Biochemical Reaction Engineering

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Half Title
Biochemical Reaction Engineering
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Contents
Preface
Authors
1. Introduction to Biochemical Engineering
	1.1 Definition of Biotechnology and Biochemical Engineering
		1.1.1 History of Biotechnology
		1.1.2 Dimensions and Units
			1.1.2.1 Fundamental Dimensions
			1.1.2.2 International System of Units
			1.1.2.3 Imperial Units
		1.1.3 Intensive and Extensive Properties
		1.1.4 Statistics
			1.1.4.1 Population
			1.1.4.2 Sample
			1.1.4.3 Parameter
			1.1.4.4 Data
			1.1.4.5 Descriptive Statistics
				1.1.4.5.1 Central Tendency
				1.1.4.5.2 Measures of Dispersion
				1.1.4.5.3 Skewness of Distribution
					1.1.4.5.3.1 Positive Skewness
					1.1.4.5.3.2 Negative Skewness
					1.1.4.5.3.3 Measures of Skewness
				1.1.4.5.4 Kurtosis of Distribution
					1.1.4.5.4.1 Types of Kurtosis
			1.1.4.6 Inferential Statistics
	1.2 Summary
	Bibliography
2. Concept of Microbiology and Biochemistry
	2.1 Introduction
		2.1.1 Concept of Living Cells, Prokaryotic and Eukaryotic, Characterization of the Cells and Their Classification
			2.1.1.1 Cell Structure and Function
		2.1.2 Concept of Carbohydrate, Fat, Protein, DNA, RNA
			2.1.2.1 Carbohydrate
			2.1.2.2 Protein
				2.1.2.2.1 Amino Acids
			2.1.2.3 Lipid/Fat
			2.1.2.4 Nucleic Acid
				2.1.2.4.1 Nucleotide
				2.1.2.4.2 Nucleosides
		2.1.3 Metabolic Pathway
			2.1.3.1 Anabolic Pathways
			2.1.3.2 Catabolic Pathway
			2.1.3.3 Amphibolic Pathway
		2.1.4 Bioenergetics
			2.1.4.1 Review of Law of Thermodynamics
				2.1.4.1.1 Concept of Free Energy
				2.1.4.1.2 Role of ATP in Biochemical Energy Transformations
	2.2 Summary
	Bibliography
3. Concept of Recombinant DNA Technology
	3.1 Introduction
	3.2 Concept of Recombinant DNA Technology
	3.3 Tools of Recombinant DNA Technology
	3.4 Process of Recombinant DNA Technology
	3.5 Concept of Gene Cloning
		3.5.1 Process of Gene Cloning
	3.6 Transgenic PlantS
	3.7 Transgenic AnimalS
	3.8 International Regulations on Genetic Engineering/ R DNA
	3.9 Summary
	Bibliography
4. Enzymatic Reaction Kinetics
	4.1 Fundamentals of Chemical Kinetics
		4.1.1 Fundamental Rate Laws
			4.1.1.1 Rate Equation
				4.1.1.1.1 First Order Reactions
				4.1.1.1.2 Second Order Reactions [Class I]
				4.1.1.1.3 Second Order Reactions [Class II]
				4.1.1.1.4 Zero-order Reactions
				4.1.1.1.5 Higher-order Reactions
		4.1.2 Concept of Free Energy
		4.1.3 Concept of Catalyst and Enzyme
	4.2 Introduction to Enzymes
		4.2.1 Nomenclature of Enzyme
			4.2.1.1 Group 1. Oxidoreductase
			4.2.1.2 Group 2. Transferase
			4.2.1.3 Group 3 Hydrolyze
			4.2.1.4 Group 4 Lyases
			4.2.1.5 Group 5: Isomerases
			4.2.1.6 Group 6 Ligase
	4.3 Enzyme Catalyzed Reaction Kinetics
		4.3.1 Importance of Km
	4.4 Enzyme–Substrate Binding
		4.4.1 Lock and Key Model and Induced Fit Model
		4.4.2 Factor Affecting Enzyme Activity
			4.4.2.1 pH
			4.4.2.2 Temperature
	4.5 Inhibition of Enzymatic Reaction
		4.5.1 Competitive Inhibition
			4.5.1.1 Reaction Mechanism
		4.5.2 Uncompetitive Inhibitor
			4.5.2.1 Non-competitive Inhibitor
		4.5.3 Substrate Inhibition
	4.6 Enzymes in Organic Media
	4.7 Catalytic Antibodies and Non-protein Biomolecules as Catalysts
		4.7.1 Different Strategies for Generating Catalytic Antibodies
			4.7.1.1 Antibodies with Catalytic Groups and Co-factors in Their Combining Sites
			4.7.1.2 Using Antibodies to Stabilize Negatively and Positively Charged Transition States
			4.7.1.3 Using Antibodies as Entropic Traps
			4.7.1.4 Using Catalytic Antibodies to Use Co-factors
		4.7.2 Biocatalysts from Extreme Thermophilic and Hyper-thermophilic Microorganisms
	4.8 Summary
	Bibliography
5. Immobilization of Enzyme
	5.1 Introduction
	5.2 Method of Immobilization and Their Comparison
