Modern Biotechnology: Connecting Innovations in Microbiology and Biochemistry to Engineering Fundamentals

1. BIOTECHNOLOGY.

Introduction.

The Directed Manipulation of Genes Distinguishes the New Biotechnology From Prior Biotechnology.

Growth of The New Biotechnology Industry Depends on Venture Capital.

Submerged Fermentations Are the Industry’s Bioprocessing Cornerstone.

Oil Prices Affect Parts Of the Fermentation Industry.

Growth of the Antibiotic/Pharmaceutical Industry.

The Existence of Antibiotics Was Recognized in 1877.

Penicillin Was The First Antibiotic Suitable for Human Systemic Use.

Genesis of the Antibiotic Industry.

Other Antibiotics Were Quickly Discovered After the Introduction of Penicillin.

Discovery and Scale-up Are Synergistic in the Development of Pharmaceutical Products.

The Success of the Pharmaceutical Industry In Research, Development and Engineering Contributed to Rapid Growth but Also Resulted in Challenges.

Growth of the Amino Acid/Acidulant Fermentation Industry.

Production of Monosodium Glutamate (MSG via Fermentation.

The Impact of Glutamic Acid Bacteria on Monosodium Glutamate Cost Was Dramatic.

Auxotrophic and Regulatory Mutants Enabled Production of Other Amino Acids.

Prices and Volumes Are Inversely Related.

Biochemical Engineers Have a Key Function in All Aspects of the Development Process for Microbial Fermentation.

Bibliography.

Homework Problems.

2. NEW BIOTECHNOLOGY.

Introduction.

Growth of The Biopharmaceutical Industry.

The Biopharmaceutical Industry Is in the Early Part of Its Life Cycle.

Discovery of Type II Restriction Endonucleases Opened A New Era in Biotechnology.

The Polymerase Chain Reaction (PCR Is An Enzyme Mediated, In vitro Amplification of DNA.

Impacts of the New Biotechnology on Biopharmaceuticals, Genomics, Plant Biotechnology and Bioproducts.

Biotechnology Developments Have Accelerated Biological Research.

Drug Discovery Has Benefited From Biotechnology Research Tools.

The Fusing of Mouse Spleen Cells with T-Cells Facilitated Production of Antibodies.

Regulatory Issues Add to The Time Required to Bringing a New Product to Market.

New Biotechnology Methods Enable Rapid Identification Of Genes and Their Protein Products.

Genomics Is the Scientific Discipline of Mapping, Sequencing, and Analyzing Genomes.

Products From the New Plant Biotechnology Are Changing The Structure of Large Companies That Sell Agricultural Chemicals.

Bioproducts from Genetically Engineered Microorganisms Will Become Economically Important to the Fermentation Industry.

Bibliography.

Homework Problems.

3. BIOPRODUCTS AND BIOFUELS.

Introduction.

Biocatalysis and the Growth of Industrial Enzymes.

Glucose Isomerase Catalyzed the Birth of A New Process For Sugar Production From Corn.

Identification of a Thermally Stable Glucose Isomerase and An Inexpensive Inducer Was Needed For An Industrial Process.

The Demand for High Fructose Corn Syrup (HFCS Resulted in Large Scale Use of Immobilized Enzymes and Liquid Chromatography.

Rapid Growth of HFCS Market Share Was Enabled by Large Scale Liquid Chromatography and Propelled by Record High Sugar Prices.

Biocatalysts Are Used in Fine Chemical Manufacture.

Growth of Renewable Resources As A Source of Specialty Products and Industrial Chemicals.

A Wide Range of Technologies Are Needed to Reduce Costs For Converting Cellulosic Substrates to Value-Added Bioproducts.

Renewable Resources Are A Source of Natural Plant Chemicals.

Bioseparations Are Important To the Extraction, Recovery, and Purification of Plant Derived Products.

Bioprocess Engineering and Economics.

Bioseparations and Bioprocess Engineering.

Bibliography.

Homework Problems.

4. MICROBIAL FERMENTATIONS.

Introduction.

Fermentations Are Carried Out In Flasks, Glass Vessels, and Specially Designed Stainless Steel Tanks.

Microbial Cells Are Either Prokaryotes or Eucaryotes.

Classification of Microorganisms are Based on Kingdoms.

