Biotechnology
Table of contents
CHAPTER 1 : THE CENTURY OF BIOTECHNOLOGY ................................................................................................ 5
1.1. What is biotechnology and what does it mean to you? ........................................................ 5
1.2. Different kinds of Biotechnology ........................................................................................... 9
1.3. Biological challenges of the 21st century ............................................................................ 12
1.4. The ‘Workforce’ in biotechnology ....................................................................................... 14
1.5. VIB (Vlaams interuniversitair instituut voor Biotechnologie) .............................................. 15
CHAPTER 2: CELLULAR LIFE AND MOLECULES OF LIFE...................................................................................... 17
2.1. All cells are either prokaryote or eukaryote ........................................................................ 17
2.2. Cells come in many sizes and shapes ................................................................................... 19
2.3. The prokaryotic cell.............................................................................................................. 20
2.4. The eukaryotic cell ............................................................................................................... 20
2.5. Prokaryotes and eukaryotes differ from each other in many ways .................................... 21
2.6. Viruses .................................................................................................................................. 22
2.7. Molecules of Life .................................................................................................................. 23
a) Fatty acids, lipids and membranes....................................................................................... 23
b) Sugars and carbohydrates.................................................................................................... 26
c) Amino acids and Proteins .................................................................................................... 28
d) Bases, Nucleosides, Nucleotides and Nucleic Acids............................................................. 44
CHAPTER 3: RECOMBINANT DNA TECHNOLOGY AND GENOMICS....................................................................... 67
3.1. Introduction to Recombinant DNA Technology and DNA Cloning ...................................... 67
Restriction enzymes ...................................................................................................................... 67
DNA ligase...................................................................................................................................... 71
Plasmid DNAs ................................................................................................................................ 72
Vectors........................................................................................................................................... 73
Transformation of bacterial cells................................................................................................... 73
3.2. What Makes a Good Vector? ............................................................................................... 74
Selection ........................................................................................................................................ 74
Practical Features of DNA Cloning Vectors ................................................................................... 74
Types of vectors (not discussed in class) ....................................................................................... 75
3.3. How Do You Identify and Clone a Gene of Interest? ........................................................... 77
Creating DNA Libraries .................................................................................................................. 77
Introduction to Biotechnology – Prof. Serge Muyldermans | 1
, Types of Libraries........................................................................................................................... 77
Comparison of a genomic DNA library and a cDNA library ........................................................... 78
Library screening ........................................................................................................................... 83
Synthesis of oligonucleotides ........................................................................................................ 84
Polymerase chain reaction (PCR) .................................................................................................. 85
Cloning PCR products .................................................................................................................... 86
3.4. What Can You Do with a Cloned Gene? Applications of Recombinant DNA Technology ... 89
DNA sequencing ............................................................................................................................ 90
Studying gene expression .............................................................................................................. 94
3.5. Genomics and Bioinformatics: Hot New Areas of Biotechnology........................................ 97
Shot-gun sequencing ..................................................................................................................... 97
The Human Genome Project ......................................................................................................... 97
Comparative genomics .................................................................................................................. 97
CHAPTER 4: PROTEINS AS PRODUCTS ............................................................................................................. 97
4.1. Introduction to Proteins as Biotech Products ...................................................................... 97
4.2. Proteins as Biotechnology Products .................................................................................... 98
Medical applications...................................................................................................................... 99
Food processing........................................................................................................................... 100
Textiles and clothing.................................................................................................................... 100
Detergents ................................................................................................................................... 100
Paper manufacturing and recycling............................................................................................. 101
Adhesives: natural glues .............................................................................................................. 101
Bioremediation: treating pollution with proteins ....................................................................... 101
4.3. Protein Structures .............................................................................................................. 101
Structural arrangement ............................................................................................................... 101
Protein folding ............................................................................................................................. 102
Glycosylation ............................................................................................................................... 102
Protein engineering ..................................................................................................................... 103
4.4. Protein Production ............................................................................................................. 104
Protein Expression: upstream processing ................................................................................... 104
Protein Purification Methods: downstream processing ............................................................. 105
Verification .................................................................................................................................. 108
Preserving Proteins...................................................................................................................... 109
Scale-Up of Protein Purification .................................................................................................. 109
Postpurification Analysis Methods .............................................................................................. 109
