Discover a detailed knowledge of concepts and techniques of this unique multi-discipline
Chemical Biology is devoted to understanding the way that Biology works at the molecular level. This is a problem-driven multi-discipline, incorporating as it does Organic, Physical, Inorganic, and Analytical Chemistry alongside newer emerging molecular disciplines. In recent years, Chemical Biology has emerged as a vibrant and growing multi-discipline distinct from Biochemistry that is focused on the quantitative analyses of the structures and functions of biological macromolecules and macromolecular lipid assemblies, at first in isolation, then in vitro and in vivo.
The second edition of the Essentials of Chemical Biology begins with a thorough introduction to the structure of biological macromolecules and macromolecular lipid assemblies, before moving on to the principles of chemical and biological synthesis, followed by descriptions of a comprehensive variety of research techniques and experimental methods. In addition, the second edition now includes new sections on the behaviour of biological macromolecules and macromolecular lipid assemblies in cells in vitro and in organisms in vivo. Given this, the second edition of the Essentials of Chemical Biology promises to cement itself as the leading introduction to Chemical Biology, incorporating descriptions of cutting-edge research wherever appropriate. Hence, readers of the second edition of the Essentials of Chemical Biology will find:
a general expansion in understanding of basic molecular mechanisms in Biology moving towards cellular and organismal mechanisms
entirely new chapters covering miniaturization and array technologies, Chemical Cell Biology, and the interface between Chemical Biology and Nanotechnology
updates to chapters reflecting recent research developments
an increased engagement with medical applications
Essentials of Chemical Biology is ideal for advanced undergraduates or (post) graduate students in Chemical Biology and adjacent fields.
Sprache
Verlagsort
Verlagsgruppe
Zielgruppe
Maße
Höhe: 274 mm
Breite: 215 mm
Dicke: 29 mm
Gewicht
ISBN-13
978-1-119-43797-0 (9781119437970)
Copyright in bibliographic data and cover images is held by Nielsen Book Services Limited or by the publishers or by their respective licensors: all rights reserved.
Schweitzer Klassifikation
Andrew D. Miller, PhD, is currently Professor of Organic Chemistry and Chemical Biology at Mendel University in Brno, Czech Republic, and founder/CSO of KP Therapeutics (Europe) s.r.o., a nanomedicine and precision therapeutics company, also based in the Czech Republic.
Julian A. Tanner, PhD, is a Professor of the School of Biomedical Sciences, the University of Hong Kong, and an Assistant Dean of the LKS Faculty of Medicine at the University of Hong Kong.
Table of Contents
0.1 Mapping the Essentials of Chemical Biology
Chapter 1 - The Structures of Biological Macromolecules and Lipid Assemblies
1.1 General Introduction
1.2 Protein Structures
Primary Structure
Repetitive Secondary Structure
Non-repetitive Secondary Structure
Alternative Secondary Structures
Tertiary Structure
Quaternary Structures
Prosthetic Groups
3. Carbohydrate Structures
Primary Structure
O-Glycosidic Link
Polysaccharides; Secondary, Tertiary and Quaternary Structures
