reading

Cover
An Introduction toMolecular Biotechnology
Copyright
Abbreviations
Part I: Fundamentals of Cellular and Molecular Biology
1. 1 The Cell as the Basic Unit of Life
  1. References
  2. Further Reading
2. 2 Structure and Function of Cellular Macromolecules
  1. 2.1 Structure and Function of Sugars
  2. 2.2 Structure of Membrane Lipids
  3. 2.3 Structure and Function of Proteins
  4. 2.4 Structure of Nucleotides and Nucleic Acids (DNA and RNA)
  5. References
  6. Further Reading
3. 3 Structure and Functions of a Cell
  1. 3.1 Structure of a Eukaryotic Cell
  2. 3.2 Structure of Bacteria
  3. 3.3 Structure of Viruses
  4. 3.4 Differentiation of Cells
  5. 3.5 Cell Death
  6. References
  7. Further Reading
4. 4 Biosynthesis and Function of Macromolecules (DNA, RNA, and Proteins)
  1. 4.1 Genomes, Chromosomes, and Replication
  2. 4.2 Transcription: From Gene to Protein
  3. 4.3 Protein Biosynthesis (Translation)
  4. Further Reading
5. 5 Distributing Proteins in the Cell (Protein Sorting)
  1. 5.1 Import and Export of Proteins via the Nuclear Pore
  2. 5.2 Import of Proteins in Mitochondria, Chloroplasts, and Peroxisomes
  3. 5.3 Protein Transport into the Endoplasmic Reticulum
  4. 5.4 Vesicle Transport from the ER via the Golgi Apparatus to the Cytoplasmic Membrane
  5. References
  6. Further Reading
6. 6 Evolution and Diversity of Organisms
  1. 6.1 Prokaryotes
  2. 6.2 Eukaryotes
  3. References
  4. Further Reading
Part II: Standard Methods in Molecular Biotechnology
1. 7 Isolation and Purification of Proteins
  1. 7.1 Introduction
  2. 7.2 Producing a Protein Extract
  3. 7.3 Gel Electrophoretic Separation Methods
  4. 7.4 Methods of Protein Precipitation
  5. 7.5 Column Chromatography Methods
  6. 7.6 Examples
  7. Further Reading
2. 8 Mass Spectrometry and Applications in Proteomics and Microbial Identification
  1. 8.1 Principles of ESI and MALDI Mass Spectrometry
  2. 8.2 Instrumental Setup
  3. 8.3 Intact Protein Analysis
  4. 8.4 Protein and Proteome Quantification
  5. 8.5 Protein–Protein Interaction Analysis
  6. 8.6 Analysis of Posttranslational Modifications
  7. 8.7 Microbial Identification and Resistance Detection
  8. References
3. 9 Isolation of DNA and RNA
  1. 9.1 Introduction
  2. 9.2 DNA Isolation
  3. 9.3 RNA Isolation
  4. Reference
4. 10 Chromatography and Electrophoresis of Nucleic Acids
  1. 10.1 Introduction
  2. 10.2 Chromatographic Separation of Nucleic Acids
  3. 10.3 Electrophoresis
  4. Further Reading
5. 11 Hybridization of Nucleic Acids
  1. 11.1 Significance of Base Pairing
  2. 11.2 Experimental Hybridization: Kinetic and Thermodynamic Control
  3. 11.3 Analytical Techniques
  4. References
  5. Further Reading
6. 12 Use of Enzymes in the Modification of Nucleic Acids
  1. 12.1 Restriction Enzymes (Restriction Endonucleases)
  2. 12.2 Ligases
  3. 12.3 Methyltransferases
  4. 12.4 DNA Polymerases
  5. 12.5 RNA Polymerases and Reverse Transcriptase
  6. 12.6 Nucleases
  7. 12.7 T4 Polynucleotide Kinase
  8. 12.8 Phosphatases
  9. Further Reading
7. 13 Polymerase Chain Reaction
  1. 13.1 Introduction
  2. 13.2 PCR Methods
  3. 13.3 PCR as a Quantitative Method
  4. 13.4 Areas of Application
  5. Further Reading
8. 14 DNA Sequencing
  1. 14.1 Introduction
  2. 14.2 The Sanger Method
  3. 14.3 Pyrosequencing
  4. 14.4 Second‐Generation Sequencing: Illumina and Ion Torrent
  5. 14.5 Third‐Generation Sequencing Techniques
  6. 14.6 The Impact of the DNA Sequencing Technology
  7. References
  8. Further Reading
  9. Websites
9. 15 Cloning Procedures
  1. 15.1 Introduction
  2. 15.2 Construction of Recombinant Vectors
  3. Further Reading
10. 16 Expression of Recombinant Proteins
  1. 16.1 Introduction
  2. 16.2 Expression of Recombinant Proteins in Host Organisms
  3. 16.3 Expression in Cell‐Free Systems
  4. Further Reading
11. 17 Patch Clamp Method
  1. 17.1 Ion Channels
  2. 17.2 Technical Requirements of the Patch Clamp Method
  3. 17.3 Patch Clamp Configurations
  4. 17.4 Applications of the Patch Clamp Method
  5. Reference
  6. Further Reading
12. 18 Cell Cycle Analysis
  1. 18.1 Introduction
  2. 18.2 Analyzing the Cell Cycle
  3. 18.3 Experimental Analysis of the Cell Cycle
  4. Acknowledgments
  5. Further Reading
13. 19 Microscopic Techniques
  1. 19.1 Introduction
  2. 19.2 Electron Microscopy
  3. 19.3 Atomic or Scanning Force Microscopy
  4. 19.4 Light Microscopy
  5. 19.5 Microscopy in the Living Cell
  6. Further Reading
14. 20 Laser Applications
  1. 20.1 Laser Development: A Historical Perspective
  2. 20.2 Types of Lasers and Setups
  3. 20.3 Properties of Laser Radiation
  4. 20.4 Applications
  5. Further Reading
Part III: Key Topics
1. 21 Sequencing the Universe of Life
  1. 21.1 What to Sequence?
