Cyclic electron flow reduces the cytochrome of the reaction center 19.3 Two Photosystems Generate a Proton Gradient and NADPH in Oxygenic Photosynthesis Photosystem II transfers electrons from water to plastoquinone and generates a proton gradient Cytochrome bf links photosystem II to photosystem I Photosystem I uses light energy to generate reduced ferredoxin, a powerful reductant Ferredoxin-NADP4 reducíase converts NADP4 into NADPH 19.4 A Proton Gradient Across the Thylakoid Membrane Drives ATP Synthesis The ATP synthase of chloroplasts closely resembles those of mitochondria and prokaryotes Cyclic electron flow through photosystem I leads to the production of ATP instead of NADPH The absorption of eight photons yields one Cb, two NADPH, and three ATP molecules 19.5 Accessory Pigments Funnel Energy into Reaction Centers Resonance energy transfer allows energy to move from the site of initial absorbance to the reaction center Light-harvesting complexes contain additional chlorophylls and carotinoids The components of photosynthesis are highly organized Many herbicides inhibit the light reactions of photosynthesis 19.6 The Ability to Convert Light into Chemical Energy Is Ancient Chapter 20 The Calvin Cycle and Pentose Phosphate Pathway 588 589 592 592 592 595 595 596 597 598 599 600 601 601 602 603 604 604 609 20.1 The Calvin Cycle Synthesizes Hexoses from Carbon Dioxide and Water 610 Carbon dioxide reacts with ribulose 1 ,5-bisphosphate to form two molecules of 3-phosphogrycerate 611 Rubisco activity depends on magnesium and carbamate 612 Rubisco also catalyzes a wasteful oxygenase reaction: Catalytic imperfection 613 Hexose phosphates are made from phosphoglycerate, and ribulose 1 ,5-bisphosphate is regenerated 614 Three ATP and two NADPH molecules are used to bring carbon dioxide to the level of a hexose 617 Starch and sucrose are the major carbohydrate stores in plants 617 20.2 The Activity of the Calvin Cycle Depends on Environmental Conditions Rubisco is activated by light-driven changes in proton and magnesium ion concentrations Thioredoxin plays a key role in regulating the Calvin cycle The C4 pathway of tropical plants accelerates photosynthesis by concentrating carbon dioxide Crassulacean acid metabolism permits growth in arid ecosystems 20.3 The Pentose Phosphate Pathway Generates NADPH and Synthesizes Five-Carbon Sugars Two molecules of NADPH are generated in the conversion of glucose 6-phosphate into ribulose 5 -phosphate The pentose phosphate pathway and glycolysis are linked by transketolase and transaldolase Mechanism: Transketolase and transaldolase stabilize carbanionic intermediates by different mechanisms 20.4 The Metabolism of Glucose 6-phosphate by the Pentose Phosphate Pathway Is Coordinated with Glycolysis The rate of the pentose phosphate pathway is controlled bythelevelofNADP+ The flow of glucose 6-phosphate depends on the need for NADPH, ribose 5 -phosphate, and ATP Through the looking-glass: The Calvin cycle and the pentose phosphate pathway are mirror images 20.5 Glucose 6-phosphate Dehydrogenase Plays a Key Role in Protection Against Reactive Oxygen Species Glucose 6-phosphate dehydrogenase deficiency causes a drug-induced hemolytic anemia A deficiency of glucose 6-phosphate dehydrogenase confers an evolutionary advantage in some circumstances Chapter 21 Glycogen Metabolism 617 618 618 619 620 621 621 621 624 626 626 627 629 629 629 631 637 Glycogen metabolism is the regulated release and storage of glucose 638 21.1 Glycogen Breakdown Requires the Interplay of Several Enzymes 639 Phosphorylase catalyzes the phosphorolytic cleavage of glycogen to release glucose 1 -phosphate 639 Mechanism: Pyridoxal phosphate participates in the phosphorolytic cleavage of glycogen 640 A debranching enzyme also is needed for the breakdown of glycogen 641 Phosphoglucomutase converts glucose 1 -phosphate into glucose 6-phosphate 642 The liver contains glucose 6-phosphatase, a hydrolytic enzyme absent from muscle 643 Contents xxv 21.2 Phosphorylase Is Regulated by Allosteric Interactions and Reversible Phosphorylation 643 Muscle phosphorylase is regulated by the intracellular energy charge 643 Liver phosphorylase produces glucose for use by other tissues 645 Phosphorylase kinase is activated by phosphorylation and calcium ions 645 21.3 