Biochemistry, 9th Edition by Berg Test Bank

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Test Bank for Biochemistry, 9th Edition, 9e by Jeremy M. Berg , John L. Tymoczko, Gregory J. Gatto,Lubert Stryer TEST BANK ISBN-13: 9781319114671 Full chapters included Part I THE MOLECULAR DES... IGN OF LIFE Chapter 1 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 DNA structure explains heredity and the storage of information 1.3 Concepts from Chemistry Explain the Properties of Biological Molecules The formation of the DNA double helix as a key example 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, Medicine, and Other Fields Genome sequencing has transformed biochemistry and other fields Environmental factors influence human biochemistry Genome sequences encode proteins and patterns of expression APPENDIX Visualizing Molecular Structures: Small Molecules APPENDIX Functional Groups Chapter 2 Protein Composition and Structure 2.1 Proteins Are Built from a Repertoire of 20 Amino Acids 2.2 Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains Proteins have unique amino acid sequences specified by genes Polypeptide chains are flexible yet conformationally restricted 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 2.4 Tertiary Structure: Proteins Can Fold into Globular or Fibrous Structures Fibrous proteins provide structural support for cells and tissues 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 〈 helices, ® sheets, and 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 Posttranslational modifications confer new capabilities to proteins APPENDIX Visualizing Molecular Structures: Proteins Chapter 3 Exploring Proteins and Proteomes 3.1 The Purification of Proteins Is an Essential First Step in Understanding Their Function The assay: How do we recognize the protein that we are looking for? Proteins must be released from the cell to be purified Proteins can be purified according to solubility, size, charge, and binding affinity Proteins can be separated by gel electrophoresis and displayed A protein purification scheme can be quantitatively evaluated Ultracentrifugation is valuable for separating biomolecules and determining their masses Protein purification can be made easier with the use of recombinant DNA technology 3.2 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 Co-immunoprecipitation enables the identification of binding partners of a protein Fluorescent markers make the visualization of proteins in the cell possible 3.3 Mass Spectrometry Is a Powerful Technique for the Identification of Peptides and Proteins Peptides can be sequenced by mass spectrometry Proteins can be specifically cleaved into small peptides to facilitate analysis Genomic and proteomic methods are complementary The amino acid sequence of a protein provides valuable information Individual proteins can be identified by mass spectrometry 3.4 Peptides Can Be Synthesized by Automated Solid-Phase Methods 3.5 Three-Dimensional Protein Structure Can Be Determined by X-ray Crystallography, NMR Spectroscopy, and Cryo-Electron Microscopy X-ray crystallography reveals three-dimensional structure in atomic detail Nuclear magnetic resonance spectroscopy can reveal the structures of proteins in solution Cryo-electron microscopy is an emerging method of protein structure determination APPENDIX Problem-Solving Strategies Chapter 4 DNA, RNA, and the Flow of Genetic Information 4.1 A Nucleic Acid Consists of Four Kinds of Bases Linked to a Sugar–Phosphate Backbone RNA and DNA differ in the sugar component and one of the bases Nucleotides are the monomeric units of nucleic acids DNA molecules are very long and have directionality 4.2 A Pair of Nucleic Acid Strands with Complementary Sequences Can Form a Double-Helical Structure The double helix is stabilized by hydrogen bonds and van der Waals interactions DNA can assume a variety of structural forms 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 Unusual circular DNA exists in the eukaryotic nucleus 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 APPENDIX Problem-Solving Strategies Chapter 5 Exploring Genes and Genomes 5.1 The Exploration of Genes Relies on Key Tools Restriction enzymes split DNA into specific fragments Restriction fragments can be separated by gel electrophoresis and visualized DNA can be sequenced by controlled termination of replication DNA probes and genes can be synthesized by automated solid-phase methods Selected DNA sequences can be greatly amplified by the polymerase chain reaction PCR is a powerful technique in medical diagnostics, forensics, and studies of molecular evolution The tools for recombinant DNA technology have been used to identify disease-causing mutations 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 ⎣ phage are choice vectors for DNA cloning in bacteria Bacterial and yeast artificial chromosomes Specific genes can be cloned from digests of genomic DNA 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 sequence of the human genome has been completed Next-generation sequencing methods enable the rapid determination of a complete 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 and genome editing provide clues to gene function and opportunities for new therapies 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 APPENDIX Biochemistry in Focus: Improved biofuel production from genetically-engineered algae Chapter 6 Exploring Evolution and Bioinformatics 6.1 Homologs Are Descended from a Common Ancestor 6.2 Statistical Analysis of Sequence Alignments Can Detect Homology The statistical significance of alignments can be estimated by shuffling Distant evolutionary relationships can be detected through the use of substitution matrices Databases can be searched to identify homologous sequences 6.3 Examination of Three-Dimensional Structure Enhances Our Understanding of Evolutionary Relationships Tertiary structure is more conserved than primary structure Knowledge of three-dimensional structures can aid in the evaluation of sequence alignments Repeated motifs can be detected by aligning sequences with themselves Convergent evolution illustrates common solutions to biochemical challenges Comparison of RNA sequences can be a source of insight into RNA secondary structures 6.4 Evolutionary Trees Can Be Constructed on the Basis of Sequence Information Horizontal gene transfer events may explain unexpected branches of the evolutionary tree 