Prokaryotes are Important Industrial Microorganisms.

Eukaryotes Are Used Industrially to Produce Ethanol Antibiotics, and Biotherapeutic Proteins.

Wild Type Organisms Find Broad Industrial Use.

Microbial Culture Requires That Energy and All Components Needed for Cell Growth Be Provided.

Media Components and Their Function (Complex and Defined Media).

Carbon Sources Provide Energy, and Sometimes Provide Oxygen.

Complex Media Have a Known Basic Composition but a Chemical Composition That is Not Completely Defined.

Industrial Fermentation Broths May Have a High Initial Carbon (Sugar Content (Ethanol Fermentation Example).

The Accumulation of Fermentation Products Is Proportional to Cell Mass In The Bioreactor.

A Microbial Fermentation is Characterized by Distinct Phases of Growth.

Expressions for Cell Growth Rate are Based on Doubling Time.

Products of Microbial Culture Are Classified In Relation To Their Energy Metabolism (Type I, II and III Fermentations).

Product Yields Are Calculated From the Stoichiometry of Biological Reactions (Yield Coefficients).

The Embden-Meyerhof Glycolysis and Citric Acid Cycles Are Regulated By The Relative Balance of ATP, ADP and AMP In The Cell.

Bibliography.

Homework Problems.

5. MODELING AND SIMULATION.

Introduction.

Simpson’s Rule.

Fourth-Order Runge-Kutta Method.

Runge-Kutta Technique Requires that Higher Order Equations be reduced to 1st Order ODEs to Obtain Their Solution.

Systems of First Order ODE’s Are Represented in Vector Form.

Kinetics of Cell Growth.

Ks Represents Substrate Concentration at Which the Specific Growth Rate is Half of its Maximum.

Simulation of a Batch Ethanol Fermentation.

Ethanol Case Study.

Luedeking-Piret Model.

Continuous Stirred Tank Bioreactor.

Batch Fermentor vs. Chemostat.

Bibliography.

Homework Problems.

6. AEROBIC BIOREACTORS.

Introduction.

Fermentation of Xylose to 2,3 Butanediol by Klebsiella oxytoca is Aerated but Oxygen Limited.

Phase I. Oxygen sufficient growth occurs early in the fermentation.

Phase II. A transition to oxygen limitation occurs at low cell concentration (1 g/L).

Phase III. Butanediol is produced under oxygen limiting conditions.

Oxygen Transfer from Air Bubble to Liquid is Controlled by Liquid-side Mass Transfer.

Bibliography.

Homework Problems.

Appendix for Chapter 6.

Excel Program for Integration of Simultaneous Differential Equations.

7. ENZYMES.

Introduction.

Enzymes and Systems Biology.

Industrial Enzymes.

Enzymes: In vivo and In vitro.

Fundamental Properties of Enzymes.

Classification of Enzymes.

Industrial Enzymes.

Assaying Enzyme Activity.

Enzyme Assays.

Batch Reactions.

Thermal Enzyme Deactivation.

Bibliography.

Homework Problems.

8. ENZYME KINETICS.

Introduction.

Initial Rate vs. Integrated Rate Equations.

Obtaining Constants from Initial Rate Data Is An Iterative Process.

Batch Enzyme Reactions: Irreversible Product Formation (No Inhibition).

Rapid Equilibrium Approach Enables Rapid Formulation of an Enzyme Kinetic Equation.

The Pseudo-steady-state Method Requires More Effort to Obtain the Hart Equation but is Necessary for Reversible Reactions.

Irreversible Product Formation in the Presence of Inhibitors and Activators.

Inhibition.

Competitive Inhibition.

Uncompetitive Inhibition.

(Classical Non-competitive Inhibition.

Substrate Inhibition.

Example of Reversible Reactions.

Coenzymes and Co-factors Interact in a Reversible Manner.

King-Altman Method.

Immobilized Enzyme.

Bibliography.

Homework Problems.

9. METABOLISM.

Introduction.

Aerobic and Anaerobic Metabolism.

Glycolysis is the Oxidation of Glucose in the Absence of Oxygen.

Oxidation Is Catalyzed by Oxidases In the Presence of O2, and by Dehydrogenases in the Absence of O2.

A Membrane Bioreactor Couples Reduction and Oxidation Reactions (R-mandelic Acid Example).