Epinephrine and Glucagon Signal the Need for Glycogen Breakdown 646 G proteins transmit the signal for the initiation of glycogen breakdown 646 Glycogen breakdown must be rapidly turned off when necessary 648 The regulation of glycogen phosphorylase became more sophisticated as the enzyme evolved 649 21.4 Glycogen Is Synthesized and Degraded by Different Pathways 649 UDP-glucose is an activated form of glucose 649 Glycogen synthase catalyzes the transfer of glucose from UDP-glucose to a growing chain 650 A branching enzyme forms α -1,6 linkages 651 Glycogen synthase is the key regulatory enzyme in glycogen synthesis 651 Glycogen is an efficient storage form of glucose 651 21.5 Glycogen Breakdown and Synthesis Are Reciprocally Regulated 652 Protein phosphatase 1 reverses the regulatory effects of kinases on glycogen metabolism 653 Insulin stimulates glycogen synthesis by inactivating glycogen synthase kinase 654 Glycogen metabolism in the liver regulates the blood-glucose level 655 A biochemical understanding of glycogen-storage diseases is possible 656 The complete oxidation of palmitate yields 106 molecules of ATP 671 Chapter 22 Fatty Acid Metabolism 663 Fatty acid degradation and synthesis mirror each other in their chemical reactions 664 22.1 Triacylglycerols Are Highly Concentrated Energy Stores 665 Dietary lipids are digested by pancreatic lipases 665 Dietary lipids are transported in chylomicrons 666 22.2 The Use of Fatty Acids As Fuel Requires Three Stages of Processing 667 Triacylglycerols are hydrolyzed by hormone-stimulated lipases 667 Fatty acids are linked to coenzyme A before they are oxidized 668 Carnitine carries long-chain activated fatty acids into the mitochondrial matrix 669 Acetyl CoA, NADH, and FADFb are generated in each round of fatty acid oxidation 670 22.3 Unsaturated and Odd-Chain Fatty Acids Require Additional Steps for Degradation 672 An isomerase and a reductase are required for the oxidation of unsaturated fatty acids 672 Odd-chain fatty acids yield propionyl CoA in the final thiolysis step 673 Vitamin B12 contains a corrin ring and a cobalt atom 674 Mechanism: Methylmalonyl CoA mutase catalyzes a rearrangement to form succinyl CoA 675 Fatty acids are also oxidized in peroxisomes 676 Ketone bodies are formed from acetyl CoA when fat breakdown predominates 677 Ketone bodies are a major fuel in some tissues 678 Animals cannot convert fatty acids into glucose 680 22.4 Fatty Acids Are Synthesized by Fatty Acid Synthase 680 Fatty acids are synthesized and degraded by different pathways 680 The formation of malonyl CoA is the committed step in fatty acid synthesis 681 Intermediates in fatty acid synthesis are attached to an acyl carrier protein 681 Fatty acid synthesis consists of a series of condensation, reduction, dehydration, and reduction reactions 682 Fatty acids are synthesized by a multifunctional enzyme complex in animals 683 The synthesis of palmitate requires 8 molecules of acetyl CoA, 14 molecules of NADPH, and 7 molecules of ATP 685 Citrate carries acetyl groups from mitochondria to the cytoplasm for fatty acid synthesis 686 Several sources supply NADPH for fatty acid synthesis 686 Fatty acid synthase inhibitors may be useful drugs 687 22.5 The Elongation and Unsaturation of Fatty Acids Are Accomplished by Accessory Enzyme Systems 687 Membrane-bound enzymes generate unsaturated fatty acids 688 Eicosanoid hormones are derived from polyunsaturated fatty acids 688 22.6 Acetyl CoA Carboxylase Plays a Key Role in Controlling Fatty Acid Metabolism 690 Acetyl CoA carboxylase is regulated by conditions in the cell 690 Acetyl CoA carboxylase is regulated by a variety of hormones 690 Chapter 23 Protein Turnover and Amino Acid Catabolism 697 23.1 Proteins Are Degraded to Amino Acids 698 The digestion of dietary proteins begins in the stomach and is completed in the intestine 698 Cellular proteins are degraded at different rates 699 xxvi Contents 701 701 23.2 Protein Turnover Is Tightly Regulated 699 Ubiquitin tags proteins for destruction 699 The proteasome digests the ubiquitin-tagged proteins The ubiquitin pathway and the proteasome have prokaryotic counterparts Protein degradation can be used to regulate biological function 02 23.3 The First Step in Amino Acid Degradation Is 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 