6.5 Modern Techniques Make the Experimental Exploration of Evolution Possible Ancient DNA can sometimes be amplified and sequenced Molecular evolution can be examined experimentally APPENDIX Biochemistry in Focus: Using sequence alignments to identify functionally important residues APPENDIX Problem-Solving Strategies Chapter 7 Hemoglobin: Portrait of a Protein in Action 7.1  Binding of Oxygen by Heme Iron Changes in heme electronic structure upon oxygen binding are the basis for functional imaging studies The structure of myoglobin prevents the release of reactive oxygen species Human hemoglobin is an assembly of four myoglobin-like subunits 7.2 Hemoglobin Binds Oxygen Cooperatively Oxygen binding markedly changes the quaternary structure of hemoglobin Hemoglobin cooperativity can be potentially explained by several models Structural changes at the heme groups are transmitted to the 〈1®1–〈2®2 interface 2,3-Bisphosphoglycerate in red cells is crucial in determining the oxygen affinity of hemoglobin Carbon monoxide can disrupt oxygen transport by hemoglobin 7.3 Hydrogen Ions and Carbon Dioxide Promote the Release of Oxygen: The Bohr Effect 7.4 Mutations in Genes Encoding Hemoglobin Subunits Can Result in Disease Sickle-cell anemia results from the aggregation of mutated deoxyhemoglobin molecules Thalassemia is caused by an imbalanced production of hemoglobin chains The accumulation of free alpha-hemoglobin chains is prevented Additional globins are encoded in the human genome APPENDIX Binding Models Can Be Formulated in Quantitative Terms: The Hill Plot and the Concerted Model APPENDIX Biochemistry in Focus: A potential antidote for carbon monoxide poisoning? Chapter 8 Enzymes: Basic Concepts and Kinetics 8.1 Enzymes are Powerful and Highly Specific Catalysts Many enzymes require cofactors for activity Enzymes can transform energy from one form into another 8.2 Gibbs Free Energy Is a Useful Thermodynamic Function for Understanding Enzymes The free-energy change provides information about the spontaneity but not the rate of a reaction The standard free-energy change of a reaction is related to the equilibrium constant Enzymes alter only the reaction rate and not the reaction equilibrium 8.3 Enzymes Accelerate Reactions by Facilitating the Formation of the Transition State The formation of an enzyme–substrate complex is the first step in enzymatic catalysis The active sites of enzymes have some common features The binding energy between enzyme and substrate is important for catalysis 8.4 The Michaelis–Menten Model Accounts for the Kinetic Properties of Many Enzymes Kinetics is the study of reaction rates The steady-state assumption facilitates a description of enzyme kinetics Variations in KM can have physiological consequences KM and Vmax values can be determined by several means KM and Vmax values are important enzyme characteristics kcat/KM is a measure of catalytic efficiency Most biochemical reactions include multiple substrates Allosteric enzymes do not obey Michaelis–Menten kinetics 8.5 Enzymes Can Be Inhibited by Specific Molecules The different types of reversible inhibitors are kinetically distinguishable Irreversible inhibitors can be used to map the active site Penicillin irreversibly inactivates a key enzyme in bacterial cell-wall synthesis Transition-state analogs are potent inhibitors of enzymes Enzymes have impact outside the laboratory or clinic 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 APPENDIX Problem-Solving Strategies APPENDIX Biochemistry in Focus: The effect of temperature rate on enzyme-catalyzed reactions and the coloring of Siamese cats Chapter 9 Catalytic Strategies 9.1 Proteases Facilitate a Fundamentally Difficult Reaction Chymotrypsin possesses a highly reactive serine residue Chymotrypsin action proceeds in two steps linked by a covalently bound intermediate Serine is part of a catalytic triad that also includes histidine and aspartate Catalytic triads are found in other hydrolytic enzymes The catalytic triad has been dissected by site-directed mutagenesis Cysteine, aspartyl, and metalloproteases are other major classes of peptide-cleaving enzymes Protease inhibitors are important drugs 9.2 Carbonic Anhydrases Make a Fast Reaction Faster Carbonic anhydrase contains a bound zinc ion essential for catalytic activity Catalysis entails zinc activation of a water molecule A proton shuttle facilitates rapid regeneration of the active form of the enzyme 9.3 Restriction Enzymes Catalyze Highly Specific DNA-Cleavage Reactions Cleavage is by in-line displacement of 3′-oxygen from phosphorus by magnesium-activated water Restriction enzymes require magnesium for catalytic activity The complete catalytic apparatus is assembled only within complexes of cognate DNA molecules, ensuring specificity Host-cell DNA is protected by the addition of methyl groups to specific bases Type II restriction enzymes have a catalytic core in common and are probably related by horizontal gene transfer 9.4 Myosins Harness Changes in Enzyme Conformation to Couple ATP Hydrolysis to Mechanical Work ATP hydrolysis proceeds by the attack of water on the gamma phosphoryl group Formation of the transition state for ATP hydrolysis is associated with a substantial conformational change The altered conformation of myosin persists for a substantial period of time Scientists can watch single molecules of myosin move Myosins are a family of enzymes containing P-loop structures APPENDIX Problem-Solving Strategies Chapter 10 Regulatory Strategies 10.1 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 T-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 Mutations in protein kinase A can cause Cushing Syndrome Exercise modifies the phosphorylation of many proteins 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 Serpins can be degraded by a unique enzyme Blood clotting is accomplished by a cascade of zymogen activations Prothrombin must bind to Ca2+ to be converted to thrombin Fibrinogen is converted by thrombin into a fibrin clot Vitamin K is required for the formation of ©-carboxyglutamate The clotting process must be precisely regulated Hemophilia revealed an early step in clotting APPENDIX Biochemistry in Focus: Phosphoribosylpyrophosphate synthetase-induced gout APPENDIX Problem-Solving Strategies 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 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 Human milk oligosaccharides