BIO 326R 1st EditionExam #4 Study Guide Lectures: 23-30 Lecture 23 (October 30) Biofilms Contd and Symbiosis- Bateria attached to surfaceo Quorum sensing- Free swimming planktonic cells- Know mechanism of antimicrobial resistanceo Know Theories of mechanism of resistance- Preventing biofilmso Biggest places where this is a problem o Change the topography Shark skin topography is resistant to biofilm formation—trying to mimic this in new developments- Symbiosis—know definition-- Rhizobia and nitrogen fixationo Symbiosis (know definition)o Rhizobia and legumes--Need to interact with bacteria to grow because most soils are nitrogen poor- conversion is very energy consuming because of the stability of the triply bonded N2- Nodulation is common to rhizobial species- Rhizospheres—know definition and mechanismo 1st step movement of the bacteria toward the root Attracted by root exudateso 2nd step communication between bacterium and plant (plant always signals first) Know mechanism of communicationo 3rd step invasion and tumor formationLecture 24 (November 1st) EndosporesEndosporeso Gram +-- know typically genuses- Hard to kill- Process-- Germinate- Know Structure o Contain the DNA of the organism, Some cytoplasm but low water, Tough coating—know components- Resistance—know what structural components allow for resistanceMyxococcus- Eats other bacteria-- hunting bacteria (wolfpacks), Digests from the outside in- Can not lyse an endospore- Transfer membrane by sliding next to each othero Makes clones-- each has the same membrane- Fruiting bodies= spore producing organo Understand structure and function- Starvation triggers the aggregation of 100,000 cells which form from fruiting bodyLecture 25 (November 4) Siderophores, Heterocysts, and ArchaeaSiderophores- Secreted outside the cell- Bind Fe3+-- know why iron is needed - small molecules secreted by a bacteria that bind iron with a high affinityo receptors in the outer membrane that uptake iron for the siderophoreHeterocysts- cyanobacteria make heterocysts- main contributors to changing the Earth’s atmosphere to an oxidizing one through CO2 fixation and photosynthesis- endosymbiotic theory—know definition and relationship between cyanobacteria and chloroplasts- fix nitrogen—nitrogenase is an issue o doesn’t work in O2 conditions and the cell is photosynthetic (liberates oxygen), so they can not exist together differentiation of vegetative (normal) cells into heterocysts allows to fix nitrogen anaerobically while maintaining oxygenic photosynthesis heterocysts don’t do photosynthesis anymore—know how it is able to grow despite this heterocysts feed vegetative cells fixed nitrogen heterocysts are terminally differentiated—know what this means know why add three membranes to vegetative cellBiofilms- exopolymeric matrix—know possible componentso also includes DNA, mportant medical discovery—treatmenat of biofilms with DnaseArchaea Domain—Comparison- know how sizes, membrane/cell wall, lipids, RNAP, ribosome operon of bacteria, archaea, and eukarya differ/relate- No discovered pathogenic archaea- Many extremophilesLecture 26 (November 6) Methanogens and MotilityArchaea—Methanogens- Know history of discovery of methanogens- Know methanogenesis reactions- Use methane as a source of natural gaso But 20 times worse than CO2 as a greenhouse gas- Know where Methanogenesis reactions occur- Mostly mesophiles, some extremophiles- Interested in methanogenesis for renewable energyMotility- Know what Brownian Motion entails- Swimming motilityo Utilizes a flagellum—know componentso Counter clockwise movement--forward motion= runo Clockwise movement--no movement= tumbleo Understand biased random walk and motive for motility Biased random walk runs are longer towards the nutrient or end destination, and short when traveling in the opposite/wrong direction Tumbles increase with unfavorable stimulio Flagella turning—proton motive force or Na+ gradiento Speed—50-60 body lengths/secondo Shape-- Rods and spiral typically have motility Spirals spirochetes= flagella inside the cell body- Twitchingo Fimbriae= NOT used in motility, adheres to hosto Pilli= type IV used in motility and conjugation Know mechanism for movement Pilli grow from base of bacterium, new subunits (pillin proteins) added at base- Gliding- SwarmingLecture 27 (November 8) More Motility and Stress ResponseMotility- Swimming—flagella- Twitching—pili- Swarming—movement on a wet surface using flagellao Know mechanism- Gliding—myxococcuso No possible mechanisms- Bacteria net movement away from low nutrients (tumble) and toward high nutrients (long run)o Recognizes with memory Understand mechanism- Taxis (bacteria can have more than one)o Know various names for different types of movement towards different stimuli- flagella and pili motility; flagella, pili, fimbriaerecognize various taxis signalsStress- defined by a change- recognize stress adapt to stress by altering gene expression for survival during stresso specific or general- stress forms are context (bacterium) dependent- bacteria create their own stresso know examples of stress- response to stress and altering gene expressiono transcriptional regulatory proteinso sigma factors RpoS—stationary phase sigma factor- Tells RNAP where to go and is required for survival under stresses in E. coli- General response o Know mechanism of responseLecture 28 (November 11) Stress Response Contd and Antibiotic ResistanceStress Response- General stress response-- RpoS- Specific stress responseo Bacterial 2 component regulatory system Know mechanism for regulationo Steps to regulatory system Sensor kinase sense stress signal and phosphorylates itself at the histidineresidue Sensor kinase then phosphorylates the response regulator Response regulator is now activated and alters transcriptionAntimicrobials- Antibiotics, disinfectants- Bacteriostatic antibiotics—know definition, difference between this and antibiotic- Antibiotic traitso Minimal side effectso Low molecular weight Easily diffusible, solubleo Low toxicityo Stops growth or kills bacteriao Naturally occurring- Know basic historyo Freudenreich-- pyocyanase, sulfa drugs, Ancient Egyptians—put moldy bread on wounds, Flemming discovers penicillin Know how