708 23.4 Ammonium Ion Is Converted into Urea in Most Terrestrial Vertebrates 709 The urea cycle begins with the formation of carbamoyl phosphate 709 The urea cycle is linked to gluconeogenesis 711 Urea-cycle enzymes are evolutionarily related to enzymes in other metabolic pathways 712 Inherited defects of the urea cycle cause hyperammonemia and can lead to brain damage 712 Urea is not the only means of disposing of excess nitrogen 713 23.5 Carbon Atoms of Degraded Amino Acids Emerge As Major Metabolic Intermediates 714 Pyruvate is an entry point into metabolism for a number of amino acids 715 Oxaloacetate is an entry point into metabolism for aspartate and asparagine 716 Alpha-ketoglutarate is an entry point into metabolism for five-carbon amino acids 716 Succinyl coenzyme A is a point of entry for several nonpolar amino acids 717 Methionine degradation requires the formation of a key methyl donor, S-adenosylmethionine 717 The branched-chain amino acids yield acetyl GoA, acetoacetate, or propionyl CoA 717 Oxygenases are required for the degradation of aromatic amino acids 719 23.6 Inborn Errors of Metabolism Can Disrupt Amino Acid Degradation 72 Ì Part ill SYNTHESIZING THE MOLECULES OF LIFE Chapter 24 The Biosynthesis of Amino Acids 729 Amino acid synthesis requires solutions to three key biochemical problems 7Л0 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 7 Л 1 Ammonium ion is assimilated into an amino acid through glutamate and glutaminę 7ЛЛ 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, alaninę, 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 737 The formation of asparagine from aspartate requires an adenylated intermediate 737 Glutamate is the precursor of glutaminę, proline, and arginine 738 S-Phosphoglycerate is the precursor of serine, cysteine, and glycine 738 Tetrahydrofolate carries activated one-carbon units at several oxidation levels 739 S-Adenosylmethionine is the major donor of methyl groups 740 Cysteine is synthesized from serine and homocysteine 742 High homocysteine levels correlate with vascular disease 743 Shikimate and chorismate are intermediates in the biosynthesis of aromatic amino acids 743 Tryptophan synthase illustrates substrate channeling in enzymatic catalysis 746 24.3 Feedback Inhibition Regulates Amino Acid Biosynthesis 747 Branched pathways require sophisticated regulation 747 An enzymatic cascade modulates the activity of glutaminę synthetase 749 24.4 Amino Acids Are Precursors of Many Biomolecules 750 Glutathione, a gamma-glutamyl peptide, serves as a sulfhy dryl buffer and an antioxidant 751 Nitric oxide, a short-lived signal molecule, is formed from arginine 751 Contents xxvii Porphyrins are synthesized from glycine and succinyl coenzyme A 752 Porphyrins accumulate in some inherited disorders of porphyrin metabolism 754 Chapter 25 Nucleotide Biosynthesis 761 Nucleotides can be synthesized by de novo or salvage pathways 762 25.1 The Pyrimidine Ring Is Assembled de Novo or Recovered by Salvage Pathways 763 Bicarbonate and other oxygenated carbon compounds are activated by phosphorylation 763 The side chain of glutaminę can be hydrolyzed to generate ammonia 763 Intermediates can move between active sites by channeling 763 Orotate acquires a ribose ring from PRPP to form a pyrimidine nucleotide and is converted into uridylate 764 Nucleotide mono-, di-, and triphosphates are interconvertible 765 GTP is formed by aminationof UTP 765 Salvage pathways recycle pyrimidine bases 766 25.2 Purine Bases Can Be Synthesized de Novo or Recycled by Salvage Pathways 766 The purine ring system is assembled on ribose phosphate 766 The purine ring is assembled by successive steps of activation by phosphorylation followed by displacement 767 AMP and GMP are formed from IMP 769 Enzymes of the purine synthesis pathway associate with one another in vivo 770 Salvage pathways economize intracellular energy expenditure 770 25.3 Deoxyribonucleotides Are Synthesized by the Reduction of Ribonucleotides Through a Radical Mechanism 771 Mechanism: A tyrosyl radical is critical to the action of ribonucleotide reducíase 771 Stable radicals other than tyrosyl radical are employed by other ribonucleotide reductases 773 Thymidylate is formed by the methylation of deoxyuridylate 774 Dihydrofolate reducíase