Contents

PREFACE

ABOUT THE AUTHORS

Part 1 The Basics of Biology: An Engineer’s Perspective

1 WHAT IS A BIOPROCESS ENGINEER?

1.1. Biotechnology and Bioprocess Engineering

1.2. Differing Approaches to Research for Biologists and Engineers

1.3. The Story of Penicillin: How Biologists and Engineers Work Together

1.4. Bioprocesses: Regulatory Constraints

Suggestions for Further Reading

Questions

2 AN OVERVIEW OF BIOLOGICAL BASICS

2.1. Microbial Diversity

2.1.1. Naming Cells,

2.1.2. Viruses,

2.1.3. Procaryotes,

2.1.4. Eucaryotes,

2.2. Cell Construction

2.2.1. Amino Acids and Proteins,

2.2.2. Carbohydrates: Mono-and Polysaccharides,

2.2.3. Lipids, Fats, and Steroids,

2.2.4. Nucleic Acids, RNA, and DNA,

2.3. Cell Nutrients

2.3.1. Macronutrients,

2.3.2. Micronutrients,

2.3.3. Growth Media,

2.4. Summary

Suggestions for Further Reading

Questions

3 ENZYMES

3.1. How Enzymes Work

3.2. Enzyme Kinetics

3.2.1. Mechanistic Models for Simple Enzyme Kinetics,

3.2.2. Determining Rate Parameters for Michaelis–Menten Kinetics,

3.2.3. Models for More Complex Enzyme Kinetics,

3.2.4. Effects of pH and Temperature,

3.2.5. Insoluble Substrates,

3.2.6. Multiphase Enzymatic Reactions,

3.3. Immobilized Enzyme Systems

3.3.1. Methods of Immobilization,

3.3.2. Diffusional Limitations in Immobilized Enzyme Systems,

3.3.3. Electrostatic and Steric Effects in Immobilized Enzyme Systems,

3.4. Large-Scale Production of Enzymes

3.5. Medical and Industrial Utilization of Enzymes

3.6. Summary

Suggestions for Further Reading

Problems

4 HOW CELLS WORK

4.1. The Central Dogma

4.2. DNA Replication: Preserving and Propagating the Message

4.3. Transcription: Sending the Message

4.4. Translation: Going from Message to Product

4.4.1. Genetic Code: Universal Message,

4.4.2. Translation: How the Machinery Works,

4.4.3. Posttranslational Processing: Making the Product Useful,

4.5. Metabolic Regulation

4.5.1. Genetic-Level Control: Which Proteins Are Synthesized?,

4.5.2. Metabolic Pathway Control,

4.6. How the Cell Senses its Extracellular Environment

4.6.1. Transporting Small Molecules across Cellular Membranes,

4.6.2. Role of Cell Receptors in Metabolism and Cellular Differentiation,

4.7. Summary

4.8. Appendix: Example Regulation of Complex Pathways

Suggestions for Further Reading

Problems

5 MAJOR METABOLIC PATHWAYS

5.1. Bioenergetics

5.2. Glucose Metabolism: Glycolysis and the TCA Cycle

5.3. Respiration

5.4. Control Sites in Aerobic Glucose Metabolism

5.5. Metabolism of Nitrogenous Compounds

5.6. Nitrogen Fixation

5.7. Metabolism of Hydrocarbons

5.8. Biodegradation of Xenobiotics

5.9. Overview of Biosynthesis

5.10. Overview of Anaerobic Metabolism

5.11. Overview of Autotrophic Metabolism

5.12. Summary

Suggestions for Further Reading

Questions

6 HOW CELLS GROW

6.1. Batch Growth

6.1.1. Quantifying Cell Concentration,

6.1.2. Growth Patterns and Kinetics in Batch Culture,

6.1.3. How Environmental Conditions Affect Growth Kinetics,

6.1.4. Heat Generation by Microbial Growth,

6.2. Quantifying Growth Kinetics

6.2.1. Unstructured Nonsegregated Models,

6.2.2. Models for Transient Behavior,

6.2.3. Cybernetic Models,

6.3. Cell Growth in Continuous Culture

6.3.1. Specific Devices for Continuous Culture,

6.3.2. The Ideal Chemostat,

6.3.3. The Chemostat as a Tool,

6.3.4. Deviations from Ideality,

6.4. Summary

Suggestions for Further Reading

Problems

7 STOICHIOMETRY OF MICROBIAL GROWTH AND PRODUCT FORMATION

7.1. Coefficients for Atp Consumption and Oxygen

