MBIO310 Exam 2 Review topics Chapter 4 Identify the four main macronutrients (excluding oxygen and hydrogen) and rank their abundance in cells Carbon~50% dry cell weight Nitrogen~12% dry vell weight Phosphorus + Sulfur~4% dry cell weight What are micronutrients? Provide some examples trace metals or elements Co, Cu, Mn, Ni, Zn What are growth factors? Provide some examples Organic compounds vitamins/coenzymes what do they do???????????????????????? Define autotrophy Uses CO2 as carbon source Define heterotrophy Uses organic compounds as carbn source Define phototrophy Uses light as energy source Define chemotrophy Uses chemicals as energy source Define lithotrophy Uses inorganic chemicals Define organotrophy Uses organic chemicals Identify the two main mechanisms in which ATP is produced substrate-level phosphorylation oxidative phosphorylation Identify and describe the three main pathways or reactions that are important in the nitrogen cycle What two sulfur sources are commonly used by microorganisms? Sulfates sulfides Which form of phosphorus compound is needed by all microorganisms? Phosphate(+5) describe the main differences between facilitated diffusion and active transport facilitated diffusion-no energy REQUIRED active transport- REQUIRES energy what do aquaporin proteins do? What type of transport mechanism is it? Aquaporins transport water, speed up process of allowing water throw. Facilitated diffusion What does the protein GlpF do? What type of transport mechanism is it? Transports glycerol in E. Coli. Facilitated diffusion Describe the main differences between uniport, symport, and antiport active transport movement of one molecule(UNIPORT) movement of second molecule in same direction(SYMPORT) movement of second molecule in opposite direction(ANITPORT) What is coupled transport? Movement of one molecule aids in movement of 2 nd molecule in same(symport) or opposite(antiport) direction Describe ABC transporters (include composition, mechanism, and movement) largest family of transport systems found in all 3 domains of life 3 components: substrate-binding protein membrane spanning protein ATP-hydrolyzing protein solute binds to periplasmic binding protein, and then binds to membrane transporter. The ATPase activity on one end of component signals opening of other end and moves the solute into the cell Describe the importance of iron and identify mechanisms used by microorganisms to acquire iron cofactor for many enzymes. Involved in e- transfer soluble and insoluble forms. Hardly any free iron in env. Siderophores used by many microorganisms as iron binding proteins What is group translocation? How is it tied into glycolysis? Transported substrate is chemically altered during th e transport process phosphotransferase system complex group trans. First rxn of glycolysis, glu-6P broken down What is a pure culture and why are pure cultures important? Composed of a single, monoclonal population free of contaminants ensures the study of only one culture and allows less error in the study of morphology and physiology Describe the main differences between a defined and complex medium in terms of composition and relative growth rates defined: exact composition known, slower growth complex: exact composition not known , faster growth What is an enrichment medium? How would you use it? Can use either defined or complex medium microbes that use a specific compound are located and grow more numerous with that compound What is a selective medium? How would you use it? Contains compounds that inhibit the growth of some microbes, but not others What is a differential medium? How would you use it? Indicator or dye used to distinguish between microbes What is the purpose of the streak plate method and how does it accomplish this? To dilute cells and obtain pure cultures Describe the main differences between the spread plate and pour plate methods spread plate: on top of agar, diluted in agar, cannot enumerate pour plate: mixed with agar, diluted before poured, used for enumeration Be prepared to calculate dilutions Be prepared to calculate cells/mL or CFUs/mL (I will not provide the equation) lab manual! Compare and contrast viable, viable nonculturable, and nonviable viable: cells will grow viable non culturable: cells will not grow, may be dead or alive nonviable: cells will not grow What is a Petroff-Hausser slide used for? Counting cells Compare and contrast plate count methods and microscopic counting methods Petroff-Hausser counting chamber on microscope slide dead and alive cells look the same cell sorter differentiate by size use flourescence to differentiat dead/alive plate counting only counts live cells disadv: hard