4. Nucleic Acid Structures
Primary Structures of DNA and RNA
Phosphodiester Link
Secondary Structure of DNA
B-Form DNA
A-Form and Z-Form DNA
Supercoiling and Tertiary Structures of DNA
Secondary and Tertiary Structures of RNA
The Genetic Code and Structure
Macromolecular Lipid Assemblies
Monomeric Lipid Structures
Lyotropic Mesophases of Phospholipids
Solid-like Mesophases
Fluid Mesophases
1.6 Structural Forces in Biological Macromolecules
Electrostatic Forces
Monopoles
Dipoles
Van der Waals and Dispersion Forces
Weak Dipole-Weak Dipole Interactions
Induced Dipole-Weak Dipole Interactions
Induced Dipole-Induced Dipole Interactions
Hydrogen Bonding
Hydrophobic Interactions
Other Forces
Chapter 2 - Chemical and Biological Synthesis
2.1 Introduction to Synthesis in Chemical Biology
2.2 Chemical Synthesis of Peptides and Proteins
2.2.1 Basic Principles - Peptide Synthesis
2.2.2 Solid Phase Peptide Synthesis (SPPS)
2.2.2.1 Solid Supports and Linkers for SPPS
2.2.2.2 Coupling Protected Amino Acids in SPPS
2.2.2.3 Protection/Deprotection Strategies in SPPS
2.2.3 Chemical Synthesis of Polypeptides
2.2.4 Chemical Synthesis of Peptide Nucleic Acids
2.3 Chemical Synthesis of Nucleic Acids
2.3.1 Chemical Synthesis of Oligodeoxynucleotides
2.3.2 Chemical Synthesis of Oligonucleotides
2.3.3 Useful Deoxynucleotide/Nucleotide Modifications
2.4 Chemical Synthesis of Oligosaccharides
2.4.1 Protecting Groups
2.4.2 Creating Glycosidic Links
2.4.3 Solid Phase Oligosaccharide Synthesis
2.5 Chemical Synthesis of Lipids
2.6 Biological Synthesis of Biological Macromolecules
2.6.1 Ion Exchange Chromatography
2.6.2 Hydrophobic Interaction Chromatography
2.6.3 Reversed-Phase Chromatography
2.6.4 Gel Filtration Chromatography
2.6.5 Hydroxyapatite Chromatography
2.7 Directed Biological Synthesis of Proteins
2.7.1 Wild-type or Recombinant Sources
2.7.2 Expression in E. coli; Early Purification
2.7.3 Affinity Chromatography
2.7.3.1 Immobilised Metal Affinity Chromatography
2.7.3.2 Glutathione-S-Transferase Tags
2.7.3.3 Maltose Binding Protein Tags
2.7.3.4 Biotinylation of Proteins
2.7.3.5 Intein Tags
2.7.3.6 Other Affinity Tags and Radiolabelling of Proteins
2.8 Biological Syntheses of Nucleic Acids, Oligosaccharides and Lipids
2.8.1 Biological Synthesis of Nucleic Acids
2.8.2 Biological Synthesis of Oligosaccharides
2.8.3 Biological Synthesis of Lipids
Chapter 3 Molecular Biology as a Toolset for Chemical Biology
3.1 Key Concepts in Molecular Biology
3.1.1 The Central Dogma of Molecular Biology
3.1.2 The Difference between Prokaryotic and Eukaryotic Genes
3.1.3 The Creation of cDNA Libraries
3.2 Tools and Techniques in Molecular Biology
3.2.1 Plasmid DNA Vectors
3.2.2 Restriction Enzymes
3.2.3 DNA Ligases
3.2.4 Hosts
3.2.5 Cellular Transformation
3.2.6 Selection
3.2.7 pDNA Purification
3.2.8 Nucleic Acid Electrophoresis
3.2.9 DNA Sequencing
3.3 Cloning and Identification of Genes in DNA
3.3.1 Direct DNA Cloning
3.3.2 Polymerase Chain Reaction
3.3.3 Gene Expression and Expression Vectors
3.3.3.1 Expression Vectors
3.3.3.2 Protein Expression Strategy
3.3.3.3 Cloning for RNA Synthesis
3.4 Integrating Cloning and Expression
3.4.1 Designing Forward and Reverse Primers
3.4.2 PCR Amplification and Product Isolation
3.4.3 Ligation and Transformation
