Biochemistry

About this Book Cover Page Accessibility Half Title Page Title Page Copyright Page Dedication Brief Contents Contents Preface Acknowledgments About the Authors Chapter 1 Biochemistry in Space and Time 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 is a key example The double helix can form from its component strands Atoms and molecules undergo random motions that help define the timescales for biochemical interactions Covalent bonds and noncovalent interactions are important for the structure and stability of biological molecules The formation of DNA’s double helix is an expression of the rules of chemistry The laws of thermodynamics govern the behavior of biochemical systems By releasing heat, the formation of the double helix obeys the Second Law of Thermodynamics Double-helix formation can be monitored one molecule at a time 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 DNA Sequencing Is Transforming Biochemistry, Medicine, and Other Fields Genome sequencing has become remarkably fast and inexpensive Characterization of genetic variation between individuals is powerful for many applications The most important function of genomic sequences is to encode proteins Comparing genomes offers great insights into evolution 1.5 Biochemistry Is an Interconnected Human Endeavor End of Chapter Summary Key Terms Problems Chapter 2 Protein Composition and Structure 2.1 Several Properties of Protein Structure Are Key to Their Functional Versatility 2.2 Proteins Are Built from a Repertoire of 20 Amino Acids The diversity of amino acids arises from the different side chains Biochemists postulate several reasons why this set of amino acids is conserved across all species 2.3 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 2.4 Secondary Structure: Polypeptide Chains Can Fold into Regular Structures 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 2.5 Tertiary Structure: Proteins Can Fold into Globular or Fibrous Structures Globular proteins form tightly packed structures Fibrous proteins form extended structures that provide support for cells and tissues 2.6 Quaternary Structure: Polypeptide Chains Can Assemble into Multisubunit Structures 2.7 The 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 Protein misfolding and aggregation are associated with some neurological diseases Posttranslational modifications confer new capabilities to proteins End of Chapter Summary Key Terms Problems Chapter 3 Binding and Molecular Recognition 3.1 Binding Is a Fundamental Process in Biochemistry Binding depends on the concentrations of the binding partners Proteins can selectively bind certain small molecules Binding is a dynamic process involving association and dissociation 3.2 Myoglobin Binds and Stores Oxygen More myoglobin binds oxygen as the oxygen partial pressure is increased A bond is formed between oxygen and iron in heme The structure of myoglobin prevents the release of reactive oxygen species Compared with model compounds, myoglobin discriminates between oxygen and carbon monoxide 3.3 Hemoglobin Is an Efficient Oxygen Carrier Human hemoglobin is an assembly of four myoglobin-like subunits 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 blood cells is crucial in determining the oxygen affinity of hemoglobin Hydrogen ions and carbon dioxide promote the release of oxygen Mutations in genes encoding hemoglobin subunits can result in disease 3.4 The Immune System Depends on Key Binding Proteins The innate immune system recognizes molecules characteristic of pathogens Antibodies bind specific molecules through specific hypervariable loops Antibodies possess distinct antigen-binding and effector units Recombination events equip the adaptive immune system with millions of unique antibodies Major-histocompatibility-complex proteins present peptide antigens on cell surfaces for recognition by T-cell receptors 3.5 Quantitative Terms Can Describe Binding Propensity Dissociation constants are useful in describing binding reactions quantitatively Specificity can be quantified by comparing dissociation constants Kinetic parameters can also describe binding processes End of Chapter Summary Key Terms Problems Chapter 4 Protein Methods 4.1 The Purification of Proteins Is an Essential First Step in Understanding Their Function The 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 A protein purification scheme can be quantitatively evaluated Ultracentrifugation is valuable for separating biomolecules and determining their masses Recombinant DNA technology can make protein purification easier 4.2 Immunology Provides Important Techniques for Investigating 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 4.3 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 approaches to deducing protein structure and function The amino acid sequence of a protein provides valuable information Individual proteins can be identified by mass spectrometry The proteome is the functional representation of the genome 4.4 Peptides Can Be Synthesized by Automated Solid-Phase Methods 4.5 Three-Dimensional Protein Structures Can Be Determined Experimentally 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 can be used to determine the structures of large proteins and macromolecular complexes End of Chapter Summary Key Terms Problems Chapter 5 Enzymes: Core Concepts and Kinetics 5.1 Enzymes Are Powerful and Highly Specific Catalysts Most enzymes are classified by the types of reactions they catalyze Many enzymes require cofactors for activity Enzymes can transform energy