Goals ch 1 and 17 Relate major scientific advances/discoveries with the individual responsible for them o Van Leeuwenhoek- 1676

6 haberdasher who constructed fist microscop 300x magnification; discovered animalcules (bact and protozoa) and described several morphologies Spallazani- 1760s sealed glass flasks and boiled contents; concludes air carries germs into broth or air is required for growth of germs o Redi- 1688 first disproved spontaneous generation of maggots from rotting meat using 3 experimental containers (open to air, covered with paper, covered with thin gauze) o Bassi -1830s showed that disease affecting silk production in silkworms was cuased by fungal infection; only worms without infection produced silk o Schwann- 1830s flasks with boild broths left open to air that passed thorugh red-hot glass tube (no growth?); concludes air carries germs o Schroder -1830s flasks with boiled broths stoppered with sterilized cotton/wool, no growth, concluded cotton/wool can keep germs out when used as stopper and that air carries gersm obstructed by cotton/wool o Pasteur- 1861 finally disproved spontaneous generation with his swan necked flasks o Lister- 1867 Founded aseptic technique; used carbolic acid (phenol)as first antiseptic; heat sterilized instruments to effectively prevent wound infections o Hess- 1876 she gave Koch the agar for his experiments o Koch- 1876 developed solid microbiological medias for obtaining isolated and pure cultures of bacteria; first used fresh cut potatoes but little grew, then used meat extract broths with gelatin but the gelatin liquefied, then used agar in place of gelatin and it was stable; also demonstrated role of bacteria in causing disease; linkined anthrax with Bacillus anthracis Germ Theory of Disease (Kochs Postulates) established relationships as causative agents of disease; used mice as models and tracked infections by symptom then isolated individual microbes in pure culture o Tyndall- 1877 notes conditions fo sterilization were differe between all those trying to repeat Pasteur; hypothesizes some germs may be more resistant to heat; help create unified concept of sterilization with Cohn, spontaneous generation refuted o Cohn- 1877 demonstrated existence of heat-resistant form of germs (endospores); he and tyndall helped creat unified concept of sterilization to support Pasteur and refute spontaneous generation o Pasteur- 1880-90s developed vaccine against anthrax bacteria and rabies virus using attenuation (via successive passage through many hosts, heat or chemical treatment) Compare and contrast the 5 kingdom vs 3 Domain classification schemes o 5 kingdom Discovered by Whittaker Used until 1970s Microorganisms were not considered to be plants or animals; they were in protists, fungi, or monera Based primarily on phenetic (overall similarity) observations (membrane presence, cell size, cell organization) Both separated prokaryotes and eukaryotes o 3 domain

5 kingdom system to simple; gives a better definition and classification of microorganisms and all organisms in general; prokaryotes (no nucleus) eukaryotes (nucleus) Based primarily on phylogenetic sequences (rRNA, DNA, protein) Both separated prokaryotes and eukaryotes List the major groups in 5 kingdom scheme o Plants, animals, protists, fungi, bacteria (monera) List the major groups in 3 Domain scheme o Superdomain Prokaryotes Domain Bacteria Domain Archaea o Superdomain Eukaryotes Domain Eukarya Fungi, protists, algae, plants, animals Explain why viruses are not included in either 5 kingdom or 3 domain system o Because they are acellular Explain why rRNA of any living organism is a suitable marker for producing phylogenetic trees o Because rRNA is present in all living organism and its function is identical in all organisms. Its isolation and sequencing is possible to compare; there are certain side chains that differ slightly from the rest of the molecule Explain how homology and lack of homology of the compared sequences can be used to determine relatedness of organisms o Homology is the similarity between the sequences o Homology in sequences means they are related and lack of it means there is a branch somewhere..duh.. List the evidence supporting the endosymbiiotic evolution theory and explain how the evidence supports it o The theory states that mitochondria, chloroplasts and hydrogenosomes likely evolved from prokaryotic symbiotes of eukaryotic partners o Evidence Mitochondria and plastids contain DNA of their own; DNA coding for rRna is 16S not 18S- the different DNA suggests a whole different organism could have been present Obligately intracellular bacteria show an evolutionary link with mitochondrial DNA- mitochondria are always in the cell, and these bacteria are in the cell perhaps they are the ancestors of mitochondria, esp if DNA is similar Cyanobacteria, which are symbiotes of many marine invertebrates, show a high homology with chloroplast DNA- basically same as abovebleh Discuss why the theory of spontaneous generation was able to return to widespread belief (post Redi) o Because science was viewed as a hobby, nobody really took it seriously, it was for the aristocrats o There was no technology to culture the microorganisms to continue study How was theory of spontaneous generation finally put to rest? By whom? o Was finally put to rest by Pasteur, winemaker, in 1861; he created swan-necked flasks; boiled the broth and there were no microorganisms, cut the neck off and microorganisms grew

