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Unformatted text preview: BioMI 2900 Study Questions #5 - Lectures 13 and 14 2 Oct 2009 Part I: BIOSYNTHESIS (ANABOLISM) 1--Define these terms: Calvin cycle, primary production, carbon fixation, RubisCO, carboxysome, secondary metabolite, central metabolite, transaminase, amino acid family, nitrate reductase, nitrogenase, nitrogen fixation 2-- Consider the bacterium, Thiobacillus ferroxidans. This Bacterium makes ATP via a respiratory an electron transport/PMF/ATPase system by oxidizing Fe2+ as an electron donor with oxygen (O2) as the terminal electron acceptor (see reduction potentials). It gets carbon strictly from CO2 fixation . NAD+/NADH E’o = -0.32V FAD/FADH E’o = -0.22V Fe3+/Fe2+ E’o = + 0.77V O2/H2O E’o = + 0.82V a) Which of the following terms would apply? autotroph/heterotroph, organotroph/phototroph/ lithotroph pyruvate b) You suspect that T. ferrooxidans fixes CO2 via the Calvin cycle. The presence of what two enzymes would indicate that this is true? c) T. ferrooxidans does not use organic carbon as an energy source; therefore, the TCA cycle is not used to generate reducing power (NADH/FADH) as is usual in aerobic respiration; yet you find it does have enzymes for the TCA cycle (at right). How can you explain the presence of these enzymes?
acetyl-CoA oxaloacetate ketoglutarate succinate d) Considering the negative reduction potentials of the NAD+/NADH and FAD/FADH couples against the positive reduction potential of the Fe3+/Fe2+ couple (see above), explain how T. ferrooxidans gets the reducing power it needs for biosynthesis? [Hint- Think about how the purple photosynthetic bacteria in question 2 generate reducing power] 3) Suppose you were a organotrophic bacterium, and you had NH4+, NO3-, organic N (RNH2) and N2 available as nitrogen sources. a) Describe what you would have to do metabolically to use each of these as a N source. b) Assuming you have the genes that code for the enzymes that are involved with the assimilation of each N source, which source would you prefer to use first? Which last? Why? 4) Review Microbial Growth--Sec. 6.1, 6.5and 6.6 in the textbook. Define lag phase, exponential phase and stationary phase for microbial cell growth curves. Would these curves look different if the culture was the yeast, Saccharomyces cerevisiae (a single-celled fungus that divides by a binary budding fission process) rather than Bacteria or Archaea? Why or Why not? 1 BioMI 2900 Study Questions #5 - Lectures 13 and 14 2 Oct 2009 5) Use the semi-logarithmic graph at the right to answer the questions below. a) Identify the phases of growth for each growth curve. b) Which experiment has the fastest growth rate? The highest cell yield? c) In one experiment, cells were taken from a complex yeastextract containing medium and were put into a tube of identical medium. For the other experiment, cells were taken from a complex yeast-extract containing medium and put into a defined glucose medium. Which is which? How can you tell? (HINT: look at the lag phase times) 6) You are working with a purple bacterium to investigate nitrogen utilization. You grow the cells in 3 tubes the following defined minimal medium with no other N source except: Acetate 0.2 g a) Tube 1: add N2; grow under oxic conditions K2HPO4 0.5g b) Tube 2: add N2; and grow under anoxic conditions MgSO4 0.2 g c) Tube 3: add NH4+ and grow under anoxic conditions CaSO4 0.1 g
CaCO3 Water 5.0 g I liter
A log of cells/ml You monitor growth over time, and get the graphs at the right. Unfortunately, your lab partner forgot to label which tube was which. Looking at the data, predict which graph (A, B or C) came from which tube above. Explain your reasoning. B C time (hrs) PART III: ENVIRONMENTAL FACTORS AFFECTING GROWTH 7) Refer to the growth vs. temperature curves (see BBOM 12e, Fig. 6.19) for psychrophiles, mesophiles, thermophiles, and hyperthermophiles. a) Based on the information shown, what do you know about lag and stationary phases in these organisms at various temperatures? b) List 2 adaptations of key macromolecules that allow thermophiles and hyperthermophiles to grow at high temperatures. 2 BioMI 2900 Study Questions #5 - Lectures 13 and 14 2 Oct 2009 c) List 2 adaptations of key macromolecules that allow psychrophiles to grow at low temperatures. d) What happens to the key macromolecules in the psychrophilic cells of Fig. 6.17 when the temperature is10° C? What happens to the key macromolecules in mesophilic cells at 10° C? e) What happens to the key macromolecules in mesophilic cells at 50° C? What happens to the key macromolecules in thermophilic cells at 50° C? 8. Answer Review Questions 10-13 in BBOM 12e Ch.6, p173. 9. Many anaerobic prokaryotes are killed by oxygen. These are called strict anaerobes. a) What makes O2 so toxic to strict anaerobes? How do aerobes overcome this? b) Why can't strict anaerobes just keep O2 out? (How does it get into the cell?) 10. For each blank below, use the term best describes each organism’s oxygen preference (see list of terms: BBOM 12e in Fig. 6.27). a) E. coli grows well on glucose, either by mixed acid fermentation in the absence of oxygen, or by respiration in the presence of oxygen. E. coli can be described as a(n) _________ b). To survive, Spirillum volutans must make its energy by the process of respiration, reducing O2 to H2O. But it fails to grow on any media at atmospheric concentrations of oxygen. S. volutans is a(n) _______________________ c) Desulfotomaculum and Clostridium are both related endospore-forming rods (Gram Positive lineage) that lack enzymes for the detoxification of oxygen radicals. Desulfotomaculum has an electron transport chain that donates electrons to SO42-, while Clostridium makes pyruvate, and then reduces it to form acids and/or alcohols. Desulfotomaculum and Clostridium are both _______________________ d) At the end of its electron transport chain, Pseudomonas denitrificans reduces O2 or—if there is no O2 present—NO3-. P. denitrificans is a(n) __________________ e) Lactic acid bacteria like Lactobacillus cannot make cytochromes . However, Lactobacillus does have enzymes to convert oxygen radicals to harmless end-products, therefore it is a(n) _________________________ 9. Refer to the example bacteria given in the previous question to answer the following questions. a) Which two of the organisms above make virtually all their ATP by substrate-level phosphorylation? b) Which 3 organisms absolutely require oxidative phosphorylation? c) Which is the only organism above that can survive on either oxidative- or substrate levelphosphorylation 3 ...
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