catalyzes the regeneration of ietrahydrofolate, a one-carbon carrier 775 Several valuable aniicancer drugs block the synthesis of thymidylaie 775 25.4 Key Steps in Nucleotide Biosynthesis Are Regulated by Feedback Inhibition 776 Pyrimidine biosynthesis is regulated by aspartaie transcarbamoylase 777 The synthesis of purine nucleotides is controlled by feedback inhibition at several sites The synthesis of deoxyribonucleotides is controlled by the regulation of ribonucleotide reducíase 25.5 Disruptions in Nucleotide Metabolism Can Cause Pathological Conditions The loss of adenosine deaminase activity results in severe combined immunodeficiency Gout is induced by high serum levels of urate Lesch—Nyhan syndrome is a dramatic consequence of mutations in a salvage-pathway enzyme Folk acid deficiency promotes birth defects such as spina bifida Chapter 26 The Biosynthesis of Membrane Lipids and Steroids III 778 778 778 779 780 781 787 26.1 Phosphatidate Is a Common Intermediate in the Synthesis of Phospholipids and Triacylglycerols 788 The synthesis of phospholipids requires an activated intermediate 789 Sphingolipids are synthesized from ceramide 791 Gangliosides are carbohydrate-rich sphingolipids that contain acidic sugars 792 Sphingolipids confer diversity on lipid structure and function 793 Respiratory distress syndrome and Тау -Sachs disease result from the disruption of lipid metabolism 793 Phosphatiditic acid phosphatase is a key regulatory enzyme in lipid metabolism 794 26.2 Cholesterol Is Synthesized from Acetyl Coenzyme A in Three Stages 795 The synthesis of mevalonate, which is activated as isopentenyl pyrophosphate, initiates the synthesis of cholesterol 795 Squalene (С30) is synthesized from six molecules of isopentenyl pyrophosphate (C5) 796 Squalene cyclizes to form cholesterol 797 26.3 The Complex Regulation of Cholesterol Biosynthesis Takes Place at Several Levels 798 Lipoproteins transport cholesterol and triacylglycerols throughout the organism 801 The blood levels of certain lipoproteins can serve diagnostic purposes 802 Low-density lipoproteins play a central role in cholesterol metabolism 803 The absence of the LDL receptor leads to hypercholesterolemia and atherosclerosis 804 Mutations in the LDL receptor prevent LDL release and result in receptor destruction 805 xxvi ïi Contents HDL appears to protect against arteriosclerosis The clinical management of cholesterol levels can be understood at a biochemical level 26.4 Important Derivatives of Cholesterol Include Bile Salts and Steroid Hormones Letters identify the steroid rings and numbers identify the carbon atoms Steroids are hydroxylated by cytochrome P450 monooxygenases that use NADPH and СЪ The cytochrome P450 system is widespread and performs a protective function Pregnenolone, a precursor of many other steroids, is formed from cholesterol by cleavage of its side chain Progesterone and corticosteroids are synthesized from pregnenolone Androgens and estrogens are synthesized from pregnenolone Vitamin D is derived from cholesterol by the ring-splitting activity of light 806 807 807 809 809 810 811 811 812 813 Chapter 27 The Integration of Metabolism 821 27.1 Caloric Homeostasis Is a Means of Regulating Body Weight 822 27.2 The Brain Plays a Key Role in Caloric Homeostasis 824 Signals from the gastrointestinal tract induce feelings of satiety 824 Leptin and insulin regulate long-term control over caloric homeostasis 825 Leptin is one of several hormones secreted by adipose tissue 826 Leptin resistance may be a contributing factor to obesity 827 Dieting is used to combat obesity 827 27.3 Diabetes Is a Common Metabolic Disease Often Resulting from Obesity 828 Insulin initiates a complex signal-transduction pathway in muscle 828 Metabolic syndrome often precedes type 2 diabetes 830 Excess fatty acids in muscle modify metabolism 830 Insulin resistance in muscle facilitates pancreatic failure 831 Metabolic derangements in type 1 diabetes result from insulin insufficiency and glucagon excess 832 27.4 Exercise Beneficially Alters the Biochemistry of Cells 833 Mitochondrial biogenesis is stimulated by muscular activity 834 Fuel choice during exercise is determined by the intensity and duration of activity 835 27.5 Food Intake and Starvation Induce Metabolic Changes 836 The starved-fed