  2. 21.2 Sequencing Projects: Human
  3. 21.3 Sequencing Other Species, Environments, …
  4. 21.4 Sequencing in the Clinics: Personalizing Oncology
  5. 21.5 Sequencing in the Private Sector: Direct to Consumer Testing (DTC)
  6. 21.6 The Information Content of a Genome Sequence and Ethical Consequences
  7. References
2. 22 Cellular Systems Biology
  1. 22.1 Introduction
  2. 22.2 Analysis of Cellular Networks by Top‐Down Approaches
  3. 22.3 Overview over Bottom‐Up Modeling of Biochemical Networks
  4. Further Reading
  5. References
3. 23 Protein–Protein and Protein–DNA Interactions
  1. 23.1 Protein–Protein Interactions
  2. 23.2 Protein–DNA Interactions
  3. References
  4. Further Reading
4. 24 Bioinformatics
  1. 24.1 Introduction
  2. 24.2 Data Sources
  3. 24.3 Sequence Analysis
  4. 24.4 Evolutionary Bioinformatics
  5. 24.5 Gene Prediction
  6. 24.6 Bioinformatics in Transcriptome and Proteome Analysis
  7. 24.7 Analysis of Ultraparallel Sequencing Data
  8. 24.8 Bioinformatic Software
  9. Further Reading
5. 25 Drug Research
  1. 25.1 Introduction
  2. 25.2 Active Compounds and Their Targets
  3. 25.3 Preclinical Pharmacology and Toxicology
  4. 25.4 Clinical Development
  5. 25.5 Clinical Testing
  6. Further Reading
6. 26 Drug Targeting and Prodrugs
  1. 26.1 Drug Targeting
  2. 26.2 Prodrugs
  3. 26.3 Penetration of Drugs Through Biological Membranes
  4. 26.4 Prodrugs to Extend Duration of Effect
  5. 26.5 Prodrugs for the Targeted Release of a Drug
  6. 26.6 Prodrugs to Minimize Side Effects
  7. References
7. 27 Molecular Diagnostics in Medicine
  1. 27.1 Introduction
  2. 27.2 Uses of Molecular Diagnostics
  3. 27.3 Which Molecular Variations Should be Detected
  4. 27.4 Molecular Diagnostic Methods
  5. 27.5 Outlook
  6. Further Reading
8. 28 Recombinant Antibodies and Phage Display
  1. 28.1 Introduction
  2. 28.2 Generation of Specific Recombinant Antibodies
  3. 28.3 Production and Purification of Recombinant Antibodies
  4. 28.4 Features and Applications of Recombinant Antibodies
  5. 28.5 Outlook
  6. Further Reading
  7. References
9. 29 Genetically Modified Mice and Their Impact in Medical Research
  1. 29.1 Overview
  2. 29.2 Transgenic Mice
  3. 29.3 Homologous Recombination: Knockout (Knock‐In) Mice
  4. 29.4 Endonuclease‐Based Knockout Mice
  5. 29.5 Endonuclease‐Based Knock‐In Mice
  6. 29.6 Conditionally Regulated Gene Expression
  7. 29.7 Gene Transfer to Subpopulations of Cells
  8. 29.8 Impact of Genetically Modified Mice in Biomedicine
  9. 29.9 Outlook
  10. Reference
  11. Further Reading
10. 30 Plant Biotechnology
  1. 30.1 Introduction
  2. 30.2 Gene Expression Control and Genome Editing
  3. 30.3 Production of Transgenic Plants
  4. 30.4 Selection of Transformed Plant Cells
  5. 30.5 Regeneration of Transgenic Plants
  6. 30.6 Plant Analysis: Identification and Characterization of Genetically Engineered Plants
  7. Further Reading
11. 31 Biocatalysis in the Chemical Industry
  1. 31.1 Introduction
  2. 31.2 Bioconversion/Enzymatic Procedures
  3. 31.3 Development of an Enzyme for Industrial Biocatalysis
  4. 31.4 Fermentative Procedures
  5. References
Part IV: Biotechnology in Industry
1. 32 Industrial Application: Biotech Industry, Markets, and Opportunities
  1. 32.1 Historical Overview and Definitions of Concepts
  2. 32.2 Areas of Industrial Application of Molecular Biotechnology
  3. 32.3 Status Quo of the Biotech Industry Worldwide
2. 33 Patents in the Molecular Biotechnology Industry: Legal and Ethical Issues
  1. 33.1 Patent Law
  2. 33.2 Ethical and Policy Issues in Biotechnology Patents
  3. 33.3 Conclusions
  4. Acknowledgments
3. 34 Drug Approval in the European Union and United States
  1. 34.1 Introduction
  2. 34.2 Regulation Within the European Union
  3. 34.3 Regulation in the United States
  4. 34.4 The Advent and Regulation of Biosimilars
  5. 34.5 International Regulatory Harmonization
  6. References
4. 35 Emergence of a Biotechnology Industry
  1. Reference
  2. Further Reading
5. 36 The 101 of Founding a Biotech Company
  1. 36.1 First Steps Toward Your Own Company
  2. 36.2 Employees: Recruitment, Remuneration, and Participation
6. 37 Marketing
  1. 37.1 Introduction
  2. 37.2 What Types of Deals Are Possible?
