Name:______________________________________ Section :______ 7.014 Problem Set 5 Answers to this problem set are to be turned in at the box outside 68-120 by 11:45 am, Wednesday, April 6. Problem sets will not be accepted late. Solutions will be posted on the web. 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 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 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 NH3 Æ NO2- Æ Fe2+ Æ CH4 Æ2 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)? 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? 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?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? 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? In general, photosynthetic organisms, such as phytoplankton, grow faster under higher light intensity. However, as we just observed, one of these ecotypes has evolved to prefer a lower light intensity. e) Why has this ecotype evolved for optimal growth at low light intensity? Question 3 Walking down the infinite corridor one day, you and your friend are suddenly engulfed in a space-time distortion and transported to a barren world covered with fake-looking rocks and sparse vegetation, strikingly similar to a set from the original Star Trek. After an indeterminate period of blind panic, you and she realize you may be stuck there for a long time, and begin to assess the situation. You find that there are only three non-microbial organisms on the planet: raspberry bushes, ants, and anteaters. Having just finished 7.014, you both realize that your introduction into this ecosystem is bound to disrupt it and, to maximize your survival, you should be careful of what you eat. Your friend starts to study the situation, and she draws the following energy flow diagram to represent the ecosystem (next page): a) You look at your friend’s diagram i) What do the arrows B, F, and J represent? ii) Why do both plants and
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