دانلود کتاب Biophysical Chemistry: Techniques and Applications

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Cover
Half Title
Biophysical Chemistry: Techniques and Applications
Copyright
Preface
Table of Contents
List of Figures
List of Tables
List of Symbols and Acronyms
Part I. Different Types of Biomolecules
1. Cell and its Biochemical Setup
1.1 Introduction
1.2 Structure of an Animal Cell
1.2.1 Principal Structures of an Animal Cell
1.2.2 Structure of a Human Cell and its Functions
1.3 Composition of Human Cell
1.3.1 Human Cell
1.3.2 Nucleus
1.3.3 Mitochondria
1.3.4 Endoplastic Reticulum (ER)
1.3.5 Golgi Apparatus
1.3.6 Lysosomes
1.3.7 Peroxisomes
1.3.8 Microfilaments and Microtubules
1.4 Eukaryotic and Prokaryotic Cells
1.4.1 Similarities and Differences Between the Two Types of Cells
1.5 Membrane-Bound Organelles
1.6 Comparison Between Lysosome and Ribosome
1.7 Types of Cells in Human Body
1.8 Peripheral Proteins
1.9 Transport Across Cell Membrane
1.9.1 Passive Transport
1.10 Facilitated Diffusion
1.10.1 Active Transport
1.11 Permeability of Molecules Across Phospholipid Bilayers
1.12 Thermodynamic basis of Transport
1.13 Examples of Antiport and Symport System
1.13.1 (Na+/K+) ATPase
1.14 Ca2+ ATPase
Questions
2. Thermodynamic Aspects of the Cell
2.1 Introduction
2.2 Enthalpy and Free Energy Changes in Biochemical Processes
2.3 Effects of Electrochemical Changes
2.4 Distribution of Ions Across Membranes
2.5 Distribution of Ions Near Charged Membranes and Macromolecules
2.6 Osmotic Effects
2.7 Role of Chemical Potential
2.8 Effects of Different Molecular Environments and Phases on Energy and Entropy
2.9 Surface Free Energies and Surface Tension
2.10 Molecular Aggregation
2.11 Non-equilibrium Thermodynamic Treatment of Bacterial Cells
2.12 Bacterial Cell as a Thermodynamic System
2.13 Physical and Chemical Features of the Cell and Environment
2.13.1 Physical Features
2.13.2 Chemical Features
2.13.3 Continuous Culture
2.14 Concept of Steady State
2.15 Non-equilibrium Thermodynamics
in Microbiology
2.16 Linear Laws
2.17 Force and Flows in Living Systems
2.17.1 Temperature and Heat Flow
2.18 Chemical Potential and Mass Transfer: Activated Support
2.19 Applicability of Linear Laws
2.20 Non-linear Descriptions
2.20.1 Systems Involving Large Affinities
2.21 Simple Cell Functions in Non-equilibrium Thermodynamics
2.22 Batch Cultures
2.23 Thermodynamic Concepts
Questions
3. Carbohydrates, their Reactions, Thermochemistry and Energetics
3.1 Introduction
3.2 General Properties of Monosaccharides
3.2.1 Ketoses
3.2.2 Oxidation
3.2.3 Reduction
3.2.4 Reaction with Phenylhydrazine
3.2.5 Reaction with Acids and Bases
3.2.6 Unusual Reactions of Monosaccharides
3.2.7 Conversion to Haworth Structures
3.3 Other Monosaccharides
3.3.1 Aldopentoses
3.3.2 Ketohexoses
3.4 Glycosides
3.5 Oligosaccharides
3.6 Polysaccharides
3.6.1 Starch
3.6.2 Glycogen
3.6.3 Cellulose
3.7 Cell Walls of Bacteria
3.8 Thermochemistry of Carbohydrates
3.9 Gibbs Free Energy Changes for Reactions
3.9.1 Glycolysis
3.10 Enolic Phosphate
3.11 Guanidinium Phosphates
3.11.1 Coupling of Reactions
3.12 Carbohydrates and Microbial Fuel Cells
Questions
4. Lipids
4.1 Introduction
4.2 Properties of Lipids
4.3 Bonding in Lipids
4.4 Classification
4.4.1 Fatty Acids
4.5 Reactions
4.5.1 Fatty Acids
4.5.2 Geometric Isomerism
4.6 Analysis of Lipids
4.7 Nomenclature of Phospholipids
