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| Biotechnology | |
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| Introduction | |
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| The Directed Manipulation of Genes Distinguishes the New Biotechnology From Prior Biotechnology | |
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| Growth of The New Biotechnology Industry Depends on Venture Capital | |
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| Submerged Fermentations Are the Industry's Bioprocessing Cornerstone | |
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| Oil Prices Affect Parts Of the Fermentation Industry | |
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| Growth of the Antibiotic/Pharmaceutical Industry | |
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| The Existence of Antibiotics Was Recognized in 1877 | |
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| Penicillin Was The First Antibiotic Suitable for Human Systemic Use | |
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| Genesis of the Antibiotic Industry | |
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| Other Antibiotics Were Quickly Discovered After the Introduction of Penicillin | |
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| Discovery and Scale-up Are Synergistic in the Development of Pharmaceutical Products | |
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| The Success of the Pharmaceutical Industry In Research, Development and Engineering Contributed to Rapid Growth but Also Resulted in Challenges | |
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| Growth of the Amino Acid/Acidulant Fermentation Industry | |
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| Production of Monosodium Glutamate MSG via Fermentation | |
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| The Impact of Glutamic Acid Bacteria on Monosodium Glutamate Cost Was Dramatic | |
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| Auxotrophic and Regulatory Mutants Enabled Production of Other Amino Acids | |
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| Prices and Volumes Are Inversely Related | |
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| Biochemical Engineers Have a Key Function in All Aspects of the Development Process for Microbial Fermentation | |
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| Bibliography | |
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| Homework Problems | |
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| New Biotechnology | |
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| Introduction | |
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| Growth of The Biopharmaceutical Industry | |
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| The Biopharmaceutical Industry Is in the Early Part of Its Life Cycle | |
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| Discovery of Type II Restriction Endonucleases Opened A New Era in Biotechnology | |
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| The Polymerase Chain Reaction PCR Is An Enzyme Mediated, In vitro Amplification of DNA | |
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| Impacts of the New Biotechnology on Biopharmaceuticals, Genomics, Plant Biotechnology and Bioproducts | |
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| Biotechnology Developments Have Accelerated Biological Research | |
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| Drug Discovery Has Benefited From Biotechnology Research Tools | |
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| The Fusing of Mouse Spleen Cells with T-Cells Facilitated Production of Antibodies | |
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| Regulatory Issues Add to The Time Required to Bringing a New Product to Market | |
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| New Biotechnology Methods Enable Rapid Identification Of Genes and Their Protein Products | |
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| Genomics Is the Scientific Discipline of Mapping, Sequencing, and Analyzing Genomes | |
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| Products From the New Plant Biotechnology Are Changing The Structure of Large Companies That Sell Agricultural Chemicals | |
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| Bioproducts from Genetically Engineered Microorganisms Will Become Economically Important to the Fermentation Industry | |
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| Bibliography | |
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| Homework Problems | |
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| Bioproducts And Biofuels | |
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| Introduction | |
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| Biocatalysis and the Growth of Industrial Enzymes | |
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| Glucose Isomerase Catalyzed the Birth of A New Process For Sugar Production From Corn | |
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| Identification of a Thermally Stable Glucose Isomerase and An Inexpensive Inducer Was Needed For An Industrial Process | |
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| The Demand for High Fructose Corn Syrup HFCS Resulted in Large Scale Use of Immobilized Enzymes and Liquid Chromatography | |
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| Rapid Growth of HFCS Market Share Was Enabled by Large Scale Liquid Chromatography and Propelled by Record High Sugar Prices | |
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| Biocatalysts Are Used in Fine Chemical Manufacture | |
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| Growth of Renewable Resources As A Source of Specialty Products and Industrial Chemicals | |
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| A Wide Range of Technologies Are Needed to Reduce Costs For Converting Cellulosic Substrates to Value-Added Bioproducts | |
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| Renewable Resources Are A Source of Natural Plant Chemicals | |
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| Bioseparations Are Important To the Extraction, Recovery, and Purification of Plant Derived Products | |
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| Bioprocess Engineering and Economics | |
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| Bioseparations and Bioprocess Engineering | |
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| Bibliography | |
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| Homework Problems | |
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| Microbial Fermentations | |
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| Introduction | |
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| Fermentations Are Carried Out In Flasks, Glass Vessels, and Specially Designed Stainless Steel Tanks | |
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| Microbial Cells Are Either Prokaryotes or Eucaryotes | |
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| Classification of Microorganisms are Based on Kingdoms | |