4.5. Proteomics ......................................................................................................................... 110
Introduction to Biotechnology – Prof. Serge Muyldermans | 2
,CHAPTER 5: MICROBIAL BIOTECHNOLOGY..................................................................................................... 110
5.1. The Structure of Microbes ................................................................................................. 110
Structural Features of Bacteria.................................................................................................... 111
Yeast ............................................................................................................................................ 112
5.2. Microorganisms as Tools.................................................................................................... 112
Microbial Enzymes....................................................................................................................... 112
Bacterial transformation ............................................................................................................. 112
Cloning and expression techniques ............................................................................................. 113
5.3. Using Microbes for a Variety of Everyday Applications ..................................................... 115
Food products.............................................................................................................................. 115
Therapeutic proteins ................................................................................................................... 116
Field applications ......................................................................................................................... 117
5.4. Vaccines ............................................................................................................................. 118
Immune system and antibodies .................................................................................................. 118
Types of vaccines: how are vaccines made? ............................................................................... 120
Bacterial and viral targets for vaccines ....................................................................................... 120
5.5. Microbial Genomes ............................................................................................................ 121
Why sequence microbial genomes?............................................................................................ 121
Viral genomics ............................................................................................................................. 122
5.6. Microbial Diagnostics ......................................................................................................... 122
Bacterial Detection Strategies ..................................................................................................... 123
Microarrays for tracking contagious diseases ............................................................................. 123
5.7. Combating Bioterrorism..................................................................................................... 124
Microbes as bioweapons ............................................................................................................. 124
5.8. Synthetic Biology................................................................................................................ 125
CHAPTER 6: ANIMAL BIOTECHNOLOGY ......................................................................................................... 125
6.1. Introduction to Animal Biotechnology............................................................................... 125
6.2. Animals in Research ........................................................................................................... 125
Why use animals in research? ..................................................................................................... 125
Regulations in animal research ................................................................................................... 126
Types of animals used in research............................................................................................... 126
Alternatives to the use of animals............................................................................................... 126
Regulation of animal research..................................................................................................... 126
Veterinary Medicine as Clinical Trials.......................................................................................... 126
6.3. Clones ................................................................................................................................. 126
Creating Dolly: a breakthrough in cloning ................................................................................... 126
Introduction to Biotechnology – Prof. Serge Muyldermans | 3
, Limits to cloning .......................................................................................................................... 127
The Future of Cloning .................................................................................................................. 128
6.4. Transgenic Animals ............................................................................................................ 128
Transgenic techniques ................................................................................................................. 128
Increasing agricultural production with transgenics ................................................................... 129
Transgenic Animals as Bioreactors .............................................................................................. 129
Knockouts: A Special Case of Transgenics .................................................................................. 130
6.5. Producing Human Antibodies in Animals........................................................................... 131
Monoclonal antibodies ................................................................................................................ 131
CHAPTER 7: MEDICAL BIOTECHNOLOGY........................................................................................................ 132
7.1. The Power of Molecular Biology: Detecting and Diagnosing Human Disease Conditions 132
Models of Human Disease ........................................................................................................... 132
Biomarkers for Disease Detection ............................................................................................... 132
The Human Genome Project Has Revealed Disease Genes on All Human Chromosomes ......... 133
Detecting Genetic Diseases: Testing for chromosome abnormalities ........................................ 133
7.2. Medical Products and Applications of Biotechnology ....................................................... 136
The search for new medicines and drugs .................................................................................... 136
Vaccines and Therapeutic Antibodies ......................................................................................... 139
7.3. Gene Therapy ..................................................................................................................... 140
How is it done? ............................................................................................................................ 140
Curing genetic diseases: targets for gene therapy ...................................................................... 142
Challenges Facing Gene Therapy................................................................................................. 144
7.4. The Potential of Regenerative Medicine ........................................................................... 144
Cell and Tissue Transplantation................................................................................................... 144
Tissue Engineering ....................................................................................................................... 145
Stem Cell Technologies................................................................................................................ 147
Cloning ......................................................................................................................................... 149
Embryonic stem cell and therapeutic cloning regulations in U.S. ............................................... 150
EXAMPLE OF 1ST QUESTION AT EXAMS ........................................................................................................ 150
Introduction to Biotechnology – Prof. Serge Muyldermans | 4
