The Cell: Organisation Functions and Regulatory Mechanisms

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Cover Contents Preface About the Author Section A: Structure, Composition and Study of the Cell Chapter 1: Cell: Structure and Composition Cell: The Unit of Life An Overview of the Structure of Cell Molecular Organisation of the Cell Elemental Composition of the Cell Water: The Natural Universal Solvent Organic Chemistry and Biomolecules Nucleic Acids Proteins Carbohydrates Lipids Review Questions Box 1.1 The Concept of Molecular Mass and Mole Box 1.2 Replication Box 1.3 Enzymes: An Overview Box 1.4 Glucose: The Most Abundant Biomolecule Box 1.5 Fat in Diet Box 1.6 Chylomicron and VLDL Chapter 2: Study of the Cell: Cell Doctrine, Diversity and Its Origin Study of the Cell: Historical Perspective Cell Doctrine and the Beginning of Cell Biology Cell Biology as an Experimental Science Aim and Scope of Modern Cell Biology Diversity of Cell: Cell Types Cell Size and Shape Prokaryotic and Eukaryotic Cells Cell and Organisms Prokaryotes: The Bacteria Archaebacteria and Eubacteria Bacterial Cell Structure Eukaryotes Salient Features of Plantae Features of Fungi Cells of the Immune System Origin of Life/Cell The First Catalytic and Replicating Molecules and Aggregates Origin of Primitive Cell and Energy Metabolism Evolutionary Lineage of Prokaryote and Eukaryote Multicellularity Adhesion Molecules and Specialised Cell Surface Structures Tissue, Organ and Organ Systems Organ and Organ Systems The Non-cellular Life and Infectious Particles: Virus, Viroid and Prion Virus: A Non-cellular Life Form Viroid: An Infectious Ribonucleic Acid Proteinaceous Infectious Particle: Prion Review Questions Box 2.1 The Largest Bacterium Box 2.2 Acetabularia Box 2.3 Classification of Organisms: The Five-Kingdom System Box 2.4 Diazotrophs and the Nitrogenase System Box 2.5 Epulopiscium fishelsoni Box 2.6 The Largest Single-Celled Organisms Box 2.7 Polyadenylation in Bacteria Box 2.8 Endospore Box 2.9 An Analogy of Major Events in Evolutionary History of Earth Chapter 3: Methods in Cell Biology Microscopy Optical Microscopes Electron Microscopes Flow Cytometry Fluorescence-Activated Cell Sorting FCM in Disease Diagnosis: An Example The Cell and Tissue Culture Primary and Secondary Cultures and Cell Lines Culture Media Centrifugation Sedimentation Coefficient and Svedberg Unit Types of Centrifugation Subcellular Fractionation Study of Cellular Macromolecules Techniques to Study Protein Structure Glycoproteins: Detection, Purification and Characterisation Methods to Study Lipids Cells and Organisms as Experimental Tool Review Questions Box 3.1 Some Stains and Specific Cell Constituents Differentiated by These Stains Box 3.2 Radionuclides Section B: Cell Membrane and Extracellular Matrix Components: Structure and Properties Chapter 4: Cell Membrane: Structure and Chemical Composition Membranes: The Basic Structural Plan Fluid Mosaic Model of Membrane Structure Chemical Composition of Membrane Membrane Lipids Membrane Proteins Glycoproteins Lipid-Anchored Proteins in Membrane Elucidation of the Structure of Membrane, and Membrane Models Davson–Danielli Sandwich Model Robertson’s Unit Membrane Model Currently Accepted Model of Membrane Structure and Lipid Rafts Membrane as a Two-Dimensional Fluid Distribution of Protein and Lipid in Membrane Erythrocyte Membrane Structure Working with Membrane Synthetic Membranes: Liposome and Black Membrane Review Questions Box 4.1 Detergent and Membrane Proteins Box 4.2 Glycosylation and Half-Life of Proteins Box 4.3 Freeze Fracture Technique Box 4.4 Erythrocyte Ghost Chapter 5: Movement of Material Across Membrane Functions of Membrane Permeability and Hydration of Membranes Factors Affecting Membrane Fluidity and Permeability Transport Across Membrane Osmosis Diffusion Passive and Active Transport Facilitated Diffusion Transport Proteins Channels and Pores ATPase Ionophores Transport Systems in Membrane Transport System for the Synthesis of Hydrochloric Acid in Stomach Solute Carrier Proteins Group Translocation Transport Across Mitochondrial Membranes Transport Proteins in Human Diseases Transport Protein in Host Parasite Relationship Endocytosis and Exocytosis Macropinocytosis and Caveolae Clathrin and Clathrin-Mediated Endocytosis