3.4.4 Validation and Sequencing
3.4.5 Protein Expression
3.4.6 Cloning and Expressing from Eukaryotic Genes
3.5 Site Directed Mutagenesis
3.5.1 PCR-based Approaches to Mutagenesis
3.5.2 Non-PCR-based Approaches to Mutagenesis
Chapter 4 - Electronic and Vibrational Spectroscopy
4.1 Electronic and Vibrational Spectroscopy in Chemical Biology
4.2 UV-Visible Spectroscopy
4.2.1 Transition Dipole Moments
4.2.2 UV-Visible Spectroscopy of Proteins
4.2.3 UV-Visible Spectroscopy of Nucleic Acids
4.2.4 Structural vs Functional Information from UV-Visible Spectroscopy
4.3 Circular Dichroism Spectroscopy
4.3.1 Circularly Polarised Light
4.3.2 Optical Activity and Circular Dichroism
4.3.3 The Circular Dichroism Spectrum
4.3.4 Structural vs Functional Information from Circular Dichroism Spectroscopy
4.4 Vibrational Spectroscopy
4.4.1 Infra-Red Vibrational Modes
4.4.2 Structural Information from Infra-Red Spectroscopy
4.4.3 Raman Spectroscopy
4.5 Fluorescence Spectroscopy
4.5.1 Rates of Emission and Lifetimes
4.5.2 Effects of Non-Radiative Competition Processes
4.5.3 Structural vs Functional Information from Fluorescence Spectroscopy
4.5.4 Extrinsic Fluorescence and FRET
4.5.5 Probing Biological Macromolecule Functions with Extrinsic Fluorescence
4.5.5.1 Chemical Conjugation of Extrinsic Fluorescent Probes
4.5.5.2 Biological Conjugation of Extrinsic Fluorescent Probes
4.5.5.3 Selecting Extrinsic Fluorescent Probes
4.5.6 Fluorescence Single Molecule Spectroscopy (SMS)
4.6 Probing Metal Centres in Biological Systems by Spectroscopy
Chapter 5 - Magnetic Resonance
5.1 Magnetic Resonance in Chemical Biology
5.2 Key Principles of NMR
5.2.1 Spin Angular Momentum
5.2.2 Magnetic Moment
5.2.3 Quantum Mechanical Description of NMR
5.2.4 Chemical Shift and Coupling
5.2.4.1 Chemical Shift
5.2.4.2 Spin-Spin Coupling
5.2.5 Vector Description of NMR
5.2.6 Spin-Lattice and Spin-Spin Relaxation
5.2.7 Nuclear Overhauser Effect
5.3 Two-dimensional NMR
5.3.1 Homonuclear 2-D COSY and TOCSY Experiments
5.3.2 Heteronuclear Correlation Experiments
5.3.3 NOESY Experiments
5.4 Multi-dimensional NMR
5.4.1 Basic Principles of 3D Experiments
5.4.2 Correlation Experiments
5.4.3 Basic Principles of 4D Experiments
5.5 Biological Macromolecule Structural Information
5.5.1 Analysing Protein Structures
5.5.1.1 3-D COSY and TOCSY Experiments of Proteins
5.5.1.2 3-D HNCA Experiment of Proteins
5.5.1.3 3D- and 4D-NOESY Experiments of Proteins
5.5.1.4 Energy Minimisations
5.5.1.5 Techniques for Overcoming the Molecular Weight Limit
5.5.2 Analysing Nucleic Acid Structures
5.5.3 Analysing Carbohydrate Structures
5.5.4 Analysing Lipid Assembly Structures
5.6 EPR Spectroscopy; Key Principles
5.6.1 Quantum Mechanical Description of EPR
5.6.2 g-Value
5.6.3 Hyperfine Splitting
5.6.4 Biological Macromolecule Structural Information
Chapter 6 - Diffraction and Microscopy
6.1 Diffraction and Microscopy in Chemical Biology
6.2 Key Principles of X-ray Diffraction
6.2.1 Unit Cell
6.2.2 Bragg Law
6.2.3 Reciprocal Lattice
6.2.4 Structure Factors
6.2.5 The Phase Problem
6.2.6 Harker Construction
6.3 Structural Information from X-ray Diffraction
6.3.1 Biological Macromolecule Crystallisation
6.3.2 X-Ray Generation
6.3.3 Determination of X-ray Diffraction Pattern
6.3.4 Heavy Atom Derivitisation