		5.2.1 Adsorption
		5.2.2 Covalent Bonding
		5.2.3 Entrapment
	5.3 Crosslinking
	5.4 Encapsulation
		5.4.1 Reversible Immobilization
	5.5 Factors Affecting Immobilized Enzyme Catalyzed Reaction
		5.5.1 pH
		5.5.2 Temperature
	5.6 Physico-chemical Characterization of Immobilized Enzyme
	5.7 Biochemical Engineering Aspects of Immobilization Methods
		5.7.1 Damköhler’s Number
		5.7.2 Diffusion Effects in Surface-bound Enzymes on Nonporous Support Materials
		5.7.3 Effects of Diffusion in Immobilized Enzyme Beads Having Porous Matrix
	5.8 Properties of Immobilized Enzyme
	5.9 Ethical and Safety Considerations Associated with the Immobilization Techniques
	5.10 Summary
	Bibliography
6. Microbial Growth Kinetics
	6.1 Introduction
	6.2 Microbial Growth
		6.2.1 Lag Phase
		6.2.2 Log Phase
		6.2.3 Stationary Phase
		6.2.4 Death Phase
	6.3 Growth Kinetics of Microorganisms
		6.3.1 Monod Equation (1949)
		6.3.2 Logistic Growth Model
	6.4 Concept of Different Yield Coefficients
		6.4.1 Yield Coefficient
	6.5 Concept of Growth- and Non-growth-associated Product Formation
	6.6 Concept of Primary and Secondary Metabolites
	6.7 Safety and Ethical Issues of Handling Microorganisms
	6.8 Summary
	Bibliography
7. Bioprocess Systems
	7.1 Introduction
	7.2 Elements of Physical Transfer Processes
	7.3 Transport Phenomena in Bioprocesses
		7.3.1 Two-film Theory
		7.3.2 Heat Transfer
			7.3.2.1 Conduction Heat Transfer
			7.3.2.2 Convection
			7.3.2.3 Radiation
	7.4 Concept of Medium and Air Sterilization
		7.4.1 Media Sterilization
		7.4.2 Theory of Thermal Death Kinetics
			7.4.2.1 Decimal Reduction Time (D-Value)
			7.4.2.2 ‘Z’-Value
			7.4.2.3 Calculation of F-Value
		7.4.3 Mode of Sterilization
			7.4.3.1 Batch Sterilization
				7.4.3.1.1 Calculation of Batch Time
			7.4.3.2 Continuous Sterilization
		7.4.4 Pasteurization
	7.5 Clean-in-Place
		7.5.1 Steps of CIP System
			7.5.1.1 Step 1 Dry Clean
			7.5.1.2 Step 2 Pre-Rinse
			7.5.1.3 Step 3 Detergent Application
			7.5.1.4 Step 4 Post-Rinse
			7.5.1.5 Step 5 Application of a Sanitizer
		7.5.2 Design of CIP System
		7.5.3 Integration Aspects of CIP System
	7.6 Summary
	Bibliography
8. Downstream Processing and Effluent Treatment
	8.1 Introduction
	8.2 Strategies to Recover and Purify Products
		8.2.1 Traditional Separation Processes
			8.2.1.1 Distillation
			8.2.1.2 Concept of Vapor–Liquid Equilibrium (VLE)
			8.2.1.3 Crystallization
			8.2.1.4 Adsorption
				8.2.1.4.1 Adsorption Isotherm
				8.2.1.4.2 Freundlich Adsorption
		8.2.2 Langmuir Isotherm
		8.2.3 Toth Isotherm
		8.2.4 Sips Isotherm
		8.2.5 BET Isotherm
			8.2.5.1 Selection of Adsorbents
			8.2.5.2 Extraction
			8.2.5.3 Filtration
			8.2.5.4 Membrane Separation Process
	8.3 Separation of Microorganisms by Microfiltration
	8.4 Extractive Fermentation
		8.4.1 Aqueous Two-Phase System (ATPS)
			8.4.1.1 ATPS in Extractive Fermentation
	8.5 Chromatography
		8.5.1 Theory of Chromatography
		8.5.2 Classification of Chromatography
			8.5.2.1 Column Chromatography
			8.5.2.2 Ion Exchange Chromatography
			8.5.2.3 Affinity Chromatography
			8.5.2.4 Thin Layer Chromatography
			8.5.2.5 Paper Chromatography
			8.5.2.6 Gas Chromatography
			8.5.2.7 High Pressure Liquid Chromatography (HPLC)
			8.5.2.8 Gel Chromatography
	8.6 Downstream Process of Aerobic and Anaerobic Treatment Processes for Handling Solid and Liquid Wastes
	8.7 Summary
	Bibliography
9. Control Systems
	9.1 Introduction
	9.2 Design Elements of Control Systems
		9.2.1 Types of Control System
			9.2.1.1 Open-Loop Systems
			9.2.1.2 Closed-Loop Systems
		9.2.2 Basic Elements of Process Control
			9.2.2.1 Process
			9.2.2.2 Measurement
			9.2.2.3 Evaluation
			9.2.2.4 Control Element
	9.3 Controlling System in Biochemical Process
		9.3.1 Fermentation Management: A Control Loop Approach
		9.3.2 Theory of PID