4.8 Lipoproteins
4.9 Role of Lipids in Cell Function
4.10 Distribution of Lipids
4.11 Physicochemical Data on Lipids
4.11.1 Physicochemical Data on Lipids
4.11.2 Waxes
4.12 Lipid Bi-layers
4.13 Glycolipids on the Surface of all Membranes
4.14 Interfacial Studies of Lipid Bilayers
Questions
5. Amino Acids
5.1 Introduction
5.2 Classification of Amino Acids
5.3 Chirality of Amino Acids
5.4 Acid-base Properties
5.6 Biochemical Importance of Amino Acids
5.7 Electrochemical Studies of Amino Acids
Questions
6. Peptides
6.1 Introduction
6.2 Classes of Peptides
6.2.1 Different Classes of Peptides
6.2.2 Natriuretic Peptides (NP’s)
6.3 Functions of Peptides
6.4 Acid-Base Properties of Peptides
6.4.1 Expansion of Symbols
6.5 Peptides as Biosensors
6.6 Current-Voltage Characteristics of Peptide Films
Questions
7. Proteins
7.1 Introduction
7.2 Composition of Proteins
7.3 Some Characteristics of Proteins
7.4 Classification of Proteins
7.5 Nature of Bonds in Protein Structure
7.6 Structure of Proteins
7.7 Role of Amino Acids in Proteins
7.8 Examples of Proteins
7.9 Hemoglobin
7.10 Antibodies
7.11 Hormones
7.11.1 Nutrient Proteins
7.12 Denaturation of Proteins
7.13 Helix-Coil Transitions in Proteins
7.14 Kinetics of Helix-Coil Transformation
7.15 Membrane Proteins
7.16 Modelling of Tertiary Structure of Proteins
7.17 Levinthal Paradox
7.18 Proteins in Nutrition
Questions
8. Nucleosides and Nucleotides
8.1 Introduction
8.2 Biological Function (DNA & RNA)
8.3 Examples of Nucleotides
8.4 Naming of Nucleosides and Nucleotides
Questions
9. Enzymes
9.1 Introduction
9.2 Different Types of Enzymes
9.3 Nature of Enzyme Action
9.3.1 Examples of Digestive Enzymes
9.3.2 Significance of Km
9.4 Michaelis-Menten Mechanism
9.5 Effect of Temperature on Enzyme-catalysed Reactions
9.6 Specificity of an Enzyme
9.7 Classification of Enzymes
9.8 Inhibitors of Enzymes
9.9 Reversible Inhibition
9.10 Uncompetitive Inhibition
9.11 Allosteric Enzymes
9.12 Oligomeric Enzymes
9.12.1 Glycolytic Enzymes
9.13 Isoenzymes
9.14 Bifunctional Oligomeric Enzymes
9.15 Multienzyme Complexes
9.16 Modification of the Specificity of an Oligomeric Enzyme
9.17 Measurement of Enzymatic Activity of Lactose Dehydrogenase (LDH) obtained from Different Organisms
9.18 Turn Over Rates (T.O.R) of Some Enzymes
9.19 Immobilisation of Enzymes
Questions
10. Co-Enzymes and Vitamins
10.1 Introduction
10.1.1 Importance and Need for Co-enzymes
10.1.2 Support for Proper Enzyme Function
10.2 Relation between Co-enzymes and Vitamins
10.3 Vitamins
10.3.1 Definition and Types
10.3.2 Some Specific Functions of Vitamins
10.4 Biochemical Functioning of the B-Vitamin Group
10.4.1 Niacin
10.4.2 Riboflavin B2
10.4.3 Flavin Adenine Dinucleotides (FAD)
10.4.4 Metalloflavoproteins
10.4.5 Lipoic Acid
10.4.6 Biotin
10.5 Biochemical Function of Biotin
10.5.1 Thiamin
10.5.2 Biochemical Function
10.5.3 Vitamin B-6 Group
10.6 Adsorption of Riboflavin
10.7 Surface Tension Data of Complexes with Vitamin-A
Questions
11. Bioenergetics
11.1 Introduction
11.2 Metabolism
11.3 Coupled Reactions
11.4 ATP as an Energy Source
11.5 High Phosphoryl Capacity of ATP
11.6 Significance of Phosphoryl Transfer Potential (PTP)
11.7 Intracellular Conditions Pertaining to ATP Hydrolysis
11.7.1 Hydrolysis Reaction
11.8 Methods by which ATP Transfers Energy
11.9 Citric Acid Cycle
11.10 Reactions of the TCA Cycle
11.10.1 Activity of TCA Cycle
Questions
