LIFE BEGINS WITH CELLS
1 CELL BIOLOGY Introduction 1 Anatomy 3 Prokaryotic Cells 4 Eukaryotic Cells5 Subcellular components 6 Membrane 6 Cytoskeleton 7 Genetic material 7 Organelles 8 Eukaryotic 8 Eukaryotic and Prokaryotic 10 Cell Wall 12 Prokaryotic 12 Flagella 12 Fimbria 12 Cellular Processes 12 Growth and Metabolism 12 Replication 13 Protein Synthesis 14 Movement or Motility 15 Multicellularity 15 Origin of Multicellularity 16 Origins 16 Origin of the first cell 16 Origin of Eukaryotic Cells 17 Multicellular Organism 17 Evolutionary History 18 1 Hypotheses for Origin 19 Advantages 21 Evolutionary History of Life 21 Earliest History of Earth 23 Earliest Evidence for Life on Earth 23 Origins of life on Earth 24 Metabolism first: Iron–sulfur world 26 Environmental and Evolutionary Impact of Microbial Mats 27 Diversification of Eukaryotes 28 Chromatin, Nucleus, Endomembrane System, and Mitochondria 29 Sexual Reproduction and Multicellular Organisms 29 Plants and the Late Devonian Wood Crisis 37 Early land Vertebrates 39 Family Tree of Tetrapods 39 Dinosaurs, Birds and Mammals 41 Social Insects 43 Humans 44 Mass Extinctions 45 References 47 2 CELL THEORY Introduction 67 Microscopes 68 Discovery of Cells 70 Cell Theory 71 Modern Interpretation 73 The Modern Version of the Cell Theory 73 Evolution of the Membrane and Bulk Phase Theories 74 The Emergence of the steady-state Membrane Pump Concept 74 The Reemergence of the Bulk Phase Theories 75 Types of Cells 75 Cell Adhesion 76 Clinical Implications 79 Measurement and Applications 79 Role of Cell Adhesions in Neural Development 79 Adhesion Classifications 79 Adhesions role in cell migration 80 Adhesion-Related Mechanisms Involved in Neuronal Tissue Development 81 Growth Cone Extensions 81 Thy-1 Adhesion Protein 81 Cell Biology 83 67 Internal Cellular Structures 83 Processes 85 Cellular Differentiation 88 Mammalian Cell Types89 Dedifferentiation 90 Mechanisms 91 Epigenetic Control of Cellular Differentiation93 Importance of Epigenetic Control 93 Mechanisms of Epigenetic Regulation 94 Epigenetics in Stem Cell Differentiation 97 Experimental Background 97 Effects of Global Histone Modifications During Embryonic Stem Cell Differentiation 98 DNA Methylation in differentiated Versus Undifferentiated Cells 98 Supplemental effects of Methylation with DNMTs 99 Epigenetic Modifications of Regulated Genes During ESC Differentiation 99 Effect of TSA on Stem Cell Differentiation 100 Alkaline Phosphatase Activity 101 HDAC1, but not HDAC2 Controls Differentiation 101 The Future 101 References 101 3 CYTOSKELETON Introduction 107 History 108 Eukaryotic Cytoskeleton 108 Microfilaments (Actin Filaments) 109 Organization 110 Mechanism of Force Generation 111 Actin in Cells 111 Associated Proteins 111 Actin Acts as a Track for Myosin Motor Motility 112 Microtubule 113 Structure 114 Intracellular Organization 115 Microtubule Polymerization 116 Microtubule Dynamics 117 Regulation of Microtubule Dynamics 118 Proteins that Interact with Microtubules 120 Functions 122 Septins 125 107 Spectrin in Erythrocytes 126 Spectrin in Invertebrates 126 Spectrin in Vertebrates 127 Role of Spectrin in Muscle Tissue 127 Spectrin 127 Structure 128 Occurrence 129 In Saccharomyces Cerevisiae 129 In Filamentous Fungi 130 In Mitochondria 133 Yeast cytoskeleton 133 Prokaryotic Cytoskeleton 133 Ftsz 133 MreB and ParM 133 Crescentin 134 References 134 4 ENDOMEMBRANE SYSTEM Introduction 137 History of the Concept 138 Components of the System 139 Nuclear Envelope 139 Endoplasmic Reticulum 140 Functions of the Smooth ER 141 Functions of the Rough ER 142 Golgi Apparatus 143 Vacuoles 143 Vesicles 144 Lysosomes 144 Discovery 145 Function and Structure 146 Formation 147 Pathogen Entry 147 Disease 148 Lysosomotropism 148 Controversy in Botany149 Etymology and Pronunciation 149 Spitzenkörper 149 Plasma Membrane 150 Evolution 151 Peroxisome 151 137 Metabolic Functions 152 Peroxisome Assembly 153 Associated Medical Conditions 153 Genes 153 Evolutionary Origins 154 Mitochondrion 154 Origin And Evolution 156 Structure 158 Perspective 164 Organization and Distribution 164 Function 165 Heat Production 167 Storage of Calcium Ions 167 Additional Functions 168 Cellular Proliferation Regulation 168 Genome 169 Alternative Genetic Code 170 Evolution and Diversity 171 Replication and Inheritance 171 Population Genetic Studies 172 Dysfunction and Disease 173 Mitochondrial Diseases 173 Possible Relationships to Aging 174 References 175 5 ENDOSYMBIONT Introduction 189 Symbiogenesis and Organelles 190 In Protists 192 Bacterial Endosymbionts in Insects 193 Viral Endosymbionts and Endogenous Retrovirus 194 Organism 194 Etymology 196 Chemistry 197 Structure 198 Evolution 199 Reproduction 200 Horizontal Gene Transfer 200 Future of Life (Cloning and Synthetic Organisms) 200 Chloroplast 201 Discovery 202 189 Primary Endosymbiosis 203 Rhodophyceae (red algae) 205 Possible cladogram of chloroplast evolution 213 Fucoxanthin-Containing Dinophyte Chloroplasts (haptophyte endosymbionts) 214 Chloroplast DNA 217 DNA Replication 218 Structure 222 Location 234 Cellular Location 235 Function and Chemistry 236 Light Reactions 237 References 245 6 RNA Introduction 257 Comparison With DNA 258 Structure 260 Synthesis 261 Types of RNA 262 Overview 262 In Length 263 In Translation 263 Regulatory RNAs 264 In RNA Processing 264 RNA Genomes 265 In Reverse Transcription 265 Double-Stranded RNA 265 Circular RNA 265 Key Discoveries in RNA Biology 265 Evolution 266 References 266 7 CYTOPLASM Introduction 273 History 274 Physical Nature 274 As a sol-gel 274 As a glass 274 Other Perspectives 275 257 273 Constituents 275 Cytosol 275 Organelles 276 Cytoplasmic Inclusions 276 Controversy and Research 276 References 276 8 PROTEASOME Introduction 279 Discovery 281 Structure and Organization 282 20S core Particle 282 19S Regulatory Particle 283 Conformational changes of 19S284 Regulation of the 20S by the 19S 285 11S regulatory particle 285 Assembly 286 The Protein Degradation Process 286 Ubiquitination and Targeting 287 Unfolding and Translocation 288 Proteolysis 289 Ubiquitin-independent degradation 289 Evolution 290 Cell Cycle Control 290 Regulation of Plant Growth 291 Apoptosis 291 Response to Cellular Stress 291 Role in the Immune System 292 Proteasome Inhibitors 293 Clinical Significance 294 References 295