Download introduction to microbiology

INTRODUCTIONTO
MICROBIOLOGY
TableofContents
Foundations of Microbiology ......................................................................................................... 8 Be able to explain how microbiology integrates into your course of study ...............................................8 List several ways in which microbes affect our lives ..................................................................................8 Know the correct taxonomic and use the correct taxonomic nomenclature to classify and name microorganisms ..........................................................................................................................................8 Name the major groups and characteristics of each group of microorganisms .........................................9 List the three domains of life ....................................................................................................................10 Know some of the key players in the history of microbiology..................................................................10 Compare spontaneous generation and biogenesis ..................................................................................11 Define bacteriology, mycology, parasitology, immunology, and virology ................................................11 Microscopy ................................................................................................................................... 12 List the metric (SI) units of measurement and know the abbreviations. Be able to estimate the size of different organisms and convert between them ......................................................................................12 Define light microscopy terms: transmission, absorption etc. .................................................................12 Be able to identify the parts of a compound microscope ........................................................................13 Be able to draw the light path through a compound microscope ............................................................13 Define total magnification, resolution, refractive index ...........................................................................14 Explain how electron microscopy differs from light microscopy ..............................................................14 Differentiate an acidic dye from a basic dye ............................................................................................14 Explain the purpose of simple staining .....................................................................................................14 List the steps in preparing a Gram stain, and describe the appearance of Gram‐positive and Gram‐
negative cells after each step ...................................................................................................................15 Compare and contrast the Gram stain and the acid‐fast stain .................................................................15 Explain why each of the following is used: capsule stain, endospore stain, flagella stain .......................15 Cell Structure ................................................................................................................................ 16 Compare and contrast the cell structure of prokaryotes and eukaryotes ...............................................16 1 Identify the basic shapes & arrangements of bacteria .............................................................................16 Describe the structure and function of the glycocalyx .............................................................................16 Differentiate flagella, axial filaments, fimbriae, and pili ...........................................................................17 Describe bacterial motility ........................................................................................................................17 Differentiate prokaryotic and eukaryotic flagella .....................................................................................17 Compare and contrast the cell walls of Gram+ with Gram‐ bacteria .......................................................18 Know the basics of the endosymbiotic theory .........................................................................................18 Microbial Metabolism ................................................................................................................... 19 Define metabolism, and describe the fundamental differences between anabolism and catabolism ....19 Identify the role of ATP as an intermediate between catabolism and anabolism ...................................19 Understand how the electron carrier NAD undergoes reversible reduction to NADH during metabolic cycles .........................................................................................................................................................20 Describe basic reactions of glycolysis and Krebs cycles ............................................................................20 Describe the chemiosmotic model for ATP generation ............................................................................21 Compare and contrast aerobic and anaerobic respiration .......................................................................22 Describe the chemical reactions of, and list some products of, fermentation .........................................22 Classify the 4 different nutritional patterns of organisms ........................................................................23 Microbial Growth .......................................................................................................................... 24 List the main requirements for growth .....................................................................................................24 Classify microbes into five groups on the basis of preferred temperature range ....................................24 Identify how and why the pH of culture media is controlled ...................................................................25 Explain the importance of osmotic pressure to microbial growth ...........................................................25 Describe a use for each of the elements needed in large amounts for microbial growth .......................25 Be familiar with trace elements and their role .........................................................................................25 Identify how aerobes avoid damage from toxic O2 species ......................................................................26 Explain how microbes are classified on the basis of oxygen requirements .............................................26 Explain the purpose of organic growth factors .........................................................................................26 Distinguish chemically defined, complex, differential, enrichment and anaerobic (reducing) media .....27 Justify the use of each of the following: anaerobic technique, living host cells, candle jars, anaerobic jar, anaerobic chamber ...................................................................................................................................27 Define what is meant by a colony on an agar plate ..................................................................................27 Describe how single colonies can be isolated by using the streak dilution plate method .......................28 Define bacterial growth, including binary fission .....................................................................................28 2 Compare the phases of microbial growth, and describe their relation to generation time .....................28 Describe four methods of measuring cell growth ....................................................................................29 Control of Microbial Growth ......................................................................................................... 