cycle is the physiological response to a fast 837 Metabolic adaptations in prolonged starvation minimize protein degradation 27.6 Ethanol Alters Energy Metabolism in the Liver Ethanol metabolism leads to an excess of NADH Excess ethanol consumption disrupts vitamin metabolism Chapter 28 DNA Replication, Repair, and Recombination 838 840 840 842 849 28.1 DNA Replication Proceeds by the Polymerization of Deoxyribonucleoside Triphosphates Along a Template 850 DNA polymerases require a template and a primer 850 AU DNA polymerases have structural features in common 851 Two bound metal ions participate in the polymerase reaction 851 The specificity of replication is dictated by complementarity of shape between bases 852 An RNA primer synthesized by primase enables DNA synthesis to begin 853 One strand of DNA is made continuously, whereas the other strand is synthesized in fragments 853 DNA ligase joins ends of DNA in duplex regions 854 The separation of DNA strands requires specific helicases and ATP hydrolysis 854 28.2 DNA Unwinding and Supercoiling Are Controlled by Topoisomerases 855 The linking number of DNA, a topological property, determines the degree of supercoiling 856 Topoisomerases prepare the double helix for unwinding 858 Type I topoisomerases relax supercoiled structures 858 Type II topoisomerases can introduce negative supercoils through coupling to ATP hydrolysis 859 28.3 DNA Replication Is Highly Coordinated 861 DNA replication requires highly processive polymerases 861 The leading and lagging strands are synthesized in a coordinated fashion 862 DNA replication in Escherickia coli begins at a unique site 864 DNA synthesis in eukaryotes is initiated at multiple sites 865 Telomeres are unique structures at the ends of linear chromosomes 866 Telomeres are replicated by telomerase, a specialized polymerase that carries its own RNA template 867 28.4 Many Types of DNA Damage Can Be Repaired 867 Errors can arise in DNA replication 867 Bases can be damaged by oxidizing agents, alkylating agents, and light 868 Contents xxix DNA damage can be detected and repaired by a variety of systems The presence of thymine instead of uracil in DNA permits the repair of deaminated cytosine Some genetic diseases are caused by the expansion of repeats of three nucleotides Many cancers are caused by the defective repair of DNA Many potential carcinogens can be detected by their mutagenic action on bacteria 28.5 DNA Recombination Plays Important Roles in Replication, Repair, and Other Processes RecA can initiate recombination by promoting strand invasion Some recombination reactions proceed through Holliday-junction intermediates RNA synthesis comprises three stages: Initiation, elongation, and termination 29.1 RNA Polymerases Catalyze Transcription RNA chains are formed de novo and grow in the б -Їо-З direction RNA polymerases backtrack and correct errors RNA polymerase binds to promoter sites on the DNA template to initiate transcription Sigma subunits of RNA polymerase recognize promoter sites RNA polymerases must unwind the template double helix for transcription to take place Elongation takes place at transcription bubbles that move along the DNA template Sequences within the newly transcribed RNA signal termination Some messenger RNAs directly sense metabolite concentrations The rho protein helps to terminate the transcription of some genes Some antibiotics inhibit transcription Precursors of transfer and ribosomal RNA are cleaved and chemically modified after transcription in prokaryotes 29.2 Transcription in Eukaryotes Is Highly Regulated Three types of RNA polymerase synthesize RNA in eukaryotic cells Three common elements can be found in the RNA polymerase II promoter region The TFIID protein complex initiates the assembly of the active transcription complex Multiple transcription factors interact with eukaryotic promoters 869 871 872 872 873 874 874 875 Chapter 29 RNA Synthesis and Processing 883 884 885 890 890 891 892 892 893 895 896 897 898 899 900 Enhancer sequences can stimulate transcription at start sites thousands of bases away 29.3 The Transcription Products of Eukaryotic Polymerases Are Processed RNA polymerase I produces three ribosomal RNAs RNA polymerase III produces transfer RNA The product of RNA polymerase II, the pre-mRNA transcript, acquires