for cells that stick together. Not perfect. What is optical density? What is turbidity? What instrument is used to measure these? How does it work? Optical density: estimates cell number based upon the amount of light that passes through the culture tube measures light scattering caused by cells in solution spectrophotometer turbidity cloudiness of a substance due to amount of particles suspended in the solute. Define binary fission one parent cell splits to form two daughter cells exponential growth Define generation time the time between two cell divisions equals the doubling time for the whole population Define a generation parent-offspring relationship? Be prepared to calculate the generations, generation time, starting cell number, or ending cell number N=N ? x 2 ^n n=generations, N= end cell #, N?=starting cell number how to calculate generation TIME??????? Diagram a standard growth curve and label each phase of growth Lag phase Log phase Stationary Phase Death Describe what is going on in the cell during each phase of growth ?or- describe what is happening during each phase of growth Lag phase: bacteria are preparing cell machinery for gr owth Log phase: growth approximates an exponential curve(straight line on a log scale) Stationary phase: cells stop growing and shut down their growth machinery while turning on stress responses to help retain viability death: cells die with a ?half-life? similar to that of radioactive decay (n eg exponential curve) How is continuous culture different than batch culture? Batch grows in tubes, controlled continuous is open ended What specific piece of equipment is used for growing a continuous culture? chemostat Chapter 5 Identify the three main temperature classifications psychrophilic, mesophilic, thermophilic Graph their relative positions based on temperature What are heat shock proteins? What do they do? Proteins that are induced when proteins start to denature. Results in production of chaperone proteins that assist in folding and proteins that alter membrane composition What is a barophile? Adapted for growth at very high pressures(many are psychrophilic) What is a halophile? REQUIRE high salt concentration for growth Describe the change in intracellular pH when the extracellular pH changes internal pH maintained by sodium/proton pumps, diffusion of weak ac ids/bases, membrane alterations what does Helicobacter pylori do to survive the low pH of the stomach? Be specific secretes enzyme urease which breaks down urea into bicarbonate and ammonia. Creates a localized increase in pH which allows cells to survive the stomach acidity. what is the basic difference between respiration and fermentation? Respiration: uses oxygen, uses ETC and external e- acceptors fermentation: does not use oxygen, uses part of starting molecules as the e- acceptor Compare and contrast a strict aerobe, microaerophile, and facultative anaerobe strict aerobe: REQUIRES oxygen for growth microaerophile: REQUIRES oxygen, only grows at low O2 levels facultative anaerobe: can go with(respiration) oxygen or without(fermentation) oxygen. Compare and contrast a strict anaerobe, aerotolerant anaerobe strict anaerobe: ONLY grows in absence of oxygen aerotolerant anaerobe: grows in presence of oxygen but NOT REQUIRED. fermentation Diagram the growth patterns of each aerobe and anaerobe in a column What does the enzyme catalase do? Write out the reaction Catalase: H2O2+H2O2 ?? 2 H2O + O2 protects organisms that grow in the presence of oxygen What does the enzyme superoxide dismutase do? Write out the reaction superoxide dismutase: O2- + O2- +2H ? ?? H2O2 + O2 same as catalase Describe the differences between sterilization, disinfection, antisepsis, and sanitation sterilization:kills all living organisms, including endospres, prions, and viruses disinfection:kill or removes pathogens from inanimate objects antisepsis; kills or removes pathogens from living tissure surfaces sanitation: reduces microbial numbers to safe levels Describe the difference between bacteriostatic and bacteriocidal bacteriostatic: inhibits growth while compound is present but doesnt kill. Growth resumes when compound is removed bacteriocidal: kills microorganisms How do you tell is a compound is bacteriocidal or bacteriostatic? Bacteriocidal will not grow again if you stop the agent. Bacteriostatic will come back. What does the D value indicate? Decimal reduction time time needed to kill 90% of population or 1-log What does 90% killing refer to? 90% of bacteria being killed, or one-log What does a 1-log reduction refer to? 90% Be prepared to calculate starting cell number, ending cell number, number of log reductions, or time needed ???????????????????????? Compare moist heat and dry heat in terms of effectiveness moist heat is more effective than dry heat boiling water kills most vegetative cells Compare boiling, autoclaving, and pasteurization in terms of effectiveness; be specific in what types of microorganisms are targteded by each method Boiling: kills most vegetative cells Autoclaving: combines high temp and high pressure.kills all cells, including endospores Pasteurization: low heat to reduce microbial numbers. Used on foods Is high temperature bacteriostatic or bacteriocidal? Bacteriocidal Is low temperature bacteriostatic or bacteriocidal? Bacteriostatic What is filtration and when would it be used? Used for heat-sensitive solutions. Viruses and bacteriophage not usually filtered Describe the effect and effectiveness of UV light poor penetration power used for sterilizing surfaces causes thymine dimers to form in DNA Describe the effect and effectiveness of ionizing radiation gamma and x-rays good penetration power used to irradiate foods and other heat-sensitive items causes hydroxyl radical formation from water Identify the chemicals that cause protein damage phenol, alcohol, iodine, chlorine, heavy metals, detergents, aldehydes, ethylene oxide Identify the chemicals that cause nucleic acid damage aldehydes Identify the chemicals that cause membrane damage phenol, alcohol, detergents Compare phenol, chlorine, alcohol, and hydrogen peroxide in terms of effectiveness against types of microorganisms phenol bact, fungi, most viruses, NOT endospores chlorine bact.endospores,fungi,viruses alcohol bact., envelo ped viruses h.perox. Bact., fungi, viruses What does penicillin do? Weakens the cell wall of bacteria through incorporation into peptidoglycan peptide cross bridge What does streptomycin do? Inhibits bacterial protein synthesis What does rifampin do? Inhibits bacterial transcription Chapter 13 Define catabolic energy releasing Define anabolic energy requiring Define exergonic releases energy Define endergonic uses energy How do you determine if a reaction will be spontaneous? What does spontaneous refer to? Energy release by products is greater than reactants (products-reactants) it is nonspontaneous(free energy is positive) energy release by products is less than reactants (products-reactants) it is spontaneous (free energy is negative) What useful information does delta G provide concerning a chemical reaction? Energy released that is avail able to do useful work Is the delta G of a chemical reaction always the same? If not, what can you do to change it? No, it is based on the concentrations. Compare prosthetic groups and coenzymes prosthetic groups: metals, tightly and permanently bound. Coenzymes: organic compounds, loosely bound, promiscuous Define oxidation loss of electrons Define reduction gain of electrons Compare NAD+ and FAD both 2 e- carriers 1 nadh-2fadh differences in ATP produced fad-lower energy, less protons, less ATP, protein bound cofactor nad-soluble cofactor, not tightly bound by enzymes Compare fermentation and respiration in terms energy ga in fermentation: (alcohol) less ATP respiration: more ATP What reasons could account for cells not getting the maximum amount of ATP from a given starting substrate? Cells ineffiicient. Most of energy is lost as heat. Not all the glucose is going to make ATP. Biosynthetic precursors proton gradients get used by other things. Keeping self regular requires energy. Not necessarily ATP Write out the entire glycolytic reaction starting from glucose; include any cofactors, co-reactants and co-products for each step What are the overall products of glycolysis? 2 Pyruvate, 2 ATP, 2 NADH What are the overall products of the citric acid cycle? 2 GTP, 6 NADH, 2 QH2, 4CO2 How is the entner-doudoroff pathway different than the embden-meyerhof-parnas pathway? Entner-doudoroff produces less ATP, and consumes less ATP than EMP found in wider range of prokaryotes than EMP What is the importance of the pentose phosphate pathway? It makes the 4,6,7,3 Carbon sugar phosphates for biosynthetic purposes Identify the three main fermentation pathways mentioned in lecture along with the products of each for 1 glucose ho molactic: produces 2 lactate per 1 glucose heterolactic: produces 1 lactate, 1 CO2, I ethanol per 1 glucose alcohol: produces 2 CO2 and 2 ethanol per 1 glucose What is the glyoxylate bypass pathway? No ATP or FADH2 production, only one NADH instead of three Describe the chemiosmotic theory What are the three main steps in the chemiosmotic theory? Electron Trasport proton gradient formation ATP production Chapter 14 Identify the order in which the electron carriers are used in aerobic respiration