  3. 37.3 What Milestone or License Fees Are Effectively Paid in a Biotech/Pharma Cooperation?
  4. 37.4 PR and IR in Biotech Companies
  5. Further Reading
  6. Websites
Glossary
Index
End User License Agreement

List of Tables

Chapter 1
1. Table 1.1 Comparison of important biochemical and molecular characteristics o...
2. Table 1.2 Compartments of animal and plant cells and their main functions.
3. Table 1.3 Important methodological tools of modern biology.
Chapter 2
1. Table 2.1 Molecular composition of cells.
2. Table 2.2 Formation and function of the cellular macromolecules.
3. Table 2.3 Important fatty acids in membrane lipids.
4. Table 2.4 Compilation and grouping of the proteinogenic amino acids: two type...
5. Table 2.5 Important classes of enzymes.
6. Table 2.6 Many vitamins serve as essential coenzymes for enzyme reactions.
7. Table 2.7 Nomenclature of DNA and RNA building blocks.
8. Table 2.8 Enzymes that use DNA as a substrate and are used in genetic enginee...
Chapter 3
1. Table 3.1 Ion concentrations inside mammalian cells and in the extracellular ...
2. Table 3.2 Most important hormones in humans.
3. Table 3.3 The role of adenylyl cyclase and phospholipase C‐β in signal ...
4. Table 3.4 Some functions of trimeric G‐proteins.
5. Table 3.5 Signal proteins that act via receptor tyrosine kinases.
6. Table 3.6 Prokaryotic properties of plastids and mitochondria.
7. Table 3.7 Classification of major animal and human pathogenic viruses.
8. Table 3.8 Viral oncogenes that may play a part in the emergence of tumors.
9. Table 3.9 Overview of important cell types in plants and animals.
Chapter 4
1. Table 4.1 Overview of a few of the genomes that are already sequenced and pub...
2. Table 4.2 Relation between genome size and the number of genes of a few selec...
3. Table 4.3 A few characteristics of the human genome.
4. Table 4.4 Spontaneous DNA damage in a single diploid mammalian cell within 24...
5. Table 4.5 Genetic diseases, which are associated with defective DNA repair sy...
6. Table 4.6 Consensus sequences in eukaryotic promoter regions.
7. Table 4.7 Protein biosynthesis in bacterial ribosomes as a target for antibio...
Chapter 5
1. Table 5.1 Examples of typical recognition sequences.
2. Table 5.2 Occurrence of some Rab proteins.
Chapter 6
1. Table 6.1 Important groups of protists (model organisms or diseases caused by...
2. Table 6.2 Systematic classification of the land plants.
3. Table 6.3 Systematic classification of multicellular animals (important phyla...
Chapter 7
1. Table 7.1 Commonly used protease inhibitors in protein purification.
2. Table 7.2 Suggestions for choosing ion exchangers when enriching proteins of ...
3. Table 7.3 Commonly used lectins for the enrichment of glycoproteins.
Chapter 12
1. Table 12.1 Features of different polymerases.
Chapter 15
1. Table 15.1 Vectors, heterologous DNA uptake capacity, and host organisms.
2. Table 15.2 Properties of enzymes for turning sticky into blunt DNA ends.
3. Table 15.3 Commonly used cytostatic or cytotoxic selection markers.
4. Table 15.4 Commonly used antigenic fusion components (tags).
5. Table 15.5 Viral expression systems for mammal cells.
Chapter 16
1. Table 16.1 Comparison of prokaryotic and eukaryotic host organisms for the ex...
2. Table 16.2 Comparison of the characteristics of the two most common modificat...
3. Table 16.3 Overview of problems for protein expression inE. coli.
4. Table 16.4 Typical properties of some yeast expression systems.
5. Table 16.5 Typical properties of some important mammalian cell lines.
Chapter 23
1. Table 23.1 Selected databases and Internet resources.
2. Table 23.2 Important biochemical and biophysical methods to examine protein–D...
3. Table 23.3 Selected DNA‐ and RNA‐binding domains in the human genome and in t...
Chapter 25
1. Table 25.1 Diagram of the position of common sequence motifs in members of th...
2. Table 25.2 Target validation.
3. Table 25.3 Screening methods that can be accomplished in high throughput.
4. Table 25.4 Overview of preclinical and clinical drug development.
Chapter 26
1. Table 26.1 Example antibodies in therapeutic use.
Chapter 28
1. Table 28.1 Clinically approved monoclonal antibody products.
Chapter 31
1. Table 31.1 Biocatalytic processes.
2. Table 31.2 The 15 top‐selling recombinant proteins (million US$) in Aggarwal ...
3. Table 31.3 Selected bioconversions.
4. Table 31.4 Annual production volumes of different bioconversions.
Chapter 32
1. Table 32.1 Selected examples of in Germany/EU in 2019 newly registered biopha...
2. Table 32.2 Selected therapeutic antibodies by highest rank of sales (US$ mill...
3. Table 32.3 Selected examples of therapeutic RNAs on the market or under devel...
4. Table 32.4 Selected biotech companies with gene therapy programs.
5. Table 32.5 Selected biotech companies with T‐cell therapy programs.
Chapter 34
1. Table 34.1 The volumes comprising the rules governing medicinal products with...
2. Table 34.2 Product categories regulated by the FDA.
3. Table 34.3 Major biotechnology/biological‐based drug types regulated by CDER ...
4. Table 34.4 ICH guidelines that specifically focus upon products of pharmaceut...
Chapter 35
1. Table 35.1 Differences between biotech and big pharma companies.
Chapter 36
1. Table 36.1 Business attitude and experience.
2. Table 36.2 Fields of competence and necessary qualifications in a startup com...
Chapter 37
1. Table 37.1 Potential revenue for the sale of developed compounds.

List of Illustrations