a 5 cap and a 3 poly(A) tail Small regulatory RNAs are cleaved from larger precursors RNA editing changes the proteins encoded by mRNA Sequences at the ends of introns specify splice sites in mRNA precursors Splicing consists of two sequential transesterification reactions Small nuclear RNAs in spliceosomes catalyze the splicing of mRNA precursors Transcription and processing of mRNA are coupled Mutations that affect pre-mRNA splicing cause disease Most human pre-mRNAS can be spliced in alternative ways to yield different proteins 29.4 The Discovery of Catalytic RNA Was Revealing in Regard to Both Mechanism and Evolution Chapter 30 Protein Synthesis 900 901 901 902 902 904 904 905 906 907 909 909 910 911 921 30.1 Protein Synthesis Requires the Translation of Nucleotide Sequences into Amino Acid Sequences The synthesis of long proteins requires a low error frequency Transfer RNA molecules have a common design Some transfer RNA molecules recognize more than one codon because of wobble in base-pairing 30.2 Aminoacyl Transfer RNA Synthetases Read the Genetic Code Amino acids are first activated by adenylation Aminoacyl-tRNA synthetases have highly discriminating amino acid activation sites Proofreading by aminoacyl-tRNA synthetases increases the fidelity of protein synthesis Synthetases recognize various features of transfer RNA molecules Aminoacyl-tRNA synthetases can be divided into two classes 30.3 The Ribosome Is the Site of Protein Synthesis Ribosomal RNAs (5S, 16S, and 23S rRNA) play a central role in protein synthesis Ribosomes have three tRNA-binding sites that bridge the 30s and 50s subunits 922 922 923 925 927 927 928 929 930 931 931 932 934 xxx Contents The start signal is usually AUG preceded by several bases that pair with 1 6S rRN A Bacterial protein synthesis is initiated by formylmethionyl transfer RNA Formylmethionyl-tRNAf is placed in the Ρ site of the ribosome in the formation of the 70S initiation complex Elongation factors deliver aminoacyl-tRNA to the ribosome Peptidyl transferase catalyzes peptide-bond synthesis The formation of a peptide bond is followed by the GTP-driven translocation of tRNAs and mRNA Protein synthesis is terminated by release factors that read stop codons 30.4 Eukaryotic Protein Synthesis Differs from Prokaryotic Protein Synthesis Primarily in Translation Initiation Mutations in initiation factor 2 cause a curious pathological condition 30.5 A Variety of Antibiotics and Toxins Can Inhibit Protein Synthesis Some antibiotics inhibit protein synthesis Diphtheria toxin blocks protein synthesis in eukaryotes by inhibiting translocation Ricin fatally modifies 28S ribosomal RNA 30.6 Ribosomes Bound to the Endoplasmic Reticulum Manufacture Secretory and Membrane Proteins Signal sequences mark proteins for translocation across the endoplasmic reticulum membrane Transport vesicles carry cargo proteins to their final destination Chapter 31 The Control of Gene Expression in Prokaryotes 934 935 936 936 937 938 940 941 942 943 943 944 945 945 945 947 957 31.1 Many DNA-Binding Proteins Recognize Specific DNA Sequences 958 The helix-turn-helix motif is common to many prokaryotic DNA-binding proteins 959 31.2 Prokaryotic DNA-Binding Proteins Bind Specifically to Regulatory Sites in Opérons 959 An operan consists of regulatory elements and protein-encoding genes 960 The lac repressor protein in the absence of lactose binds to the operator and blocks transcription 961 Ligand binding can induce structural changes in regulatory proteins 962 The operon is a common regulatory unit in prokaryotes 962 Transcription can be stimulated by proteins that contact RNA polymerase 963 31.3 Regulatory Circuits Can Result in Switching Between Patterns of Gene Expression Lambda repressor regulates its own expression A circuit based on lambda repressor and Cro form a genetic switch Many prokaryotic cells release chemical signals that regulate gene expression in other cells Biofilms are complex communities of prokaryotes 31.4 Gene Expression Can Be Controlled at Posttranscriptional Levels Attenuation is a prokaryotic mechanism for regulating transcription through the modulation of nascent RNA secondary structure Chapter 32 The Control of Gene Expression in Eukaryotes 32.2 Transcription Factors Bind DNA and Regulate Transcription