30 Define the key terms: sterilization, disinfection, antisepsis, sanitization, biocide, germicide, bacteriostasis, and asepsis ........................................................................................................................30 Describe the patterns of microbial death caused by treatments with microbial control agents .............30 Describe the effects of microbial control agents on cellular structures ...................................................30 Compare the effectiveness of moist heat, boiling, autoclaving, pasteurization and dry heat .................30 Describe how filtration, low temperatures, high pressure suppress microbial growth ...........................32 Interpret the results of the disk‐diffusion method ...................................................................................32 Identify the methods of action and preferred uses of chemical disinfectants .........................................33 Identify the appropriate uses for surface‐active agents ...........................................................................34 Explain how the type of microbe affects the control of microbial growth ...............................................34 Be familiar with aseptic technique ...........................................................................................................34 Know Paul Erlich’s and Alexander Fleming’s contributions to antibiotics ................................................34 Explain the difference between broad and narrow‐spectrum antibiotics ...............................................35 List the 5 modes‐of‐action of antibiotics; illustrate mode‐of‐action using penicillin ...............................35 Microbial Genetics ........................................................................................................................ 36 Define genetics, genome, genomics, chromosome, gene, genotype and phenotype .............................36 Describe how DNA serves as genetic information ....................................................................................36 Describe the process of DNA replication ..................................................................................................36 Describe the process of transcription .......................................................................................................37 Describe the process of translation ..........................................................................................................38 Define operon ...........................................................................................................................................39 Explain the regulation of gene expression in an operon ..........................................................................39 Classify mutations by type ........................................................................................................................39 Describe ways mutations can be repaired ................................................................................................39 Define mutagen ........................................................................................................................................39 Outline the procedure/purpose of the Ames test ....................................................................................40 Differentiate horizontal and vertical gene transfer ..................................................................................40 Compare the mechanisms of genetic recombination in bacteria .............................................................40 Describe the functions of plasmids and transposons ...............................................................................41 3 Fungi ............................................................................................................................................. 42 Be able to describe how fungi influence our everyday lives ....................................................................42 List the defining characteristics of fungi. ..................................................................................................42 Differentiate asexual from sexual reproduction, and describe each of these processes in fungi. ...........43 List the characteristics of five groups of fungi. .........................................................................................43 Differentiate fungal sexual and asexual spores coming from five different fungal phyla ........................44 Identify two beneficial and two harmful effects of fungi. ........................................................................45 List the distinguishing characteristics of lichens, and describe their nutritional needs. ..........................45 Describe the roles of the fungus and the alga in a lichen. ........................................................................45 Describe an oomycetes .............................................................................................................................46 Viruses, viroids, prions and parasites ............................................................................................ 