			9.3.2.1 Proportional Controller (PC)
			9.3.2.2 Integration Controller
			9.3.2.3 Derivative Controller
			9.3.2.4 Proportional-Integral-Derivative (PID) Control
	9.4 Instrumentation Symbol
	9.5 Introduction to Process Flow Diagram and Piping Instrumentation Diagram
	9.6 Summary
	Bibliography
10. Bioprocess Technology
	10.1 Introduction
		10.1.1 Bioprocessing versus Chemical Processing
		10.1.2 Substrates for Bioconversion Processes and Design of Media
		10.1.3 Cell Culture Techniques
			10.1.3.1 Primary Cell Culture
				10.1.3.1.1 Cell Line
				10.1.3.1.2 Cell Strain
			10.1.3.2 In-Vitro Cell Culture Technique (Animal)
				10.1.3.2.1 Substrate for cell growth
				10.1.3.2.2 Culture Media
				10.1.3.2.3 Natural Media
				10.1.3.2.4 Synthetic Media
					10.1.3.2.4.1 Serum-containing media
					10.1.3.2.4.2 Serum-free media
		10.1.4 Concept of Metabolites
			10.1.4.1 Primary Metabolites
				10.1.4.1.1 Production Pathway of Ethanol
				10.1.4.1.2 Production Pathway of Butanol
				10.1.4.1.3 Production Pathway of Citric Acid
				10.1.4.1.4 Production Pathway of Amino Acid
		10.1.5 Production of Industrial Enzymes Using Microorganisms
			10.1.5.1 Glucose Isomerase (EC 5.3.1.5)
			10.1.5.2 Penicillin Acylase
			10.1.5.3 Amylase
		10.1.6 Production of Secondary Metabolites
		10.1.7 Mushroom Production from Agriculture Residue
		10.1.8 Cultivation Technology of Paddy Straw Mushroom (Volvariella volvacea)
			10.1.8.1 Requirement of Materials
			10.1.8.2 Method of Cultivation
			10.1.8.3 Storage
		10.1.9 Biopesticide
			10.1.9.1 Limitations and Prospects of Biopesticides
		10.1.10 Biofertilizers
		10.1.11 Wastewater Treatment Process
			10.1.11.1 Physical Treatment Process
			10.1.11.2 Chemical Pre-treatment Process
				10.1.11.2.1 Neutralization
				10.1.11.2.2 Addition of Flocculating Agent and Oxidation
				10.1.11.2.3 Ion Exchange Process
				10.1.11.2.4 Disinfection
			10.1.11.3 Biological Treatment of Wastewater
			10.1.11.4 Reaction Kinetics
	10.2 Summary
	Bibliography
11. Bioprocess Plant Design
	11.1 Introduction
		11.1.1 General Design Information
	11.2 Mass and Energy Balance
	11.3 Flow Sheeting, Piping, and Instrumentation
		11.3.1 Flow Sheeting in a Bioprocess
		11.3.2 Principle of Piping and Instrumentation in Bioprocess Plant
	11.4 Materials of Construction for Bioprocess Plants
		11.4.1 Mechanical Design of Process Equipment
		11.4.2 Vessels for Biotechnology Application
	11.5 Design of Fermenters
		11.5.1 Classification of Fermenter/Bioreactor
	11.6 Concept of Scale-up and Scale-down of Bioreactors
		11.6.1 Theory of Scale-up and Scale-down of Bioreactor
		11.6.2 Commercial Impact of Scale-up and Scale-down Approaches
		11.6.3 Case Studies on Scale-up and Scale-down Approaches
	11.7 Selection and Specification of Equipment for Handling Fluids and Solids
	11.8 Design of Heat and Mass Transfer Equipment Used in Bioprocess Industries
		11.8.1 Designing of a Pasteurizer
		11.8.2 Designing of a Spray Drier
	11.9 Summary
	Bibliography
12. MATLAB Basics and Data Analysis
	12.1 Introduction
		12.1.1 Creation and Run Scripts, Functions, and Models in MATLAB
	12.2 Data Analysis and Curve Fitting
	12.3 Numerical Integration
		12.3.1 Euler and Fourth-order Runge–Kutta Method
	12.4 Input and Output Function in MATLAB
	12.5 Summary
	Bibliography
13. MATLAB and Simulink
	13.1 Introduction
	13.2 Application in Bioprocess Systems: Solving Problems Using MATLAB by Numerical Integration
		13.2.1 Numerical Integration Techniques
	13.3 Simulation of Gravity Flow Tank in MATLAB
	13.4 Simulation of CSTR in Series
	13.5 Simulation of Non-isothermal CSTR Simulation of Batch Reactor Using MATLAB
		13.5.1 Simulation in batch reactor
	13.6 Euler Method in MATLAB
		13.6.1 Fourth-order Runge-Kutta Method in MATLAB:
	13.7 SIMULINK for Dynamic Systems
	13.8 Summary
	Bibliography
Index