Explain the process in which a disease is determined to be caused by a specific agent (bacterial species) o Microbe must be present in every case of disease byt absent in healthy organisms o Microbe must be isolated and grown in pure culture o Disease must result when isolated organism is inoculated into healthy host o Microbe must be re-isolated from diseased host Explain the significance of isolation in obtaining pure cultures o How else are you gonna know that is the organism youre looking for.. Explain the importance of studying pure cultures themselves o bleh List and discuss the roles of microbes outside of medicine and disease o Produce and preserve foods o Recycle nutrients and fertilize soils o Industrialized synthesis of natural and engineered products o Bioremediation (GEMs used to degrade toxic compounds like PCBs, DDt, and oil spills) Goals ch 2 Compare and contrast benefits and limitations of each subtype of light and electron microscopy techniques o Light Brightfield Images dark, background white Specimens need natural pigments or staining (not good for live material) Light pass through and around specimen and up into objective Darkfield Images bright, background dark No need for natural pigments or stain (good for live material) Light is blocked and scattered by disc (patch stop), creating outer ring of illumination, scattered light collected and passed into objective lens Phase contrast Images bright, background dark No need for natural pigments or stain (good for live material) Light passes through specimen and recombined with scattered light, dense structures appear darker than background and glow around edges Fluorescence Dyes or natural pigment (some work for live cells) Light pass through specimen using excitation filter so only certain range of wavelengths pass into specimen; pigments/dyes emit different wavelength of light after excitation and only those are passed through barrier filter and then transmitted to eye o Electron microscopy Transmission E- beam penetrates specimen then scatters; e- bounce back to detector and are collected to produce images Used to study intracellular detail 1000x better resolution than light microscopy Scanning

Electron beams hit surface of metal coate specimen and bounce back to detector to produce image Used to study surface structures 100x better resolution than light microscopy List and explain the types of information that can be obtained from: o Unstained cells o Gram stained cells Peptidoglycan content; if purple there is a lot of pep and is gram positive; red is opposite o Endospore stained cells o Acid fast stained cells Waxy Mycolic acid content; if fuschia there is a lot of acid and is acid fast; blue is opposite Diagnostic for presence of pathogens (mycobacterium, nocardia, tuberculosis, leprosy) o Capsule stained cells Reveals presence of capsules, which are made of polysaccharides that surround many bacteria and some fungi o Flagella stained cells Reveals presence of flagella, presence, number and position of them canhelp identify unknown bacterial specimens Explain the relationship between refraction and resolution o Resolution is the ability to distinguish two points from each other. o Refraction is the bending of light o Refraction occurs when light passes through two different media; the more difference in refractive index the more refraction. o More refraction means lower resolution. Explain how the use of immersion oil impacts both resolution and refraction. Be able to analyze a scenario or create an example o Immersion oil has same refractive index as glass of slide/coeverslip and lens; less refraction, higher resolution Explain the role that fixation plays in slide preparation o It sticks the specimens to the slide so you dont wash them off when staining o It kills the specimens so they dont move around (if motile) o Preserves structure and inactivated enzymes within cells that may alter morphology; o toughens cell wall and other structures Compare and contrast the benefits and limitations of heat fixation vs. chemical fixation o Heat fixation Bene: good preservation of cell morphology Lim: bad preservation of delicate internal cell structures; if not air- dried completely, internal water will boil and cause lysis o Chemical fixation Bene: toughens internal structures and makes them easy to see Lim: some chemicals very toxic to us and bacteria o Be able to analyze scenario and predict results of: Forgetting to perform this process Not performing the process correctly