Initiation A range of DNA-binding structures are employed by eukaryotic DNA-binding proteins Activation domains interact with other proteins Multiple transcription factors interact with eukaryotic regulatory regions Enhancers can stimulate transcription in specific cell types Induced pluripotent stem cells can be generated by introducing four transcription factors into differentiated cells 32.3 The Control of Gene Expression Can Require Chromatin Remodeling The methylation of DNA can alter patterns of gene expression Steroids and related hydrophobic molecules pass through membranes and bind to DNA-binding receptors Nuclear hormone receptors regulate transcription by recruiting coactivators to the transcription complex Steroid-hormone receptors are targets for drugs Chromatin structure is modulated through covalent modifications of histone tails Histone deacetylases contribute to transcriptional repression 32.4 Eukaryotic Gene Expression Can Be Controlled at Posttranscriptional Levels Genes associated with iron metabolism are translationally regulated in animals Small RNAs regulate the expression of many eukaryotic genes 964 964 965 965 966 967 967 973 32.1 Eukaryotic DNA Is Organized into Chromatin Nucleosomes are complexes of DNA and histones DNA wraps around histone octamers to form nucleosomes 974 975 975 977 977 978 979 979 980 980 981 982 982 984 985 986 987 987 989 Contents xxxi Part IV RESPONDING TO ENVIRONMENTAL CHANGES Chapter 33 Sensory Systems 995 33.1 A Wide Variety of Organic Compounds Are Detected by Olfaction 996 Olfaction is mediated by an enormous family of seven-transmembrane-helix receptors 996 Odorants are decoded by a combinatorial mechanism 998 33.2 Taste Is a Combination of Senses That Function by Different Mechanisms 1000 Sequencing of the human genome led to the discovery of a large family of 7TM bitter receptors 1001 A heterodimeric 7TM receptor responds to sweet compounds 1002 Umami, the taste of glutamate and aspartate, is mediated by a heterodimeric receptor related to the sweet receptor 1003 Salty tastes are detected primarily by the passage of sodium ions through channels 1003 Sour tastes arise from the effects of hydrogen ions (acids) on channels 1003 33.3 Photoreceptor Molecules in the Eye Detect Visible Light 1004 Rhodopsin, a specialized 7TM receptor, absorbs visible light 1004 Light absorption induces a specific isomerization of bound ll-ds-retinal 1005 Light-induced lowering of the calcium level coordinates recovery 1006 Color vision is mediated by three cone receptors that are homologs of rhodopsin 1007 Rearrangements in the genes for the green and red pigments lead to color blindness 1008 33.4 Hearing Depends on the Speedy Detection of Mechanical Stimuli 1009 Hair cells use a connected bundle of stereocilia to detect tiny motions 1009 Mechanosensory channels have been identified in Drosophila and vertebrates 1010 33.5 Touch Includes the Sensing of Pressure, Temperature, and Other Factors 1011 Studies of capsaicin reveal a receptor for sensing high temperatures and other painful stimuli 1011 More sensory systems remain to be studied 1012 Chapter 34 The Immune System 34.1 Antibodies Possess Distinct Antigen-Binding and Effector Units 34.2 Antibodies Bind Specific Molecules Through Hypervariable Loops The immunoglobulin fold consists of a beta-sandwich framework with hypervariable loops X-ray analyses have revealed how antibodies bind antigens Large antigens bind antibodies with numerous interactions 34.3 Diversity Is Generated by Gene Rearrangements J (joining) genes and D (diversity) genes increase antibody diversity More than 10 antibodies can be formed by combinatorial association and somatic mutation The oligomerization of antibodies expressed on the surfaces of immature В cells triggers antibody secretion Different classes of antibodies are formed by the hopping of Vh genes 34.4 Major-Histocompatibility-Complex Proteins Present Peptide Antigens on Cell Surfaces for Recognition by Т -Cell Receptors Peptides presented by MHC proteins occupy a deep groove flanked by alpha helices Т -cell receptors are antibody-like proteins containing variable and constant regions GD8 on cytotoxic T cells acts in concert with T -cell receptors Helper T cells stimulate cells that display foreign peptides bound to class II MHC