12. Biosensors
12.1 Introduction
12.2 Components of a Biosensor
12.2.1 Working of a Biosensor
12.2.2 Applications
12.3 Different Types of Biosensors
12.4 Electrochemical Biosensors
12.4.1 Amperometric Biosensors
12.5 Enzymatic Sensing of Glucose
12.5.1 Experimental Details
12.5.2 Mechanism of Detection
12.6 Estimation of Michaelis-Menten Constants
12.7 Non-enzymatic Sensing of Glucose
12.7.1 Interference Studies
12.8 Enzymatic Sensing of Urea
12.8.1 Potentiometric Sensors
12.8.2 Voltammetric Biosensors
12.8.3 Impedimetric Biosensors
Questions
Part II. Biochemical Techniques
13. Surface Plasmon Resonance Spectroscopy
13.1 Introduction
13.2 Details of SPR Set Up
13.2.1 Surface Plasmon
13.3 Surface Plasmon Resonance and Refractive Indices
13.4 Kinetic Applications of SPR Spectroscopy
Questions
14. Affinity Chromatography
14.1 Introduction
14.2 Methodology
14.2.1 Support Material
14.2.2 Ligand
14.2.3 Immobilization of Ligand
14.2.4 N-hydroxy Succinimide Method (NHS)
14.2.5 Carbonyl Diimidazole Method (CDI)
14.2.6 Elution
14.3 Types of Affinity Chromatography (A.C.)
14.3.1 Applications
14.3.2 Purification of Specific Groups of Molecules
14.4 Kinetic Applications of Affinity Chromatography
Questions
15. Capillary Electrophoresis
15.1 Introduction
15.2 Basic Instrumentation
15.3 Capillary Diameter and Joule Heating
15.4 Various Types of Electrophoresis
15.5 Chiral Recognition
Questions
16. NMR Technique in the Elucidation of Biochemical Problems
16.1 Introduction
16.2 Basics of NMR
16.3 Applications of NMR
16.4 Applications of NMR in Biomedical Research
16.4.1 Determination of Protein Structure
Questions
17. Applications of ESR Spectroscopy for the Solution of Biological Problems
17.1 Introduction
17.2 Advances in Magic Angle Spinning (MAS) NMR
17.3 Protein Structure Determination
17.4 Electron Nuclear Double Resonance Spectroscopy (ENDOR), Electron Spin Echo Envelope Modulation (ESEEM) and Hyperfine Sub-Level Correlation (HYScore) Spectroscopic Techniques
17.5 Structural and Dynamical Information of Biological Systems
17.6 Topology of Proteins
17.7 SDSLEPR Methods Under High Fields/High Frequencies
17.8 Double Site-Directed Spin Labeling Methods
17.9 Other Important Biological Systems
Questions
18. Flow Methods for the Kinetic Study of Fast Biochemical Reactions
18.1 Introduction
18.2 Experimental Arrangement
18.3 Reactions Studied Using this Technique
18.4 Applications to Unimolecular Reactions
18.5 Applications Involving Competitive Reactions
18.6 Applications Involving Multi-step Reactions
Questions
19. Temperature Jump Relaxation Technique for the Kinetic Study of Fast Biochemical Reactions
19.1 Introduction
19.2 Schematic Diagram of the Apparatus
19.3 Follow Up of the Change in Concentration of Reactants by Spectrophotometry
19.4 Applications
Questions
20. Flash Photolysis Technique for the Kinetic Study of Fast Biochemical Reactions
20.1 Introduction
20.2 Principle of the Method
20.3 Applications
Questions
21. Pressure Jump Relaxation Method for the Kinetic Study of Fast Biochemical Reactions
21.1 Introduction
21.2 Experimental Arrangement and Methodology
21.3 Applications
Questions
22. Circular Dichroism as a Tool for the Analysis of Biochemical Reactions
22.1 Introduction
22.2 Principle
22.3 Experimental Set Up
22.3.1 Units for CD
22.3.2 Amount of Sample Required
22.4 Methodology
22.4.1 CD Studied by Using Synchrotron Radiation