protect newborns from infection 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 Glycosylation functions in nutrient sensing Proteoglycans, composed of polysaccharides and protein, have important structural roles Proteoglycans are important components of cartilage Mucins are glycoprotein components of mucus Chitin can be processed to a molecule with a variety of uses 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 and within cells Lectins are organized into different classes Influenza virus binds to sialic acid residues APPENDIX Biochemistry in Focus: α-Glucosidase (maltase) inhibitors can help to maintain blood glucose homeostsis Chapter 12 Lipids and Cell 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 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 APPENDIX Biochemistry in Focus: The curious case of cardiolipin Chapter 13 Membrane Channels and Pumps 13.1 The Transport of Molecules Across a Membrane May Be Active or Passive Many molecules require protein transporters to cross membranes Free energy stored in concentration gradients can be quantified 13.2 Two Families of Membrane Proteins Use ATP Hydrolysis to Pump Ions and Molecules Across Membranes P-type ATPases couple phosphorylation and conformational changes to pump calcium ions across membranes Digitalis specifically inhibits the Na+–K+ pump by blocking its dephosphorylation P-type ATPases are evolutionarily conserved and play a wide range of roles Multidrug resistance highlights a family of membrane pumps with ATP-binding cassette domains 13.3 Lactose Permease Is an Archetype of Secondary Transporters That Use One Concentration Gradient to Power the Formation of Another 13.4 Specific Channels Can Rapidly Transport Ions Across Membranes Action potentials are mediated by transient changes in Na+ and K+ permeability Patch-clamp conductance measurements reveal the activities of single channels The structure of a potassium ion channel is an archetype for many ion-channel structures The structure of the potassium ion channel reveals the basis of ion specificity The structure of the potassium ion channel explains its rapid rate of transport Voltage gating requires substantial conformational changes in specific ion-channel domains A channel can be inactivated by occlusion of the pore: the ball-and-chain model The acetylcholine receptor is an archetype for ligand-gated ion channels Action potentials integrate the activities of several ion channels working in concert Disruption of ion channels by mutations or chemicals can be potentially life-threatening 13.5 Gap Junctions Allow Ions and Small Molecules to Flow Between Communicating Cells 13.6 Specific Channels Increase the Permeability of Some Membranes to Water APPENDIX Biochemistry in Focus: Setting the pace is more than funny business APPENDIX Problem-Solving Strategies Chapter 14 Signal-Transduction Pathways 14.1  Epinephrine and Angiotensin II Signaling: Heterotrimeric G Proteins Transmit Signals and Reset Themselves Ligand binding to 7TM receptors leads to the activation of heterotrimeric G proteins Activated G proteins transmit signals by binding to other proteins Cyclic AMP stimulates the phosphorylation of many target proteins by activating protein kinase A G proteins spontaneously reset themselves through GTP hydrolysis Some 7TM receptors activate the phosphoinositide cascade Calcium ion is a widely used second messenger Calcium ion often activates the regulatory protein calmodulin 14.2 Insulin Signaling: Phosphorylation Cascades Are Central to Many Signal-Transduction Processes The insulin receptor is a dimer that closes around a bound insulin molecule Insulin binding results in the cross-phosphorylation and activation of the insulin receptor The activated insulin-receptor kinase initiates a kinase cascade Insulin signaling is terminated by the action of phosphatases 14.3 EGF Signaling: Signal-Transduction Pathways Are Poised to Respond EGF binding results in the dimerization of the EGF receptor The EGF receptor undergoes phosphorylation of its carboxyl-terminal tail EGF signaling leads to the activation of Ras, a small G protein Activated Ras initiates a protein kinase cascade EGF signaling is terminated by protein phosphatases and the intrinsic GTPase activity of Ras 14.4 Many Elements Recur with Variation in Different Signal-Transduction Pathways 14.5 Defects in Signal-Transduction Pathways Can Lead to Cancer and Other Diseases Monoclonal antibodies can be used to inhibit signal-transduction pathways activated in tumors Protein kinase inhibitors can be effective anticancer drugs Cholera and whooping cough are the result of altered G-protein activity APPENDIX Biochemistry in Focus: Gases get in on the signaling game Part II TRANSDUCING AND STORING ENERGY Chapter 15 Metabolism: Basic Concepts and Design 15.1 Metabolism Is Composed of Many Coupled, Interconnecting Reactions Metabolism consists of energy-yielding and energy-requiring reactions A thermodynamically unfavorable reaction can be driven by a favorable reaction 15.2 ATP Is the Universal Currency of Free Energy in Biological Systems ATP hydrolysis is exergonic ATP hydrolysis drives metabolism by shifting the equilibrium of coupled reactions The high phosphoryl potential of ATP results from structural differences between ATP and its hydrolysis products Phosphoryl-transfer potential is an important form of cellular energy transformation 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 Phosphates play a prominent role in biochemical processes 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 APPENDIX Problem-Solving Strategies Chapter 16 Glycolysis and Gluconeogenesis 16.1 Glycolysis Is an Energy-Conversion Pathway in Many Organisms The enzymes of glycolysis are associated with one another Glycolysis can be divided into two parts Hexokinase traps glucose in the cell and begins glycolysis Fructose 1,6-bisphosphate is generated from glucose 6-phosphate The six-carbon sugar is cleaved into two three-carbon fragments Mechanism: Triose phosphate isomerase salvages a three-carbon fragment The oxidation of an aldehyde to an acid powers the formation of a compound with high phosphoryl-transfer potential Mechanism: Phosphorylation is coupled to the oxidation of glyceraldehyde 3-phosphate by a thioester intermediate ATP is formed by phosphoryl transfer from 1,3-bisphosphoglycerate Additional ATP is generated with the formation of pyruvate Two ATP molecules are