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Preface Chapter 1¿Introduction to Microbiology 1.1 Most microorganisms are microscopic, and they include all life forms other than the plants and animals. 1.2 Most microorganisms are unicellular; if multicellular, they lack highly differentiated tissues. 1.3 Microbial life originated shortly after the earth was formed 1.4 There are two fundamentally different types of cells: procaryotic and eucaryotic 1.5 Microbes, especially procaryotic ones, are unbelievably numerous 1.6 The tree of life is almost entirely microbial 1.7 There are three major lineages of life on earth. 1.8 Procaryotes inhabit an immense range of habitats 1.9 Procaryotes are essential to all life on earth 1.10 The dry weight of microbial cells consists mainly of macromolecules and lipids. 1.11 Among the macromolecules, proteins are the largest and most diverse category 1.12 The cytosol is a dense suspension of ribosomes 1.13 The small molecules of the cell are in constant flux Reprise Box 1-1 The Search for Microbial Fossils CHAPTER 2¿HISTORY OF MICROBIOLOGY 2.1 Microbiology is founded on two basic methodologies: microscopy, and pure culture technique 2.2 Leeuwenhoek discovered microbes because he used a single lens of unusually high quality 2.3 Advances in optics in the mid-19th century led to much improved microscopes, allowing a rapid expansion of exploration of the microbial world 2.4 Advances in light microscopy in the 20th century were largely confined to improved methods of enhancing contrast 2.5 The most significant advance in microscopy in the 20th century was the development of electron microscopy 2.6 The controversy over spontaneous generation required the development of methods of sterilizing media, and keeping it sterile while in contact with air 2.7 The development of the germ theory of disease provided an explanation for most disease, and for the phenomenon of contagion 2.8 Pure culture technique was necessary to show that different diseases were caused by different microbes 2.9 Koch¿s postulates define what is logically necessary and sufficient to prove the microbial etiology of a disease. 2.10 Enrichment culture allows the isolation of microbes that are present in the source material in very low numbers 2.11 Several microbes have become model systems for the study of cell biology, molecular genetics, development, etc. Reprise Box 2¿1 Joblot¿s Experiments on Spontaneous Generation Box 2¿2 Anthrax [head added by DD based on material included in art package] CHAPTER 3¿METHODS OF MICROBIOLOGY MICROSCOPY 3.1 Compound microscopes are used for observing microbes 3.2 Resolution of the light microscope is normally limited to about 0.2mðm 3.3 Brightfield microscopy is used for observing stained cells 3.4 Darkfield microscopy can resolve very small objects 3.5 Phase-contrast is routinely used for observing live microbial cells 3.6 Phase-contrast is achieved by modifications to the condenser and the objective lens 3.7 Fluorescence microscopy can locate specific molecules within cells 3.8 The electron microscope uses electromagnetic lenses to bend a beam of electrons 3.9 The resolution of the electron microscope is a thousand-fold better than the light microscope 3.10 Specimens in the electron microscope need to be dehydrated 3.11 Thin sectioning slices through cells shows interior structures 3.12 Negative staining reveals the texture of the outside of cells and isolated subcellular organelles 3.13 Shadow casting shows the surface of very small isolated organelles 3.14 Freeze-etching does not require fixation or dehydration 3.15 Scanning electron microscopy shows surfaces with great depth of field PURE CULTURE TECHNIQUE 3.16 Pure cultures do not consist of identical cells 3.17 Pure culture technique consists of three interrelated techniques 3.18 The most common method of sterilizing is autoclaving 3.19 Heat-sensitive solutions are sterilized by filtration 3.20 Glassware is sterilized by dry heat 3.21 Bunsen burner flames help to prevent contamination during transfer into or out of containers 3.22 Pure cultures are isolated by streaking on solid media 3.23 Different media are necessary for different microbes 3.24 Cultures are incubated under different conditions according to their relations with oxygen 3.25 Some pathogenic microbes require special containment facilities Reprise Box 3--1 Image Formation in the Phase-Contrast Microscope CHAPTER 4 PROCARYOTIC CELL STRUCTURE AND FUNCTION 4.1 The procaryotic cell is small and structurally simple 4.2 Most procaryotes are unicellular THE CELL ENVELOPE 4.3 Procaryotic cells protect themselves against osmotic lysis with a cell envelope 4.4 There are four major types of cell