Chapter 1
1. Figure 1.1 Tree of life – phylogeny of life domains.
2. Figure 1.2 Schematic structure of prokaryotic and eukaryotic cells. (a) Bact...
3. Figure 1.3 Schematic structure of bacteriophages and viruses. (a) Bacterioph...
Chapter 2
1. Figure 2.1 Composition and structure of sugar molecules. (a) Structures of t...
2. Figure 2.2 Structure of the cytoplasmic membrane. Schematic diagram of the l...
3. Figure 2.3 Structures of important phospholipids. Phosphatidylcholine, phosp...
4. Figure 2.4 Chemical structure of cerebrosides (glycolipids). (a) Galactocere...
5. Figure 2.5 Cholesterol and related sterols. Cholesterol; β‐sitosterol r...
6. Figure 2.6 General structure of amino acids and peptides.
7. Figure 2.7 Structures of proteinogenic amino acids. (Cysteine muss zu den am...
8. Figure 2.8 Important hydrogen bonds in biomolecules.
9. Figure 2.9 Noncovalent bonds and disulfide bridges lead to a spatial folding...
10. Figure 2.10 Folding of peptide chains under aqueous conditions leads to a co...
11. Figure 2.11 Importance of hydrogen bonds for the construction of α‐heli...
12. Figure 2.12 Size of proteins in yeast (Saccharomyces cerevisiae). The yeast ...
13. Figure 2.13 Structure of Src protein with four domains. The four domains are...
14. Figure 2.14 Occurrence of domains in different proteins.
15. Figure 2.15 Structure of binding sites within proteins. (a) Schematic illust...
16. Figure 2.16 Reversible activation and inactivation of enzymes and regulatory...
17. Figure 2.17 Structure of nucleotides. (a) Structures of purine and pyrimidin...
18. Figure 2.18 Linear structure of DNA and RNA. In nucleic acid biosynthesis, t...
19. Figure 2.19 Structure of the DNA double helix. The spatial orientation of th...
20. Figure 2.20 Structure of RNA molecules. (A) Yeast tRNA. The base sequence is...
21. Figure 2.21 Structure and function of a hammerhead ribozyme.
Chapter 3
1. Figure 3.1 Mobility of phospholipids in a biomembrane. Three types of moveme...
2. Figure 3.2 Vesicle and liposome formation. (a) In an aqueous environment, li...
3. Figure 3.3 Asymmetric structure of biomembranes.
4. Figure 3.4 Permeability of artificial lipid membranes for biologically relev...
5. Figure 3.5 Important membrane proteins and transport processes. (a) Schemati...
6. Figure 3.6 Glucose transporters in an intestinal cell. Glucose is pumped fro...
7. Figure 3.7 Schematic view of communication pathways between cells. (a) Endoc...
8. Figure 3.8 Schematic representation of receptor classes on the cell surface....
9. Figure 3.9 Activation of adenylyl cyclase and formation from cAMP as second ...
10. Figure 3.10 Role of phospholipase C‐β in the production of second messe...
11. Figure 3.11 Signal transduction after activation of G‐protein and enzyme‐lin...
12. Figure 3.12 Schematic representation of the endomembrane system of the cell:...
13. Figure 3.13 Similarities of lysosomes and plant vacuoles. (a) Schematic stru...
14. Figure 3.14 Composition of a mitochondrion. (a) Electron microscope photogra...
15. Figure 3.15 Function of mitochondrion: metabolism and respiratory chain. (a)...
16. Figure 3.16 Schematic overview of the arrangement of genes in the mtDNA of m...
17. Figure 3.17 Development of an early eucyte and origin of mitochondria. α‐Pur...
18. Figure 3.18 Structure of a chloroplast. (a) Electron microscope photo of a c...
19. Figure 3.19 Essential steps in photosynthesis. (a) Overview of photosyntheti...
20. Figure 3.20 Overview of the arrangement of genes in chloroplast genomes.
21. Figure 3.21 Development of chloroplasts through phagocytosis of cyanobacteri...
22. Figure 3.22 Synopsis of the breakdown pathways and energy‐producing pathways...
23. Figure 3.23 Importance of glycolysis and the citric acid cycle as a point of...
24. Figure 3.24 Schematic composition of actin filaments (microfilaments).
25. Figure 3.25 Mechanism of muscle contraction. (a) Molecular mechanism of musc...
26. Figure 3.26 Schematic view of microtubules and cilia structures. Tubulin dim...
27. Figure 3.27 Schematic view of bacterial cell walls. (a) Gram‐positive bacter...