Table of contents
CHAPTER 1 : THE CENTURY OF BIOTECHNOLOGY ................................................................................................ 5
1.1. What is biotechnology and what does it mean to you? ........................................................ 5
1.2. Different kinds of Biotechnology ........................................................................................... 9
1.3. Biological challenges of the 21st century ............................................................................ 12
1.4. The ‘Workforce’ in biotechnology ....................................................................................... 14
1.5. VIB (Vlaams interuniversitair instituut voor Biotechnologie) .............................................. 15
CHAPTER 2: CELLULAR LIFE AND MOLECULES OF LIFE...................................................................................... 17
2.1. All cells are either prokaryote or eukaryote ........................................................................ 17
2.2. Cells come in many sizes and shapes ................................................................................... 19
2.3. The prokaryotic cell.............................................................................................................. 20
2.4. The eukaryotic cell ............................................................................................................... 20
2.5. Prokaryotes and eukaryotes differ from each other in many ways .................................... 21
2.6. Viruses .................................................................................................................................. 22
2.7. Molecules of Life .................................................................................................................. 23
a) Fatty acids, lipids and membranes....................................................................................... 23
b) Sugars and carbohydrates.................................................................................................... 26
c) Amino acids and Proteins .................................................................................................... 28
d) Bases, Nucleosides, Nucleotides and Nucleic Acids............................................................. 44
CHAPTER 3: RECOMBINANT DNA TECHNOLOGY AND GENOMICS....................................................................... 67
3.1. Introduction to Recombinant DNA Technology and DNA Cloning ...................................... 67
Restriction enzymes ...................................................................................................................... 67
DNA ligase...................................................................................................................................... 71
Plasmid DNAs ................................................................................................................................ 72
Vectors........................................................................................................................................... 73
Transformation of bacterial cells................................................................................................... 73
3.2. What Makes a Good Vector? ............................................................................................... 74
Selection ........................................................................................................................................ 74
Practical Features of DNA Cloning Vectors ................................................................................... 74
Types of vectors (not discussed in class) ....................................................................................... 75
3.3. How Do You Identify and Clone a Gene of Interest? ........................................................... 77
Creating DNA Libraries .................................................................................................................. 77
Introduction to Biotechnology – Prof. Serge Muyldermans | 1
, Types of Libraries........................................................................................................................... 77
Comparison of a genomic DNA library and a cDNA library ........................................................... 78
Library screening ........................................................................................................................... 83
Synthesis of oligonucleotides ........................................................................................................ 84
Polymerase chain reaction (PCR) .................................................................................................. 85
Cloning PCR products .................................................................................................................... 86
3.4. What Can You Do with a Cloned Gene? Applications of Recombinant DNA Technology ... 89
DNA sequencing ............................................................................................................................ 90
Studying gene expression .............................................................................................................. 94
3.5. Genomics and Bioinformatics: Hot New Areas of Biotechnology........................................ 97
Shot-gun sequencing ..................................................................................................................... 97
The Human Genome Project ......................................................................................................... 97
Comparative genomics .................................................................................................................. 97
CHAPTER 4: PROTEINS AS PRODUCTS ............................................................................................................. 97
4.1. Introduction to Proteins as Biotech Products ...................................................................... 97
4.2. Proteins as Biotechnology Products .................................................................................... 98
Medical applications...................................................................................................................... 99
Food processing........................................................................................................................... 100
Textiles and clothing.................................................................................................................... 100
Detergents ................................................................................................................................... 100
Paper manufacturing and recycling............................................................................................. 101
Adhesives: natural glues .............................................................................................................. 101
Bioremediation: treating pollution with proteins ....................................................................... 101
4.3. Protein Structures .............................................................................................................. 101
Structural arrangement ............................................................................................................... 101
Protein folding ............................................................................................................................. 102
Glycosylation ............................................................................................................................... 102
Protein engineering ..................................................................................................................... 103
4.4. Protein Production ............................................................................................................. 104
Protein Expression: upstream processing ................................................................................... 104
Protein Purification Methods: downstream processing ............................................................. 105
Verification .................................................................................................................................. 108
Preserving Proteins...................................................................................................................... 109
Scale-Up of Protein Purification .................................................................................................. 109
Postpurification Analysis Methods .............................................................................................. 109