Three Stages of Catabolism Generate Energy, Intermediate Molecules and Waste Products.

The Glycolysis Pathway Utilizes Glucose Both In the Presence (Aerobic and Absence of O2 (Anaerobic to Produce Pyruvate.

Glycolysis Is Initiated By the Transfer of a High Energy Phosphate Group to Glucose.

Products of Anaerobic Metabolism Are Secreted or Processed by Cells to Allow Continuous Metabolism of Glucose by Glycolysis.

Other Metabolic Pathways That Utilize Glucose Under Anaerobic Conditions (Pentose Phosphate, Entner-Doudoroff, and Hexose Monophosphate Shunt Pathways).

Knowledge of Anaerobic Metabolism Enables Calculation of Theoretical Yields of Products Derived From Glucose.

Economics Favors the Glycolytic Pathway for Obtaining Oxygenated Chemicals from Renewable Resources.

Citric Acid Cycle and Aerobic Metabolism.

Respiration Is The Aerobic Oxidation of Glucose And Other Carbon-Food-Sources (Citric Acid Cycle).

The Availability of Oxygen, Under Aerobic Conditions, Enables Microorganisms to Utilize Pyruvate Via the Citric Acid Cycle.

The Citric Acid Cycle Generates Precursors for Biosynthesis of Amino Acids and Commercially Important Fermentation Products.

Glucose Is Transformed to Commercially Valuable Products Via Fermentation Processes: A Summary.

Essential Amino Acids Not Synthesized By Microorganisms Must Be Provided As Nutrients (Auxotrophs).

The Utilization of Fats in Animals Occurs By a Different Mechanism than the TCA Cycle.

Some Bacteria and Molds Can Grow on Hydrocarbons or Methanol in Aerated Fermentations (Single Cell Protein Case Study).

Extremophiles: Microorganisms That Do Not Require Glucose, Utilize H2, and Grow At 80 to 100?C and 200 Atmospheres Have Industrial Uses.

The Terminology For Microbial Culture Is Inexact: Fermentation Refers to Both Aerobic and Anaerobic Conditions While Respiration Can Denote Anaerobic Metabolism.

Metabolism and Biological Energetics.

Bibliography.

Homework Problems.

10. BIOLOGICAL ENERGETICS.

Introduction.

Redox Potential and Gibbs Free Energy in Biochemical Reactions.

Heat: Byproduct of Metabolism.

Bibliography.

Homework Problems.

11. METABOLIC PATHWAYS.

Introduction.

Living Organisms Control Metabolic Pathways at Strategic and Operational Levels.

Auxotrophs Are Nutritionally Deficient Microorganisms That Enhance Product Yields In Controlled Fermentations (Relief of Feedback Inhibition and Depression).

Both Branched and Unbranched Pathways Cause Feedback Inhibition and Repression (Purine Nucleotide Example).

The Accumulation of An End Metabolite of A Branched Pathway Requires A Different Strategy Than Accumulation of An Intermediate Metabolite.

Amino Acids.

The Formulation of Animal Feed Rations With Exogeneous Amino Acids Is A Major Market For Amino Acids.

Microbial Strain Discovery, Mutation, Screening and Development Facilitated Introduction of Industrial, Aerated Fermentations for Amino Acid Production by C. glutamicum.

Overproduction of Glutamate by C. Glutamicum Depends on An Increase in Bacterial Membrane Permeability (Biotin Deficient Mutant).

A Threonine and Methionine Auxotroph of C. glutamicum Avoids Concerted Feedback Inhibition and Enables Industrial Lysine Fermentations.

Cell (Protoplast Fusion Is A Method for Breeding Amino Acid Producers That Incorporate Superior Characteristics of Each Parent (Lysine Fermentation).

Amino Acid Fermentations Represent Mature Technologies.

Antibiotics.

Secondary Metabolites Formed During Idiophase Are Subject to Catabolite Repression and Feedback Regulation (Penicillin and Streptomycin).

The Production of Antibiotics Was Viewed as a Mature Field Until Antibiotic Resistant Bacteria Began to Appear.

Bacteria Retain Antibiotic Resistance Even When Use of the Antibiotic Has Been Stopped For Thousands of Generations.

Antibiotic Resistance Involves Many Genes (Vancomycin Example).

Bibliography.