7.2. Stoichiometric Calculations

7.2.1. Elemental Balances,

7.2.2. Degree of Reduction,

7.3. Theoretical Predictions of Yield Coefficients

7.4. Estimation of Elemental Cell Composition

7.5. Stoichiometry by Oxidation-Reduction Half-Reactions

7.6. Thermodynamics of Biological Reactions

7.7. Summary

Suggestions for Further Reading

Problems

8 HOW CELLULAR INFORMATION IS ALTERED

8.1. Evolving Desirable Biochemical Activities Through Mutation and Selection

8.1.1. How Mutations Occur,

8.1.2. Selecting for Desirable Mutants,

8.2. Natural Mechanisms for Gene Transfer and Rearrangement

8.2.1. Genetic Recombination,

8.2.2. Transformation,

8.2.3. Transduction,

8.2.4. Episomes and Conjugation,

8.2.5. Transposons: Internal Gene Transfer,

8.3. Genetically Engineering Cells

8.3.1. Basic Elements of Genetic Engineering,

8.3.2. Genetic Engineering of Higher Organisms,

8.3.3. Genome Engineering,

8.4. Genomics

8.4.1. Experimental Techniques,

8.4.2. Computational Techniques,

8.5. Summary

Suggestions for Further Reading

Problems

Part 2 Engineering Principles for Bioprocesses

9 OPERATING CONSIDERATIONS FOR BIOREACTORS FOR SUSPENSION AND IMMOBILIZED CULTURES

9.1. Choosing the Cultivation Method

9.2. Modifying Batch and Continuous Reactors

9.2.1. Chemostat with Recycle,

9.2.2. Multistage Chemostat Systems,

9.2.3. Fed-Batch Operation,

9.2.4. Perfusion Systems,

9.2.5. Membrane Bioreactors,

9.3. Immobilized Cell Systems

9.3.1. Active Immobilization of Cells,

9.3.2. Passive Immobilization: Biological Films,

9.3.3. Diffusional Limitations in Immobilized Cell Systems,

9.3.4. Bioreactor Considerations in Immobilized Cell Systems,

9.4. Hybrid Bioreactors: Attached and Suspended Cells

9.5. Solid-State Fermentations

9.6. Summary

Suggestions for Further Reading

Problems

10 SELECTION, SCALE-UP, OPERATION, AND CONTROL OF BIOREACTORS

10.1. Scale-Up and its Difficulties

10.1.1. Overview of Traditional Reactor Types,

10.1.2. Reactors with Internal Mechanical Agitation,

10.1.3. Bubble Column and Loop Reactor,

10.1.4. Single-Use Bioreactors,

10.1.5. Considerations in Aeration, Agitation, and Heat Transfer,

10.1.6. Approaches to Scale-Up,

10.1.7. Scale-Down and Microbioreactors,

10.2. Bioreactor Instrumentation and Control

10.2.1. Instrumentation for Measurements of Active Fermentation,

10.2.2. Using the Information Obtained,

10.3. Sterilization of Process Fluids

10.3.1. The Kinetics of Death,

10.3.2. Sterilization of Liquids,

10.3.3. Sterilization of Gases,

10.4. Summary

Suggestions for Further Reading

Problems

11 RECOVERY AND PURIFICATION OF PRODUCTS

11.1. Strategies to Recover and Purify Products

11.2. Separation of Insoluble Products

11.2.1. Filtration,

11.2.2. Centrifugation,

11.2.3. Coagulation and Flocculation,

11.3. Cell Disruption

11.3.1. Mechanical Methods,

11.3.2. Nonmechanical Methods,

11.4. Separation of Soluble Products

11.4.1. Liquid–Liquid Extraction,

11.4.2. Aqueous Two-Phase Extraction,

11.4.3. Precipitation,

11.4.4. Dialysis,

11.4.5. Reverse Osmosis,

11.4.6. Ultrafiltration and Microfiltration,

11.4.7. Cross-Flow Ultrafiltration and Microfiltration,

11.4.8. Adsorption,

11.4.9. Chromatography,

11.4.10. Electrophoresis,

11.4.11. Electrodialysis,

11.5. Finishing Steps for Purification

11.5.1. Crystallization,

11.5.2. Drying,

11.6. Integration of Reaction and Separation

11.7. Summary

Suggestions for Further Reading

Problems

12 BIOPROCESS CONSIDERATIONS IN USING ANIMAL CELL CULTURES

12.1. Structure and Biochemistry of Animal Cells