envelope among the bacteria; the most common is the Gram negative envelope 4.5 There are three types of Archaeal cell envelopes; the most common is a layer of protein 4.6 Procaryotes without a defined cell envelope layer have their membranes strengthened by glycolipids 4.7 Murein is a form of peptidoglycan, whose individual glycan strands (polysaccharide) are cross-linked to each other by the peptides 4.8 Murein consists of a single giant molecule, a single layer thick in the Gram negative bacteria, many layers thick in the Gram positive bacteria 4.9 Archaeal pseudomurein is a peptidoglycan similar to bacterial murein 4.10 Gram positive bacterial walls contain teichoic acids 4.11 The Gram negative outer membrane protects the murein 4.12 The outer membrane is highly asymmetric 4.13 The outer membrane is impermeable to both hydrophobic and hydrophilic compounds 4.14 Dissolved compounds enter the Gram negative periplasm via porins 4.15 The outer membrane is physically linked to the murein 4.16 The periplasm is a dense solution of protein THE CELL MEMBRANE 4.17 The procaryotic cell membrane contains hopanoids in place of sterols 4.18 The cell membrane is a two dimensional fluid 4.19 The procaryotic cell membrane has more protein, and more different proteins, that most membranes. 4.20 The cell membrane may invaginate into the cell to provide extra surface area 4.21 Some procaryotes have intracellular membane-bound organelles 4.22 The archaeal cell membrane is a bilayer or monolayer of ether lipids THE NUCLEOID 4.23 The nucleoid is haploid and usually contains a single, circular chromosome 4.24 The procaryotic chromosome is supercoiled 4.25 The nucleoid is a highly ordered structure 4.26 Transcription and translation are coupled in procaryotes 4.27 Compaction of DNA into the nucleoid requires neutralization of DNA charges by polyamines THE BACTERIAL CYTOSKELETON 4.28 An actin-like cytoskeleton maintains cell shape and forms the procaryotic mitotic apparatus 4.29 A tubulin-like protein is involved in bacterial cytokinesis THE CYTOPLASM 4.30 The cytoplasm is a dense suspension of ribosomes 4.31 Storage granules are polymeric reserves of nutrients 4.32 Phosphate is stored in membrane-bound vesicles termed acidocalcisomes 4.33 Gas vacuoles provide buoyancy to aquatic cells 4.34 Magnetosomes allow procaryotic cells to distinguish north from south SURFACE LAYERS AND APPENDAGES 4.35 Many procaryotes have a surface layer of protein external to the envelope 4.36 Capsules are gelatinous layers of polysaccharide external to the wall 4.37 Procaryotic cells often are found as biofilms 4.38 Pili mediate the specific attachment of cells to other cells MOTILITY 4.39 Flagella are rigid, helical organelles whose rotation moves cells through liquid 4.40 Flagella are rotated by the entry of ions through the basal body 4.41 Gliding motility requires contact with a surface REPRISE BOX4-1 How Do We Know Procaryotic Transcription Is Localized on Cytoplasmic Loops of Dna? CHAPTER 5: CELL STRUCTURE AND FUNCTION IN PROTISTS 5.1 Most eucaryotes are microbes 5.2 Eucaryotic cells are characterized by an endomembrane system and a cytoskeletal system 5.3 Special signal sequences on proteins target them to particular places in the eucaryotic cell 5.4 There are two types of targeting mechanism 5.5 Proteins that cross two membranes have two signal sequences THE ENDOMEMBRANE SYSTEM 5.6 The endomembrane system exchanges materials by the budding and fusion of membrane vesicles 5.7 The nuclear envelope encloses the chromosomes 5.8 Pore complexes in the nuclear envelope regulate the passage of materials between the cytoplasm and the nucleoplasm 5.9 mRNA molecules are capped and tailed to mark them for export 5.10 The endoplasmic reticulum is responsible for membrane synthesis 5.11 The ER is also the site of synthesis of secretory proteins, digestive enzymes, and cell walls 5.12 The Golgi sorts the mixed contents of ER membranes and lumen into different vesicles 5.13 Secretory vesicles fuse with the cell membrane 5.14 Lysosomal vesicles fuse with the endosome, which then targets proteins to the lysosome 5.15 Endocytosis is the first step in intracellular digestion, and in recycling surface 5.16 The endosome recycles membrane proteins 5.17 Vesicles containing material to be digested fuse with lysosomes 5.18 Exocytosis eliminates indigestible residue 5.19 Many protists are armed with extrusomes MITOCHONDRIA AND CHLOROPLASTS 5.20 Mitochondria and chloroplasts are not part of the endomembrane system 5.21 Mitochondria and chloroplasts have their own chromosomes and their own protein-synthesizing system 5.22 Many mitochondrial and chloroplast proteins, and some lipids, are imported from