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Unformatted text preview: Boundless Microbiology Boundless Microbiology 1. Introduction to Microbiology 1. Introduction to Microbiology 1. Defining Microbes 2. History of Microbiology: Hooke, van Leeuwenhoek, and Cohn 3. Pasteur and Spontaneous Generation 4. Koch and Pure Culture 5. Attributions 2. Microbes and the World 1. Types of Microorganisms 2. Classification of Microorganisms 3. Microbes and the Origin of Life on Earth 4. Environmental Diversity of Microbes 5. Attributions 3. The Science of Microbiology 1. Basic Microbiology 2. Applied Microbiology 3. Immunization, Antiseptics, and Antibiotics 4. Modern Microbiology 5. Attributions 2. Chemistry 1. Atomic Structure 1. Overview of Atomic Structure 2. Electron Orbitals 3. Attributions 2. Chemical Bonds 1. Ions and Ionic Bonds 2. Covalent Bonds and Other Bonds and Interactions 3. Hydrogen Bonding 4. Avogadro's Number and the Mole 5. Average Atomic Mass 6. Attributions 3. Chemical Reactions 1. The Chemical Basis for Life 2. Energy Changes in Chemical Reactions 3. Attributions 4. Inorganic Compounds 1. Water’s States: Gas, Liquid, and Solid 2. pH, Buffers, Acids, and Bases 3. Overview of the Acid-Base Properties of Salt 4. Attributions 5. Organic Compounds 1. Carbohydrate Molecules 2. Lipid Molecules 3. DNA and RNA 4. Amino Acids 5. Types and Functions of Proteins 6. ATP: Adenosine Triphosphate 7. Attributions 6. Energy 1. Metabolism of Carbohydrates 2. Free Energy Changes in Chemical Reactions 3. Internal Energy and Enthalpy 4. Attributions 7. Enzymes 1. Control of Metabolism Through Enzyme Regulation 2. Enzyme Active Site and Substrate Specificity 3. Attributions 3. Microscopy 1. Looking at Microbes 1. Microbe Size 2. Units of Measurement for Microbes 3. Refraction and Magnification 4. Magnification and Resolution 5. Attributions 2. Light Microscopy 1. Microscopy 2. General Staining Methods 3. Attributions 3. Other Types of Microscopy 1. Dark-Field Microscopy 2. Phase-Contrast Microscopy 3. Interference Microscopy 4. Fluorescence Microscopy 5. Confocal Microscopy 6. Electron Microscopy 7. Scanned-Probe Microscopy 8. X-Ray Diffraction Analysis 9. Attributions 4. Cell Structure of Bacteria, Archaea, and Eukaryotes 1. Overview of Prokaryotic and Eukaryotic Cells 1. Characteristics of Prokaryotic Cells 2. Attributions 2. The Cytoplasmic Membrane of Prokaryotic and Eukaryotic Cells 1. Components of Plasma Membranes 2. Attributions 3. Transport Across the Cell Membrane 1. Facilitated transport 2. Primary Active Transport 3. ABC Transporters 4. Siderophores 5. Group Translocation 6. Attributions 4. Cell Walls of Prokaryotes 1. The Cell Wall of Bacteria 2. Gram-Negative Outer Membrane 3. Gram-Positive Cell Envelope 4. Mycoplasmas and Other Cell-Wall-Deficient Bacteria 5. Cell Walls of Archaea 6. Damage to the Cell Wall 7. Attributions 5. Specialized External Structures of Prokaryotes 1. Endospores 2. Attributions 6. Specialized Internal Structures of Prokaryotes 1. Ribosomes 2. Cell Inclusions and Storage Granules 3. Carboxysomes 4. Magnetosomes 5. Gas Vesicles 6. Attributions 7. Internal Structures of Eukaryotic Cells 1. The Nucleus and Ribosomes 2. Mitochondria 3. Comparing Plant and Animal Cells 4. The Endoplasmic Reticulum 5. The Golgi Apparatus 6. Attributions 8. Other Eukaryotic Components 1. Peroxisomes 2. Lysosomes 3. Intermediate Filaments and Microtubules 4. Extracellular Matrix of Animal Cells 5. Attributions 9. Protein Export and Secretion 1. Endocytosis 2. Attributions 10. Studying Cells 1. Microscopy 2. Crystallographic Analysis 3. Genetic Analysis 4. Attributions 5. Microbial Metabolism 1. Types of Metabolism 2. 