28. Figure 3.28 Infection cycle and genome of retroviruses. (a) Genome compositi...
29. Figure 3.29 Schematic outline of apoptotic pathways.
Chapter 4
1. Figure 4.1 Number of nucleotides in the haploid genomes of important groups ...
2. Figure 4.2 Composition of eukaryotic genomes and a fraction of a few DNA ele...
3. Figure 4.3 Schematic illustration of human chromosomes. The indentations ind...
4. Figure 4.4 Important structural elements of chromosomes necessary for the re...
5. Figure 4.5 Principle of telomere replication. The telomerase exhibits an RNA...
6. Figure 4.6 From the nucleosome to the condensed metaphase chromosome. The DN...
7. Figure 4.7 Schematic overview of mitosis and meiosis.
8. Figure 4.8 Schematic summary of DNA replication. SSB, single‐strand binding ...
9. Figure 4.9 Asymmetric composition of replication bubbles. DNA is unwound at ...
10. Figure 4.10 Depurination, deamination, oxidation, and dimerization as exampl...
11. Figure 4.11 Consequences of deamination, depurination, and oxidation. Cytidi...
12. Figure 4.12 Base pairing of tautomeric DNA bases. The correct base pairings ...
13. Figure 4.13 Consequences of gene mutations.
14. Figure 4.14 Inheritance of mutations leading to the loss of protein function...
15. Figure 4.15 From gene to protein: comparison of prokaryotes and eukaryotes. ...
16. Figure 4.16 Schematic overview of the function of RNA polymerase and transcr...
17. Figure 4.17 Simplified schematic illustration of the control of gene express...
18. Figure 4.18 Structure of a eukaryotic gene. NCS, noncoding sequence.
19. Figure 4.19 Schematic representation of alternative splicing processes. The ...
20. Figure 4.20 Differences between genetic and epigenetic inheritance.
21. Figure 4.21 Structure of RNA cassettes and synthesis of rRNA. ITSs, internal...
22. Figure 4.22 Structure of (a) prokaryotic and (b) eukaryotic ribosomes. For t...
23. Figure 4.23 Schematic illustration of protein biosynthesis in ribosomes. Thr...
24. Figure 4.24 Loading tRNA with an amino acid. First the amino acid is activat...
25. Figure 4.25 rRNA‐catalyzed peptide transfer in ribosomes. (a) Possible react...
Chapter 5
1. Figure 5.1 Schematic overview of protein transport inside a cell.
2. Figure 5.2 Structure of a nuclear pore (reconstructed from electron microsco...
3. Figure 5.3 Simplified model of the import and export of proteins via the nuc...
4. Figure 5.4 Schematic overview of the uptake of a precursor protein by the mi...
5. Figure 5.5 Simplified scheme of the import of a protein into the ER lumen.
6. Figure 5.6 Simplified scheme of the integration of a membrane protein into t...
7. Figure 5.7 Assembly of glycoproteins in the ER. The oligosaccharide exists a...
8. Figure 5.8 Vesicle transport pathways in the cell.
9. Figure 5.9 Structure of clathrin‐coated vesicles: (a) electron micrograph an...
10. Figure 5.10 Schematic progression of receptor‐mediated endocytosis of LDL....
Chapter 6
1. Figure 6.1 A phylogenetic tree of life, showing the relationship between spe...
2. Figure 6.2 Phylogenetic relationships between protists and transition to pla...
3. Figure 6.3 Phylogeny of land plants.
4. Figure 6.4 Phylogeny of Deuterostomia and vertebrates.
5. Figure 6.5 Evolutionary trends in animal phylogeny.
Chapter 7
1. Figure 7.1 SDS gel electrophoresis. (a) Denaturing effect of SDS. (b) Setup ...
2. Figure 7.2 Size exclusion chromatography. (a) Time course of size exclusion ...
3. Figure 7.3 Anion exchange chromatography. Illustration of the time course of...
4. Figure 7.4 Purification of NDPK with a Cibacron Blue‐Sepharose column. Plot ...
5. Figure 7.5 Purification of His₆‐RGS16: Coomassie Blue R‐250 stain of a 15% S...
Chapter 8
1. Figure 8.1 Key features of a mass spectrum: (a) natural isotope pattern of a...
2. Figure 8.2 Setup of a tandem mass spectrometer allowing the recording of MS1...
3. Figure 8.3 Collision‐induced fragment ion spectrum of the peptide FSGSGSGTSY...
4. Figure 8.4 Metabolic stable isotope labeling. (a) Schematic setup of a SILAC...
5. Figure 8.5 Label‐based quantification strategies in quantitative proteomics ...
6. Figure 8.6 Identification of specific protein interaction partners by Co‐IP,...
