Introduction to Pharmaceutical Biotechnology: Applications and Issues

by Saurabh Bhatia

Overview

This book addresses the characteristics of genomics, genome sequencing, comparative genomics and genomic evolution, and will be of interest to biochemists, biologists, microbiologists, biotechnologists, food technologists and all others involved in the research and development of the biological applications of proteins and enzymes.

Product Details

ISBN-13:	9780750313032
Publisher:	Iop Publishing Ltd
Publication date:	03/15/2019
Series:	IPH001 , #2
Pages:	350
Product dimensions:	7.51(w) x 10.52(h) x 0.82(d)

Table of Contents

Preface xiv

Acknowledgments xv

Author biography xvi

1 Introduction to enzymes and their applications 1-1

1.1 Introduction 1-1

1.2 Properties of enzymes 1-3

1.3 Catalysis 1-5

1.4 The structure of enzymes 1-5

1.5 Structural features: primary and secondary structures 1-7

1.6 The mechanism of action of enzymes 1-7

1.6.1 The Fisher template model (lock and key model) 1-7

1.6.2 Induced fit model 1-8

1.6.3 Covalent catalysis 1-8

1.7 Catalysis via chymotrypsin 1-9

1.7.1 Intermediary stages of chymotrypsin 1-9

1.7.2 Kinetic behavior of α-chymotrypsin 1-9

1.7.3 Selective proteolysis in creation of the catalytic sites of enzymes 1-10

1.7.4 Kinetic models for enzymes 1-11

1.7.5 Enzyme mediated acid-base (general) catalysis 1-15

1.7.6 Metallozymes 1-15

1.8 Enzyme inhibition 1-17

1.9 Pharmaceutical applications 1-17

1.9.1 Diagnostic applications of enzymes 1-18

1.9.2 Enzymes in therapeutics 1-20

1.10 Plants and algae enzyme systems 1-25

References 1-26

2 Technologies and procedures involved in enzyme production 2-1

2.1 Introduction 2-1

2.1.1 Sources of enzymes 2-2

2.2 Enzyme production technology 2-6

2.2.1 Selection of micro-organisms 2-6

2.2.2 Medium selection 2-8

2.2.3 Production process 2-9

2.2.4 Recovery and purification of enzymes 2-10

2.2.5 Cell debris removal 2-10

2.2.6 Nucleic acid removal 2-11

2.2.7 Precipitation of enzymes 2-11

2.2.8 Liquid-liquid partition 2-11

2.2.9 Chromatographic separation 2-12

2.2.10 Drying and packing 2-12

2.2.11 Regulation of microbial enzyme production 2-13

2.2.12 Induction 2-13

2.2.13 Feedback repression 2-14

2.2.14 Nutrient repression 2-14

2.3 Procedures involved in enzyme production 2-15

2.3.1 Source and location of enzymes 2-15

2.3.2 The variety of micro-organisms 2-16

2.3.3 Media for fermentation 2-17

2.3.4 Fermentation 2-17

2.3.5 Enzyme extraction 2-19

2.4 Recombinant proteins from algae 2-35

References 2-36

3 Industrial enzymes and their applications 3-1

3.1 Industrial enzymes 3-1

3.2 Bacterial a-amylases 3-1

3.3 Fungal a-amylases 3-6

3.4 Bacterial proteases 3-8

3.5 Fungal proteases 3-9

3.6 Glucose isomerase (D-xylose ketol-isomerase; EC. 5.3.1.5) 3-9

3.7 Penicillinase 3-11

3.8 Chloramphenicol acetyltransferase 3-13

3.9 Aminoglycoside antibiotic inactivating enzymes 3-14

3.10 Fibrinolytic enzymes 3-14

3.10.1 Streptokinase 3-15

3.10.2 Urokinase 3-17

3.10.3 Tissue plasminogen activator (t-PA) 3-17

3.11 Biotechnological applications of enzymes 3-18

3.11.1 Algae and plant research 3-18

3.11.2 Immobilization 3-18

References 3-19

4 Immobilization of enzymes 4-1

4.1 Introduction 4-1

4.2 Types of immobilization 4-3

4.2.1 Surface immobilization by covalent coupling 4-3

4.2.2 Adsorption 4-6