3. 4. 5. 6. 7. 8. 9. 1. Photoautotrophs and Photoheterotrophs 2. Chemoautotrophs and Chemoheterotrophs 3. Attributions Energy Production 1. Control of Catabolic Pathways 2. Transforming Chemical Energy 3. Connecting Other Sugars to Glucose Metabolism 4. Attributions Catabolism 1. Types of Catabolism 2. Pyruvic Acid and Metabolism 3. Attributions Glycolysis 1. Importance of Glycolysis 2. Electron Donors and Acceptors 3. ATP Yield 4. Respiration and Proton Motive Force 5. Attributions Respiratory ETS and ATP Synthase 1. Cofactors and Energy Transitions 2. Oxidoreductase Protein Complexes 3. F10 ATP Synthase 4. Sodium Pumps as an Alternative to Proton Pumps 5. Attributions The Citric Acid (Krebs) Cycle 1. Citric Acid Cycle 2. Breakdown of Pyruvate 3. Acetyl CoA and the Citric Acid Cycle 4. Attributions Alternatives to Glycolysis 1. The Entner–Doudoroff Pathway 2. Aerobic Hydrocarbon Oxidation 3. The Pentose Phosphate Shunt 4. Organic Acid Metabolism 5. Lipid Metabolism 6. Connecting Proteins to Glucose Metabolism 7. Methylotrophy and Methanotrophy 8. Attributions Fermentation 1. Anaerobic Cellular Respiration 2. Clostridial and Propionic Acid Fermentation 3. Fermentation Without Substrate-Level Phosphorylation 4. Syntrophy 5. Attributions Anaerobic Respiration 1. Electron Donors and Acceptors in Anaerobic Respiration 2. Nitrate Reduction and Denitrification 3. Sulfate and Sulfur Reduction 4. Methanogenesis 5. Proton Reduction 6. Anoxic Hydrocarbon Oxidation 7. Attributions 10. Chemolithotrophy 1. The Energetics of Chemolithotrophy 2. Hydrogen Oxidation 3. Oxidation of Reduced Sulfur Compounds 4. Iron Oxidation 5. Nitrification 6. Anammox 7. Benzoate Catabolism 8. Polycyclic Aromatic Hydrocarbons 9. Attributions 11. Phototrophy 1. The Purpose and Process of Photosynthesis 2. Main Structures and Summary of Photosynthesis 3. The Two Parts of Photosynthesis 4. Bacteriorhodopsin 5. Carotenoids and Phycobilins 6. Facultative Phototrophy 7. Oxygenic Photosynthesis 8. Anoxygenic Photosynthesis 9. Attributions 12. Biosynthesis 1. Substrates for Biosynthesis 2. Biosynthesis and Energy 3. The Calvin Cycle 4. Intermediates Produced During the Calvin Cycle 5. Regulation of the Calvin Cycle 6. The Reverse TCA Cycle 7. The Acetyl-CoA Pathway 8. The 3-Hydroxypropionate Cycle 9. Attributions 13. Anabolism 1. Polysaccharide Biosynthesis 2. Lipid Biosynthesis 3. Regulation by Biosynthetic Enzymes 4. Bacterial Polyesters 5. Polyketide Antibiotics 6. Attributions 14. Amino Acid and Nucleotide Biosynthesis 1. Amino Acid Synthesis 2. Purine and Pyrimidine Synthesis 3. Nonribosomal Peptide Antibiotics 4. Biosynthesis of Tetrapyrroles 5. Attributions 15. Nitrogen Fixation 1. Nitrogenase and Nitrogen Fixation 2. Early Discoveries in Nitrogen Fixation 3. Nitrogen Fixation Mechanism 4. Anaerobiosis and N2 Fixation 5. Genetics and Regulation of N2 Fixation 6. Attributions 6. Culturing Microorganisms 1. Microbial Nutrition 1. Chemical Analysis of Microbial Cytoplasm 2. Sources of Essential Nutrients 