7.014 Solution Set 5 Question 1 Organisms can use a variety of carbon and energy sources, depending on their availability in the environment. Oxidation and reduction reactions play critical roles in metabolism, and the relative favorability of these reactions often dictates the type of metabolism an organism will employ in a given situation. For example, organisms that conduct aerobic respiration (like humans) use organic carbon compounds (like glucose) as both their carbon source and their energy source. a) What compound is reduced by the transfer of electrons from glucose? What are the oxidized and reduced forms of this compound? Electrons in glucose are transferred to reduce NAD+ (oxidized) to NADH (reduced). Electrons are then passed down the electron transport chain, sequentially reducing proteins in the chain, in the process creating a proton gradient for ATP synthesis. b) What is the final electron acceptor for organisms performing aerobic respiration? Why do organisms need a final electron acceptor? The terminal electron acceptor for aerobes is oxygen. The electrons that are being passed down ETC have to go somewhere so the chain doesn’t get backed up, and that is why the final electron acceptor is needed. The reduction of oxygen is a very favorable reaction; in fact oxygen is the most favorable electron acceptor. Organisms conducting respiration in the absence of oxygen do so anaerobically, using other compounds as electron acceptors. c) Consider the following environments where different compounds are present. Circle the compound in each environment most likely to be used as an electron acceptor. Top portion of the table from the Redox handout has been reproduced on page 6 (last page) to help you decide. Environment 1 Environment 2 Environment 3 NO3- Fe3+ CH3OH NO2- NO2- NO3- O2 NO3- fumarate Just as electron acceptors are selected in evolution based on thermodynamic favorability, so are electron donors. Whereas respiration uses organic compounds as electron donors, and photosynthesis uses water as an electron donor (to replace the electron excited by light), many organisms use inorganic compounds as electron donors and sources of energy. d) For each electron donor below, give the compound it will be converted to upon oxidation. Circle the compound that will yield the most energy upon oxidation. H2S Æ S or SO42- NH3 Æ NH2OH or N2 or NO2- NO2- Æ NO3- Fe2+ Æ Fe3+ CH4 Æ CH3OH or CH2O or HCOO- or CO22 Question 1, continued e) Organisms using the above compounds as electron donors are employing what type of metabolism? Are these organisms most likely prokaryotes, archea, or eukaryotes (pick all that apply)? These organisms are employing chemosynthesis. These organisms are likely to be bacteria or archea. Question 2 Curious about the Sorcerer II expedition of Craig Venter, you take your own research vessel to the Sargasso Sea to study the phytoplankton community there. At a particular location in the open ocean, you measure several environmental parameters (nutrient and light levels) down the water column as well as the relative abundances of two ecotypes (i.e. strains), I and II, of Prochlorococcus, a unicellular cyanobacterium. Inexplicably, as you are returning to Woods Hole to analyze your data, your ship is raided by pirates, who steal your data on the abundance of the two ecotypes. Fortunately, the pirates did not take your data on nutrient and light levels. You remember that you have genome sequences for the two strains, providing you with information on which genes each ecotype has. Based on this genomic information (in the questions, below) and the depth profile data, answer the following questions. Figure: Depth profile for the region of the Sargasso Sea where you measured the abundance of two Prochlorococcus strains. solid black line: dissolved NH4+ and urea dashed black line: nitrate (NO3-) solid gray line: phosphate (PO43-) The genome of ecotype II appears to have nitrate reductase, allowing it to utilize nitrate as a nitrogen source. Ecotype I does not appear to have nitrate reductase. a) Based on this observation and the nitrogen data above, which ecotype should dominate which part of the water column (shallow/0-100 m or deep/100-200 m) and why? Nitrate is more concentrated in the deep waters. And since ecotype II has the nitrate reductase gene, it is likely that ecotype II dominates deep water, while ecotype I dominates shallow water. b) Name two important molecules in the cell that require nitrogen for biosynthesis. In which redox form does the cell require its nitrogen, oxidized or reduced? Proteins and DNA require nitrogen for biosynthesis. Both use nitrogen in its reduced form.3 Question 2, continued c) Without using the graph, would you expect one or both of these ecotypes to have genes for phosphate transport proteins in their genomes? If yes, which one(s) and why? Why don’t you need to use the graph? Both ecotypes would need phosphate transport genes because phosphorus is an essential nutrient and no living organism is capable of getting phosphorus from the air. We do not need to use the graph because the need for phosphorus is universal and does not depend on the particular organisms in the graph. Prochlorococcus possesses two types of chlorophyll, a and b. Chlorophyll a (Chl a) absorbs longer wavelengths (red) better than chlorophyll b (Chl b), whereas Chl b absorbs shorter wavelengths (blue) better than Chl a. Blue wavelengths penetrate deeper down the water column because they are scattered and absorbed less by water than red wavelengths. The operons for Chl a and Chl b biosynthesis are expressed at different levels in these two ecotypes, such that ecotype II has a higher Chl b/a ratio than ecotype I (ecotype I has a comparatively low Chl b/a ratio). d) Which ecotype would you expect to dominate shallow (0-100 m) water and which would you expect to dominate deep (100-200 m) water? Why? Ecotype I would dominate shallow water because it is better suited to exploit longer wavelength light, and that is the light that is available in the shallow but not deep water. Ecotype II would dominate deep water because it is better suited to exploit shorter wavelength light, and any deep water photosynthesizer would have to rely primarily on this type of light. This is because the longer wavelength light does not penetrate well that
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