4.2.3 Complexation and chelation 4-6

4.2.4 Within-support immobilization 4-7

4.2.5 Cell immobilization 4-8

4.2.6 Commercial production of enzymes 4-10

4.3 Genetic engineering for microbial enzyme production 4-10

4.3.1 Cloning methods 4-11

4.4 Protein studies for modification of commercial enzymes 4-12

4.5 Enzyme and cell immobilization 4-13

4.6 Immobilization methods 4-14

4.6.1 Adsorption methods 4-14

4.6.2 Nonspecific adsorption 4-14

4.6.3 Ionic binding 4-15

4.6.4 Hydrophobic adsorption 4-15

4.6.5 Affinity binding 4-15

4.6.6 Entrapment method 4-16

4.6.7 Covalent binding 4-17

4.6.8 Cross-linking 4-19

4.7 Choice of immobilization technique 4-20

4.7.1 Immobilization of L-amino acid acylase 4-20

4.7.2 Stabilization of soluble enzymes 4-20

4.8 Immobilization of cells 4-21

4.8.1 Immobilization of viable cells 4-22

4.8.2 Immobilized non-viable cells 4-22

4.8.3 Drawbacks of immobilizing eukaryotic cells 4-23

4.8.4 The effect of immobilization on enzyme properties 4-23

4.8.5 Immobilized enzyme reactors 4-23

4.8.6 Applications of immobilized enzymes and cells 4-25

4.9 Manufacture of commercial products 4-25

4.9.1 Production of L-amino acids 4-26

4.9.2 Production of high-fructose syrup 4-26

4.9.3 Immobilized enzyme and cell analytical applications 4-27

4.10 Application of various immobilization techniques for algal bio processes 4-28

References 4-30

5 Biosensors 5-1

5.1 Introduction 5-1

5.2 Principles of a biosensor 5-2

5.3 Different types of biosensors 5-3

5.3.1 Electrochemical biosensors 5-4

5.3.2 Thermometric biosensors 5-9

5.3.3 Optical biosensors 5-10

5.3.4 Piezoelectric biosensors 5-13

5.3.5 Whole-cell biosensors 5-14

5.3.6 Immunobiosensors 5-14

5.4 Applications of biosensors 5-15

5.4.1 Applications in medicine and health 5-16

5.4.2 Applications in industry 5-16

5.4.3 Applications in pollution control 5-16

5.4.4 Applications in the military 5-16

5.4.5 Immobilized enzymes and cell therapeutic applications 5-16 References 5-18

6 Biotransformation and enzymes 6-1

6.1 Introduction 6-1

6.2 Types of biotransformation reactions 6-1

6.3 Sources of biocatalysts and techniques for biotransformation 6-2

6.3.1 Growing cells 6-3

6.3.2 Non-growing cells 6-3

6.3.3 Immobilized cells 6-3

6.3.4 Immobilized enzymes 6-3

6.4 Product recovery in biotransformations 6-3

6.5 Application of biotransformation in the production of pharmaceutical products 6-4

6.5.1 Biotransformation of steroids 6-4

6.5.2 Biotransformation of antibiotics 6-6

6.5.3 Biotransformation of arachidonic acid to prostaglandins 6-10

6.5.4 Biotransformation for the production of ascorbic acid 6-11

6.5.5 Biotransformation of glycerol to dihydroxyacetone 6-11

6.5.6 Biotransformation for the production of indigo 6-11

References 6-11

7 Introduction to genomics 7-1

7.1 Introduction 7-1

7.2 Characterizations in genomics 7-2

7.3 Historical background 7-2

7.4 Genome sequencing 7-3

7.4.1 Clone-by-clone sequencing 7-4

7.4.2 Human whole-genome shotgun sequencing 7-5

7.4.3 Compilation of genome resources 7-7

7.5 Understanding bioinformatics and sequencing 7-8

7.6 Comparative genomics as a technique to understand evolution 7-12

7.6.1 The role of exon shuffling 7-12

7.6.2 Horizontal or lateral gene transfer 7-13

7.6.3 Genome similarity or homology 7-14

7.6.4 SNPs 7-15

7.6.5 Inferences from comparative genomics 7-17