proteins Helper T cells rely on the Т -cell receptor and CD4 to recognize foreign peptides on antigen-presenting cells MHC proteins are highly diverse Human immunodeficiency viruses subvert the immune system by destroying helper T cells 34.5 The Immune System Contributes to the Prevention and the Development of Human Diseases T cells are subjected to positive and negative selection in the thymus Autoimmune diseases result from the generation of immune responses against self-antigens The immune system plays a role in cancer prevention Vaccines are a powerful means to prevent and eradicate disease Innate immunity is an evolutionarily ancient defense system 1018 The adaptive immune system responds by using the principles of evolution 1019 1017 chapter 35 Molecular Motors 1021 1023 1024 1024 1026 1027 1027 1028 1029 1030 1031 1032 1034 1034 1036 1036 1038 1039 1040 1040 1041 1041 1042 1049 35.1 Most Molecular-Motor Proteins Are Members of the P-Loop NTPase Superfamily 1050 Molecular motors are generally oligomeric proteins with an ATPase core and an extended structure 1050 xxxii Contents ATP binding and hydrolysis induce changes in the conformation and binding affinity of motor proteins 35.2 Myosins Move Along Actin Filaments Actin is a polar, self-assembling, dynamic polymer Myosin head domains bind to actin filaments Motions of single motor protems can be directly observed Phosphate release triggers the myosin power stroke Muscle is a complex of myosin and actin The length of the lever arm determines motor velocity 35.3 Kinesin and Dynein Move Along Microtubules Microtubules are hollow cylindrical polymers Kinesin motion is highly processive 35.4 A Rotary Motor Drives Bacterial Motion Bacteria swim by rotating their flagella Proton flow drives bacterial flagellar rotation Bacterial chemotaxis depends on reversal of the direction of flagellar rotation Chapter 36 Drug Development 1052 1054 1054 1056 1056 1057 1057 1060 1060 1060 1062 1064 1064 1064 1066 1073 36.1 The Development of Drugs Presents Huge Challenges 1074 Drug candidates must be potent modulators of their targets 1074 Drugs must have suitable properties to reach their targets 1075 Toxicity can limit drug effectiveness 1080 36.2 Drug Candidates Can Be Discovered by Serendipity, Screening, or Design 1081 Serendipitous observations can drive drug development 1081 Screening libraries of compounds can yield drugs or drug leads 1083 Drugs can be designed on the basis of three-dimensional structural information about their targets 1086 36.3 Analyses of Genomes Hold Great Promise for Drug Discovery 1089 Potential targets can be identified in the human proteome 1089 Animal models can be developed to test the validity of potential drug targets 1090 Potential targets can be identified in the genomes of pathogens 1090 Genetic differences influence individual responses to drags 1091 36.4 The Development of Drugs Proceeds Through Several Stages 1092 Clinical trials are time consuming and expensive 1092 The evolution of drug resistance can limit the utility of drugs for infectious agents and cancer 1094 Answers to Problems Al Index Bl
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indexdate	2024-12-20T14:47:52Z
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spellingShingle	Berg, Jeremy M. 1958- Tymoczko, John L. 1948-2019 Stryer, Lubert 1938-2024 Biochemistry Biochemie (DE-588)4006777-4 gnd Physiologische Chemie (DE-588)4076124-1 gnd
subject_GND	(DE-588)4006777-4 (DE-588)4076124-1 (DE-588)4151278-9 (DE-588)4123623-3
title	Biochemistry
title_auth	Biochemistry
title_exact_search	Biochemistry
title_full	Biochemistry Jeremy M. Berg ; John L. Tymoczko ; Lubert Stryer
title_fullStr	Biochemistry Jeremy M. Berg ; John L. Tymoczko ; Lubert Stryer
title_full_unstemmed	Biochemistry Jeremy M. Berg ; John L. Tymoczko ; Lubert Stryer
title_short	Biochemistry
title_sort	biochemistry
topic	Biochemie (DE-588)4006777-4 gnd Physiologische Chemie (DE-588)4076124-1 gnd
topic_facet	Biochemie Physiologische Chemie Einführung Lehrbuch
url	http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=021174175&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
work_keys_str_mv	AT bergjeremym biochemistry AT tymoczkojohnl biochemistry AT stryerlubert biochemistry

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