the cytoplasm 5.23 Mitochondria and chloroplasts exchange small molecules with the cytoplasm via permeases in their inner membrane 5.24 Mitochondria and chloroplasts have an evolutionary origin different that that of the nucleus 5.25 Hydrogenosomes are another relict symbiosis 5.26 Some chloroplasts appear to be more recent endosymbioses THE CYTOSKELETAL SYSTEM 5.27 Microtubules are hollow tubes composed of thousands of molecules of tubulin 5.28 Centrosomes organize the cell¿s microtubule network 5.29 Microtubules serve as tracks for endomembrane vesicles to slide on 5.30 Microfilaments are chains of actin monomers 5.31 Microfilaments maintain cell shape and stabilizes the membrane 5.32 Microfilaments also provide tracks for membrane vesicles to slide along MOTILITY 5.33 Amoeboid movement is mediated by microfilaments and myosin 5.34 Flagella and cilia contain a bundle of microtubules that slide against each other 5.35 Dynein binding to flagellar microtubules controls the state of the flagellum/cilium 5.36 Flagella and cilia originate in a centriole-like basal body 5.37 Flagella and cilia differ in their beat pattern and in their length THE CELL WALL AND PELLICLE 5.38 The eucaryotic cell wall is usually composed of polysaccharide 5.39 Some protists make walls that are heavily impregnated with inorganic salts 5.40 The pellicle is a complex structure that includes the cell membrane and an underlying layer of protein or polysaccharide 5.41 Some amoebas make shells for protection against predation THE CONTRACTILE VACUOLE 5.42 The contractile vacuole collects water from the cytoplasm and expels it to the outside by exocytosis 5.43 The contractile vacuole collects water through a system of tubules or vesicles REPRODUCTION IN PROTISTS 5.44 Open mitosis is common in protists 5.45 Sex is occasional in protists; reproduction is normally asexual REPRISE CHAPTER 6 VIRUSES AND OTHER ACELLULAR ENTITIES 6.1 Viruses have an acellular stage in their life cycle 6.2 Virions contain one or more chromosomes of either DNA or RNA, double-stranded or single-stranded 6.3 Viral genomes are incomplete; the host cell provides most genetic information needed by the infected cell 6.4 Viral capsids are usually symmetrical 6.5 Envelopes are obtained by budding 6.6 Virus multiplication is a five-stage process ATTACHMENT AND PENETRATION 6.7 Attachment of virion to host cell is highly specific 6.8 Bacteriophage penetration is by nucleic acid injection 6.9 Penetration is by membrane fusion in enveloped viruses, followed by uncoating 6.10 Plant viruses penetrate via wounds, or they are injected by insects 6.11 Plant viruses are transmitted from cell to cell within the same plant through plasmodesmata MACROMOLECULAR SYNTHESIS 6.12 DNA viruses of eucaryotic cells usually replicate in the nucleus, RNA viruses in the cytoplasm 6.13 DNA phages often replicate by a ¿rolling circle¿ mechanism 6.14 The chromosome of (+) strand RNA viruses acts as mRNA to produce a replicase 6.15 A replicase enters the host cell along with the chromosome of (-) strand RNA viruses and double-stranded RNA viruses 6.16 Retroviruses copy their ss-RNA chromosome into DNA, using reverse transcriptase 6.17 Viral protein synthesis is regulated 6.18 Eucaryotic viruses often make polyproteins ASSEMBLY AND RELEASE 6.19 Capsid assembly and nucleic acid packaging are tightly linked processes 6.20 Assembly of simple viruses occurs spontaneously; more complex viruses have regulated assembly pathways 6.21 Release of unenveloped virions is normally by the lysis of the host cell 6.22 Release of enveloped virions is a continuous process that often does little damage to the host cell LYSOGENY AND LATENCY 6.23 Prophages make their host cells immune to subsequent infection by another virion of the same kind 6.24 Proviruses can be induced to reenter active multiplication 6.25 Latency is a strategy for intergenerational transmission VIRAL TAXONOMY 6.26 Viruses are classified into artificial groups on the basis of their molecular biology, life cycles, and host organisms VIROIDS AND PRIONS 6.27 Viroid RNA is not translated; it is replicated by a rolling circle mechanism 6.28 Prions are aberrant conformations of a normal mammalian brain protein, that replicate by catalyzing a conformational change in the normal proteins REPRISE Box 1-6 The Hershey-Chase Experiment Chapter 7: Microbial Metabolism: Fermentation and Respiration Microbial Nutrition, Central Metabolism, and Biosynthesis 7.1 Microbes are divided into four basic nutritional categories 7.2 Microbial metabolism is also categorized on the basis of its relationship to oxygen 7.3 Many microbes can switch from one category to another, depending on the conditions 7.4 