formed in the conversion of glucose into pyruvate NAD+ is regenerated from the metabolism of pyruvate Fermentations provide usable energy in the absence of oxygen Fructose is converted into glycolytic intermediates by fructokinase Excessive fructose consumption can lead to pathological conditions Galactose is converted into glucose 6-phosphate 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 Aerobic glycolysis is a property of rapidly growing cells Cancer and endurance 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 alanine formed by contracting muscle are used by other organs Glycolysis and gluconeogenesis are evolutionarily intertwined APPENDIX Biochemistry in Focus: Triose phosphate isomerase deficiency (TPID) APPENDIX Biochemistry in Focus: Pyruvate carboxylase deficiency (PCD) APPENDIX Problem-Solving Strategies Chapter 17 The Citric Acid Cycle 17.1 The Pyruvate Dehydrogenase Complex Links Glycolysis to the Citric Acid Cycle Mechanism: The synthesis of acetyl coenzyme A from pyruvate requires three enzymes and five coenzymes Flexible linkages allow lipoamide to move between different active sites 17.2 The Citric Acid Cycle Oxidizes Two-Carbon Units Citrate synthase forms citrate from oxaloacetate and acetyl coenzyme A Mechanism: The mechanism of citrate synthase prevents undesirable reactions Citrate is isomerized into isocitrate Isocitrate is oxidized and decarboxylated to alpha-ketoglutarate Succinyl coenzyme A is formed by the oxidative decarboxylation of alpha-ketoglutarate A compound with high phosphoryl-transfer potential is generated from succinyl coenzyme A Mechanism: Succinyl coenzyme A synthetase transforms types of biochemical energy Oxaloacetate is regenerated by the oxidation of succinate The citric acid cycle produces high-transfer-potential electrons, ATP, and CO2 17.3 Entry to the Citric Acid Cycle and Metabolism Through It Are Controlled The pyruvate dehydrogenase complex is regulated allosterically and by reversible phosphorylation The citric acid cycle is controlled at several points Defects in the citric acid cycle contribute to the development of cancer An enzyme in lipid metabolism is hijacked to inhibit pyruvate dehydrogenase activity 17.4 The Citric Acid Cycle Is a Source of Biosynthetic Precursors The citric acid cycle must be capable of being rapidly replenished The disruption of pyruvate metabolism is the cause of beriberi and poisoning by mercury and arsenic The citric acid cycle may have evolved from preexisting pathways 17.5 The Glyoxylate Cycle Enables Plants and Bacteria to Grow on Acetate APPENDIX Biochemistry in Focus: New treatments for tuberculosis may be on the horizon APPENDIX Problem-Solving Strategies Chapter 18 Oxidative Phosphorylation 18.1 Eukaryotic Oxidative Phosphorylation Takes Place in Mitochondria Mitochondria are bounded by a double membrane Mitochondria are the result of an endosymbiotic event 18.2 Oxidative Phosphorylation Depends on Electron Transfer The electron-transfer potential of an electron is measured as redox potential Electron flow from NADH to molecular oxygen powers the formation of a proton gradient 18.3 The Respiratory Chain Consists of Four Complexes: Three Proton Pumps and a Physical Link to the Citric Acid Cycle Iron–sulfur clusters are common components of the electron-transport chain The high-potential electrons of NADH enter the respiratory chain at NADH-Q oxidoreductase Ubiquinol is the entry point for electrons from FADH2 of flavoproteins Electrons flow from ubiquinol to cytochrome c through Q-cytochrome c oxidoreductase The Q cycle funnels electrons from a two-electron carrier to a one-electron carrier and pumps protons Cytochrome c oxidase catalyzes the reduction of molecular oxygen to water Much of the electron-transport chain is organized into a complex called the respirasome Toxic derivatives of molecular oxygen such as superoxide radicals are scavenged by protective enzymes Electrons can be transferred between groups that are not in contact The conformation of cytochrome c 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 c 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 NADH enter mitochondria by shuttles The entry of ADP 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 phosphorylation is determined by the need for ATP ATP synthase can be regulated Regulated uncoupling leads to the generation of heat Reintroduction of UCP-1 into pigs may be economically valuable Oxidative phosphorylation 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 APPENDIX Biochemistry in Focus: Leber hereditary optic neuropathy can result from defects in Complex I Chapter 19 The Light Reactions of Photosynthesis 19.1 Photosynthesis Takes Place in Chloroplasts The primary events of photosynthesis take place in thylakoid membranes Chloroplasts arose from an endosymbiotic event 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–NADP+ reductase converts NADP+ 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 The activity of chloroplast ATP synthase is regulated Cyclic electron flow through photosystem I leads to the production of ATP instead of NADPH The absorption of eight photons yields one O2, 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 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 Artificial photosynthetic systems may provide clean, renewable energy APPENDIX Biochemistry in Focus: Increasing the efficiency of photosynthesis will increase crop yields APPENDIX Problem-Solving Strategies Chapter 20 The Calvin Cycle and the Pentose Phosphate Pathway 20.1 The Calvin Cycle Synthesizes Hexoses from Carbon Dioxide and Water Carbon dioxide reacts with ribulose 1,5-bisphosphate to form two molecules of 3-phosphoglycerate Rubisco activity depends on magnesium and carbamate Rubisco activase is essential for rubisco activity Rubisco also catalyzes a wasteful oxygenase reaction: Catalytic imperfection Hexose phosphates are made from phosphoglycerate, and ribulose 1,5-bisphosphate is regenerated Three ATP and two NADPH molecules are used to bring carbon dioxide to the level of a hexose Starch and sucrose are the major carbohydrate stores in plants 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 oxidative phase of the pentose phosphate pathway is controlled by the level of NADP+ The flow of glucose 6-phosphate depends on the need for NADPH, ribose 5-phosphate, and ATP The pentose phosphate pathway is required for rapid cell growth 