NADH, FADH2, quinone pool, cytochromes How is a proton gradient established and how is it used? Having a higher concentrations of protons outside the inner membrane of the mitochondria than on the inside of the membrane. Drives flagellar motor rotation, drug efflux pumps, active transport, ion transport What two components comprise the proton motive force? Electric potential pH difference Which electron carriers are free? Which are protein-bound? Which are membrane embedded? Free: NAD+ protein-bound: FMN/FAD, Fe/S clusters, cytochromes membrane-embedded: quinones How many protons are pumped by the NADH dehydrogenase complex starting from 1 NADH? 4 How many protons are pumped by the quinone pool starting from 1 NADH? Include individual number and total number 2 from quinone, +6 from NADH dehydrogenase How many protons are pumped by the terminal oxidase starting from 1 NADH? Include individual number and total number 2 from terminal oxidase. +2 from quinone What is the range of total protons pumped per 1 NADH in E. coli and mitochondria? E.Coli: 2-8 mitochondria: 10-12 How many total protons are pumped across th e membrane for 1 FADH2? 6 Calculate the number of ATP generated by the ATP synthase through oxidative phosphorylation starting from 1 glucose on paper..number 7** NADH 10 8H+/NADH 1ATP/3H+ = 26.7 ATP FADH2 2 6H+/FADH2 1ATP/3H+ = 4 ATP oxidative =30ish ATP Calculate the number of total ATP generated through substrate-level phosphorylation and by oxidative phosphorylation starting from 1 glucose on page also...substrate-level---4ATP + last answer oxidative=30ish + 4ATP = 34ish ATP total Describe the composition of the F0F1 ATP synthase; include the location of each component F0: 12 subunits. Membrane spanning, proton channel F1: 6 subunits. Cytoplasmic side Describe the mechanism of ATP generation by the F0F1 ATP synthase F0: H+ go in a create rotation, as soon as one goes in, it is full and must rotate. F1: revolving door. ADP+Pi(substrates bind), ATP is produced, ATP is spit out. Continues rotation Besides ATP generation, what other cellular functions use the proton gradient? Flagella, moving stuff across membrane(active transport), maintain intercellular pH Rank the following electron acceptors in terms of energy gain: carbon dioxide, iron hydroxide, manganese oxide, nitrate, oxygen, sulfate oxygen(highest) nitrate iron manganese sulfate CO2(lowest) What are the steps in nitrate reduction? You may use compound names or chemical formulas nitrate ??nitrite??nitric oxide??nitrous oxide??nitrogen gas What name is given to nitrate reduction? denitrification What name is given to aerobic ammonia oxidation? Nitrogen oxidation How is anaerobic ammonia oxidation different than aerobic ammonia oxidation? What is the ultimate end product of sulfate reduction? Hydrogen sulfide What is the ultimate end product of hydrogen sulfide oxidation? Sulfuric acid What interesting reaction does Geobacter perform? Does not require a chemical equation clean up uranium contaminated sites? What interesting reaction does Ferroplasma perform? Does not require a chemical equation oxidizes both iron and sulfur What interesting reaction does Thiobacillus perform? Does not require a chemical equation helps mining of copper Define hydrogenotrophy use of hydrogen as an electron donor??? What are the three methanogenic reactions discussed in lecture? CO2 reductions CH3OH(methyl) acetate How is ATP produced during methanogenesis? From oxidative phosphorylation using proton gradient and sodium ion gradient What reactions are bacteriorhodopsin and proteorhodopsin involved in? Bacteriorhodopsin: light-driven proton pump in halophilic archaea proteorhodopsin: in proteobacteria, especially those on top of water. Reflects lights How are rhodopsin proteins different than chlorophyll? Rhodopsin: cofactor, excessive for extra energy chlorophyll:protein. Needed for energy by light different absorption Chapter 15 What role do glycolysis and the TCA cycle play in biosynthesis? TCA: 1 st step in oxidative phosphorylation What are the three main pathways for CO2 fixation? Calvin cycle reductive TCA Reductive acetyl-CoA How many ATP are required per 1 CO2 for each pathway? What is gluconeogenesis and why is it important? Glucose synthesis when glucose is not main energy and carbon source What two compounds are needed or used in fatty acid biosynthesis? Acetyl-CoA Acyl-ACP How many ATP are required to reduce N2 to NH3? 40 What is the Haber process? Industrial process N2+CH4 to produce NH3 What is the importance of ? -ketoglutarate, glutamate, and glutamine in nitrogen assimilation? How does transamination differ?
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