Compare and contrast the benefits and limitations of : o Simple vs. differential staining Simple Bene: use only one dye Lim: may not be able to differentiate between different types of bacteria Differential Bene: divides bacteria into two distinct groups Lim:what if there is a third group? (help..); must be careful to do steps correctly or else false neg or false positive o Positive vs. negative staining Positive Bene: get better picture of internal structures, in color Lim: Negative Bene: get better morphology idea Lim: Explain the role of each step of the gram stain process and list the chemical (s) involved o Crystal violet- primary stain; stain all cells purple o Lugols/grams iodine- mordant; chemical mordant, crystallizes purple stain in cells o 95% ethanol- decolorizer; dissolved lipopolysaccharide layers in cell walls, allows crystallized purple to wash out of those cells with a lot of lipopolysaccharide o Safranin- counterstain; enters vacant cells and makes them pink/red o If a step is forgotten what impact would you predict to occur on: Gram negative cells No Crystal violet- they will still turn out red No Lugols- they will still turn out red No 95%ethanol- they will be purple No Safranin- they will be purple Gram positive cells No crystal violet- not purple No lugols- not as purple, very little to no purple No ethanol- still purple No safranin- still purple Both No c- mostly red /pink cells No l- mostly red/pink cells No e- all purple No saf- all purple Explain the role of each step of the acid fast stain process and list the chemical(s) involved o If a step is forgotten what impact would you predict to occur on: Acid fast cells Non-acid fast cells Both Explain the role of each step of the endospore stain process and list the chemical(s) involved o If a step is forgotten what impact would you predict to occur on: vegetative cells

 endospore cells Both Expaline the value (information) you get from: o Gram stain o Endospore stain o Capsule stain o Flagella stain o Acid fast stain Compare and contrast acidic and basic dyes and explain why one is used more often than the other to stain bacterial cells Goals ch 3 What are the different morphologies of cells What are the different arrangements of cells Identify the function of prokaryotic cell components and describe their importance to the cells functions Be able to make comparisons/contrasts with prokaryotic and eukaryotic cell components Explain why some genes are housed on the chromosome and others can be found on plasmids Explain the conditions which impact the cells conversion from vegetative cell to endospore and vice versa; what stages are involved in the process Compare and contrast the chemical an dphysical structural differences found between gram ositive and gram negative cells walls (including difference within the peptidoglycan layers themselves) Be able to label a diagram of both gram positive and gram negative cell walls Explain the impact penicillin and lysozyme have on Gram negative and Gram positive cell walls and why the differences occur Goals Ch 6 Compare and contrast the 4 major transport mechanisms that prokaryotes use to obtain nutrients: o Active transport o Passive diffusion o Facilitated diffusion o Group translocation Be able to examine a descriptive scenario and determine the type of transport a cellwill utilize int aht situation Identify the major players in coupled transport pathway and explain how they interact in order for a cell to successfully transport solutes using this mechanism Identify the major players in ABC transport pathway and explain how they interact in order for a cell to successfully transport solutes using this mechanism Identify the major players in group translocation pathway and explain how they interact in order for a cell to successfully transport solutes using this mechanism Given a scenario, determine the term(s) that should be applied to an organism to fully describe its nutritional requirements. Alternatively, starting with a term such as photolithoautotroph, be able to identify each of the organism's nutritional requirmetns and provide an example (i.e. photo refers to the requirement for light to drive carbon fixation). Explain the importance of each major element and trace element for the cell (i.e. why is nitrogen essential for growth?) Compare and contrast auxotrophy with prototrophy and relate growth actors into the discussion

Compare and contrast autotrophy with heterotrophy in relation to carbon sources used and what the overall processes provide nutritionally to the cells Compare and contrast complex media with defined (synthetic) media. Compare and contrast selective media with differential media Compare and contrast selective media with selective and differential media Compare and contrast isolation methods (not which are quantitative and which are qualitative) Goals ch 7 Analyze a given scenario and determine the cardinal groupings for: o Temperature o pH o osmotic pressure o oxygen requirements o pressure of the organism described discuss how each of the physical or chemical factors given affect the actual growth/survival of a bacterial cell and how it may compensate to survive: o temperature o pH o osmotic pressure o oxygen availability/absence o hydrostatic pressure o radiation explain how cells remove toxic oxygen species from their environments, what enzymes are involved and what (oxygen use) cardinal groups have which enzymes. What happens when some or all of these enzymes are lacking given cardinal group terms, draw a simple sketch fo where the microbes would best grow in a broth medium or vice versa explain what is happening at the cellular and population levels during o lag o exponential o stationary o death phases of the batch culture growth curve Given all but one of the following pieces of information be able to solve for the missing data o Generation time o Starting cell number o Ending cell number o Number of generations o Amount of time needed to reach a certain cell number Compare and contrast the three major theories that explain the decline phase ina batch culture growth cycle Compare and contrast the effect of these on bacterial cells and how they may over come these effects: o UV o Gamma o Ionizing radiation Compare and contrast the ways that microbial growth can be estimated, explaining the benefits and limitations associated with each method