Homework Problems.

12. GENETIC ENGINEERING: DNA, RNA, AND GENES.

Introduction.

DNA.

DNA Is A Double Stranded Polymer of the Nucleotides: Thymine, Adenine, Cytosine and Guanine.

The Information Contained in DNA Is Huge.

Genes Are Nucleotide Sequences That Contain the Information Required for the Cell to Make Proteins.

Transcription Is A Process Whereby Specific Regions of the DNA (Genes Serve As A Template to Synthesize Another Nucleotide, Ribonucleic Acid (RNA).

Chromosomal DNA In A Prokaryote (Bacterium Is Anchored to The Cell?s Membrane While Plasmids are in the Cytoplasm.

Chromosomal DNA In A Eukaryote (Yeast, Animal or Plant Cells Is Contained In The Nucleus.

Microorganisms Carry Genes In Plasmids Consisting of Shorter Lengths of Circular, Extrachromosomal DNA.

Restriction Enzymes Enable Directed In Vitro Cleavage of DNA.

Different Type II Restriction Enzymes Give Different Patterns of Cleavage And Different Single Stranded Terminal Sequences.

DNA Ligase Covalently Joins The Ends of DNA Fragments.

DNA Fragments and Genes of Up To 150 Nucleotides Can Be Chemically Synthesized If The Nucleotide Sequence Has Been Previously Determined.

Protein Sequences Can Be Deduced And Genes Synthesized Based On Complementary DNA Obtained From Messenger RNA.

Selectable Markers Are Genes That Facilitate Identification of Transformed Cells That Contain Recombinant DNA.

A Second Protein Fused to The Protein Product Is Needed To Protect The Product From Proteolysis (?-Gal-Somatostatin Fusion Protein Example).

Recovery of Protein Product From Fusion Protein Requires Correct Selection of Amino Acid That Links The Two Proteins (Met Linker).

Chemical Modification and Enzyme Hydrolysis Recovers An Active Molecule Containing Met Residues From A Fusion Protein (?-endorphin Example).

Metabolic Engineering Differs From Genetic Engineering By the Nature of The End Product.

Bibliography.

Homework Problems.

13. METABOLIC ENGINEERING.

Introduction.

Building Blocks.

L-Threonine Overproducing Strains of E. coli K-12.

Genetically Altered Brevibacterium lactoferrin Has Yielded Improved Amino Acid Producing Strains.

Metabolic Engineering May Catalyze Development of New Processes for Manufacture of Oxygenated Chemicals.

Gene Chips Enable Examination of Glycolytic and Citric Acid Cycle Pathways in Yeast At a Genomic Level (Yeast Genome Microarray Case Study).

The Fermentation of Pentoses to Ethanol Is A Goal of Metabolic Engineering (Recombinant Bacteria and Yeast Examples).

Metabolic Engineering For a 1,3 Propanediol Producing Organism to Obtain Monomer for Polyester Manufacture.

Redirection of Cellular Metabolism to Overproduce An Enzyme Catalyst Results In An Industrial Process For Acrylamide Production (Yamada-Nitto Process).

Bibliography.

Homework Problems.

14. GENOMES AND GENOMICS.

Introduction.

Human Genome Project.

Deriving Commercial Potential From Information Contained in Genomes.

The Genome for E. coli Consists of 4288 Genes That Code for Proteins.

DNA Sequencing is Based on Electrophoretic Separations of Defined DNA Fragments.

Sequence Tagged Sites (STSs Determined From Complimentary DNA (cDNA Give Locations of Genes.

Single Nucleotide Polymorphisms (SNPs Are Stable Mutations Distributed Throughout the Genome That Locate Genes More Efficiently Than STSs.

Gene Chip Probe Array.

Polymerase Chain Reaction (PCR).

The Polymerase Chain Reaction Enables DNA to be Copied In Vitro.

Thermally Tolerant DNA Polymerase From Thermus aquaticus Facilitated Automation of PCR.

Only the 5’ Terminal Primer Sequence Is Needed To Amplify the DNA By PCR.

The Sensitivity of PCR Can Be A Source of Significant Experimental Error.

Applications of PCR Range From Obtaining Fragments of Human DNA For Sequencing To Detecting Genes Associated With Diseases.

Conclusions.

Bibliography.

Homework Problems.