6.3.5 Fitting an Electron Density Map
6.3.6 Biological Macromolecular Structures by X-ray Crystallography
6.4 Neutron Diffraction
6.5 Key Principles of Electron Microscopy
6.5.1 Duality of Matter
6.5.2 Electron Wavelengths
6.5.3 Sample Preparation
6.5.4 Contrast Imaging
6.5.5 Image Processing
6.5.6 Biological Macromolecular Structures from Electron Microscopy
6.6 Key Principles of Scanning Probe Microscopy
6.6.1 STM Concept
6.6.2 Electron Tunnelling
6.6.3 Piezo Electric Drives
6.6.4 STM Scanning Modes
6.6.5 Origin of AFM
6.6.6 AFM Cantilever
6.6.7 AFM Scanning Modes
6.6.8 Biological Structural Information from STM and AFM
Chapter 7 - Molecular Recognition and Binding
7.1 Molecular Recognition and Binding in Chemical Biology
7.1.1 Roles of Molecular Recognition and Binding
7.1.1.1 Acetyl Choline, Receptor and Esterase
7.1.1.2 Adaptive Immunity, Antibodies and Myasthenia Gravis
7.1.1.3 DNA Packaging and Expression Control
7.1.2 Theoretical Framework for Molecular Recognition and Binding
7.1.2.1 Motion in Solution
7.1.2.2 Long Range Molecular Recognition
7.1.2.3 Short Range Molecular Recognition and Binding
7.2 Theoretical Models of Binding
7.2.1 Single Site Single Affinity Binding
7.2.2 Independent Multiple Site, Equal Affinity Binding
7.2.3 Independent Multiple Site, Variable Affinity Binding
7.2.4 Dependent Multiple Site Cooperative Binding and Hill Equation
7.3 Analysing Molecular Recognition and Binding
7.3.1 Equilibrium Dialysis
7.3.2 Titration Methodologies
7.3.2.1 Titration Data Estimates
7.3.2.2 Physical Properties vs Spectroscopic Signatures
7.3.3 Isothermal Titration Calorimetry and Binding Thermodynamics
7.3.3.1 Equilibrium Thermodynamics of Molecular Recognition and Binding
7.3.3.2 Enthalpy of Binding and ITC
7.3.3.3 Van't Hoff Relationships
7.3.4 Capillary Electrophoresis
7.3.5 Resonant Mirror Biosensing (Surface Plasmon Resonance)
7.4 Biological Molecular Recognition Studies
7.4.1 LysU Enzyme Substrate Recognition
7.4.2 Stress Protein Molecular Chaperones
7.4.2.1 GroEL
7.4.2.2 Hsp47
7.4.3 Complementary Peptides
Chapter 8 - Kinetics and Catalysis
8.1 Catalysis in Chemical Biology
8.1.1 Simple Principles in Biocatalysis
8.1.2 Steady State Kinetics in Biocatalysis
8.1.3 Steady-state Bioassays
8.2 Steady State Kinetic Schemes
8.2.1 Simple Steady State Kinetics and Michaelis-Menten Equation
8.2.2 Interpretation of kcatand KM
8.2.3 Determination of kcatand KM
8.2.4 Effect of Steady State Inhibitors
8.2.4.1 Competitive Inhibition
8.2.4.2 Non-competitive Inhibition
8.2.4.3 Un-competitive Inhibition
8.2.5 Applicability of Michaelis-Menten Equation
8.2.6 Multiple Substrate/Product Steady State Kinetics
8.2.6.1 Multiple Catalytic Sites, Non-cooperative Uni-Uni Kinetic Scheme
8.2.6.2 Multiple Catalytic Sites, Cooperative Uni Uni Kinetic Scheme and Hill Equation
8.2.6.3 Ordered Uni-Bi Kinetic Scheme 8.2.6.4 Ordered Bi-Uni Kinetic Scheme
8.2.7 Multiple Substrate/Product King-Altman Kinetics
8.2.7.1 Reversible Uni-Uni Kinetic Scheme
8.2.7.2 Ordered Bi-Bi Kinetic Scheme
8.2.7.3 Ping-Pong Bi-Bi Kinetic Scheme
8.2.7.4 Ordered Ter Bi and Ter Ter Kinetic Scheme
8.3 Pre-steady State Kinetics
8.3.1 Pre-steady State Bioassays
8.3.2 First-Order Pre-steady State Equations
8.3.3 Further Pre-steady State Equations
8.4 Theories of Biocatalysis