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 APPENDIX Biochemistry in Focus APPENDIX Biochemistry in Focus: Hummingbirds and the pentose phosphate pathway APPENDIX Problem-Solving Strategies Chapter 21 Glycogen Metabolism 21.1 Glycogen Breakdown Requires the Interplay of Several Enzymes Phosphorylase catalyzes the phosphorolytic cleavage of glycogen to release glucose 1-phosphate Mechanism: Pyridoxal phosphate participates in the phosphorolytic cleavage of glycogen A debranching enzyme also is needed for the breakdown of glycogen Phosphoglucomutase converts glucose 1-phosphate into glucose 6-phosphate The liver contains glucose 6-phosphatase, a hydrolytic enzyme absent from muscle 21.2 Phosphorylase Is Regulated by Allosteric Interactions and Reversible Phosphorylation Liver phosphorylase produces glucose for use by other tissues Muscle phosphorylase is regulated by the intracellular energy charge Biochemical characteristics of muscle fiber types differ Phosphorylation promotes the conversion of phosphorylase b to phosphorylase a Phosphorylase kinase is activated by phosphorylation and calcium ions An isomeric form of glycogen phosphorylase exists in the brain 21.3 Epinephrine and Glucagon Signal the Need for Glycogen Breakdown G proteins transmit the signal for the initiation of glycogen breakdown Glycogen breakdown must be rapidly turned off when necessary The regulation of glycogen phosphorylase became more sophisticated as the enzyme evolved 21.4 Glycogen Is Synthesized and Degraded by Different Pathways UDP-glucose is an activated form of glucose Glycogen synthase catalyzes the transfer of glucose from UDP-glucose to a growing chain A branching enzyme forms 〈-1,6 linkages Glycogen synthase is the key regulatory enzyme in glycogen synthesis Glycogen is an efficient storage form of glucose 21.5 Glycogen Breakdown and Synthesis Are Reciprocally Regulated Protein phosphatase 1 reverses the regulatory effects of kinases on glycogen metabolism Insulin stimulates glycogen synthesis by inactivating glycogen synthase kinase Glycogen metabolism in the liver regulates the blood-glucose concentration A biochemical understanding of glycogen-storage diseases is possible APPENDIX Biochemistry in Focus: McArdle disease results from a lack of skeletal muscle glycogen phosphorylase APPENDIX Problem-Solving Strategies Chapter 22 Fatty Acid Metabolism 22.1 Triacylglycerols Are Highly Concentrated Energy Stores Dietary lipids are digested by pancreatic lipases Dietary lipids are transported in chylomicrons 22.2 The Use of Fatty Acids as Fuel Requires Three Stages of Processing Triacylglycerols are hydrolyzed by hormone-stimulated lipases Free fatty acids and glycerol are released into the blood Fatty acids are linked to coenzyme A before they are oxidized Carnitine carries long-chain activated fatty acids into the mitochondrial matrix Acetyl CoA, NADH, and FADH2 are generated in each round of fatty acid oxidation The complete oxidation of palmitate yields 106 molecules of ATP 22.3 Unsaturated and Odd-Chain Fatty Acids Require Additional Steps for Degradation An isomerase and a reductase are required for the oxidation of unsaturated fatty acids Odd-chain fatty acids yield propionyl CoA in the final thiolysis step Vitamin B12 contains a corrin ring and a cobalt atom Mechanism: Methylmalonyl CoA mutase catalyzes a rearrangement to form succinyl CoA Fatty acids are also oxidized in peroxisomes Some fatty acids may contribute to the development of pathological conditions 22.4 Ketone Bodies Are a Fuel Source Derived from Fats Ketone bodies are a major fuel in some tissues Animals cannot convert fatty acids into glucose 22.5 Fatty Acids Are Synthesized by Fatty Acid Synthase Fatty acids are synthesized and degraded by different pathways The formation of malonyl CoA is the committed step in fatty acid synthesis Intermediates in fatty acid synthesis are attached to an acyl carrier protein Fatty acid synthesis consists of a series of condensation, reduction, dehydration, and reduction reactions Fatty acids are synthesized by a multifunctional enzyme complex in animals The synthesis of palmitate requires 8 molecules of acetyl CoA, 14 molecules of NADPH, and 7 molecules of ATP Citrate carries acetyl groups from mitochondria to the cytoplasm for fatty acid synthesis Several sources supply NADPH for fatty acid synthesis Fatty acid metabolism is altered in tumor cells Triacylglycerols may become an important renewable energy source 22.6 The Elongation and Unsaturation of Fatty Acids are Accomplished by Accessory Enzyme Systems Membrane-bound enzymes generate unsaturated fatty acids Eicosanoid hormones are derived from polyunsaturated fatty acids Variations on a theme: Polyketide and nonribosomal peptide synthetases resemble fatty acid synthase 22.7 Acetyl CoA Carboxylase Plays a Key Role in Controlling Fatty Acid Metabolism Acetyl CoA carboxylase is regulated by conditions in the cell Acetyl CoA carboxylase is regulated by a variety of hormones AMP-activated protein kinase is a key regulator of metabolism APPENDIX Biochemistry in Focus: Ethanol consumption results in triacylglycerol accumulation in the liver APPENDIX Problem-Solving Strategies Chapter 23 Protein Turnover and Amino Acid Catabolism 23.1 Proteins are Degraded to Amino Acids The digestion of dietary proteins begins in the stomach and is completed in the intestine Cellular proteins are degraded at different rates 23.2 Protein Turnover Is Tightly Regulated Ubiquitin tags proteins for destruction 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 23.3 The First Step in Amino Acid Degradation Is the Removal of Nitrogen Alpha-amino groups are converted into ammonium ions by the oxidative deamination of glutamate Mechanism: Pyridoxal phosphate forms Schiff-base intermediates in aminotransferases Aspartate aminotransferase is an archetypal pyridoxal-dependent transaminase Blood levels of aminotransferases serve a diagnostic function Pyridoxal phosphate enzymes catalyze a wide array of reactions Serine and threonine can be directly deaminated Peripheral tissues transport nitrogen to the liver 23.4 Ammonium Ion Is Converted into Urea in Most Terrestrial Vertebrates The urea cycle begins with the formation of carbamoyl phosphate Carbamoyl phosphate synthetase is the key regulatory enzyme for urea synthesis Carbamoyl phosphate reacts with ornithine to begin the urea cycle The urea cycle is linked to gluconeogenesis