7.6.6 Gene order comparisons (for phylogenetic inference) 7-21

7.6.7 Phylogenetic footprinting (computational method) 7-21

7.6.8 Origins, evolution and phenotypie impact of new genes 7-22

7.6.9 The concept of minimum genome size 7-22

7.6.10 Comparative genomics analysis of mitochondria and chloroplasts 7-24

7.7 Gene estimation and counting 7-25

7.7.1 Genome similarity, SNPs and comparative genomics 7-26

7.8 Genomes: genome evolution 7-27

7.8.1 Microbial genome reduction in bacteria 7-28

7.8.2 Role of duplications in the origin and evolution of the eukaryotic genome 7-29

7.8.3 Gene duplications increase genetic diversity and complexity 7-31

7.9 Algae bioinformatics 7-32

7.9.1 Scope of algae bioinformatics 7-32

7.9.2 What is involved in algae bioinformatics 7-32

7.9.3 Role of algae bioinformatics 7-32

7.9.4 Steps involved in obtaining the data for analysis using bioinformatics 7-32

References 7-33

8 Basics of proteomics 8-1

8.1 Introduction 8-1

8.2 Types of proteomics 8-2

8.2.1 Structural proteomics 8-2

8.2.2 Functional proteomics (strategy) 8-3

8.2.3 Expression proteomics 8-4

8.3 Basic techniques involved in proteomics 8-5

8.3.1 Sequence alignment (algorithms) 8-5

8.3.2 Protein structure (annotation resources) 8-6

8.3.3 Protein structural investigation 8-7

8.3.4 Two-dimensional gel electrophoresis in proteomics 8-8

8.3.5 Domain fusion method (or Rosetta stone method) 8-8

8.4 Complete proteome of Mycoplasma genitalium 8-9

8.5 Architecture and design of the nuclear pore complex 8-10

8.6 Functional genomics and systems biology 8-10

8.6.1 Gene expression profiling 8-12

8.6.2 Transcriptome, proteome and genomes 8-14

8.6.3 DNA arrays: a potential genomic tool 8-16

8.6.4 Gene function determination from sequence information 8-20

8.6.5 Protein interactions 8-22

8.7 Synthetic genomics 8-28

References 8-30

9 Bioinformatics 9-1

9.1 Introduction 9-1

9.2 History of bioinformatics 9-2

9.3 Sequences and nomenclature 9-4

9.3.1 DNA sequences 9-5

9.3.2 Amino acid sequences of proteins 9-5

9.3.3 Types of sequences in nucleotide sequence databases 9-5

9.3.4 Databases 9-7

9.3.5 Search engines and analysis tools 9-9

9.3.6 Various Indian databases 9-12

9.4 Investigation by means of bioinformatics tools 9-12

9.4.1 Identification of genes 9-13

9.4.2 Identification of the function of a new gene 9-14

9.4.3 Identification of functional domains 9-14

9.4.4 Detection of noncoding RNA 9-14

9.4.5 Genome annotation 9-15

9.4.6 Molecular phylogenetics 9-15

References 9-15

10 Protein and enzyme engineering 10-1

10.1 Protein and enzyme engineering 10-1

10.2 Designing macromolecules 10-1

10.3 Protein engineering versus enzyme engineering 10-4

10.4 Protein engineering 10-5

10.5 Foundation of protein (enzyme) engineering 10-6

10.6 Basic assumptions for protein engineering 10-7

10.7 Steps involved in protein engineering 10-8

10.7.1 Studying three-dimensional protein structure 10-8

10.7.2 Protein modeling 10-9

10.7.3 Perturbation theory 10-9

10.8 Methods of protein engineering 10-10

10.9 Mutagenesis and selection of mutant enzymes 10-10

10.10 Gene modifications or gene synthesis for protein engineering 10-11

10.11 Multi-enzyme systems 10-12

10.12 Chemical modification of enzyme 10-12

10.13 Some early achievements of protein engineering 10-13

References 10-14