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| Prokaryotes are Important Industrial Microorganisms | |
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| Eukaryotes Are Used Industrially to Produce Ethanol Antibiotics, and Biotherapeutic Proteins | |
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| Wild Type Organisms Find Broad Industrial Use | |
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| Microbial Culture Requires That Energy and All Components Needed for Cell Growth Be Provided | |
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| Media Components and Their Function Complex and Defined Media | |
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| Carbon Sources Provide Energy, and Sometimes Provide Oxygen | |
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| Complex Media Have a Known Basic Composition but a Chemical Composition That is Not Completely Defined | |
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| Industrial Fermentation Broths May Have a High Initial Carbon Sugar Content Ethanol Fermentation Example | |
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| The Accumulation of Fermentation Products Is Proportional to Cell Mass In The Bioreactor | |
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| A Microbial Fermentation is Characterized by Distinct Phases of Growth | |
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| Expressions for Cell Growth Rate are Based on Doubling Time | |
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| Products of Microbial Culture Are Classified In Relation To Their Energy Metabolism Type I II and III Fermentations | |
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| Product Yields Are Calculated From the Stoichiometry of Biological Reactions Yield Coefficients | |
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| The Embden-Meyerhof Glycolysis and Citric Acid Cycles Are Regulated By The Relative Balance of ATP, ADP and AMP In The Cell | |
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| Bibliography | |
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| Homework Problems | |
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| Modeling And Simulation | |
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| Introduction | |
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| Simpson's Rule | |
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| Fourth-Order Runge-Kutta Method | |
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| Runge-Kutta Technique Requires that Higher Order Equations be reduced to 1st Order ODEs to Obtain Their Solution | |
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| Systems of First Order ODE's Are Represented in Vector Form | |
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| Kinetics of Cell Growth | |
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| Ks Represents Substrate Concentration at Which the Specific Growth Rate is Half of its Maximum | |
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| Simulation of a Batch Ethanol Fermentation | |
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| Ethanol Case Study | |
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| Luedeking-Piret Model | |
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| Continuous Stirred Tank Bioreactor | |
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| Batch Fermentor vs. Chemostat | |
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| Bibliography | |
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| Homework Problems | |
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| Aerobic Bioreactors | |
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| Introduction | |
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| Fermentation of Xylose to 2,3 Butanediol by Klebsiella oxytoca is Aerated but Oxygen Limited | |
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| Oxygen sufficient growth occurs early in the fermentation | |
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| A transition to oxygen limitation occurs at low cell concentration (1 g/L) | |
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| Butanediol is produced under oxygen limiting conditions | |
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| Oxygen Transfer from Air Bubble to Liquid is Controlled by Liquid-side Mass Transfer | |
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| Bibliography | |
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| Homework Problems | |
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| Appendix for Chapter 6 | |
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| Excel Program for Integration of Simultaneous Differential Equations | |
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| Enzymes | |
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| Introduction | |
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| Enzymes and Systems Biology | |
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| Industrial Enzymes | |
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| Enzymes: In vivo and In vitro | |
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| Fundamental Properties of Enzymes | |
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| Classification of Enzymes | |
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| Industrial Enzymes | |
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| Assaying Enzyme Activity | |
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| Enzyme Assays | |
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| Batch Reactions | |
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| Thermal Enzyme Deactivation | |
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| Bibliography | |
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| Homework Problems | |
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| Enzyme Kinetics | |
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| Introduction | |
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| Initial Rate vs. Integrated Rate Equations | |
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| Obtaining Constants from Initial Rate Data Is An Iterative Process | |
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| Batch Enzyme Reactions: Irreversible Product Formation No Inhibition | |
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| Rapid Equilibrium Approach Enables Rapid Formulation of an Enzyme Kinetic Equation | |
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| The Pseudo-steady-state Method Requires More Effort to Obtain the Hart Equation but is Necessary for Reversible Reactions | |
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| Irreversible Product Formation in the Presence of Inhibitors and Activators | |
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| Inhibition | |
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| Competitive Inhibition | |
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| Uncompetitive Inhibition | |
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| (Classical Non-competitive Inhibition) | |