22.5 Disadvantages as Limitations
22.6 Applications
22.6.1 Effect of Cofactors and Ligands on CD
22.6.2 Specific Examples
Questions
23. Applications of Isothermal Calorimetry in the Study of Biochemical Reactions
23.1 Introduction
23.2 Experimental Set Up
23.3 Applications
23.4 Mutational Studies
23.5 Interaction of Transducer Fragments
Questions
24. Principles of Differential Scanning Calorimetry and its Applications in the Study of Biochemical Reactions
24.1 Introduction
24.2 Experimental Set Up
24.3 Methodology
24.4 Illustrative Application of DSC
Questions
25. Applications of Gel Filtration Technique in the Separation of Biomolecules
25.1 Introduction
25.2 Methodology of Gel Filtration
25.3 Principle of Gel Filtration
25.4 Applications
Questions
26. Gel Electrophoresis and its Applications to Biochemical Analysis
26.1 Introduction
26.2 Nature of Gels Commonly Employed
26.3 Experimental Arrangement
26.4 Applications of Gel Electrophoresis
26.5 Isoelectric Focusing (IEF)
Questions
27. Uses of Analytical Ultracentrifugation Methods in the Analysis of Biomolecules
27.1 Introduction
27.2 Details of the Apparatus
27.3 Detection Method and Data Collection
27.4 Rayleigh Interference Optics
27.5 Applications
27.6 Determination of Sedimentation Coefficient
27.7 Effect of Association on Sedimentation Coefficient
27.8 Active Enzyme Sedimentation
27.9 Estimation of Diffusion Coefficients
27.10 Estimation of Molar Mass
27.11 Thermodynamic Parameters of Association Reactions
27.12 Sedimentation in Biological Environments
27.13 Density Gradient Sedimentation Equilibrium
Questions
28. Ion Exchange Chromatography and its Applications in the Separation of Biomolecules
28.1 Introduction
28.2 Mechanism of Ion Exchange
28.3 Applications
28.4 Purification of Adenovirus
28.5 Separation of Membrane Phospholipids
28.6 Separation of Soyabean Proteins
28.7 Choice of Column Media
Questions
29. Surface Enhanced Raman Scattering and its Bioanalytical Applications
29.1 Introduction
29.2 Principle of SERS
29.3 Experimental Aspects
29.4 Applications of SERS
Questions
30. Mass Spectrometry and its Applications in the Analysis of Biomolecules
30.1 Introduction
30.2 Principle of the Technique
30.3 Basic Components of a Mass Spectrometer
30.4 Ionisation Methods in Mass Spectrometry
30.5 Applications
30.6 Analysis of Glycoproteins
30.7 ESI of Equine Apomyoglobin
30.8 Analysis of Phosphoproteins
30.9 Protein Ladder Sequencing
30.10 Specific Examples of Biomolecules
30.11 Peptides, Proteins and Polynucleotides
30.12 Polysaccharides
Questions
31. X-Ray Studies in the Elucidation of Structure of Biomolecules
31.1 Introduction
31.2 Bragg’s Law
31.3 Structural Determination of Proteins
31.4 X-ray Structures of Haemoglobin and Myoglobin
31.5 Photosynthetic Reaction Centers
31.6 Ribosomal Subunit
Questions
32. CRISPR-CAS-9, A Method for Genome Editing
32.1 Introduction to CRISPR-CAS-9
32.2 Genesis of the Discovery
32.3 Details on Enzyme “CAS-9”
32.4 CAS-9 Mechanism
32.5 Target DNA Binding and Cleavage by CAS-9
Questions
Appendix A. Donnan Membrane Potential
Appendix B. Nernst Planck Equation
B.1 Nernst–Planck Equation from Onsager’s Linear Flux-Force Relation
Appendix C. Goldman-Hodgkin-Katz Equation
Appendix D. Salient Aspects of COVID-19
D.1 Introduction
D.2 Composition of the COVID-19 Virus
D.3 Symptoms and Other Effects of COVID-19
D.4 Remedial Measures
Notes and Bibliography
Index