Urea-cycle enzymes are evolutionarily related to enzymes in other metabolic pathways Inherited defects of the urea cycle cause hyperammonemia and can lead to brain damage Urea is not the only means of disposing of excess nitrogen 23.5 Carbon Atoms of Degraded Amino Acids Emerge as Major Metabolic Intermediates Pyruvate is an entry point into metabolism for a number of amino acids Oxaloacetate is an entry point into metabolism for aspartate and asparagine Alpha-ketoglutarate is an entry point into metabolism for five-carbon amino acids Succinyl coenzyme A is a point of entry for several amino acids Methionine degradation requires the formation of a key methyl donor, S-adenosylmethionine Threonine deaminase initiates the degradation of threonine The branched-chain amino acids yield acetyl CoA, acetoacetate, or propionyl CoA Oxygenases are required for the degradation of aromatic amino acids Protein metabolism helps to power the flight of migratory birds 23.6 Inborn Errors of Metabolism Can Disrupt Amino Acid Degradation Phenylketonuria is one of the most common metabolic disorders Determining the basis of the neurological symptoms of phenylketonuria is an active area of research APPENDIX Biochemistry in Focus: Methylmalonic acidemia results from an inborn error of metabolism APPENDIX Problem-Solving Strategies Part III SYNTHESIZING THE MOLECULES OF LIFE Chapter 24 The Biosynthesis of Amino Acids 24.1 Nitrogen Fixation: Microorganisms Use ATP and a Powerful Reductant to Reduce Atmospheric Nitrogen to Ammonia The iron–molybdenum cofactor of nitrogenase binds and reduces atmospheric nitrogen Ammonium ion is assimilated into an amino acid through glutamate and glutamine 24.2 Amino Acids Are Made from Intermediates of the Citric Acid Cycle and Other Major Pathways Human beings can synthesize some amino acids but must obtain others from their diet Aspartate, alanine, and glutamate are formed by the addition of an amino group to an alpha-ketoacid A common step determines the chirality of all amino acids The formation of asparagine from aspartate requires an adenylated intermediate Glutamate is the precursor of glutamine, proline, and arginine 3-Phosphoglycerate is the precursor of serine, cysteine, and glycine Tetrahydrofolate carries activated one-carbon units at several oxidation levels S-Adenosylmethionine is the major donor of methyl groups Cysteine is synthesized from serine and homocysteine High homocysteine levels correlate with vascular disease Shikimate and chorismate are intermediates in the biosynthesis of aromatic amino acids Tryptophan synthase illustrates substrate channeling in enzymatic catalysis 24.3 Feedback Inhibition Regulates Amino Acid Biosynthesis Branched pathways require sophisticated regulation The sensitivity of glutamine synthetase to allosteric regulation is altered by covalent modification 24.4 Amino Acids Are Precursors of Many Biomolecules Glutathione, a gamma-glutamyl peptide, serves as a sulfhydryl buffer and an antioxidant Nitric oxide, a short-lived signal molecule, is formed from arginine Amino acids are precursors for a number of neurotransmitters Porphyrins are synthesized from glycine and succinyl coenzyme A Porphyrins accumulate in some inherited disorders of porphyrin metabolism APPENDIX Biochemistry in Focus: Tyrosine is a precursor for human pigments APPENDIX Problem-Solving Strategies Chapter 25 Nucleotide Biosynthesis 25.1 The Pyrimidine Ring Is Assembled de Novo or Recovered by Salvage Pathways Bicarbonate and other oxygenated carbon compounds are activated by phosphorylation The side chain of glutamine can be hydrolyzed to generate ammonia Intermediates can move between active sites by channeling Orotate acquires a ribose ring from PRPP to form a pyrimidine nucleotide and is converted into uridylate Nucleotide mono-, di-, and triphosphates are interconvertible CTP is formed by amination of UTP Salvage pathways recycle pyrimidine bases 25.2 Purine Bases Can Be Synthesized de Novo or Recycled by Salvage Pathways The purine ring system is assembled on ribose phosphate The purine ring is assembled by successive steps of activation by phosphorylation followed by displacement AMP and GMP are formed from IMP Enzymes of the purine synthesis pathway associate with one another in vivo Salvage pathways economize intracellular energy expenditure 25.3 Deoxyribonucleotides Are Synthesized by the Reduction of Ribonucleotides Through a Radical Mechanism Mechanism: A tyrosyl radical is critical to the action of ribonucleotide reductase Stable radicals other than tyrosyl radical are employed by other ribonucleotide reductases Thymidylate is formed by the methylation of deoxyuridylate Dihydrofolate reductase catalyzes the regeneration of tetrahydrofolate, a one-carbon carrier Several valuable anticancer drugs block the synthesis of thymidylate 25.4 Key Steps in Nucleotide Biosynthesis Are Regulated by Feedback Inhibition Pyrimidine biosynthesis is regulated by aspartate transcarbamoylase The synthesis of purine nucleotides is controlled by feedback inhibition at several sites The synthesis of deoxyribonucleotides is controlled by the regulation of ribonucleotide reductase 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 Folic acid deficiency promotes birth defects such as spina bifida APPENDIX Biochemistry in Focus: Uridine plays a role in caloric homeostasis APPENDIX Problem-Solving Strategies Chapter 26 The Biosynthesis of Membrane Lipids and Steroids 26.1 Phosphatidate Is a Common Intermediate in the Synthesis of Phospholipids and Triacylglycerols The synthesis of phospholipids requires an activated intermediate Some phospholipids are synthesized from an activated alcohol Phosphatidylcholine is an abundant phospholipid Excess choline is implicated in the development of heart disease Base-exchange reactions can generate phospholipids Sphingolipids are synthesized from ceramide Gangliosides are carbohydrate-rich sphingolipids that contain acidic sugars Sphingolipids confer diversity on lipid structure and function Respiratory distress syndrome and Tay–Sachs disease result from the disruption of lipid metabolism Ceramide metabolism stimulates tumor growth Phosphatidic acid phosphatase is a key regulatory enzyme in lipid metabolism 26.2 Cholesterol Is Synthesized from Acetyl Coenzyme A in Three Stages The synthesis of mevalonate, which is activated as isopentenyl pyrophosphate, initiates the synthesis of cholesterol