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• Title:Biochemistry / Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto, Jr., Lubert Stryer.
  
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• Author/Creator:Berg, Jeremy M. (Jeremy Mark), 1958- author.
  
• Other Contributors/Collections:Tymoczko, John L., 1948-2019, author.
  Gatto, Gregory J., Jr. (Gregory Joseph), author.
  Stryer, Lubert, author.
  
• Published/Created:New York : W.H. Freeman, [2019]
  

• Holdings

  Holdings Record Display

  • Location: c.1  Temporarily shelved at WOODWARD LIBRARY reserve collectionWhere is this?
    
  • Call Number: QU4 .B493b 2019
    
  • Number of Items:1
    
  • Status:Available
    

   
• Library of Congress Subjects:Biochemistry--Textbooks.
  
• Medical Subjects: Biochemistry.
  Biochemical Phenomena.
  
• Edition:Ninth edition.
  
• Description:xlii, 1,096, A45, B60, C45 pages ; 29 cm
  
• Summary:"For four decades, this extraordinary textbook played an pivotal role in the way biochemistry is taught, offering exceptionally clear writing, innovative graphics, coverage of the latest research techniques and advances, and a signature emphasis on physiological and medical relevance. Those defining features are at the heart of this edition."-- Provided by publisher.
  
• Notes:Includes bibliographical references and index.
  