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| Substrate Inhibition | |
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| Example of Reversible Reactions | |
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| Coenzymes and Co-factors Interact in a Reversible Manner | |
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| King-Altman Method | |
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| Immobilized Enzyme | |
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| Bibliography | |
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| Homework Problems | |
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| Metabolism | |
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| Introduction | |
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| Aerobic and Anaerobic Metabolism | |
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| Glycolysis is the Oxidation of Glucose in the Absence of Oxygen | |
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| Oxidation Is Catalyzed by Oxidases In the Presence of O2, and by Dehydrogenases in the Absence of O2 | |
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| A Membrane Bioreactor Couples Reduction and Oxidation Reactions (R-mandelic Acid Example | |
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| Three Stages of Catabolism Generate Energy, Intermediate Molecules and Waste Products | |
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| The Glycolysis Pathway Utilizes Glucose Both In the Presence Aerobic and Absence of O2 Anaerobic to Produce Pyruvate | |
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| Glycolysis Is Initiated By the Transfer of a High Energy Phosphate Group to Glucose | |
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| Products of Anaerobic Metabolism Are Secreted or Processed by Cells to Allow Continuous Metabolism of Glucose by Glycolysis | |
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| Other Metabolic Pathways That Utilize Glucose Under Anaerobic Conditions Pentose Phosphate Entner-Doudoroff, and Hexose Monophosphate Shunt Pathways | |
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| Knowledge of Anaerobic Metabolism Enables Calculation of Theoretical Yields of Products Derived From Glucose | |
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| Economics Favors the Glycolytic Pathway for Obtaining Oxygenated Chemicals from Renewable Resources | |
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| Citric Acid Cycle and Aerobic Metabolism | |
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| Respiration Is The Aerobic Oxidation of Glucose And Other Carbon-Food-Sources Citric Acid Cycle | |
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| The Availability of Oxygen, Under Aerobic Conditions, Enables Microorganisms to Utilize Pyruvate Via the Citric Acid Cycle | |
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| The Citric Acid Cycle Generates Precursors for Biosynthesis of Amino Acids and Commercially Important Fermentation Products | |
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| Glucose Is Transformed to Commercially Valuable Products Via Fermentation Processes: A Summary | |
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| Essential Amino Acids Not Synthesized By Microorganisms Must Be Provided As Nutrients (Auxotrophs) | |
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| The Utilization of Fats in Animals Occurs By a Different Mechanism than the TCA Cycle | |
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| Some Bacteria and Molds Can Grow on Hydrocarbons or Methanol in Aerated Fermentations Single Cell Protein Case Study | |
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| Extremophiles: Microorganisms That Do Not Require Glucose, Utilize H2, and Grow At 80 to 100?C and 200 Atmospheres Have Industrial Uses | |
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| The Terminology For Microbial Culture Is Inexact: Fermentation Refers to Both Aerobic and Anaerobic Conditions While Respiration Can Denote Anaerobic Metabolism | |
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| Metabolism and Biological Energetics | |
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| Bibliography | |
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| Homework Problems | |
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| Biological Energetics | |
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| Introduction | |
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| Redox Potential and Gibbs Free Energy in Biochemical Reactions | |
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| Heat: Byproduct of Metabolism | |
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| Bibliography | |
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| Homework Problems | |
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| Metabolic Pathways | |
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| Introduction | |
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| Living Organisms Control Metabolic Pathways at Strategic and Operational Levels | |
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| Auxotrophs Are Nutritionally Deficient Microorganisms That Enhance Product Yields In Controlled Fermentations Relief of Feedback Inhibition and Depression | |
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| Both Branched and Unbranched Pathways Cause Feedback Inhibition and Repression Purine Nucleotide Example | |
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| The Accumulation of An End Metabolite of A Branched Pathway Requires A Different Strategy Than Accumulation of An Intermediate Metabolite | |
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| Amino Acids | |
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| The Formulation of Animal Feed Rations With Exogeneous Amino Acids Is A Major Market For Amino Acids | |
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| Microbial Strain Discovery, Mutation, Screening and Development Facilitated Introduction of Industrial, Aerated Fermentations for Amino Acid Production by C. glutamicum | |
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| Overproduction of Glutamate by C. Glutamicum Depends on An Increase in Bacterial Membrane Permeability Biotin Deficient Mutant | |
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| A Threonine and Methionine Auxotroph of C. glutamicum Avoids Concerted Feedback Inhibition and Enables Industrial Lysine Fermentations | |
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| Cell Protoplast Fusion Is A Method for Breeding Amino Acid Producers That Incorporate Superior Characteristics of Each Parent Lysine Fermentation | |
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| Amino Acid Fermentations Represent Mature Technologies | |
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| Antibiotics | |
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| Secondary Metabolites Formed During Idiophase Are Subject to Catabolite Repression and Feedback Regulation Penicillin and Streptomycin | |
