Bioprocess Engineering

Preface xvii

About the Authors xxi



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




Chapter 1: What Is a Bioprocess Engineer? 1

1.1 Biotechnology and Bioprocess Engineering 2

1.2 Differing Approaches to Research for Biologists and Engineers 3

1.3 The Story of Penicillin: How Biologists and Engineers Work Together 4

1.4 Bioprocesses: Regulatory Constraints 9

Suggestions for Further Reading 11

Questions 11



Chapter 2: An Overview of Biological Basics 13

2.1 Microbial Diversity 13

2.2 Cell Construction 28

2.3 Cell Nutrients 51

2.4 Summary 56

Suggestions for Further Reading 58

Questions 58



Chapter 3: Enzymes 61

3.1 How Enzymes Work 62

3.2 Enzyme Kinetics 63

3.3 Immobilized Enzyme Systems 86

3.4 Large-Scale Production of Enzymes 98

3.5 Medical and Industrial Utilization of Enzymes 100

3.6 Summary 103

Suggestions for Further Reading 104

Problems 104



Chapter 4: How Cells Work 113

4.1 The Central Dogma 114

4.2 DNA Replication: Preserving and Propagating the Message 117

4.3 Transcription: Sending the Message 119

4.4 Translation: Going from Message to Product 123

4.5 Metabolic Regulation 130

4.6 How the Cell Senses its Extracellular Environment 135

4.7 Summary 139

4.8 Appendix: Example Regulation of Complex Pathways 140

Suggestions for Further Reading 142

Problems 143



Chapter 5: Major Metabolic Pathways 145

5.1 Bioenergetics 146

5.2 Glucose Metabolism: Glycolysis and the TCA Cycle 149

5.3 Respiration 152

5.4 Control Sites in Aerobic Glucose Metabolism 154

5.5 Metabolism of Nitrogenous Compounds 155

5.6 Nitrogen Fixation 156

5.7 Metabolism of Hydrocarbons 156

5.8 Biodegradation of Xenobiotics 157

5.9 Overview of Biosynthesis 158

5.10 Overview of Anaerobic Metabolism 161

5.11 Overview of Autotrophic Metabolism 163

5.12 Summary 165

Suggestions for Further Reading 166

Questions 168



Chapter 6: How Cells Grow 169

6.1 Batch Growth 170

6.2 Quantifying Growth Kinetics 191

6.3 Cell Growth in Continuous Culture 208

6.4 Summary 219

Suggestions for Further Reading 219

Problems 220



Chapter 7: Stoichiometry of Microbial Growth and Product Formation 227

7.1 Coefficients for ATP Consumption and Oxygen 227

7.2 Stoichiometric Calculations 229

7.3 Theoretical Predictions of Yield Coefficients 235

7.4 Estimation of Elemental Cell Composition 236

7.5 Stoichiometry by Oxidation-Reduction Half-Reactions 237

7.6 Thermodynamics of Biological Reactions 240

7.7 Summary 242

Suggestions for Further Reading 242

Problems 243



Chapter 8: How Cellular Information Is Altered 247

8.1 Evolving Desirable Biochemical Activities Through Mutation and Selection 247

8.2 Natural Mechanisms for Gene Transfer and Rearrangement 252

8.3 Genetically Engineering Cells 257

8.4 Genomics 267

8.5 Summary 272

Suggestions for Further Reading 272

Problems 273



Part 2: Engineering Principles for Bioprocesses 275




Chapter 9: Operating Considerations for Bioreactors for Suspension and Immobilized Cultures 275

9.1 Choosing the Cultivation Method 276

9.2 Modifying Batch and Continuous Reactors 278

9.3 Immobilized Cell Systems 298

9.4 Hybrid Bioreactors: Attached and Suspended Cells 311

9.5 Solid-State Fermentations 313

9.6 Summary 316

Suggestions for Further Reading 317

Problems 318



Chapter 10: Selection, Scale-Up, Operation, and Control of Bioreactors 323

10.1 Scale-Up and its Difficulties 323

10.2 Bioreactor Instrumentation and Control 349

10.3 Sterilization of Process Fluids 356

10.4 Summary 364

Suggestions for Further Reading 365

Problems 366



Chapter 11: Recovery and Purification of Products 371

11.1 Strategies to Recover and Purify Products 371

11.2 Separation of Insoluble Products 374

11.3 Cell Disruption 382

11.4 Separation of Soluble Products 385

11.5 Finishing Steps for Purification 422

11.6 Integration of Reaction and Separation 424

11.7 Summary 426

Suggestions for Further Reading 426

Problems 427



Chapter 12: Bioprocess Considerations in Using Animal Cell Cultures 431

12.1 Structure and Biochemistry of Animal Cells 431

12.2 Methods Used for the Cultivation of Animal Cells 434

12.3 Bioreactor Considerations for Animal Cell Culture 443

12.4 Bioreactor Systems for Animal Cell Culture 444

12.5 Products of Animal Cell Cultures 447

12.6 Summary 448

Suggestions for Further Reading 449

Problems 450



Chapter 13: Bioprocess Considerations in Using Plant Cell Cultures 451

13.1 Why Plant Cell Cultures? 451

13.2 Plant Cells in Culture Compared to Microbes 457

13.3 Bioreactor Considerations 461

13.4 Economics of Plant Cell Tissue Cultures 467

13.5 Summary 468

Suggestions for Further Reading 468

Problems 469



Chapter 14: Utilizing Genetically Engineered Organisms 471

14.1 How the Product Influences Process Decisions 471

14.2 Guidelines for Choosing Host-Vector Systems 474

14.3 Process Constraints: Genetic Instability 485

14.4 Avoiding Process Problems in Plasmid Design 490

14.5 Predicting Host-Vector Interactions and Genetic Instability 493

14.6 Regulatory Constraints on Genetic Processes 503

14.7 Metabolic Engineering 506

14.8 Synthetic and Systems Biology 509

14.9 Protein Engineering 511

14.10 Summary 513

Suggestions for Further Reading 514

Problems 516



Chapter 15: Medical Applications of Bioprocess Engineering 519

15.1 Tissue Engineering 519

15.2 Gene Therapy Using Viral Vectors 523

15.3 Bioreactors 528

15.4 Summary 531

Suggestions for Further Reading 532

Problems 532



Chapter 16: Bioprocesses Utilizing Mixed Cultures 535

16.1 Major Classes of Interactions in Mixed Cultures 536

16.2 Simple Models Describing Mixed-Culture Interactions 539

16.3 Mixed Cultures in Nature 545

16.4 Industrial Utilization of Mixed Cultures 546

16.5 Biological Waste Treatment 549

16.6 Summary 572

Suggestions for Further Reading 572

Problems 573



Appendix: Traditional Industrial Bioprocesses 577

A.1 Anaerobic Bioprocesses 577

A.2 Aerobic Processes 586

A.3 Bioprocess Technologies: Biofuel and Bioenergy Production from Biomass 596

Suggestions for Further Reading 600



Index 601