7. Figure 8.7 MALDI‐TOF fingerprinting of microorganisms. (a) Generation and an...
Chapter 9
1. Figure 9.1 Mammalian chromosomal DNA in solution (right) precipitated after ...
2. Figure 9.2 Separated plasmid DNA after ultracentrifugation in a CsCl–EtBr gr...
3. Figure 9.3 Scheme of DNA purification for prokaryotes or eukaryotes using a ...
Chapter 10
1. Figure 10.1 Agarose gel electrophoresis of plasmid DNA in the presence of Et...
Chapter 11
1. Figure 11.1 Classical setup of a Southern blot after.
2. Figure 11.2 Genetic analysis of transgenic mice by Southern blotting. Genomi...
3. Figure 11.3 Analysis of gene expression in two strains of transgenic mice (2...
4. Figure 11.4 Result of the expression screening of thousands of genes using l...
5. Figure 11.5 FISH in chromosome preparations. (a) Detection of a deletion in ...
6. Figure 11.6 ISH of two developmental genes (even skipped [blue] and fushi ta...
Chapter 12
1. Figure 12.1 The discovery of restriction endonucleases such as HindIII was a...
2. Figure 12.2 Palindromic sequence recognized by a restriction enzyme. The sym...
3. Figure 12.3 Restriction sites of the restriction enzymes XbaI, AluI, and Pst...
4. Figure 12.4 In order to incorporate nucleotides, a polymerase requires a DNA...
Chapter 13
1. Figure 13.1 Schematic outline of PCR. (a) Basic principle: double‐stranded D...
2. Figure 13.2 Increase in DNA copies, determined by using quantitative real‐ti...
3. Figure 13.3 Schematic representation of the quantitative real‐time detection...
Chapter 14
1. Figure 14.1 Schematic representation of the Sanger sequencing technique. The...
2. Figure 14.2 Schematic representation of the pyrosequencing technique. (a) Nu...
3. Figure 14.3 Schematic representation of the Illumina sequencing system. (a) ...
4. Figure 14.4 Schematic representation of the Ion Torrent sequencing system. (...
Chapter 15
1. Figure 15.1 Cloning, amplification, and selection of heterologous DNA in hos...
Chapter 16
1. Figure 16.1 Which organism for recombinant protein expression?
2. Figure 16.2 Growth and protein induction in an E. coli culture using an...
3. Figure 16.3 Life cycle of wild‐type and recombinant baculoviruses. (a) After...
Chapter 17
1. Figure 17.1 Patch clamp setup. Motorized micromanipulators (a) are mounted o...
2. Figure 17.2 Working principle of a patch clamp amplifier and the effect of t...
3. Figure 17.3 Patch clamp configurations. When the patch pipette touches the c...
4. Figure 17.4 Paired whole‐cell recording of pyramidal neurons from mouse cere...
Chapter 18
1. Figure 18.1 The cell cycle and its phases in S. cerevisiae.
2. Figure 18.2 Regulation of the cell cycle in the yeast S. cerevisiae. Ad...
3. Figure 18.3 Elutriation – schematic view.
4. Figure 18.4 Mating cycle of S. cerevisiae. The presence of a‐ and α‐fac...
5. Figure 18.5 DAPI staining and differential interference contrast (DIC) micro...
6. Figure 18.6 Cell cycle profiles after DNA staining and fluorescence‐activate...
7. Figure 18.7 Schematic configuration of a laser scanning microscope. PMT, pho...
8. Figure 18.8 Plotting the progression throughout the cell cycle in yeast cell...
9. Figure 18.9 Visualization of cell cycle phases using the FUCCI expression an...
Chapter 19
1. Figure 19.1 Layout of optical components in a basic TEM.
2. Figure 19.2 Functional principle of the AFM. The scan table moves the sample...
3. Figure 19.3 Functional principle of the confocal microscope. Through the bea...
Chapter 20
1. Figure 20.1 Setup of a ruby laser.
2. Figure 20.2 Effect of optical tweezers or trap on an object.
Chapter 21
1. Figure 21.1 Cost estimate for sequencing of a single human genome and its pr...
2. Figure 21.2 Just a minor fraction of the human genome encodes proteins (i.e....
3. Figure 21.3 ENCODE encyclopedia of DNA Elements. The goal of ENCODE is to bu...
4. Figure 21.4 Major types of variation found in genomes. A lot of such variati...
Chapter 22
1. Figure 22.1 The three networks of a cell.
2. Figure 22.2 A linear regression function (red line) is fitted to the express...
3. Figure 22.3 The machine learning system needs features of the network, the g...