Central metabolism interconverts a small number of small organic compounds needed for biosynthesis 7.5 The pathways of central metabolism, biosynthesis, and macromolecule assembly are nearly identical in all organisms 7.6 Oxoglutarate dehydrogenase is found principally in aerobic chemoheterotrophs 7.7 Chemoheterotrophs normally use the same organic compound for both biosynthesis and respiration 7.8 Macromolecules are hydrolyzed by extracellular enzymes 7.9 Most solute uptake by procaryotes is by active transport 7.10 In many bacteria, sugar uptake is by a phosphotransferase systems Energy Metabolism 7.11 Cells interconvert two forms of energy: an ionic potential, and ATP FERMENTATION 7.12 Fermentation is a mode of chemotrophic energy metabolism in which most or all of the ATP is made by substrate-level phosphorylation 7.13 Fermentation produces end-products at the same average redox level as the substrates. 7.14 Some fermentations do not involve redox reactions 7.15 Many fermentations involve a minor component of chemiosmotic energy generation 7.16 Many different kinds of compounds can be fermented CHEMOHETEROTROPHIC RESPIRATION 7.17 Respiration is a type of chemotrophic energy metabolism in which most or all of the ATP is made by chemiosmotic means 7.18 Most oxidations of organic compounds reduce NAD+ 7.19 The electron transport system consists of two or three separate complexes of protein 7.20 Organisms that lack the cytochrome b/c complex transfer electrons directly from quinol to the oxidase complex 7.21 Electron transport chains often branch 7.22 Alternate dehydrogenase complexes are used for different compounds 7.23 Alternate oxidases are used for different electron acceptors 7.24 ATP yields of microbial respiration differ greatly CHEMOAUTOTROPHIC RESPIRATION 7.25 Electrons from inorganic substrates normally enter the electron transport system at the level of quinone or cytochrome c 7.26 Oxidation of inorganic electron donors usually occurs in the periplasm 7.27 Reverse electron transport is necessary for chemoautotrophs to generate reductant 7.28 Transhydrogenase couples NADPH production to proton entry 7.29 Chemoautotrophic respiration is very inefficient 7.30 Anaerobic chemoautotrophic respirations commonly use H2 as electron donor 7.31 Methanogenesis pumps ions without a cytochrome-based electron transport system REPRISE Chapter 8: Microbial Metabolism: photosynthesis, autotrophic growth, and nitrogen fixation Photosynthesis 8.1 Photochemistry is mediated by membrane-embedded reaction centers containing chlorophyll and other electron carriers 8.2 Reaction centers are associated with pigment antennas 8.3 Photosynthesis is based on the cyclic transformations of chlorophyll through three different states 8.4 Cyclic photophosphorylation generates energy in the light with no material input 8.5 Electron donors and noncyclic photophosphorylation are needed for autotrophic growth only, not for energy metabolism 8.6 Photoheterotrophic growth does not need an electron donor 8.7 There are two fundamentally different types of reaction center 8.8 There are three distinct types of photosynthesis 8.9 Photosynthesis is confined to the bacteria and their descendants the chloroplasts Type I Photosynthesis 8.12 Cyclic photophosphorylation in type I photosynthesis uses photosystem I 8.13 Non-cyclic photophosphorylation in type I photosynthesis utliizes photosystem I only Type II Photosynthesis 8.10 Cyclic photophosphorylation in purple bacterial photosynthesis uses photosystem II 8.11 In type II photosynthesis, non-cyclic photophosphorylation requires reverse electron transport Type I/II Photosynthesis 8.14 Cyclic photophosphorylation in cyanobacterial photosynthesis uses photosystem I only 8.15 Non-cyclic photophosphorylation in cyanobacterial photosynthesis uses both photosystem I and II 8.16 The oxygen-evolving complex, combined with a high-potential photosystem II, allows cyanobacteria and their descendants to use water as electron donor 8.17 Oxygen evolution on the early earth may have been advantageous because of its toxicity 8.18 An alternative form of photophosphorylation is based on retinal instead of chlorophyll Carbon Dioxide Fixation 8.18 The Calvin-Benson cycle is the most common pathway of CO2 fixation 8.19 Oxygen competes with CO2 for the active site of RuBisCO 8.20 The reverse TCA cycle is used by a diverse group of autotrophic bacteria and archaea 8.21 The Ljungdahl-Wood pathway is common in strictly anaerobic autotrophs 8.22 The hydroxypropionic acid cycle is used by the green non-sulfur bacteria 8.23 Nitrogen fixation is a very expensive process 8.24 Nitrogen fixation is an intrinsically anaerobic process REPRISE CHAPTER 9: MICROBIAL