12.2. Methods Used for the Cultivation of Animal Cells

12.2.1. Basic Techniques for Animal Cell Culture,

12.2.2. Growth Media,

12.2.3. Growth Dynamics for Animal Cells,

12.3. Bioreactor Considerations for Animal Cell Culture

12.4. Bioreactor Systems for Animal Cell Culture

12.4.1. Nonstirred Reactor Systems,

12.4.2. Systems for Entrapped Cells in Stirred Reactors,

12.4.3. Suspended Cultures,

12.5. Products of Animal Cell Cultures

12.6. Summary

Suggestions for Further Reading

Problems

13 BIOPROCESS CONSIDERATIONS IN USING PLANT CELL CULTURES

13.1. Why Plant Cell Cultures?

13.2. Plant Cells in Culture Compared to Microbes

13.3. Bioreactor Considerations

13.3.1. Bioreactors for Suspension Cultures,

13.3.2. Reactors Using Cell Immobilization,

13.3.3. Bioreactors for Organized Tissues,

13.4. Economics of Plant Cell Tissue Cultures

13.5. Summary

Suggestions for Further Reading

Problems

14 UTILIZING GENETICALLY ENGINEERED ORGANISMS

14.1. How the Product Influences Process Decisions

14.2. Guidelines for Choosing Host–Vector Systems

14.2.1. Escherichia Coli,

14.2.2. Gram-Positive Bacteria,

14.2.3. Lower Eucaryotic Cells,

14.2.4. Mammalian Cells,

14.2.5. Insect Cell–Baculovirus System,

14.2.6. Transgenic Animals,

14.2.7. Transgenic Plants and Plant Cell Culture,

14.2.8. Cell-Free Protein Synthesis,

14.2.9. Comparison of Strategies,

14.3. Process Constraints: Genetic Instability

14.3.1. Segregational Loss,

14.3.2. Plasmid Structural Instability,

14.3.3. Host Cell Mutations,

14.3.4. Growth-Rate-Dominated Instability,

14.4. Avoiding Process Problems in Plasmid Design

14.5. Predicting Host–Vector Interactions and Genetic Instability

14.6. Regulatory Constraints on Genetic Processes

14.7. Metabolic Engineering

14.8. Synthetic and Systems Biology

14.9. Protein Engineering

14.10. Summary

Suggestions for Further Reading

Problems

15 MEDICAL APPLICATIONS OF BIOPROCESS ENGINEERING

15.1. Tissue Engineering

15.1.1. What Is Tissue Engineering?,

15.1.2. Tissue-Engineered Skin Replacements,

15.1.3. Chondrocyte Culture for Cartilage Replacement,

15.2. Gene Therapy Using Viral Vectors

15.2.1. Models of Viral Infection,

15.2.2. Mass Production of Retrovirus,

15.3. Bioreactors

15.3.1. Stem Cells and Hematopoiesis,

15.3.2. Extracorporeal Artificial Liver,

15.3.3. Body-on-a-Chip Systems,

15.4. Summary

Suggestions for Further Reading

Problems

16 BIOPROCESSES UTILIZING MIXED CULTURES

16.1. Major Classes of Interactions in Mixed Cultures

16.2. Simple Models Describing Mixed-Culture Interactions

16.3. Mixed Cultures in Nature

16.4. Industrial Utilization of Mixed Cultures

16.5. Biological Waste Treatment

16.5.1. Biological Waste-Treatment Processes,

16.5.2. Advanced Wastewater Treatment Systems,

16.5.3. Conversion of Wastewater to Useful Products,

16.6. Summary

Suggestions for Further Reading

Problems

APPENDIX TRADITIONAL INDUSTRIAL BIOPROCESSES

A.1. Anaerobic Bioprocesses

A.1.1. Ethanol Production,

A.1.2. Lactic Acid Production,

A.1.3. Acetone–Butanol Production,

A.2. Aerobic Processes

A.2.1. Citric Acid Production,

A.2.2. Production of Baker’s Yeast,

A.2.3. Production of Penicillins,

A.2.4. Production of High-Fructose Corn Syrup,

A.3. Bioprocess Technologies: Biofuel and Bioenergy Production from Biomass

A.3.1. Production of Liquid Fuels,

A.3.2. Production of Gaseous Fuels from Biomass,

A.3.3. Bioelectricity Generation from Wastes Using Microbial Fuel Cells,

Suggestions for Further Reading

INDEX

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