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| The Production of Antibiotics Was Viewed as a Mature Field Until Antibiotic Resistant Bacteria Began to Appear | |
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| Bacteria Retain Antibiotic Resistance Even When Use of the Antibiotic Has Been Stopped For Thousands of Generations | |
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| Antibiotic Resistance Involves Many Genes Vancomycin Example | |
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| Bibliography | |
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| Homework Problems | |
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| Genetic Engineering: DNA, RNA, And Genes | |
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| Introduction | |
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| DNA | |
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| DNA Is A Double Stranded Polymer of the Nucleotides: Thymine, Adenine, Cytosine and Guanine | |
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| The Information Contained in DNA Is Huge | |
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| Genes Are Nucleotide Sequences That Contain the Information Required for the Cell to Make Proteins | |
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| Transcription Is A Process Whereby Specific Regions of the DNA | |
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| Chromosomal DNA In A Prokaryote Bacterium Is Anchored to The Cell?s Membrane While Plasmids are in the Cytoplasm | |
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| Chromosomal DNA In A Eukaryote (Yeast, Animal or Plant Cells Is Contained In The Nucleus | |
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| Microorganisms Carry Genes In Plasmids Consisting of Shorter Lengths of Circular, Extrachromosomal DNA | |
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| Restriction Enzymes Enable Directed In Vitro Cleavage of DNA | |
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| Different Type II Restriction Enzymes Give Different Patterns of Cleavage And Different Single Stranded Terminal Sequences | |
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| DNA Ligase Covalently Joins The Ends of DNA Fragments | |
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| DNA Fragments and Genes of Up To 150 Nucleotides Can Be Chemically Synthesized If The Nucleotide Sequence Has Been Previously Determined | |
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| Protein Sequences Can Be Deduced And Genes Synthesized Based On Complementary DNA Obtained From Messenger RNA | |
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| Selectable Markers Are Genes That Facilitate Identification of Transformed Cells That Contain Recombinant DNA | |
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| A Second Protein Fused to The Protein Product Is Needed To Protect The Product From Proteolysis (?-Gal-Somatostatin Fusion Protein Example) | |
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| Recovery of Protein Product From Fusion Protein Requires Correct Selection of Amino Acid That Links The Two Proteins Met Linker | |
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| Chemical Modification and Enzyme Hydrolysis Recovers An Active Molecule Containing Met Residues From A Fusion Protein (?-endorphin Example) | |
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| Metabolic Engineering Differs From Genetic Engineering By the Nature of The End Product | |
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| Bibliography | |
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| Homework Problems | |
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| Metabolic Engineering | |
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| Introduction | |
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| Building Blocks | |
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| L-Threonine Overproducing Strains of E. coli K-12 | |
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| Genetically Altered Brevibacterium lactoferrin Has Yielded Improved Amino Acid Producing Strains | |
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| Metabolic Engineering May Catalyze Development of New Processes for Manufacture of Oxygenated Chemicals | |
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| Gene Chips Enable Examination of Glycolytic and Citric Acid Cycle Pathways in Yeast At a Genomic Level Yeast Genome Microarray Case Study | |
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| The Fermentation of Pentoses to Ethanol Is A Goal of Metabolic Engineering | |
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| Metabolic Engineering For a 1,3 Propanediol Producing Organism to Obtain Monomer for Polyester Manufacture | |
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| Redirection of Cellular Metabolism to Overproduce An Enzyme Catalyst Results In An Industrial Process For Acrylamide Production (Yamada-Nitto Process | |
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| Bibliography | |
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| Homework Problems | |
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| Genomes And Genomics | |
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| Introduction | |
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| Human Genome Project | |
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| Deriving Commercial Potential From Information Contained in Genomes | |
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| The Genome for E. coli Consists of 4288 Genes That Code for Proteins | |
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| DNA Sequencing is Based on Electrophoretic Separations of Defined DNA Fragments | |
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| Sequence Tagged Sites STSs Determined From Complimentary DNA cDNA Give Locations of Genes | |
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| Single Nucleotide Polymorphisms SNPs Are Stable Mutations Distributed Throughout the Genome That Locate Genes More Efficiently Than STSs | |
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| Gene Chip Probe Array | |
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| Polymerase Chain Reaction (PCR | |
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| The Polymerase Chain Reaction Enables DNA to be Copied In Vitro | |
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| Thermally Tolerant DNA Polymerase From Thermus aquaticus Facilitated Automation of PCR | |
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| Only the 5' Terminal Primer Sequence Is Needed To Amplify the DNA By PCR | |
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| The Sensitivity of PCR Can Be A Source of Significant Experimental Error | |
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| Applications of PCR Range From Obtaining Fragments of Human DNA For Sequencing To Detecting Genes Associated With Diseases | |
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| Conclusions | |
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| Bibliography | |
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| Homework Problems | |