47 Differentiate a virus from a bacterium .....................................................................................................47 List the properties of an enveloped & non‐enveloped virus ....................................................................47 Describe the structure of a complex virus ................................................................................................48 Define viral species ...................................................................................................................................48 Give an example of a family, genus, and common name for a virus ........................................................48 Describe how bacteriophage are cultured ...............................................................................................49 Describe how animal viruses are cultured and their growth curve ..........................................................49 List three techniques used to identify viruses ..........................................................................................50 Describe the lytic cycle of T‐even bacteriophages ....................................................................................50 Describe the lysogenic cycle of bacteriophage lambda ............................................................................51 Describe the life cycle of an animal virus..................................................................................................51 Provide an example of a latent viral infection ..........................................................................................51 Give an example of a plant virus and viroid ..............................................................................................52 Discuss how a protein can be infectious ...................................................................................................52 Describe the different types of parasitism ...............................................................................................53 List the defining characteristics of protozoans .........................................................................................53 Name two diseases caused by protozoans and give the genus name of the protozoan in each case. ....53 List the distinguishing characteristics of parasitic helminths ...................................................................54 Describe a parasitic infection which has as a definitive and intermediate host . .....................................54 Principals of Disease ..................................................................................................................... 55 Define pathology, aetiology, infection, and disease .................................................................................55 4 Define normal and transient microbiota ..................................................................................................55 Compare commensalism, mutualism, and parasitism, and give an example of each ..............................55 Contrast normal microbiota and transient microbiota with opportunistic microorganisms ...................56 List Koch’s postulates ................................................................................................................................56 Differentiate a communicable from a non‐communicable disease .........................................................56 Categorize diseases according to frequency of occurrence .....................................................................57 Categorize diseases according to severity ................................................................................................57 Define herd immunity ...............................................................................................................................58 Identify four predisposing factors for disease ..........................................................................................58 Put the following in proper sequence: period of decline, period of convalescence, period of illness, prodromal period, incubation period .......................................................................................................58 Define reservoir of infection .....................................................................................................................58 Contrast human, animal, and nonliving reservoirs, and give one example of each .................................59 Explain three methods of disease transmission .......................................................................................59 Define nosocomial infections, and explain their importance ...................................................................59 Define compromised host.........................................................................................................................59 List several methods of disease transmission in hospitals .......................................................................60 Explain how nosocomial infections can be prevented .............................................................................60 Mechanisms of Pathogenicity ....................................................................................................... 61 Identify how pathogens get into the cell (portals of entry) and requirements for infection ...................61 Define ID50 and LD50 ..................................................................................................................................61 Explain how microbes adhere to host cells, give an examples .................................................................62 Explain how capsules and cell wall components contribute to pathogenicity .........................................62 Compare the effects of: coagulases, kinases, hyaluronidase and collagenase ........................................62 Define and give an example of antigenic variation...................................................................................63 Describe how bacteria use the host cell’s cytoskeleton to enter the cell ................................................63 Give an example of direct damage ...........................................................................................................63 Contrast the nature and effects of exotoxins and endotoxins .................................................................63 Describe the roles of plasmids and lysogeny in pathogenicity .................................................................64 List nine cytopathic effects of viruses .......................................................................................................64 Discuss the causes of symptoms in fungal, protozoan and helminthic diseases ......................................64 List & describe the portals of exit .............................................................................................................65 Differentiate innate from adaptive immunity ..........................................................................................65 5 Describe the role of the skin and mucous membranes in innate immunity .............................................65 Differentiate physical from chemical factors; list five examples of each .................................................65 Classify leukocytes, and describe their roles ............................................................................................66 Define phagocyte and phagocytosis .........................................................................................................66 Describe the process of phagocytosis .......................................................................................................67 Identify six mechanisms of avoiding destruction by phagocytosis ...........................................................67 Environmental Microbiology ......................................................................................................... 