• ISBN:1319114679 hardcover
  9781319114671 hardcover
  
• Contents:Machine generated contents note: 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
  formation of the DNA double helix as a key example
  double helix can form from its component strands
  Covalent and noncovalent bonds are important for the structure and stability of biological molecules
  double helix is an expression of the rules of chemistry
  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. 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
  2.1. Proteins Are Built from a Repertoire of
  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
  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. Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure
  Amino acids have different propensities for forming α helices, β 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
  proteome is the functional representation of the genome
  3.1. Purification of Proteins Is an Essential First Step in Understanding Their Function
  assay: How do we recognize the protein 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
  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
  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
  4.1. 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. Pair of Nucleic Acid Strands with Complementary Sequences Can Form a Double-Helical Structure
  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. Double Helix Facilitates the Accurate Transmission of Hereditary Information
  Differences in DNA density established the validity of the semiconservative replication hypothesis
  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
  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
  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
  5.1. 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
  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 lipase are key tools in forming recombinant DNA molecules
  Plasmids and A 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
  genomes of organisms ranging from bacteria to multicellular eukaryotes have been sequenced
  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
  6.1. Homologs Are Descended from a Common Ancestor
  6.2. Statistical Analysis of Sequence Alignments Can Detect Homology
  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
  Contents note continued: 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
  Appendix: Problem-Solving Strategies
  7.1. Binding of Oxygen by Heme Iron
  Changes in heme electronic structure upon oxygen binding are the basis for functional imaging studies
  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 α1β1-α2β2 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
  accumulation of free α-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
  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
  free-energy change provides information about the spontaneity but not the rate of a reaction
  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
  formation of an enzyme-substrate complex is the first step in enzymatic catalysis
  active sites of enzymes have some common features
  binding energy between enzyme and substrate is important for catalysis
  8.4. Michaelis-Menten Model Accounts for the Kinetic Properties of Many Enzymes
  Kinetics is the study of reaction rates
  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
  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: Biochemistry in Focus
  Appendix: Problem-Solving Strategies
  few basic catalytic principles are used by many enzymes
  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
  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
  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
  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
  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
  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's 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
  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 γ-carboxyglutamate
  clotting process must be precisely regulated
  Hemophilia revealed an early step in clotting
  Appendix: Biochemistry in Focus
  Appendix: Problem-Solving Strategies
  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
  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
  Contents note continued: Influenza virus binds to sialic acid residues
  Appendix: Biochemistry in Focus
  Appendix: Problem-Solving Strategies
  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
  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
  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
  expression of transporters largely defines the metabolic activities of a given cell type
  13.1. 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
  structure of a potassium ion channel is an archetype for many ion-channel structures
  structure of the potassium ion channel reveals the basis of ion specificity
  structure of the potassium ion channel explains its rapid rate of transport
  Voltage gating requires substantial conformational changes in specific ion-channel domains
  channel can be inactivated by occlusion of the pore: the ball-and-chain model
  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
  Appendix: Problem-Solving Strategies
  Signal transduction depends on molecular circuits
  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
  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
  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
  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
  15.1. Metabolism Is Composed of Many Coupled, Interconnecting Reactions
  Metabolism consists of energy-yielding and energy- requiring reactions
  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
  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
  ATP may have roles other than in energy and signal transduction
  15.3. 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
  Glucose is generated from dietary carbohydrates
  Glucose is an important fuel for most organisms
  16.1. Glycolysis Is an Energy-Conversion Pathway in Many Organisms
  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
  six-carbon sugar is cleaved into two three-carbon fragments
  Mechanism: Triose phosphate isomerase salvages a three-carbon fragment
  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. Glycolytic Pathway Is Tightly Controlled
  Glycolysis in muscle is regulated to meet the need for ATP
  regulation of glycolysis in the liver illustrates the biochemical versatility of the liver
  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
  conversion of pyruvate into phosphoenolpyruvate begins with the formation of oxaloacetate
  Oxaloacetate is shuttled into the cytoplasm and converted into phosphoenolpyruvate
  conversion of fructose 1,6-bisphosphate into fructose 6-phosphate and orthophosphate is an irreversible step
  generation of free glucose is an important control point
  Contents note continued: 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
  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
  Biochemistry in Focus 1
  Biochemistry in Focus 2
  Appendix: Problem-Solving Strategies
  citric acid cycle harvests high-energy electrons
  17.1. 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. 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
  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
  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
  pyruvate dehydrogenase complex is regulated allosterically and by reversible phosphorylation
  citric acid cycle is controlled at several points
  Defects in the citric acid cycle contribute to the development of cancer
  enzyme in lipid metabolism is hijacked to inhibit pyruvate dehydrogenase activity
  17.4. Citric Acid Cycle Is a Source of Biosynthetic Precursors
  citric acid cycle must be capable of being rapidly replenished
  disruption of pyruvate metabolism is the cause of beriberi and poisoning by mercury and arsenic
  citric acid cycle may have evolved from preexisting pathways
  17.5. Glyoxylate Cycle Enables Plants and Bacteria to Grow on Acetate
  Appendix: Biochemistry In Focus
  Biochemistry in Focus 1
  Biochemistry in Focus 2
  Appendix: Problem-Solving Strategies
  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
  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. 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
  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
  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
  Most 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
  conformation of cytochrome c has remained essentially constant for more than a billion years
  18.4. 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
  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. Regulation of Cellular Respiration Is Governed Primarily by the Need for ATP
  complete oxidation of glucose yields about 30 molecules of ATP
  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
  Appendix: Problem-Solving Strategies
  Photosynthesis converts light energy into chemical energy
  19.1. Photosynthesis Takes Place in Chloroplasts
  primary events of photosynthesis take place in thylakoid membranes