3. Limitation of Microbial Growth by Nutrient Supply 4. Attributions 2. Cell Differentiation and Starvation 1. Activation of Starvation by Survival Genes 2. Oligotrophs 3. Starvation-Induced Fruiting Bodies 4. Bacterial Differentiation 5. Attributions 3. Culturing Bacteria 1. Culture Media 2. Complex and Synthetic Media 3. Selective and Differential Media 4. Aseptic Technique, Dilution, Streaking, and Spread Plates 5. Special Culture Techniques 6. Attributions 4. Microbial Culture Methods 1. Enrichment and Isolation 2. Pure Culture 3. Preserving Bacterial Cultures 4. The FISH Technique 5. Coupling Specific Genes to Specific Organisms Using PCR 6. Attributions 5. Bacterial Identification 1. Chemical Assays, Radioisotopic Methods, and Microelectrodes 2. Stable Isotopes 3. Attributions 6. Microbial Growth 1. Binary Fission 2. Fts Proteins and Cell Division 3. MreB and Determinants of Cell Morphology 4. Peptidoglycan Synthesis and Cell Division 5. Generation Time 6. Attributions 7. Bacterial Population Growth 1. Microbial Growth Cycle 2. Growth Terminology 3. Attributions 8. Counting Bacteria 1. Direct Counting 2. Viable Cell Counting 3. Measurements of Microbial Mass 4. Detecting Acid and Gas Production 5. Attributions 9. Temperature and Microbial Growth 1. Growth Rate and Temperature 2. Classification of Microorganisms by Growth Temperature 10. 11. 12. 13. 14. 15. 7. 3. The Heat-Shock Response 4. Attributions Other Environmental Growth Factors 1. Gas Requirements 2. Osmotic Pressure 3. Microbial Growth at Low or High pH 4. Oxygen 5. Attributions Microbial Growth in Communities 1. Ecological Associations Among Microorganisms 2. Biofilms 3. Attributions Control of Microbial Growth 1. Considerations in Microbial Control 2. Rate of Microbial Death 3. Relative Resistance of Microbes 4. Attributions Mechanisms of Microbial Control 1. Alteration of Membrane Permeability 2. Damage to Proteins and Nucleic Acids 3. Attributions Physical Antimicrobial Control 1. Heat 2. Radiation 3. Low Temperatures 4. High Pressure 5. Desiccation 6. Osmotic Pressure 7. Filtration 8. Attributions Chemical Antimicrobial Control 1. Effective Disinfection 2. Factors that Affect Germicidal Activity of Chemicals 3. Types of Disinfectants 4. Biological Control of Microbes 5. Attributions Microbial Genetics 1. Genes 1. Bacterial Genomes 2. DNA Replication in Prokaryotes 3. Gene Inversion 4. Slipped-Strand Mispairing 5. Attributions 2. Prokaryotic Genomes 1. Bacterial Chromosomes in the Nucleoid 2. Supercoiling 3. Size Variation and ORF Contents in Genomes 4. Bioinformatic Analyses and Gene Distributions 5. Attributions 3. DNA Replication 1. Basics of DNA Replication 2. DNA Replication in Eukaryotes 3. Attributions 4. Plasmids 1. Introduction to Plasmids 2. Types of Plasmids and Their Biological Significance 3. Attributions 5. RNA Synthesis: Transcription 1. Elongation and Termination in Eukaryotes 2. The Promoter and the Transcription Machinery 3. Attributions 6. Translation: Protein Synthesis 1. Processing of tRNAs and rRNAs 2. The Protein Synthesis Machinery 3. Prokaryotic Transcription and Translation Are Coupled 4. The Incorporation of Nonstandard Amino Acids 5. Unsticking Stuck Ribosomes 6. Attributions 7. Protein Modification, Folding, Secretion, and Degradation 1. mRNA Processing 2. Denaturation and Protein Folding 3. Protein