68 What is Environmental Microbiology? .....................................................................................................68 Define Biosphere, Hydrosphere, Lithosphere and Atmosphere ...............................................................68 Define extremophile, and identify two extreme habitats ........................................................................68 Define symbiosis .......................................................................................................................................68 Define mycorrhiza, distinguish between endomycorrhizae from ectomycorrhizae ................................69 Define biogeochemical cycle ....................................................................................................................69 Describe soil & soil microbes’ contribution to the biogeochemical cycle. ...............................................69 Define rhizosphere. ...................................................................................................................................69 Compare different methods for growing & studying soil microbes .........................................................69 Outline the carbon cycle and roles of microorganisms in this cycle ‐5a) .................................................70 Outline the nitrogen cycle and roles of microorganisms in this cycle ......................................................70 Define ammonification, nitrification, denitrification, and nitrogen fixation. ...........................................71 Explain why wastewater pollution is a public health and ecological problem .........................................71 Discuss the causes and effects of eutrophication .....................................................................................72 Describe how pathogens are removed from drinking water ....................................................................72 Compare primary, secondary, and tertiary sewage treatment ................................................................72 Define BOD, activated sludge system, trickling filter, septic tank, and oxidation pond ...........................73 Applied & Industrial Microbiology ................................................................................................ 74 Explain how foods were preserved before industrial canning and refrigeration .....................................74 Why preserve foods, food safety, HACCP .................................................................................................74 Preservation by industrial food canning ...................................................................................................74 Distinguish commercial sterilisation from complete sterilisation ............................................................74 Distinguish the main types of can spoilage by bacteria: thermophilic anaerobic spoilage, flat sour spoilage; and mesophilic spoilage ............................................................................................................75 Understand the use of aseptic packaging .................................................................................................75 Describe food preservation by radiation ..................................................................................................75 6 Describe food preservation by high pressure ...........................................................................................75 Name four beneficial activities of microorganisms and describe the organisms involved ......................76 Define microbial biotechnology, industrial fermentation and bioreactor................................................76 Differentiate primary from secondary metabolites ..................................................................................76 Describe the role of microorganisms in the production of industrial chemicals and pharmaceuticals ...78 Define bioconversion, and list its advantages ..........................................................................................78 List biofuels that can be made by microorganisms ..................................................................................78 7 FoundationsofMicrobiology
Beabletoexplainhowmicrobiologyintegratesintoyourcourseofstudy
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Production of yoghurt, wine and vinegar 
Fermentation processes 
Preservation of foods and HACCP 
Aseptic technique 
Diseases & their etiological agents 
Host/Pathogen interactions 
Antibiotics spectrum & mode‐of‐action 
Clinical hygiene Listseveralwaysinwhichmicrobesaffectourlives
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A few are pathogenic 
Some decompose organic waste or fix nitrogen so in the big picture they recycle carbon and nitrogen 
Microbes make 50% of the world’s oxygen and are the foundation of food webs 
Some make industrial chemicals such as ethanol and acetone 
Some produce fermented foods such as vinegar, cheese, bread, beer, wine & sauerkraut 
Some help us make biotechnology products like: cellulase and human insulin. 
Some make recombinant vaccines and pharmaceuticals Knowthecorrecttaxonomicandusethecorrecttaxonomicnomenclature
toclassifyandnamemicroorganisms
To remember, use the mnemonic Dumb Kids Playing Chicken On Freeways Get Squashed Scientific names were devised by Carolus Linnaeus, they have 2 parts (binomial) 1. Genus (e.g. Escherichia) 2. Specific epithet (e.g. coli) 8 Namethemajorgroupsandcharacteristicsofeachgroupof
microorganisms
1. Bacteria 
Prokaryotes (have no nuclear membrane holding genetic material) 
Peptidoglycan cell walls 
Relatively simple, single‐celled (unicellular) organisms. 
reproduce by dividing into two equal cells (binary fission) 
For energy, use organic chemicals, inorganic chemicals, or photosynthesis 2. Archaea 
Prokaryotes (have no nuclear membrane holding genetic material) 
Lack peptidoglycan in cell walls 
Live in extreme environments o
Methanogens (produce methane as a waste product from respiration) o
Extreme halophiles (salt loving) o
Extreme thermophiles (heat loving) 3. Fungi 
Eukaryotes (cell walls have a nucleus surrounded by a membrane) 
Chitin cell walls 
Use organic chemicals for energy 
Maybe multicellular (moulds) or unicellular (yeasts) 4. Protozoa 
Eukaryotes 
Absorb or ingest organic chemicals 
May be motile via pseudopods, cilia or flagella 5. Algae 
Eukaryotes 
Cellulose cell walls 
Use photosynthesis for energy 
Produce molecular oxygen and organic compounds 6. Multicellular animal parasites 
Eukaryotes 
Multicellular animals 
Parasitic flatworms and roundworms are called helminths. 