GROWTH Growth and Division of Individual Cells 9.1 The growth of individual cells is exponential 9.2 Most procaryotes divide by binary fission 9.3 Some cells divide by budding or multiple fission 9.4 The interdivision times of individual cells are quite variable 9.5 Procaryotic growth rates can be highly variable 9.6 Procaryotic chromosomes replicate bidirectionally from a single origin 9.7 Segregation of the bacterial chromosome is mediated by the bacterial cytoskeleton 9.8 In procaryotes, successive cell cycles can overlap Microbial Population Growth 9.8 Microbial population growth is normally measured by spectrophotometry 9.9 Microbial population growth is exponential 9.10 Populations enter stationary phase when they run out of nutrients or accumulate toxic quantities of waste materials 9.11 Cells that have been in exponential growth for several generations are in balanced growth 9.12 Maintenance metabolism is necessary for cells in stationary phase 9.13 Microbial death is exponential 9.14 A subpopulation of stationary phase cells can survive for months 9.15 Growth at low nutrient concentrations is studied in the chemostat 9.16 Growth in nature is usually continuous like a chemostat, or episodic like successive batch cultures The Effect of Environmental Conditions on Growth 9.17 Each strain is characterized by a set of cardinal temperatures 9.18 Collectively, procaryotes grow over the entire range of temperature from ¿10°C to about 120°C 9.19 Procaryotes grow over a range of pH values, while maintaining constant internal pH 9.20 Osmoregulation in procaryotes involves the synthesis or uptake of solutes to keep the cytosol more concentrated than the environment 9.21 Aerobic growth requires several protections against the toxic effects of oxygen REPRISE Chapter 10: PROCARYOTIC genome organization and regulation PROCARYOTIC GENOME STRUCTURE AND TRANSCRIPTION 10.1 Most procaryotes have a single circular chromosome 10.2 The DNA in procaryotic chromosomes is supercoiled 10.3 Most of the procaryotic genome is coding 10.4 Procaryotic chromosomes contain multiple transposons 10.5 Many procaryotes have plasmids that encode dispensable functions 10.6 Procaryotic genes are often organized into operons 10.7 Promoter recognition by RNA polymerase is different in bacteria than in archaea and eucarya 10.8 Promotors may be ¿weak¿ or ¿strong¿ 10.9 There are two types of bacterial transcription termination 10.10 Every transcriptional unit has a common set of signals REGULATION OF INDIVIDUAL TRANSCRIPTIONAL UNITS 10.11 Transcription initiation is controlled by allosteric proteins¿repressors or transcription factors 10.12 Repressors and transcription factors bind to DNA sequences in the major groove 10.13 Repressors bind to DNA sequences adjacent to promoters and prevent RNA polymerase binding 10.14 Transcription factors bind to DNA sequences adjacent to weak promotors and allow RNA polymerase to recognize them 10.15 Repressors and transcription factors often bind at two sites to form DNA loops 10.16 Repressors and transcription factors can control multiple operons 10.17 Some proteins can be both repressors and transcription factors 10.18 Many biosynthetic operons are controlled by attenuation, regulating early termination 10.19 Antitermination is another mechanism regulating termination 10.20 Procaryotic mRNA is rapidly degraded, so continued gene expression requires continued transcription 10.21 Translational repressors prevent translation of mRNA 10.22 Antisense RNA can prevent translation of mRNA 10.23 Some operons are turned on and off by DNA rearrangements GLOBAL CONTROL BY MODULONS 10.24 There are many different global control systems 10.25 Catabolite repression is mediated by the transcription factor CRP 10.26 Glucose permease indirectly controls the cAMP concentration 10.27 The heat shock response is mediated by an alternate sigma factor 10.28 Growth rate regulation is principally the regulation of the ribosome supply 10.29 Rapidly growing cells are bigger and have more ribosomes than slowly growing ones 10.30 Slowly growing cells retain a reservoir of ribosomal subunits 10.31 Multiple rRNA operons are transcribed from two promoters 10.32 The stringent response is mediated by ppGpp REPRISE Chapter 11: Microbial BEHAVIOR and DEVELOPMENT TACTIC BEHAVIOR 11.1 Tactic responses can be positive or negative 11.2 Tactic responses depend on reversals of direction or on biased random walks 11.3 Tumbling is caused by a reversal of flagellar rotation 11.4 Many tactic responses are mediated by two-component regulatory systems 11.5 Gradient sensing depends on sensory adaptation 11.6 The two component chemotactic system integrates many signals through a single