8.4.1 Intramolecular Catalysis and Stereo-control in Catalysis
8.4.2 "Orbital Steering"
8.4.3 Induced-Fit and Strain
8.4.4 General-Acid-Base Catalysis
8.4.4.1 Dixon-Webb Log Plots
8.4.5 Electrophilic and Nucleophilic Catalysis
8.46 Mechanisms of Biocatalysis by Selected Biocatalysts
8.47 Transition State Stabilisation and Biocatalysis
8.4.7.1 Basic Transition-State Concepts
8.4.7.2 Binding Energy in Biocatalysis
8.4.8 "Perfect Biocatalyst" Theory
8.4.9 Linear-Free Energy Relationships
8.5 Electron Transfer
8.5.1 Electron Transfer Kinetics
8.5.2 Electron Transfer Step
Chapter 9 - Mass Spectrometry and Proteomics
9.1 Mass Spectrometry in Chemical Biology
9.2 Key Principles in Mass Spectrometry
9.2.1 Ionisation Sources
9.2.1.1 Traditional Techniques of Ionisation
9.2.1.2 Desorption Ionisation Techniques - FAB and MALDI
9.2.1.3 Spray Ionisation Techniques - Thermospray and Electrospray
9.2.2 Mass Analysers in Mass Spectrometry
9.2.2.1 Time of Flight (TOF) Mass Analysers
9.2.2.2 Quadrupole Mass Analysers
9.2.2.3 Ion Trap Mass Analysers
9.2.2.4 Fourier Transform Ion Cyclotron Resonance (FTICR) and Orbitrap Mass Analysers
9.2.2.5 Tandem Mass Analysers (MS/MS)
9.3 Structural Analysis of Biological Macromolecules and Lipids by Mass Spectrometry
9.3.1 Analysis of Individual Peptides by Mass Spectrometry
9.3.2 Analysis of Proteins by Mass Spectrometry
9.3.2.1 Protein Molecular Weight Determination
9.3.2.2 Gel-Based Isolation and Digestion of a Protein for Mass Spectrometry
9.3.2.3 Peptide Mass Fingerprinting for Protein Identification
9.3.2.4 Tandem Mass Spectrometery for Protein Identification
9.3.3 Analysis of Oligonucleotides by Mass Spectrometry
9.3.4 Analysis of Carbohydrates and Glycoproteins by Mass Spectrometry
9.3.5 Analysis of Lipids by Mass Spectrometry
9.4 The Challenge of Proteomics
9.4.1 Early Developments in Proteomics
9.4.2 Using 2-D Gel Electrophoresis with Mass Spectrometry
9.4.3 Isotope-Coded Affinity Tags
9.4.4 Deciphering Protein Networks by Tandem Affinity Purification
9.4.5 The Challenge of Membrane Proteins in Proteomics
9.4.6 Proteomics and Post-Translational Modifications
9.4.6.1 Comprehensive PTM Analysis of a Single Protein
9.4.6.2 PTM Analysis of Protein Populations
9.5 Genomics - Assigning Function to Genes and Proteins
9.5.1 Protein Microarrays
9.5.1.1 Analytical Arrays
9.5.1.2 Functional Arrays
9.5.2 Biochemical Genomics
9.5.3 Chemical Genomics
9.5.4 Structural Genomics
9.5.5 Perspectives on the Future of Proteomics with Genomics
Chapter 10 - Molecular Selection and Evolution
10.1 Chemical Biology and the Origins of Life
10.1.1 Order from Complexity
10.1.2 Evolution from the Molecular Level
10.1.3 Chemical Self-Organisation from Complexity
10.1.4 Origins of Biological Macromolecules of Life
10.2 Molecular Breeding; Natural Selection Acting on Self-Organisation
10.3 Directed Evolution of Protein Function
10.3.1 Random Mutagenesis and PCR
10.3.2 Mutagenesis and DNA Shuffling
10.3.3 Oligodeoxynucleotide Cassette Mutagenesis
10.3.4 Screening Strategies
Directed Evolution of Nucleic Acids
10.4.1 Aptamers
10.4.1.1 Design and Construction of Polydeoxynucleotide/Polynucleotide Libraries
10.4.1.2 Partition, Amplification and Iteration
10.4.1.3 Applications of Aptamers
10.4.2 Selection of Catalytic RNA