  Chloroplasts arose from an endosymbiotic event
  19.2. Light Absorption by Chlorophyll Induces Electron Transfer
  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. Proton Gradient across the Thylakoid Membrane Drives ATP Synthesis
  ATP synthase of chloroplasts closely resembles those of mitochondria and prokaryotes
  activity of chloroplast ATP synthase is regulated
  Cyclic electron flow through photosystem I leads to the production of ATP instead of NADPH
  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
  components of photosynthesis are highly organized
  Many herbicides inhibit the light reactions of photosynthesis
  19.6. Ability to Convert Light into Chemical Energy Is Ancient
  Artificial photosynthetic systems may provide clean, renewable energy
  Appendix: Biochemistry in Focus
  Appendix: Problem-Solving Strategies
  20.1. 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. 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
  C4 pathway of tropical plants accelerates photosynthesis by concentrating carbon dioxide
  Crassulacean acid metabolism permits growth in arid ecosystems
  20.3. 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
  pentose phosphate pathway and glycolysis are linked by transketolase and transaldolase
  Mechanism: Transketolase and transaldolase stabilize carbanionic intermediates by different mechanisms
  20.4. Metabolism of Glucose 6-Phosphate by the Pentose Phosphate Pathway Is Coordinated with Glycolysis
  rate of the oxidative phase of the pentose phosphate pathway is controlled by the level of NADP+
  flow of glucose 6-phosphate depends on the need for NADPH, ribose 5-phosphate, and ATP
  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
  deficiency of glucose 6-phosphate dehydrogenase confers an evolutionary advantage in some circumstances
  Appendix: Biochemistry In Focus
  Biochemistry in Focus 1
  Biochemistry in Focus 2
  Appendix: Problem-Solving Strategies
  Glycogen metabolism is the regulated release and storage of glucose
  21.1. Glycogen Breakdown Requires the Interplay of Several Enzymes
  Phosphorylase catalyzes the phosphorolytic cleavage of glycogen to release glucose 1-phosphate
  Contents note continued: Mechanism: Pyridoxal phosphate participates in the phosphorolytic cleavage of glycogen
  debranching enzyme also is needed for the breakdown of glycogen
  Phosphoglucomutase converts glucose 1-phosphate into glucose 6-phosphate
  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
  isozymic 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
  regulation of glycogen phosphorylase became more sophisticated as the enzyme evolved
  21.4. Glycogen Synthesis Requires Several Enzymes and Uridine Diphosphate Glucose
  UDP-glucose is an activated form of glucose
  Glycogen synthase catalyzes the transfer of glucose from UDP-glucose to a growing chain
  branching enzyme forms α-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
  biochemical understanding of glycogen-storage diseases is possible
  Appendix: Biochemistry in Focus
  Appendix: Problem-Solving Strategies
  Fatty acid degradation and synthesis mirror each other in their chemical reactions
  22.1. Triacylglycerols Are Highly Concentrated Energy Stores
  Dietary lipids are digested by pancreatic lipases
  Dietary lipids are transported in chylomicrons
  22.2. 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
  complete oxidation of palmitate yields 106 molecules of ATP
  22.3. Unsaturated and Odd-Chain Fatty Acids Require Additional Steps for Degradation
  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
  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
  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 renewal energy source
  22.6. 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
  Appendix: Problem-Solving Strategies
  23.1. Proteins Are Degraded to Amino Acids
  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
  proteasome digests the ubiquitin-tagged proteins
  ubiquitin pathway and the proteasome have prokaryotic counterparts
  Protein degradation can be used to regulate biological function
  23.3. 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
  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
  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
  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
  Appendix: Problem-Solving Strategies
  Amino acid synthesis requires solutions to three key biochemical problems
  24.1. Nitrogen Fixation: Microorganisms Use ATP and a Powerful Reductant to Reduce Atmospheric Nitrogen to Ammonia
  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
  common step determines the chirality of all amino acids
  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
  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
  Contents note continued: Appendix: Problem-Solving Strategies
  Nucleotides can be synthesized by de novo or salvage pathways
  25.1. Pyrimidine Ring Is Assembled de Novo or Recovered by Salvage Pathways
  Bicarbonate and other oxygenated carbon compounds are activated by phosphorylation
  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
  purine ring system is assembled on ribose phosphate
  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
  synthesis of purine nucleotides is controlled by feedback inhibition at several sites
  synthesis of deoxyribonucleotides is controlled by the regulation of ribonucleotide reductase
  25.5. Disruptions in Nucleotide Metabolism Can Cause Pathological Conditions
  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
  Appendix: Problem-Solving Strategies
  26.1. Phosphatidate Is a Common Intermediate in the Synthesis of Phospholipids and Triacylglycerols
  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
  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. 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
  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
  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
  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
  Appendix: Problem-Solving Strategies
  27.1. Caloric Homeostasis Is a Means of Regulating Body Weight
  27.2. 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
  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
  Biochemistry in Focus 1
  Biochemistry in Focus 2
  Appendix: Problem-Solving Strategies
  28.1. Compounds Must Meet Stringent Criteria to Be Developed into Drugs
  Drugs 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. Clinical Development of Drugs Proceeds Through Several Phases
  Clinical trials are time-consuming and expensive
  evolution of drug resistance can limit the utility of drugs for infectious agents and cancer
  Appendix: Biochemistry in Focus
  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
  specificity of replication is dictated by complementarity of shape between bases
  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 lipase joins ends of DNA in duplex regions
  separation of DNA strands requires specific helicases and ATP hydrolysis
  29.2. DNA Unwinding and Supercoiling Are Controlled by Topoisomerases
  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
  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
  presence of thymine instead of uracil in DNA permits the repair of deaminated cytosine
  Contents note continued: 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
  RNA synthesis comprises three stages: Initiation, elongation, and termination
  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
  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
  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. Transcription Products of Eukaryotic Polymerases Are Processed
  RNA polymerase I produces three ribosomal RNAs
  RNA polymerase III produces transfer RNA
  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. Discovery of Catalytic RNA Was Revealing in Regard to Both Mechanism and Evolution
  Appendix: Biochemistry in Focus
  31.1. Protein Synthesis Requires the Translation of Nucleotide Sequences into Amino Acid Sequences
  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. 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
  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
  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. 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 modifiy 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
  Appendix: Problem-Solving Strategies
  32.1. Many DNA-Binding Proteins Recognize Specific DNA Sequences
  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
  operon consists of regulatory elements and protein-encoding genes
  lac repressor protein in the absence of lactose binds to the operator and blocks transcription
  Ligand binding can induce structural changes in regulatory proteins
  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
  λ repressor regulates its own expression
  circuit based on the X 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
  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
  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. Control of Gene Expression Can Require Chromatin Remodeling
  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.