response protein DIMORPHIC CELL DIVISION IN CAULOBACTER 11.7 Cell division in Caulobacter produces one stalked cell and one flagellated cell 11.8 Flagellar sythesis is controlled by a regulatory cascade 11.9 Transcription of flagellar genes is compartment specific ENDOSPORE FORMATION IN BACILLUS 11.10 Endospores are highly durable and long-lived 11.11 Sporulation is a last-ditch response to starvation 11.12 Sporulation occurs in a series of defined morphological stages 11.13 Initiation of sporulation involves a two-component regulatory system and a protein kinase cascade 11.14 Endospore development depends on the sequential action of a series of different sigma factors 11.15 DNA rearrangements are required in the mother cell 11.16 Germination of endospores is a three-step process Heterocyst formation in Anabaena 11.17 Heterocysts lose photosystem II and the OEC, and undergo significant morphological differention 11.18 Nitrogen fixation requires material transport between heterocyst and adjacent vegetative cells 11.19 Heterocyst spacing is determined by an oligopeptide repressor of development 11.20 DNA rearrangements are required in the developing heterocyst FRUITING BODY FORMATION AND SPORULATION IN MYXOCOCCUS 11.21 Myxobacteria are highly social procaryotes 11.22 Myxobacteria have two different systems of gliding motility 11.23 Myxobacteria locate prey by sensing their physical presence 11.24 Aggregation is triggered by starvation, and is mediated by a series of intercellular signals 11.25 A subpopulation of cells are programmed to develop into myxospores; the rest lyse 11.26 Fruiting body formation insures that spores remain together and can immediately re-establish swarms 11.27 Myxospores are formed from entire vegetative cells REPRISE CHAPTER 12: MICROBIAL GENETICS 12.1 Recombination is separate from multiplication in microbes 12.2 Genetic exchange in procaryotes is directional, incomplete, and polarized 12.3 Genetic exchange often involves the transfer of a plasmid from donor to recipient 12.4 There are three principal mechanisms by which procaryotes can exchange chromosomal genes GENETIC MAPPING 12.5 Mapping a gene requires that there be at least two known alleles of that gene 12.6 Mapping usually involves three basic steps: crossing, selection, and scoring TRANSFORMATION 12.7 Gram positive transformation is non-specific, and DNA enters the recipient cell in single-stranded form 12.8 Competence to be transformed is subject to a quorum sensing mechanism 12.9 Gram negative transformation is species-specific, and takes in DNA in double-stranded form 12.10 Donor cells may actively release DNA CONJUGATION 12.11 Transmissible plasmids encode special pili to bind donor cells to recipient cells 12.12 DNA transfer to the recipient and plasmid replication by a rolling circle mechanism occur simultaneously 12.13 Transfer genes are normally repressed 12.14 F is derepressed for transfer because it has an insertion mutation in a regulatory gene 12.15 F has several insertion sequences that allow recombination with the chromosome 12.16 Hfr strains donate chromosomal genes to recipients at high frequency 12.17 Hfrs can be used to map genes on the bacterial chromosome 12.18 F' plasmids are created by recombination between insertion sequences in an Hfr 12.19 F' plasmids can be used to construct stable partial diploids TRANSDUCTION 12.20 There are two principal forms of transduction, with different mechanisms 12.21 Generalized transduction results from mistakes during packaging 12.22 Generalized transduction is used for precise mapping of nearby genes 12.23 Specialized transduction results from a mistaken excision of an integrated prophage 12.24 Specialized transduction produces partial diploids GENOMIC MAPPING 12.25 Genomic sequencing allows the identification of genes on the chromosome GENETIC RECOMBINATION IN EUCARYOTIC MICROBES 12.26 Most eucaryotic microbes multiply mainly by asexual means; genetic recombination is rare 12.27 Most unicellular eucaryotic microbes have morphologically indistinguishable mating types 12.28 Yeast cells switch their mating type frequently 12.29 Mating type switching is a form of gene conversion REPRISE CHAPTER 13: MICROBIAL SYSTEMATICS 13.1 Classification aims to group related organisms 13.2 Convergence can confuse the determination of relationships 13.3 Molecular sequences avoid convergence and allow evolutionary classification of microbes 13.4 The small subunit ribosomal RNA gene is the most commonly used sequence for phylogeny reconstruction 13.5 Extensive secondary structure in rRNA helps with sequence alignment 13.6 After homologous sequences are aligned, phylogenetic trees are reconstructed by computers 13.7 