from one form into another 5.2 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 5.3 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 Because the transition state collapses randomly, the activation energies determine the accumulation of either product or substrate 5.4 The Michaelis–Menten Model Accounts for the Kinetic Properties of Many Enzymes Kinetics is the study of reaction rates The steady-state assumption aids a description of enzyme kinetics The Michaelis–Menten model explains many observations of enzyme kinetics The Michaelis–Menten equation describes the relationship between initial velocity and substrate concentration Variations in KM can have physiological consequences KM and Vmax values can be determined by several means KM and kcat values are important enzyme characteristics kcat/KM is a measure of catalytic efficiency Most biochemical reactions include multiple substrates Allosteric enzymes often do not obey Michaelis–Menten kinetics Temperature affects enzymatic activity 5.5 Enzymes Can Be Studied One Molecule at a Time Single-molecule kinetics confirm results obtained from ensemble studies Single-molecule studies continue to reveal new information about enzyme molecular dynamics 5.6 Enzymes Can Be Inhibited by Specific Molecules The different types of reversible inhibitors are kinetically distinguishable Transition-state analogs are potent competitive inhibitors Irreversible inhibitors can be used to map the active site Penicillin irreversibly inactivates a key enzyme in bacterial cell-wall synthesis End of Chapter Summary Key Terms Problems Chapter 6 Enzyme Catalytic Strategies 6.1 Enzymes Use a Core Set of Catalytic Strategies 6.2 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 Scientists have dissected the catalytic triad using site-directed mutagenesis Some proteases cleave peptides at other locations besides serine residues Protease inhibitors are important drugs 6.3 Carbonic Anhydrases Make a Fast Reaction Faster Carbonic anhydrase contains a bound zinc ion essential for catalytic activity Catalysis involves zinc activation of a water molecule Rapid regeneration of the active form of carbonic anhydrase depends on proton availability 6.4 Restriction Enzymes Catalyze Highly Specific DNA-Cleavage Reactions Cleavage is by direct 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 6.5 Molecular Motor Proteins 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 Actin forms filaments along which myosin can move End of Chapter Summary Key Terms Problems Chapter 7 Enzyme Regulatory Strategies 7.1 Allosteric Regulation Enables Control of Metabolic Pathways Many 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 7.2 Isozymes Provide a Means of Regulation Specific to Distinct Tissues and Developmental Stages 7.3 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 The phosphorylation states of the proteome can be measured 7.4 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 7.5 Enzymatic Cascades Allow Rapid Responses Such as Blood Clotting 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 The clotting process must be precisely regulated End of Chapter Summary Key Terms Problems Chapter 8 DNA, RNA, and the Flow of Genetic Information 8.1 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 8.2 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 The major and minor grooves are lined by sequence-specific hydrogen-bonding groups Some DNA molecules are circular and supercoiled Single-stranded nucleic acids can adopt elaborate structures 8.3 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 8.4 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 8.5 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 8.6 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 8.7 Most Eukaryotic Genes Are Mosaics of Introns and Exons RNA processing generates mature RNA Many exons encode protein domains End of Chapter Summary Key Terms Problems Chapter 9 Nucleic Acid Methods 9.1 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 9.2 Recombinant DNA Technology Has Revolutionized All Aspects of Biology Restriction enzymes and DNA ligase are key tools in forming recombinant DNA molecules Plasmids and λ phage are choice vectors for DNA cloning in bacteria 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 9.3 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 is a powerful research tool 9.4 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 enables disruption of gene expression and presents new therapeutic opportunities Foreign DNA can be introduced into plants End of Chapter Summary Key Terms Problems Chapter 10 Exploring Evolution and Bioinformatics 10.1 Homologs Are Descended from a Common Ancestor and Can Be Detected by Sequence Alignments Orthologs and paralogs are two different classes of homologous proteins 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 10.2 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 10.3 Evolutionary Trees Can Be Constructed on the Basis of Sequence Information Evolutionary trees can be calibrated using fossil record data Horizontal gene transfer events may explain unexpected branches of the evolutionary tree 10.4 Modern Techniques Make the Experimental Exploration of Evolution Possible Ancient DNA can sometimes be amplified and sequenced Molecular evolution can be examined experimentally End of Chapter Summary Key Terms Problems Chapter 11 Carbohydrates and Glycoproteins 11.1 Monosaccharides Are the Simplest Carbohydrates There are many monosaccharides but they are structurally similar