Phagocytosis Autophagy Exocytosis Transcytosis Review Questions Box 5.1 Phase Transition and Phase Transition or Melting Temperature Box 5.2 The Bulk Flow of Water Box 5.3 Identification and Purification of a Transport Protein, Glucose Permease Box 5.4 Band 3 Protein Box 5.5 Catabolism of Amino Acids, and Glutamine as a Major Body Fuel Box 5.6 The Phosphocreatine/Creatine Shuttle Box 5.7 ATP and Receptor Mediated Endocytosis Chapter 6: Membrane Electric Potential and Conduction of Nerve Impulse The Membrane Electric Potential Free Energy and Equilibrium Membrane Potential Donnan Equilibrium Nernst Equation Goldman Equation Excitable Assemblies in Membranes Action Potential and Its Propagation Voltage-Gated Sodium Channels Nerve Impulse Synapses and Neurotransmitters Acetylcholine Amino Acids and Derivatives Catecholamines Neuropeptides Review Questions Box 6.1 Biomembranes: Resistance and Capacitance Box 6.2 Voltage Clamp Technique Box 6.3 Patch Clamp Technique Chapter 7: The Extracellular Matrix and Cell Junctions Extracellular Matrix Components Collagen and Elastin Proteoglycan Fibronectin and Laminin Glycocalyx Cell Recognition and Adhesion Cell Junctions Adhesive Junctions Tight Junction Gap Junction The Plant Cell Wall and Plasmodesmata Chemical Composition of Plant Cell Wall Expansin and Plant Cell Growth Mechanism Plasmodesmata Review Questions Section C: Cytoplasm and Organelles Chapter 8: The Intracellular Fluid and Cytoskeleton Protoplasm and Cytoplasm Ultrastructure of Eukaryotic Cytoplasm Cytosol: Composition and Functions Cytoskeleton Methods to Study the Cytoskeleton Eukaryotic Cytoskeleton Microtubule Microfilament Intermediate Filament Intermediate Filament Versus Actin Filament and Microtubule Erythrocyte Membrane Skeleton Review Questions Box 8.1 DG: The Gibbs Free Energy Box 8.2 Multiple Roles of Lactic Acid Box 8.3 MAPs in Brain Box 8.4 Profilin Box 8.5 Molecular Motors Chapter 9: The Endomembrane System and Associated Organelles The Endomembrane System Endoplasmic Reticulum Ultrastructure of ER Composition of Endoplamsic Reticulum Functions of ER Golgi Body Ultrastructure of Golgi Body Movement of Material Through Golgi Body Transport Vesicles Coated Vesicles Fusion of the Vesicle and Acceptor Membranes Protein Secretion Lysosome: The Suicide-Sac of the Cell Origin of Lysosome and Its Types Functions of Lysosome Intracellular Protein Degradation Systems and Protein Turnover Lysosomal Storage Diseases Lysosome-related Organelles Melanosome Vacuole Review Questions Box 9.1 ER Stress and Unfolded Protein Response Box 9.2 Lysosomal Enzymes: TGN to Lysosome Box 9.3 The Age Pigment: Lipofuscin Chapter 10: Energy Processing Organelles: Mitochondrion and Chloroplast Energy Metabolism: An overview of Energy Transformation and Energy Organelles The Energy Organelles: Mitochondrion and Chloroplast Mitochondrion Ultrastructure of Mitochondrion Functions of Mitochondria Mitochondrial Dysfunction and Diseases Chloroplast Plastids Development of Chloroplast Ultrastructure of Chloroplast Nuclear DNA-Coded Chloroplast Proteins: Targeting to Chloroplast and Its Various Compartments Functions of Chloroplast: Photosynthesis Reactions of Photosynthesis: The Light and Dark Reactions Dark Reaction Origin of the Energy Processing Organelles: Endosymbiotic Theory Review Questions Box 10.1 Translocases of Outer and Inner Membranes of Mitochondria Box 10.2 Ammonia and Ammonium Ion Box 10.3 Plastids and Biological Containment Box 10.4 The Tat Pathway Box 10.5 Anoxygenic Photosynthesis: A Form of Phototrophy Box 10.6 Live Evidences Supporting the Origin of Chloroplast from Primitive Bacteria Chapter 11: Microbodies Microbodies Peroxisome Peroxisome: Structure and Catabolic Functions Plant Peroxisome Leaf Peroxisome Glyoxysome and Oleosome Biogenesis and Origin of Peroxisome Delivery of Peroxisomal Proteins to Peroxisome Peroxisomal Disorders Glycosome Review Questions Box 11.1 Uric Acid Box 11.2 The β-Oxidation in Peroxisome and Mitochondria Box 11.3 The Glyoxylate Cycle Chapter 12: The Nucleus: Ultrastructure and Functions Nucleus: An Introduction to the Structure and Function Internal Organisation and Composition of the Nucleus Macromolecular Composition of the Nucleus The Nuclear Pore Complex: Ultrastructure and Functions Transport Function of Nuclear Pore