Microscopic stages in life cycles. 7. Viruses 
Acellular (not cellular) 
Consist of either DNA or RNA core which is surrounded by a protein coat 
Coat may be enclosed in a lipid envelope 
Viruses are replicated only when they are in a living host cell 9 Listthethreedomainsoflife
1. Bacteria 2. Archaea 3. Eukarya 
Protists 
Fungi 
Plants 
Animals Knowsomeofthekeyplayersinthehistoryofmicrobiology
1665 Robert Hooke coined the term “Cells” to describe the box‐like structures he saw in cork tissue. They reminded him of monk’s small rooms – cells. This marked the beginning of the cell theory – that all living things are composed of cells 1673 Anton van Leeuwenhoek observed the first microbes. He was a Dutch clothes merchant. Now considered to be a genius. He originally made microscopes to look at cloth fibres but ended up looking at things like his teeth scrapings, his faeces and pond water. He was the first to see bacteria and protozoa which he called “animalcules” (little animals) 1735 Carolus Linnaeus devised a binomial nomenclature (two part names) for organisms that avoided confusion with common names 1798 Edward Jenner Produced the first vaccine against the deadly smallpox using scrapings from cowpox blisters (Vacca = cow) 1835 Agostino Bassi de Lodi showed that a disease affecting silkworms was caused by a fungus ‐ the first micro‐organism to be recognised as a contagious agent of animal disease 1840 Ignaz Semmelweiss, a Hungarian physician demonstrated that doctors in Vienna hospitals were spreading childbed fever while delivering babies. He started forcing doctors under his supervision to wash their hands before touching patients 1857‐1864 Louis Pasteur Discovered fermentation, disproved spontaneous generation ‐confirming the Germ theory of disease and invented pasteurization 1858 Robert Virchow introduced the concept of biogenesis (the cell theory) that living cells arise from pre‐existing cells. 1867 Joseph Lister convinced by the germ theory of disease introduced antiseptics in surgery. By spraying carbolic acid (phenol) on surgical instruments, wounds and dressings, he reduced surgical mortality due to bacterial infection considerably. Before this 50% of patients died during surgery. 1876: Robert Koch, a German bacteriologist was the first to cultivate anthrax bacteria outside the body using blood serum at body temperature. Building on Pasteur's "germ theory he proposed in "Koch's postulates", the critical test for the involvement of a microorganism in a disease: 1. The microbe must be present in every case of the disease. 10 2. The microbe must be identified, isolated and grown in pure culture 3. The disease must be reproduced when a pure culture of the microbe is inoculated into a susceptible host. 4. The microbe must be recoverable and identified from the experimentally‐infected host. 1880 ‐1910 Paul Erlich dreamed of a chemical “magic bullet” to hunt down and destroy disease. He discovered salvarsan an arsenic derivative effective against syphilis, so started the chemotherapy era. Ironically chemicals that killed bacteria were dyes used in the clothing industry (dressed to kill!?) 1928 Alexander Fleming accidentally discovered that a Penicillium mould killed Staphylococcus on contaminated Petri dishes. He coined the word Penicillin for the active ingredient. Fleming shared the Nobel prize with Aussie Howard Florey and Ernst Chain who isolated the active ingredient and when the USA entered the second world war Penicillin was produced in Industrial quantities saving millions of lives. 2005 Aussies Barry J. Marshall and J. Robin Warren get Nobel prize for discovering that Helicobacter pylori is the cause of peptic ulcers Comparespontaneousgenerationandbiogenesis
Spontaneous generation: The hypothesis that living organisms arise from nonliving matter; a “vital force” forms life Biogenesis: The hypothesis that the living organisms arise from pre‐existing life. Definebacteriology,mycology,parasitology,immunology,andvirology
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Bacteriology is the study of bacteria 
Mycology is the study of fungi 
Parasitology is the study of protozoa and parasitic worms 
Immunology is the study of immunity 
Virology is the study of viruses 11