Most monosaccharides exist as interchanging cyclic forms Pyranose and furanose rings can assume different conformations D-Glucose is an important fuel for most organisms Glucose is a reducing sugar and reacts nonenzymatically with hemoglobin Monosaccharides are joined to alcohols and amines through glycosidic linkages by specific enzymes Phosphorylated sugars are key intermediates in metabolism 11.2 Monosaccharides Are Linked to Form Complex Carbohydrates Sucrose, lactose, and maltose are common disaccharides Maltase inhibitors can help to maintain blood glucose homeostasis Human milk oligosaccharides protect newborns from infection Glycogen and starch are storage polysaccharides of glucose Cellulose is the main structural polysaccharide of plants Chitin is the main structural polysaccharide of fungi and arthropods Chitin can be processed to a molecule with a variety of uses 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 have important structural roles Proteoglycans are important components of cartilage Mucins are glycoprotein components of mucus Protein glycosylation takes place in the lumen of the endoplasmic reticulum and in the Golgi complex Specific enzymes are responsible for oligosaccharide assembly Blood groups are based on protein glycosylation patterns Errors in glycosylation can result in pathological conditions Biochemists use several techniques to analyze the oligosaccharide components of glycoproteins 11.4 Lectins Are Specific Carbohydrate-Binding Proteins Lectins promote interactions between cells and within cells Lectins are organized into two large classes Influenza virus binds to sialic acid residues End of Chapter Summary Key Terms Problems Chapter 12 Lipids and Biological Membranes 12.1 Fatty Acids Are Key Constituents of Lipids Fatty acid names are based on their parent hydrocarbons Chain length and degree of unsaturation affect fatty acid properties 12.2 Biological Membranes Are Composed of Three Common Types of Membrane Lipids Phospholipids are the major class of membrane lipids Glycolipids 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 Prokaryotes and Eukaryotes Differ in Their Use of Biological Membranes Eukaryotic cells contain compartments bounded by internal membranes Membrane budding and fusion are highly controlled processes End of Chapter Summary Key Terms Problems 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 Actively Transport Ions and Molecules Across Membranes P-type ATPases couple phosphorylation and conformational changes to pump calcium ions across membranes Digoxin 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 Hyperpolarization-activated ion channels enable pacemaker activity in the heart 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 End of Chapter Summary Key Terms Problems Chapter 14 Signal-Transduction Pathways 14.1 Many Signal-Transduction Pathways Share Common Themes Signal transduction depends on molecular circuits 14.2 Epinephrine 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 Some receptors signal through G proteins that inhibit rather than stimulate adenylate cyclase G-protein βγ-dimers can also directly participate in signaling 7TM receptors trigger signaling through G proteins in many other cell types 14.3 Insulin Signaling: Phosphorylation Cascades Are Central to Many Signal-Transduction Processes The insulin receptor is a protein kinase that is autoinhibited prior to insulin binding 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 14.4 Epidermal Growth Factor: Receptor Dimerization Can Drive Signaling 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 14.5 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 14.6 Sensory Systems Are Based on Specialized Signal-Transduction Pathways A huge family of 7TM receptors detect a wide variety of organic compounds Vision relies on a specialized 7TM receptor to signal in response to absorbed light Light absorption induces a specific isomerization of bound 11-cis-retinal Color vision is mediated by three cone receptors that are homologs of rhodopsin Hearing depends on hair cells that use mechanosensitive ion channels to detect tiny motions Comparison of different organisms yields insights into sensory system evolution End of Chapter Summary Key Terms Problems Chapter 15 Metabolism: Basic Concepts and Themes 15.1 Metabolism Is Composed of Many Interconnected Reactions Metabolism consists of destructive and constructive reactions that typically yield or require energy 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 food is extracted in three stages 15.4 Metabolic Pathways Contain Many Recurring Motifs Activated carriers exemplify the modular structure 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 End of Chapter Summary Key Terms Problems Chapter 16 Glycolysis and Gluconeogenesis 16.1 Glycolysis Is an Energy-conversion Pathway in Most Organisms Glucose is generated from dietary carbohydrates A family of transporters enables glucose to enter and leave animal cells 16.2 Glycolysis Can Be Divided into Two Parts Stage 1 begins: 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 Stage 2 begins: The oxidation of an aldehyde 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 Galactose is converted into glucose 6-phosphate Galactose can be highly toxic with a defective metabolic pathway Many adults worldwide are intolerant of milk because they are deficient in lactase 16.3 The Glycolytic Pathway is Tightly Controlled Glycolysis in muscle is regulated to meet the need for ATP The regulation of glycolysis in the l