4.5. Proteomics ......................................................................................................................... 110
Introduction to Biotechnology – Prof. Serge Muyldermans | 2
,CHAPTER 5: MICROBIAL BIOTECHNOLOGY..................................................................................................... 110
5.1. The Structure of Microbes ................................................................................................. 110
Structural Features of Bacteria.................................................................................................... 111
Yeast ............................................................................................................................................ 112
5.2. Microorganisms as Tools.................................................................................................... 112
Microbial Enzymes....................................................................................................................... 112
Bacterial transformation ............................................................................................................. 112
Cloning and expression techniques ............................................................................................. 113
5.3. Using Microbes for a Variety of Everyday Applications ..................................................... 115
Food products.............................................................................................................................. 115
Therapeutic proteins ................................................................................................................... 116
Field applications ......................................................................................................................... 117
5.4. Vaccines ............................................................................................................................. 118
Immune system and antibodies .................................................................................................. 118
Types of vaccines: how are vaccines made? ............................................................................... 120
Bacterial and viral targets for vaccines ....................................................................................... 120
5.5. Microbial Genomes ............................................................................................................ 121
Why sequence microbial genomes?............................................................................................ 121
Viral genomics ............................................................................................................................. 122
5.6. Microbial Diagnostics ......................................................................................................... 122
Bacterial Detection Strategies ..................................................................................................... 123
Microarrays for tracking contagious diseases ............................................................................. 123
5.7. Combating Bioterrorism..................................................................................................... 124
Microbes as bioweapons ............................................................................................................. 124
5.8. Synthetic Biology................................................................................................................ 125
CHAPTER 6: ANIMAL BIOTECHNOLOGY ......................................................................................................... 125
6.1. Introduction to Animal Biotechnology............................................................................... 125
6.2. Animals in Research ........................................................................................................... 125
Why use animals in research? ..................................................................................................... 125
Regulations in animal research ................................................................................................... 126
Types of animals used in research............................................................................................... 126
Alternatives to the use of animals............................................................................................... 126
Regulation of animal research..................................................................................................... 126
Veterinary Medicine as Clinical Trials.......................................................................................... 126
6.3. Clones ................................................................................................................................. 126
Creating Dolly: a breakthrough in cloning ................................................................................... 126
Introduction to Biotechnology – Prof. Serge Muyldermans | 3
, Limits to cloning .......................................................................................................................... 127
The Future of Cloning .................................................................................................................. 128
6.4. Transgenic Animals ............................................................................................................ 128
Transgenic techniques ................................................................................................................. 128
Increasing agricultural production with transgenics ................................................................... 129
Transgenic Animals as Bioreactors .............................................................................................. 129
Knockouts: A Special Case of Transgenics .................................................................................. 130
6.5. Producing Human Antibodies in Animals........................................................................... 131
Monoclonal antibodies ................................................................................................................ 131
CHAPTER 7: MEDICAL BIOTECHNOLOGY........................................................................................................ 132
7.1. The Power of Molecular Biology: Detecting and Diagnosing Human Disease Conditions 132
Models of Human Disease ........................................................................................................... 132
Biomarkers for Disease Detection ............................................................................................... 132
The Human Genome Project Has Revealed Disease Genes on All Human Chromosomes ......... 133
Detecting Genetic Diseases: Testing for chromosome abnormalities ........................................ 133
7.2. Medical Products and Applications of Biotechnology ....................................................... 136
The search for new medicines and drugs .................................................................................... 136
Vaccines and Therapeutic Antibodies ......................................................................................... 139
7.3. Gene Therapy ..................................................................................................................... 140
How is it done? ............................................................................................................................ 140
Curing genetic diseases: targets for gene therapy ...................................................................... 142
Challenges Facing Gene Therapy................................................................................................. 144
7.4. The Potential of Regenerative Medicine ........................................................................... 144
Cell and Tissue Transplantation................................................................................................... 144
Tissue Engineering ....................................................................................................................... 145
Stem Cell Technologies................................................................................................................ 147
Cloning ......................................................................................................................................... 149
Embryonic stem cell and therapeutic cloning regulations in U.S. ............................................... 150
EXAMPLE OF 1ST QUESTION AT EXAMS ........................................................................................................ 150
Introduction to Biotechnology – Prof. Serge Muyldermans | 4