10.4.3 DNA Aptamers and Catalytic DNA
10.5 Catalytic Antibodies
Chapter 11 - Chemical Biology of Cells
11.1 General Introduction
11.2 Array Technologies, Microfluidics, and Miniaturization
11.2.1 Arrays from Past to Present
11.2.2 Micropatterned and Microfluidic Devices
11.3 Chemical Genetics and Potential New Therapeutics
11.3.1 Early Chemical Genetics
11.3.2 More Recnt Chemical Genetics
11.3.2.1 Chemical Genetics in MoA Identification
11.3.2.2 Chemical Genetics in Drug Resistance and Drug-Drug Interactions
11.4 Chemical Cellular Dynamics
11.5 Chemical Biology and in vivo Cell Connectomics
11.5.1 Brainbow Connectomics
11.5.2 Brainbow Applications
Chapter 12 - Chemical Biology of Stem Cells to Tissue Engineering
12.1 General Introduction
12.2 Chemical Stem Cell Biology
12.2.1 Stem Cell Regulation
12.2.1.1 Biochemical Regulation
12.2.1.2 Biophysical Regulation
12.2.2 Controlling Stem Cell Regulation by Biochemical and Biophysical Means
12.2.3 Controlling Stem Cell Regulation by Genetic Means
12.2.4 Stem Cell Modelling
12.2.4.1 Deterministic Modelling
12.2.4.2 Other Modelling Approaches
12.3 The Road to Cell Therapies
12.3.1 The Need for Bioreactors
12.3.2 Practical Bioreactors
12.3.3 Practical Cell Therapies
12.4 Tissue Engineering
12.4.1 Biomaterials to Tissue Engineering
12.4.2 Tissue Engineering and Regenerative Medicine
Chapter 13 - Chemical Biology, Nanomedicine and Advanced Therapeutics
13.1 General Introduction
13.2 The Chemical Biology Approach to Gene Therapy
13.2.1 Nantechnology to Nanomedicine
13.2.2 Advanced Therapeutics - Gene Therapy
13.2.3 Gene Therapy Strategies
13.2.4 First Applications of Synthetic Nanoparticles in Gene Therapy Strategies
13.2.5 Improving on the Therapeutic Nucleic Acid APIs
13.2.6 The ABCD Nanoparticle Concept
13.2.7 Formation of ABC/ABCD Nanoparticles for in vivo and Clinical Use
13.2.8 Nanoparticles in Clinic
13.2.9 Desiging Future ABC/ABCD Nanoparticles
13.2.10 4Ss or Nanotechnology; Impact on 4 Ts of Delivery
13.2.11 Future Prospects for Gene Therapy Enabled by LNP Nanomedicine
13.3 Biophysical Characterisation of LNPs
13.3.1 Dynamic Light Scattering
13.3.2 Measuring Nanoparticulate Zeta-potentials
13.3.3 Measuring Nanoparticle Properties in Complex Solutions
13.4 Applications of LNPs with Small Molecule Drugs
Chapter 14 - Chemical Biology and Advanced Diagnostics Leading to Precision
Therapeutic Approaches
14.1 General Introduction
14.2 MRI Basic Principles Leading to Diagnostic Applications
14.2.1 Small Molecule Positive Contrast Agents
14.2.2 Imaging Nanoparticles
14.3 PET/CT and SPECT Fundamentals
14.3.1 Tracer Agents
14.3.2 Nanomolecular Tracer Agents
14.4 Understanding How to Control Nanoparticle Biodistribution Behaviour in vivo
14.4.1 Designing Future Theranostic ABC/ABCD Nanoparticles
14.5 Theranostics
14.5.1 Multimodal "hard" TNPs
14.5.2 Multimodal "soft" TNPs
14.5.3 Towards Precision Therapeutic Approaches for Treatment
14.5.4 Devising Precision Therapeutic Approaches for Treatment
Chapter 15 - DNA Nanotechnology
15.1 Background
15.1.1 From Holliday Junctions to Double-Crossover and Paranemic DNA
15.1.2 Scaffolded DNA Origami
15.1.3 Single-Stranded Tile (SST) Assembly
15.2 Three-Dimensional DNA Nanostructures
15.3 Dynamic DNA Nanostructures
15.4 Biomedical Applicationns of DNA Nanostructures