Complex Transport-Independent Functions of NPC Eukaryotic Chromosome: Levels of Structural Organisation Chromosome Packaging of DNA: Nucleosome, Chromatin and Chromosome Chromatin Condensation/Decondensation and Genomic Control Polytene Chromosome Extra Chromosomal DNA and Plasmid Nucleolus and Nuclear Bodies Organisation of the Nucleolus Techniques to Study the Nucleolus Review Questions Box 12.1 Histone Variants Box 12.2 Histone Modification and Epigenetics Box 12.3 Heterochromatin and Euchromatin Box 12.4 Determining the Diameter of Aqueous Diffusion Channel in Nuclear Envelope Box 12.5 Importin Box 12.6 Size of DNA in Haploid Cells of Some Species Chapter 13: The Ribosome: Molecular Machine for Protein Synthesis Ribosome: Molecular Machine for the Synthesis of Polypeptide Protein Synthesis: An Overview Stages in Polypeptide Synthesis: Initiation, Elongation and Termination Structure and Types of Ribosome Types of Ribosome Ribosomal Subunits Ribosome Self-assembly Biogenesis of Ribosome Synthesis of Ribosomal RNA Assembly and Transport of Ribosome Antibiotics and Ribosome Polysome Synthesis of Secretory Proteins Signal Hypothesis Synthesis of Membrane Proteins Protein Processing and Degradation Polypeptide Folding: Chaperones Post-Translational Chemical Modifications Intracellular Degradation of Proteins: Ubiquitination Review Questions Box 13.1 tRNA Binding Sites on Ribosome: A, P and E Sites Section D: Regulatory Mechanisms and Cellular Processes Chapter 14: Regulatory Mechanisms of the Cell and Signal Transduction Pathways Regulatory Mechanisms of the Cell Metabolic Control Mechanisms Cell Signalling Receptor and Ligand Steroid Receptors Cell Surface Receptors Attributes of Receptor–Ligand Interaction Receptor Isolation and Functional Assay Signal Transduction Signal Transduction via G Protein Inositol Phospholipid Signalling Pathway Receptor Tyrosine Kinase Pathway Second Messengers and Protein Kinases Second Messengers Protein Kinases Rationale of Signal Transduction Review Questions Box 14.1 Okadaic Acid: A Phosphatase Inhibitor Box 14.2 Hormone Box 14.3 Monomeric G Proteins and Associated Proteins Box 14.4 Bacterial Toxins and Membrane G Protein Box 14.5 cAMP: Experimental Evidence Demonstrating the Role of cAMP as Second Messenger Box 14.6 Phosphoinositides Box 14.7 Classes of Gα Box 14.8 Measurement of Free Ca2+ in a Living Cell Chapter 15: Cell Cycle and Cell Death Cell Division and Growth Cell Culture Cell Cycle Study of the Cell Cycle Synchrony and Karyotyping Determination of Cell Cycle Time Regulation of Cell Cycle: Cyclins Cyclin-Dependent Kinases M Phase Mitosis Meiosis Fertilisation and the Regulation of Meiosis in Oocyte Cell Death Apoptosis Apoptosis versus Necrosis Apoptotic Pathways Caspase-dependent Apoptotic Pathways: Activation Regulation of Apoptosis Apoptosis and Human Diseases Review Questions Box 15.1 Ubiquitin-Mediated Degradation of Protein Box 15.2 PCNA Box 15.3 Efferocytosis Box 15.4 Morphological Patterns of Necrosis Box 15.5 Caspases Chapter 16: Cell Differentiation, Stem Cell and Regeneration Cell Differentiation Differentiation and Gene Expression Cell Proliferation Control of Cell Differentiation Differentiation and Early Development in Drosophila Melanogaster Anterior–Posterior and Dorsal–Ventral Gradients in the Development of Fruit Fly Bicoid: A Regulator of Anterior-Posterior Differentiation in Drosophila Gap Genes and Segmentation Stem Cell iPS: The Induced Pluripotent Stem Cell Embryonic Stem Cell and Therapeutic Cloning Embryonal Carcinoma Cells Regeneration Review Questions Box 16.1 Development of Early Embryo: The Germ Layers Chapter 17: Cancer Tumours Types of Cancer Cancer-causing Agents Carcinogen Development of Cancer Metastasis Angiogenesis Tumour Viruses and Other Cancer Causing Infectious Agents Oncogene and Protooncogene Conversion of Protooncogene to Oncogene Oncoproteins: The Mechanisms of Action Tumour Suppressor Genes Genetic Instability: Caretaker, Gatekeeper and Landscaper Genes Properties of Cancer Cell Telomerase and Cancer Cancer Therapy and Its Limitations Review Questions Box 17.1 Ames Test Box 17.2 Induction of Tumour in Mouse Box 17.3 Src: A Tyrosine Kinase Box 17.4 BRCA1 Appendix: Biochemical Pathways Glycolysis Krebs Cycle Fatty Acid Synthesis Fatty Acid β-Oxidation Pathway Index