Genetic exchange among distantly related organisms can confuse phylogenies 13.8 ssu rRNA phylogenies show three major lines of descent, or ¿domains¿ 13.9 Each of the three domains contains multiple major lineages, or ¿kingdoms¿ 13.10 Close relationships are measured by DNA/DNA hybridization 13.11 The concept of a procaryotic species is fundamentally different from the traditional species concept 13.12 Most procaryotes have never been cultured REPRISE CHAPTER 14: PROCARYOTIC MICROBES BACTERIAL DIVERSITY 14.1 Hyperthermophilic Bacterial kingdoms 14.2 Green nonsulfur bacteria 14.3 Deinococci 14.4 Proteobacteria 14.5 Gram positive bacteria 14.6 Cyanobacteria 14.7 Spirochetes 14.8 Green sulfur bacteria 14.9 Bacteroides group 14.10 Planctomyces group 14.11 Chlamydia THE ARCHAEA 14.12 Euryarchaeotes 14.13 Crenarchaeotes 14.14 Nanoarchaeotes REPRISE CHAPTER 14: PROCARYOTIC MICROBES BACTERIAL DIVERSITY 14.1 Hyperthermophilic Bacterial kingdoms 14.2 Green nonsulfur bacteria 14.3 Deinococci 14.4 Proteobacteria 14.5 Gram positive bacteria 14.6 Cyanobacteria 14.7 Spirochetes 14.8 Green sulfur bacteria 14.9 Bacteroides group 14.10 Planctomyces group 14.11 Chlamydia THE ARCHAEA 14.12 Euryarchaeotes 14.13 Crenarchaeotes 14.14 Nanoarchaeotes REPRISE CHAPTER 15: EUCARYOTIC MICROBES ANAEROBIC PROTOZOA 15.1 Microsporidia 15.2 Diplomonads 15.3 Parabasalids AEROBIC PROTOZOA 15.4 Euglenids 15.5 Kinetoplastids 15.6 Amoebas and amoeboflagellates 15.7 Actinopoda 15.8 Slime molds 15.9 Cryptomonads 15.10 Ciliates 15.11 Dinoflagellates 15.12 Apicomplexans 15.13 Choanoflagellates THE ALGAE 15.14 Red Algae 15.15 Stramenopiles 15.16 Chrysophytes 15.17 Diatoms 15.18 Oomycetes FUNGI 15.19 Chytrids 15.20 Zygomycetes 15.21 Ascomycetes 15.22 Basidiomycetes REPRISE CHAPTER 16: BIOGEOCHEMISTRY AND MICROBIAL ECOLOGY BIOGEOCHEMISTRY 16.1 Chemical transformations on earth are cyclic 16.2 Terrestrial life depends on gaseous or mineral reservoirs 16.3 Anaerobic ecosystems are maintained by oxygen consumption 16.4 Some carbon is sequestered in geological formations 16.5 Gaseous products transfer carbon from anaerobic sediments to the aerobic zone 16.6 Syntrophy is common in anaerobic ecosystems MICROBIAL HABITATS 16.7 The minimal conditions for life are quite broad 16.8 Microbial communities consist of physiological guilds 16.9 Microbial communities create steep chemical gradients 16.10 Procaryotes grow on surfaces as biofilms 16.11 Microbial habitats generally allow periods of rapid growth alternating with starvation, or continuous slow growth REPRISE CHAPTER 17: SYMBIOSIS 17.1 Symbiosis benefits one partner; the other may benefit, be harmed, or be unaffected 17.2 The benefit of symbiosis to microbial symbionts is usually nutritional 17.3 In ruminant animals, microbial fermentation is the first step in digesting food 17.4 In many symbioses the microbial partner provides fixed nitrogen 17.5 The water fern is important in rice cultivation 17.6 The most important N2-fixing symbiosis is the rhizobium-legume one 17.7 Establishment of the legume-rhizobium symbiosis involves an exchange of chemical signals 17.8 N2 fixation requires regulation of oxygen concentration within the nodule 17.9 The actinomycete Frankia forms N2-fixing symbioses with many host plants 17.10 Lichens consist of highly coadapted fungi and either algae or cyanobacteria 17.11 Mycorrhizae are mutualistic association of fungi with the roots of angiosperm plants 17.12 Luminescent bacteria form mutualistic associations with deep-sea fish 17.13 Geothermal vent animals host chemoautotrophic symbionts REPRISE CHAPTER 18: HOST DEFENSES AGAINST MICROBIAL INFECTION 18.1 Host defenses confine microbial growth to the outside surfaces of the body 18.2 The normal flora is usually protective to the host 18.3 The normal flora occasionally causes disease Constitutive (INNATE) Host Defenses 18.4 Many defenses are mechanical 18.5 Some nutrients are sequestered in the animal body 18.6 Phagocytes prey on invading microbes 18.7 Natural killer cells destroy virus-infected host cells 18.8 Antimicrobial peptides of many kinds are found in all plants and animals INDUCIBLE (ADAPTIVE) HOST DEFENSES--INFLAMMATION, INTERFERON, AND RNA INTERFERFENCE 18.9 Inflammation increases host defenses at the site of infections 18.10 Interferon reduces the ability of viruses to spread 18.11 Small interfering RNAs can destroy viral mRNA INDUCIBLE HOST DEFENSES--THE IMMUNE SYSTEM AND HUMORAL IMMUNITY 18.12 The immune system recognizes only foreign molecules 18.13 The immune system has two principal branches 18.14 Antibodies are proteins that have several identical, highly specific, binding sites 18.15 Antibody binding to antigens protects by enhancing phagocytosis