EBIO 3400 1st EditionExam # 2 Study Guide Lectures: 10-18Lecture 10 Explain what a biofilm is, the importance, why microbes congregate there and where else biofilms reside in? * 145-150, 686-687- Biofilm: colonial microbes attached to the surface- Importance of growth in medicine and the environment- Microbes congregate in rich environments (shower curtain)- Also found in: catheters tubes, ventilators, on teeth (& many other parts of the body causing infections) How do cells in a biofilm talk to each other? And how do they sense their crowdedness?- Microbes express different genes when they are in biofilms- They sense their degree of crowdedness using quorum sensing What is quorum sensing? How does it work? * page 397-399 and 1037- Quorum Sensing is how microbes sense that they are crowded (or not). Very important to microbes that act in unison (e.g. pathogens, decomposers, predators etc.)- Use chemicals and turn on certain genes to do whatever they need to do together - How it works: Cells of a species make basal levels of low molecular weight compounds (e.g. homoserine lactones or HSLs) that diffuse out of the cell  The cell can sense these compounds (with surface receptors)  When con-specific cells are densely packed (e.g. in a biofilm) their receptors are full and they express genes that are advantageous for the group (e.g. pathogenicity genes, bioluminescence genes-con-specific: belong to same species - The one known case of Quorum sensing in Archaea involves a HSL (slide 4)What happens ecologically when microbes reach high population densities?- They are finally numerous enough to affect the world at a macro scale- * watch quorum sensing video What special genes are turned on via Quorum sensing? And what species are capable of this trait? What is the enzyme involved?- Bioluminescence - Many oceanic Vibrio (and Photobacterium) species are capable of bioluminescence live symbiotically with squid or fish- Enzyme luciferase (same as in fire flies)  the reaction involves shuttling electrons to O2without an e- transport chain - energy is released as light instead of heat or going to ATP productionExplain the one known case of quorum sensing in archaea?- Has been studied in the haloalkaliphile Natronococcus occultus- Quorum Sensing controls the synthesis of its extracellular protease - So that it doesn’t waste energy making this expensive, extracellular enzyme (protease) unless there is a big enough population to benefit, and the amino acids that are produced by the protease don’t diffuse away so easily - (Only make extracellular proteases when they are crowded- Releasing HSL)List some characteristics of Pseudomonas- Very metabolically diverse, but strictly respiratory (no fermentations), Gram- Gammaproteobacterium- Fast growing / opportunistic / not fastidious (demanding)- Plant and animal pathogens, P. syringae and P. aeruginosa, respectivelyLecture 11List P. aeruginosa features: - So metabolically versatile that it can grow in distilled water- Found in soil and on plants, including flower petals- Very common as an opportunistic pathogen and in nosocomial infections (infections acquired in the hospital) - Affects 2/3 of burn patients in hospitals and about 10% of patients with cystic fibrosis- Utilizes Quorum Sensing - only turns on virulence genes if it is in a biofilm. This allows it to avoid detection until its numbers are high enough to do real harmWhat does it mean when we say most microbes that use Quorum Sensing lead double lives?- Lone cells (planktonic) don’t need group genes turned on (Can also live planktonically but oncethey find another organism can turn on genes for biofilm or luminescence)- Cells in biofilm can cause macroscopic effects such as disease or light productionWhat are the two major energy processes?- Catabolic: Breakdown molecules into simpler ones release energy and heat (energy stored in ATP)- Catabolic reactions involve the oxidation and reduction of molecules - Anabolic: use (require) energy to build new molecules and store energy  simpler substances are combined to form more complex molecules- The energy of catabolic reactions is used to drive anabolic reactions - use metabolic intermediates and ATP to build new cells Main ways that microbes oxidize molecules for energy:1) Fermentation Pages 516-527- Redox reactions take place in the absence of terminal electron acceptors (no glucose or nitrate)- ATP is produced by substrate-level phosphorylation- Electrons need to be shuttled around between organic molecules 2) Respiration pages 546 – 563- Oxygen or another oxidant serves as the terminal electron acceptor- ATP is generated via oxidative or electron transport phosphorylation using a proton motive force - Oxygen plentiful so sucks up a ton of electrons a. Aerobic b. AnaerobicWhat are the main aerobic/anaerobic reactions presented in class?- All respiratory reactions (aerobic and anaerobic) could be summarized using the simple formula:AH2 + B -----> A + BH2- Electron donor + electron acceptor  oxidized donor + reduced acceptor - Aerobic resp.: Beggiatoa H2S + O2 -----> So + H2O (H2S e donor, water reduced)Chemoheterotrophs: CH2O + O2 -----> CO2 + H2O (Oxygen e acceptor)- Anaerobic resp: chemoheterotrophs: CH2O + NO3 -----> CO2 + N2OThe final e acceptor is something other than O2, its nitrate NO3What is the electron transport chain and what are the main points?- The flow of electrons works in pumping protons (H+) across the membrane- Electron acceptor more electronegative (more affinity for electrons) to pump protons across the membrane- More positive ions outside than inside- Know that movement of electrons down the chain leads to:1) Pumping of protons across the membrane This establishes the “Proton Motive Force”2) The reduction of oxygen at the end of the chain forming water molecules** Also know where the electrons came fromWhere is the ETC and ATP synthase in bacteria compared to eukaryotes?- In bacteria: the ETC and ATP synthase is in the plasma membrane- In eukaryotes: the ETC is in the inner membrane of the mitochondria Define chemical energy and free energy.- Chemical energy is the energy released from organic or inorganic compounds when they are oxidized - Some is host as heat but some energy of chemical reaction is free energy (G)- Free energy: the energy that is available to do work - Change in free energy: delta GWhat are exergonic and endergonic reactions?- The reaction