Squalene (C30) is synthesized from six molecules of isopentenyl pyrophosphate (C5) Squalene cyclizes to form cholesterol 26.3 The Complex Regulation of Cholesterol Biosynthesis Takes Place at Several Levels Lipoproteins transport cholesterol and triacylglycerols throughout the organism Low-density lipoproteins play a central role in cholesterol metabolism The absence of the LDL receptor leads to hypercholesterolemia and atherosclerosis Mutations in the LDL receptor prevent LDL release and result in receptor destruction Inability to transport cholesterol from the lysosome causes Niemann-Pick disease Cycling of the LDL receptor is regulated HDL appears to protect against atherosclerosis The clinical management of cholesterol levels can be understood at a biochemical level 26.4 Important Biochemicals Are Synthesized from Cholesterol and Isoprene Letters identify the steroid rings and numbers identify the carbon atoms Steroids are hydroxylated by cytochrome P450 monooxygenases that use NADPH and O2 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 Five-carbon units are joined to form a wide variety of biomolecules Some isoprenoids have industrial applications APPENDIX Biochemistry in Focus: Excess ceramides may cause insulin insensitivity APPENDIX Problem-Solving Strategies Chapter 27 The Integration of Metabolism 27.1 Caloric Homeostasis Is a Means of Regulating Body Weight 27.2 The Brain Plays a Key Role in Caloric Homeostasis Signals from the gastrointestinal tract induce feelings of satiety Leptin and insulin regulate long-term control over caloric homeostasis Leptin is one of several hormones secreted by adipose tissue Leptin resistance may be a contributing factor to obesity Dieting is used to combat obesity 27.3 Diabetes Is a Common Metabolic Disease Often Resulting from Obesity Insulin initiates a complex signal-transduction pathway in muscle Metabolic syndrome often precedes type 2 diabetes Excess fatty acids in muscle modify metabolism Insulin resistance in muscle facilitates pancreatic failure Metabolic derangements in type 1 diabetes result from insulin insufficiency and glucagon excess 27.4 Exercise Beneficially Alters the Biochemistry of Cells Mitochondrial biogenesis is stimulated by muscular activity Fuel choice during exercise is determined by the intensity and duration of activity 27.5 Food Intake and Starvation Induce Metabolic Changes The starved–fed cycle is the physiological response to a fast 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 APPENDIX Biochemistry in Focus: Adipokines help to regulate metabolism in the liver APPENDIX Biochemistry in Focus: Exercise alters muscle and whole-body metabolism APPENDIX Problem-Solving Strategies Chapter 28 Drug Development 28.1 Compounds Must Meet Stringent Criteria to be Developed Into Drugs Drug must be potent and selective Drugs must have suitable properties to reach their targets Toxicity can limit drug effectiveness 28.2 Drug Candidates Can Be Discovered by Serendipity, Screening, or Design Serendipitous observations can drive drug development Natural products are a valuable source of drugs and drug leads Screening libraries of synthetic compounds expands the opportunity for identification of drug leads Drugs can be designed on the basis of three-dimensional structural information about their targets 28.3 Genomic Analyses Can Aid Drug Discovery Potential targets can be identified in the human proteome Animal models can be developed to test the validity of potential drug targets Potential targets can be identified in the genomes of pathogens Genetic differences influence individual responses to drugs 28.4 The Clinical Development of Drugs Proceeds Through Several Phases Clinical trials are time consuming and expensive The evolution of drug resistance can limit the utility of drugs for infectious agents and cancer APPENDIX Biochemistry in Focus: Monoclonal antibodies: Expanding the drug developer’s toolbox Chapter 29 DNA Replication, Repair, and Recombination 29.1 DNA Replication Proceeds by the Polymerization of Deoxyribonucleoside Triphosphates Along a Template DNA polymerases require a template and a primer All DNA polymerases have structural features in common Two bound metal ions participate in the polymerase reaction The specificity of replication is dictated by complementarity of shape between bases An RNA primer synthesized by primase enables DNA synthesis to begin One strand of DNA is made continuously, whereas the other strand is synthesized in fragments DNA ligase joins ends of DNA in duplex regions The separation of DNA strands requires specific helicases and ATP hydrolysis 29.2 DNA Unwinding and Supercoiling Are Controlled by Topoisomerases The linking number of DNA, a topological property, determines the degree of supercoiling Topoisomerases prepare the double helix for unwinding Type I topoisomerases relax supercoiled structures Type II topoisomerases can introduce negative supercoils through coupling to ATP hydrolysis 29.3 DNA Replication Is Highly Coordinated DNA replication requires highly processive polymerases The leading and lagging strands are synthesized in a coordinated fashion DNA replication in Escherichia coli begins at a unique site and proceeds through initiation, elongation, and termination DNA synthesis in eukaryotes is initiated at multiple sites Telomeres are unique structures at the ends of linear chromosomes Telomeres are replicated by telomerase, a specialized polymerase that carries its own RNA template 29.4 Many Types of DNA Damage Can Be Repaired Errors can arise in DNA replication Bases can be damaged by oxidizing agents, alkylating agents, and light 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 29.5 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 APPENDIX Biochemistry in Focus: Identifying amino acids crucial for DNA replication fidelity Chapter 30 RNA Synthesis and Processing 30.1 RNA Polymerases Catalyze Transcription RNA chains are formed de novo and grow in the 5′-to-3′ 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 30.2 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 Enhancer sequences can stimulate transcription at start sites thousands of bases away 30.3 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 30.4 The Discovery of Catalytic RNA was Revealing in Regard to Both Mechanism and Evolution APPENDIX Biochemistry in Focus: Discovering enzymes made of RNA Chapter 31 Protein Synthesis 31.1 