and by preventing antigen entry into host cells 18.16 Antibody binding activates the complement system 18.17 Antibody-producing cells are generated by a process of clonal selection 18.18 Induction of B-cell multiplication requires bound antigen and helper T-cells INDUCIBLE DEFENSES--CELL-MEDIATED IMMUNITY 18.19 CTL's target cells that are making foreign proteins 18.20 CTL's and TH cells are produced by a process of clonal selection similar to the production of B-cells 18.21 Much of the immune system activity occurs in lymph nodes 18.22 Vaccination is the deliberate stimulation of the immune system 18.23 Vaccines may be live or dead organisms, or inactivated toxins REPRISE CHAPTER 19: MICROBIAL PATHOGENESIS 19.1 Many pathogens infect surfaces only 19.2 Bacterial adaptations may increase invasiveness or toxigenicity INVASIVENESS 19.3 Pathogens are transferred among hosts by several routes 19.4 Establishing an infection is often an improbable event 19.5 Access to deep tissues requires wounds, or active penetration of mucous membranes 19.6 Intracellular growth protects some pathogens from host defenses 19.7 Intracellular pathogens may induce phagocytosis 19.8 Many Gram negative pathogens secrete defensive proteins directly into phagocytes 19.9 Capsules can protect against phagocytosis 19.10 Antigenic variation reduces the effectiveness of the immune system 19.11 Rapid mutation rates of some viruses slow an effective immune response 19.12 Some pathogens block the action of antibodies 19.13 Many pathogens disrupt defenses by blocking cellular communication 19.14 Antibiotic resistance is an increasingly common defense TOXIGENICITY 19.15 Exotoxins are proteins with specific enzymatic activity 19.16 Many exotoxins have two subunits, one of which is a transporter 19.17 Some diseases are intoxications 19.18 Some exotoxins disrupt host cell membranes 19.19 Endotoxin is the lipopolysaccharide of the Gram negative wall 19.20 Genes for virulence factors are often clustered in "pathogenicity islands" or located on plasmids or prophages 19.21 Host damage in viral infections is mainly caused by host defenses REPRISE CHAPTER 20: EPIDEMIOLOGY AND HUMAN DISEASE 20.1 An epidemic is the occurrence of disease at higher than expected frequency 20.2 Disease at expected frequency is endemic 20.3 Distinguishing between endemic and epidemic disease requires background information derived from surveillance 20.4 Epidemic detection requires alert physicians 20.5 Epidemic investigation follows standard procedures 20.6 The rate of transmission determines the course of epidemics 20.7 Population structure is a major determinant of the rate of transmission 20.8 High-speed transportation allows global dissemination of diseases 20.9 Some animal disease are communicable to humans 20.10 Many zoonoses are not contagious among humans 20.11 Species-specific strains of influenza virus cause avian and human flu 20.12 Diseases that provoke immunity become childhood diseases 20.13 Many human disease are evolutionarily recent phenomena 20.14 Many of the disease of urbanized humans came from domestic animals 20.15 New diseases are continuously emerging 20.16 Infectious disease is a major cause of death world-wide REPRISE CHAPTER 21: HUMAN EXPLOITATION OF MICROBES FOOD MICROBIOLOGY 21.1 The lactic acid fermentation preserves food 21.2 Cheese production usually involves secondary microbial transformations 21.3 The ethanol fermentation of fruit juice produces wine 21.4 Beer is the other major beverage made by an alcohol fermentation 21.5 Distillation of wines and beers produce liquor 21.6A partial oxidation of wine produces vinegar 21.7 The ethanol fermentation is also used to raise bread 21.8 Soy fermentations are common in the Far East 21.9 Microbes are used to produce many food additives 21.10 Microbial cells themselves can be food USEFUL PRODUCTS FROM MICROBES 21.11 Antibiotics are microbial products 21.12 Antibiotics are secondary metabolites 21.13 Antibiotics are often modified chemically after synthesis 21.14 Antibiotics often bind to uniquely bacterial targets BIOCONTROL 21.15 The most widely used biocontrol agent is Bacillus thuringiensis WASTEWATER TREATMENT 21.16 Wastewater treatment has two principal goals 21.17 Primary treatment removes particulate matter from sewage 21.18 Solids are digested anaerobically 21.19 Secondary treatment oxidizes dissolved organic material 21.20 Wastewater treatment is subject to periodic failures BIOLOGICAL WEAPONS 21.21 Biological weapons were used in both World Wars 21.22 Biological weapons are banned by international law REPRISE Glossary Appendices Index
Library of Congress Subject Headings for this publication:
Microbiology -- Textbooks.