Folding, Modification, and Targeting 4. Regulating Protein Activity and Longevity 5. Attributions 8. Archaeal Genetics 1. Chromosomes and DNA Replication in the Archaea 2. Shared Features of Bacteria and Archaea 3. Shared Features of Archaea and Eukaryotes 4. Attributions 9. Eukaryotic Genetics 1. The Role of the Cell Cycle 2. The Relationship Between Genes and Proteins 3. Attributions 10. Mutation 1. DNA Repair 2. Attributions 11. Genetic Transfer in Prokaryotes 1. Generalized Recombination and RecA 2. Bacterial Transformation 3. Bacterial Transduction 4. Prokaryotic Reproduction 5. Complementation 6. Gene Transfer in Archaea 7. Attributions 12. Tools of Genetic Engineering 1. Recombinant DNA Technology 2. Selection 3. Mutation 4. Reproductive Cloning 5. Basic Techniques to Manipulate Genetic Material (DNA and RNA) 6. Molecular and Cellular Cloning 13. 14. 15. 16. 17. 18. 19. 20. 7. Plasmids as Cloning Vectors 8. Attributions Bioinformatics 1. Strategies Used in Sequencing Projects 2. Annotating Genomes 3. Homologs, Orthologs, and Paralogs 4. Synthesizing DNA 5. Amplifying DNA: The Polymerase Chain Reaction 6. DNA Sequencing Based on Sanger Dideoxynucleotides 7. Metagenomics 8. Reporter Fusions 9. Attributions Cloning Techniques 1. Putting Foreign DNA into Cells 2. Obtaining DNA 3. Hosts for Cloning Vectors 4. Shuttle Vectors and Expression Vectors 5. Bacteriophage Lambda as a Cloning Vector 6. Vectors for Genomic Cloning and Sequencing 7. Attributions Genome Evolution 1. Gene Families 2. Genomics and Biofuels 3. Genome Reduction 4. Pathogenicity Islands 5. Attributions Environmental Genomics 1. Detecting Uncultured Microorganisms 2. Viral Genomes in Nature 3. Attributions Molecular Regulation 1. Catabolite Activator Protein (CAP): An Activator Regulator 2. The Initiation Complex and Translation Rate 3. Attributions Global Regulatory Mechanisms 1. Transcription in Prokaryotes 2. The trp Operon: A Repressor Operon 3. The Stringent Response 4. Repression of Anabolic Pathways 5. The AraC Regulator 6. Attributions RNA-Based Regulation 1. RNA Regulation and Antisense RNA 2. Attenuation 3. Riboswitches 4. Regulation of Sigma Factor Activity 5. Regulation of Sigma Factor Translation 6. Proteolytic Degradation 7. Small Regulatory RNAs 8. Attributions Developmental Regulation 1. Sporulation in Bacillus 21. 22. 23. 24. 25. 26. 8. 2. Caulobacter Differentiation 3. Attributions Sensing and Signal Transduction 1. Chemotaxis 2. Two-Component Regulatory Systems 3. Quorum Sensing 4. Control of Transcription in Archaea 5. Attributions Genomics and Proteomics 1. Microarrays and the Transciptome 2. Proteomics 3. Metabolomics 4. Attributions Genetic Engineering Products 1. Overview of Biotechnology 2. Applications of Genetic Engineering 3. Biochemical Products of Recombinant DNA Technology 4. Mammalian Gene Expression in Bacteria 5. Mammalian Proteins and Products 6. Attributions Transgenic Organisms 1. Genetically Engineered Vaccines 2. Genetic Engineering in Animals 3. Biotechnology in Medicine 4. Attributions Molecular Techniques 1. Inactivating and Marking Target Genes with Transposons 2. DNA Sequencing of Insertion Sites 3. Northern Blots 4. Western Blots 5. DNA Mobility Shifts 6. Purifying Proteins by Affinity Tag 7. Primer Extension Analysis 8. DNA Protection Analysis 9. Whole-Genome DNA-Binding Analysis 