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 31.2 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 31.3 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 The start signal is usually AUG preceded by several bases that pair with 16S rRNA Bacterial protein synthesis is initiated by formylmethionyl transfer RNA Formylmethionyl-tRNAf is placed in the P 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 31.4 Eukaryotic Protein Synthesis Differs from Bacterial Protein Synthesis Primarily in Translation Initiation Mutations in initiation factor 2 cause a curious pathological condition 31.5 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 Some toxins modify 28S ribosomal RNA 31.6 Ribosomes Bound to the Endoplasmic Reticulum Manufacture Secretory and Membrane Proteins Protein synthesis begins on ribosomes that are free in the cytoplasm Signal sequences mark proteins for translocation across the endoplasmic reticulum membrane Transport vesicles carry cargo proteins to their final destination APPENDIX Biochemistry in Focus: Selective control of gene expression by ribosomes APPENDIX Problem-Solving Strategies Chapter 32 The Control of Gene Expression in Prokaryotes 32.1 Many DNA-Binding Proteins Recognize Specific DNA Sequences The helix-turn-helix motif is common to many prokaryotic DNA-binding proteins 32.2 Prokaryotic DNA-Binding Proteins Bind Specifically to Regulatory Sites in Operons An operon consists of regulatory elements and protein-encoding genes The lac repressor protein in the absence of lactose binds to the operator and blocks transcription Ligand binding can induce structural changes in regulatory proteins The operon is a common regulatory unit in prokaryotes Transcription can be stimulated by proteins that contact RNA polymerase 32.3 Regulatory Circuits Can Result in Switching Between Patterns of Gene Expression The ⎣ repressor regulates its own expression A circuit based on the ⎣ repressor and Cro forms a genetic switch Many prokaryotic cells release chemical signals that regulate gene expression in other cells Biofilms are complex communities of prokaryotes 32.4 Gene Expression Can Be Controlled at Posttranscriptional Levels Attenuation is a prokaryotic mechanism for regulating transcription through the modulation of nascent RNA secondary structure APPENDIX Biochemistry in Focus: Regulating gene expression through proteolysis Chapter 33 The Control of Gene Expression in Eukaryotes 33.1 Eukaryotic DNA Is Organized into Chromatin Nucleosomes are complexes of DNA and histones DNA wraps around histone octamers to form nucleosomes 33.2 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 33.3 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 Transcriptional repression can be achieved through histone deacetylation and other modifications 33.4 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 APPENDIX Biochemistry in Focus: A mechanism for consolidating epigenetic modifications Part IV RESPONDING TO ENVIRONMENTAL CHANGES (Online Only) Chapter 34 Sensory Systems (Online Only) 34.1 A Wide Variety of Organic Compounds Are Detected by Olfaction Olfaction is mediated by an enormous family of seven-transmembrane-helix receptors Odorants are decoded by a combinatorial mechanism 34.2 Taste Is a Combination of Senses That Function by Different Mechanisms Sequencing of the human genome led to the discovery of a large family of 7TM bitter receptors A heterodimeric 7TM receptor responds to sweet compounds Umami, the taste of glutamate and aspartate, is mediated by a heterodimeric receptor related to the sweet receptor Salty tastes are detected primarily by the passage of sodium ions through channels Sour tastes arise from the effects of hydrogen ions (acids) on channels 34.3 Photoreceptor Molecules in the Eye Detect Visible Light Rhodopsin, a specialized 7TM receptor, absorbs visible light Light absorption induces a specific isomerization of bound 11-cis-retinal Light-induced lowering of the calcium level coordinates recovery Color vision is mediated by three cone receptors that are homologs of rhodopsin Rearrangements in the genes for the green and red pigments lead to “color blindness” 34.4 Hearing Depends on the Speedy Detection of Mechanical Stimuli Hair cells use a connected bundle of stereocilia to detect tiny motions Mechanosensory channels have been identified in Drosophila and vertebrates 34.5 Touch Includes the Sensing of Pressure, Temperature, and Other Factors Studies of capsaicin reveal a receptor for sensing high temperatures and other painful stimuli APPENDIX Biochemistry in Focus: Binding many palatable tastants with a single receptor Chapter 35 The Immune System (Online Only) 35.1 Antibodies Possess Distinct Antigen-Binding and Effector Units 35.2 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 35.3 Diversity Is Generated by Gene Rearrangements J (joining) genes and D (diversity) genes increase antibody diversity More than 108 antibodies can be formed by combinatorial association and somatic mutation The oligomerization of antibodies expressed on the surfaces of immature B cells triggers antibody secretion Different classes of antibodies are formed by the hopping of VH genes 35.4 Major-Histocompatibility-Complex Proteins Present Peptide Antigens on Cell Surfaces for Recognition by T-Cell Receptors Peptides presented by MHC proteins occupy a deep groove flanked by alpha helices T-cell receptors are antibody-like proteins containing variable and constant regions CD8 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 T-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 35.5 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 APPENDIX Biochemistry in Focus Chapter 36 Molecular Motors (Online Only) 36.1 Most Molecular-Motor Proteins Are Members of the P-Loop NTPase Superfamily Molecular motors are generally oligomeric proteins with an ATPase core and an extended structure ATP binding and hydrolysis induce changes in the conformation and binding affinity of motor proteins 36.2 Myosins Move Along Actin Filaments Actin is a polar, self-assembling, dynamic polymer Myosin head domains bind to actin filaments Motions of single motor proteins 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 36.3 Kinesin and Dynein Move Along Microtubules Microtubules are hollow cylindrical polymers Kinesin motion is highly processive 36.4 A Rotary Mo [Show More]

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