4. Figure 22.4 (a) An example of a simple network. Knocking out reaction (22.3)...
5. Figure 22.5 TCA cycle and glyoxylate shunt of E. coli for the example in the...
6. Figure 22.6 Numerical simulation of the Michaelis–Menten equations, (a) fast...
7. Figure 22.7 Stimulus response of the Hill equation for increasing Hill expon...
8. Figure 22.8 Model of the MAPK signaling pathway. (a) Schematic representatio...
9. Figure 22.9 Euler integration scheme for two consecutive time steps. Note ho...
10. Figure 22.10 Linear regression and parameter estimation. (a) The true output...
11. Figure 22.11 Schematic representation of the signaling pathway leading to ca...
12. Figure 22.12 Caspase‐3 levels can reach two different steady states, dependi...
13. Figure 22.13 Phase‐space plot of Eq. (22.21). The rate of change dC3/dt is p...
14. Figure 22.14 The steady states (stable, solid line; unstable, dotted line) o...
15. Figure 22.15 Architecture of an autocatalytic positive feedback of the rtTA...
16. Figure 22.16 Mutual inhibition of two molecules on transcription (a) and pro...
17. Figure 22.17 Simulation of the mutual inhibition mechanism (Eq. (22.23)). Pa...
Chapter 23
1. Figure 23.1 Protein domains of the Src oncoprotein. The Src protein has thre...
2. Figure 23.2 RNA polymerase II, a multimeric protein complex. (a) Crystal str...
3. Figure 23.3 Protein interaction network of Helicobacter pylori. This map was...
4. Figure 23.4 Selected methods for the study of protein–protein interactions. ...
5. Figure 23.5 Predicting protein–protein interactions using docking and evolut...
6. Figure 23.6 The NF‐κB signaling pathway as an example for protein–protein an...
7. Figure 23.7 Crystal structure of the Zinc uptake regulator (Zur) in complex ...
8. Figure 23.8 Watson–Crick pairing and hydrogen bond pattern of the 2 bp A–T a...
9. Figure 23.9 ChIP‐Seq, a global method to map binding sites of DNA‐binding pr...
10. Figure 23.10 Network representation of transcriptional regulation (a) transc...
11. Figure 23.11 Crystal structure of EthR from Mycobacterium tuberculosis. This...
12. Figure 23.12 Schematic representation of the Cas9 endonuclease with its gui...
Chapter 24
1. Figure 24.1 Kyte–Doolittle plot of bacteriorhodopsin from Halobacterium spp....
2. Figure 24.2 Part of a multiple alignment of sequences of the a subunit of ca...
3. Figure 24.3 Jukes–Cantor model. Each single nucleotide changes to any other ...
4. Figure 24.4 Consequences of time reversibility. Two actual sequences, 1 and ...
5. Figure 24.5 Multiple substitutions. Several types of multiple substitutions ...
6. Figure 24.6 Operating principle of a simple HMM. In this case, there are onl...
7. Figure 24.7 Results of a classification experiment. Bone marrow samples from...
Chapter 25
1. Figure 25.1 Distribution of targets of known therapeutic agents over protein...
2. Figure 25.2 Domain structure of GPCRs. H1–H7 are the seven α‐helices, e...
3. Figure 25.3 Target validation pyramid. Genomic methods (sequence analysis, e...
4. Figure 25.4 Filter‐binding and FRET assays. The top part shows a FRET assay ...
5. Figure 25.5 Potency and efficiency. Compounds A and B are similar in potency...
Chapter 26
1. Figure 26.1 EPR effect. Drug carriers permeate through the pathologically ch...
2. Figure 26.2 Schematic diagram to illustrate physical targeting. The active s...
3. Figure 26.3 Structure of liposomes that can be used for drug targeting. (a) ...
4. Figure 26.4 Prodrug principle. The free drug cannot cross a membrane barrier...
5. Figure 26.5 Phenytoin and fosphenytoin. Fosphenytoin is around 40 times more...
6. Figure 26.6 Prodrugs of ampicillin. The functional acid group makes it diffi...
7. Figure 26.7 Pivaloyloxyethyl ester of methyldopa. Esterification greatly imp...
8. Figure 26.8 Dipivefrin, a dipivalyl ester of epinephrine, is used to treat g...
9. Figure 26.9 Targeting of the CNS using a redox‐based prodrug system. The dru...
10. Figure 26.10 Azo prodrugs of aminosalicylic acid, used to treat inflammatory...
11. Figure 26.11 Dexamethasone‐21‐β‐D‐glucoside. Following administration, up to...