10. Two-Hybrid Analysis 11. Attributions Cell Physiology Techniques 1. Mapping Protein-Protein Interactions 2. Tracking Cells with Light 3. Multiplex and Real-Time PCR 4. Phage Display 5. Attributions Microbial Evolution, Phylogeny, and Diversity 1. Origins of Life 1. Evidence of Evolution 2. Elements of Life 3. Unresolved Questions About the Origins of Life 4. Attributions 2. Astrobiology 1. Mars and a Biosphere 2. Martian Biosignatures 3. Terraforming Mars 4. Europa's Possible Ocean 5. Attributions 3. Microbial Phylogeny 1. Processes and Patterns of Evolution 2. Distinguishing between Similar Traits 3. The Levels of Classification 4. Attributions 4. Classification of Microorganisms 1. The Taxonomic Scheme 2. The Diagnostic Scheme 3. The Species Concept in Microbiology 4. Classification and Nomenclature 5. Attributions 5. Methods of Classifying and Identifying Microorganisms 1. Phenotypic Analysis 2. Classification of Prokaryotes 3. Phylogenetic Analysis 4. Nongenetic Categories for Medicine and Ecology 5. Attributions 6. Bacterial Diversity 1. Common Bacterial Traits 2. Unclassified and Uncultured Bacteria 3. Attributions 7. Proteobacteria 1. Overview of Proteobacteria 2. Alphaproteobacteria 3. Betaproteobacteria 4. Morphologically Unusual Proteobacteria 5. Gammaproteobacteria 6. The Deltaproteobacteria 7. Epsilonproteobacteria 8. Attributions 8. Gram-Positive Bacteria and Actinobacteria 1. Overview of Gram-Positive Bacteria and Actinobacteria 2. Non-Spore-Forming Firmicutes 3. Firmicutes 4. Actinobacteria (High G + C Gram-Positive Bacteria) 5. Attributions 9. Nonproteobacteria Gram-Negative Bacteria 1. Cyanobacteria 2. Anoxygenic Photosynthetic Bacteria 3. Prochlorophytes 4. Attributions 10. Irregular Bacterial Cells 1. Chlamydiae 2. Planctomycetes 3. Verrucomicrobia 4. Attributions 11. Other Bacterial Groups 1. Bacteroides and Flavobacterium 2. Acidobacteria 3. Cytophaga and Relatives 4. Bacteroidetes and Chlorobi 5. Fusobacteria 6. Spirochaetes 7. Attributions 12. Thermophiles 1. Aquificales and Thermotogales 2. Deinococcus and Thermus 3. Chloroflexus and Relatives 4. Nitrospirae and Deferribacter 5. Aquifex, Thermocrinis, and Related Bacteria 6. Attributions 13. Archaeal Diversity 1. Energy Conservation and Autotrophy in Archaea 2. Archaeal Gene Regulation 3. Attributions 14. Crenarchaeota 1. Habitats and Energy Metabolism of Crenarchaeota 2. Hyperthermophiles from Terrestrial Volcanic Habitats 3. Hyperthermophiles from Submarine Volcanic Habitats 4. Nonthermophilic Crenarchaeota 5. Psychrophilic Crenarchaeota 6. Attributions 15. Euryarchaeota 1. Diverse Cell Forms of Methanogens 2. Extremely Halophilic Archaea 3. Methane-Producing Archaea: Methanogens 4. Thermoplasmatales, Thermocaccales, and Methanopyrus 5. Archaeoglobus 6. Nanoarchaeum and Aciduliprofundum 7. Hyperthermophilic Archaea, H2, and Microbial Evolution 8. Attributions 16. Eukaryotic Microbial Diversity 1. Phylogeny of the Eukarya 2. Historical Overview of Eukaryotes 3. Opisthokonts: Animals and Fungi 4. Endosymbiotic Theory and the Evolution of Eukaryotes 5. Cell Structure, Metabolism, and Motility 6. Newly Discovered Eukaryotes 7. Attributions 17. Fungi 1. Characteristics of Fungi 2. Fungi as Plant, Animal, and Human Pathogens 3. Fungi Habitat, Decomposition, and Recycling 4. Chytridiomycota: The Chytrids 5. Zygomycota: The Conjugated Fungi 6. Glomeromycota 7. Ascomycota: The Sac Fungi 8. Basidiomycota: The Club Fungi 9. Attributions 18. Protists 1. Early Eukaryotes 2. Excavata 3. Chromalveolata: Alveolates 4. Chromalveolata: Stramenopiles 5. Rhizaria 6. Amoebozoa and Opisthokonta 7. Attributions 19. Algae 1. Archaeplastida 2. Protists as Primary Producers, Food Sources, and Symbionts 3. Attributions 20. Helminths 1. Characteristics of Helminths 2. Classification and Identification of Helminths 3. Distribution and Importance of Parasitic Worms 4. Arthropods as Vectors 5. Attributions 9. Viruses 1. Overview of Viruses 1. Discovery and Detection of Viruses 2. Nature of the Virion 3. Viral Genomes 4. Host Range 5. Viral Size 6. Attributions 2. Structure of Viruses 1. Viral Morphology 2. General Morphology 3. Complex and Asymmetrical Virus Particles 4. Attributions 3. Classifying Viruses 1. The International Committee on Taxonomy of Viruses 2. The Baltimore Virus Classification 3. Evolution of Viruses 4. Medical Importance of Viruses 5. Attributions 4. Culturing Viruses 1. Batch Culture of Bacteriophages 2. Tissue Culture of Animal Viruses 3. Inoculation of Live Animals 4. Viral Identification 5. Attributions 5. Viral Replication 1. General Features of Virus Replication 2. Steps of Virus Infections 3. Tissue Tropism in Animal Viruses 4. Animal Viruses 6. 7. 8. 9. 10. 11. 12. 13. 5. Plant Virus Life Cycles 6. Attributions Subviral Entities 1. Defective Viruses 2. Viroids 3. Prions 4. Attributions Viral Diversity 1. Overview of Bacterial Viruses 2. RNA Bacteriophages 3. Single-Stranded DNA Bacteriophages 4. Double-Stranded DNA Bacteriophages 5. Mu: A Double-Stranded Transposable DNA Bacteriophage 6. Virulent Bacteriophages and T4 7. Temperate Bacteriophages: Lambda and P1 8. Viruses of Archaea 9. Attributions Positive-Strand RNA Viruses in Animals 1. Positive-Strand RNA Viruses of Animals 2. Virus Attachment and Genome Entry 3. Viral Replication and Gene Expression 4. Viral Exit 5. Attributions Negative-Strand RNA Viruses in Animals 1. Negative-Strand RNA Viruses of Animals 2. Attachment and Entry to the Host Cell 3. Replicative Cycle of Influenza A 4. Attributions Retroviruses: Double-Stranded RNA Viruses 1. Double-Stranded RNA Viruses: Retroviruses 2. HIV Attachment and Host Cell Entry 3. Retroviral RNA Genome 4. Replicative Cycle of HIV 5. Attributions DNA Viruses in Eukaryotes 1. Plant DNA Viruses 2. Replication of Double-Stranded DNA Viruses of Animals 3. Double-Stranded DNA Viruses: Herpesviruses 4. Attachment and Entry of Herpes Simplex 5. Replication of Herpes Simplex Virus 6. Immunodeficiency 7. Double-Stranded DNA Viruses: Pox Viruses 8. Double-Stranded DNA Viruses: Adenoviruses 9. Retroviruses and Hepadnavirus 10. Treatment of Animal Viral Infections 11. Attributions Viruses and Cancer 1. Cancer Viruses 2. DNA Oncogenic Viruses 3. RNA Oncogenic Viruses 4. Attributions Viral Ecology 1. Emergence of Viral Pathogens 2. Viral Roles in Ecosystems 3. Attributions 10. Epidemiology 1. Principles of Epidemiology 1. History of Epidemiology 2. The Science of Epidemiology 3. The Vocabulary Epidemiology 4. Koch's Postulates 5. Exceptions to Koch's Postulates 6. Attributions 2. Pathogen Identification 1. Occurrence of a Disease 2. Disease Severity and Duration 3. Ex...
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