12. Figure 26.12 Ftorafur [1‐(2‐tetrahydrofuranyl)‐5‐fluorouracil]. This has an ...
Chapter 27
1. Figure 27.1 Overview of mutations in a protein‐coding gene that can influenc...
2. Figure 27.2 Mutation of a single nucleotide. A given nucleic acid sequence (...
3. Figure 27.3 Mutations through repeat expansion or reduction. The repeat of a...
4. Figure 27.4 Gene duplication. In a few cases the duplication of an entire ge...
5. Figure 27.5 Epigenetics: DNA methylation. The expression of a gene can also ...
6. Figure 27.6 Overview of PCR‐based approaches for the detection of target seq...
7. Figure 27.7 DNA microarrays: the principle. DNA microarrays are a further de...
8. Figure 27.8 PCR detection of a length polymorphism. Length insertions and de...
9. Figure 27.9 RFLP. If a mutation disrupts a given restriction enzyme recognit...
10. Figure 27.10 ARCS. If the mutation of interest does not alter a restriction ...
11. Figure 27.11 ARMS. PCR analysis of the negative influence of a mismatch on t...
12. Figure 27.12 Minisequencing. If, in a sequence reaction, instead of a mixtur...
Chapter 28
1. Figure 28.1 Schematic (a) and crystal (b) structure of an immunoglobulins ga...
2. Figure 28.2 Experimental flowchart for the production of an antibody gene li...
3. Figure 28.3 Different selection systems for human antibodies based on recomb...
4. Figure 28.4 Phage display using M13K07 or Hyperphage. After electroporating ...
5. Figure 28.5 From people to people: the human antibody generation cycle. With...
6. Figure 28.6 Modes of action of various antibody‐based anticancer therapies. ...
7. Figure 28.7 Numbers of antibody‐based therapeutics approved by FDA and Europ...
Chapter 29
1. Figure 29.1 First example of a human gene (growth hormone gene) expressed in...
2. Figure 29.2 Experimental flowchart. All gene manipulations are performed in ...
3. Figure 29.3 Gene manipulations in early mouse embryos. Holding pipette (H), ...
4. Figure 29.4 Examples for strategies to make a gene accessible for Cre‐mediat...
5. Figure 29.5 Chimeric founders. The efficiency of ES cell integration into C5...
6. Figure 29.6 Gene editing. Gene editing by CRISPR/Cas9 works in every strain ...
7. Figure 29.7 Conditional gene expression in “compound transgenic” mice. (a, C...
8. Figure 29.8 Virus‐mediated Venus expression in the mouse brain. Expression o...
Chapter 30
1. Figure 30.1 Expression cassette for plant transformation and examples for pl...
2. Figure 30.2 Binary vector for plant transformation. The binary vector system...
3. Figure 30.3 Cre/lox‐based DNA excision. The loxP (locus of excision) system ...
Chapter 31
1. Figure 31.1 Biotechnological processes can differentiate between fermentatio...
2. Figure 31.2 Screening of strain collections can make new enzymes available. ...
3. Figure 31.3 In addition to classical screening of culturable microorganisms,...
4. Figure 31.4 Nitrilases are suitable biocatalysts for the production of optic...
5. Figure 31.5 Reaction mechanism of lipase.
6. Figure 31.6 Lipase‐catalyzed racemic resolution of amines gives access to an...
7. Figure 31.7 Directed evolution increases the stability of pyruvate decarboxy...
8. Figure 31.8 n‐Butanol. Using metabolic engineering, pathways for the synthes...
9. Figure 31.9 Systematic representation of glutamate biosynthesis in C. glutam...
10. Figure 31.10 Influence of penicillin on glutamate formation and on the enzym...
11. Figure 31.11 Selection of feedback‐deregulated mutants with antimetabolites....
Chapter 34
1. Figure 34.1 Simplified structural overview of the EMA.
2. Figure 34.2 Overview of the EU centralized procedure. Refer to text for deta...
3. Figure 34.3 Partial organizational structure of the FDA.
4. Figure 34.4 Summary overview of the main points during a drug's lifetime at ...
Chapter 35
1. Figure 35.1 From descriptive biology towards microbiology.
2. Figure 35.2 Medical and genetic discoveries in the first half of the twentie...
3. Figure 35.3 1953–1976: from molecular genetics toward genetic engineering....
4. Figure 35.4 From genetic engineering toward biotechnology.
5. Figure 35.5 From biotechnology toward genomics.