APh161: Physical Biology of the CellHomework 2Due Date: Tuesday, February 3, 2009“To do successful research, you don’t need to know everything. You justneed to know of one thing that isn’t known.” – A. L. SchawlowReading: Read chap. 14 of “Molecular Biology of the Cell” by Alberts etal. See the online version of the book posted on the website and read thesection on “Chloroplasts and Photosynthesis”. This will give you a bettersense of the energetics of the photosynthetic process and on the managementof charges (electron and proton transfer). Read chap. 6 of PBoC.1. Photosynthesis: Your Turn.(a) Write a two-paragraph description of the nature of photosynthesisthat would be appropriate for readers of “Scientific American”. Key pointsthat you should touch upon include: relevance of photosynthesis to life onEarth and the mechanisms of photosynthesis. Your essay should be readableby an interested high-school student.(b) Make a syllabus for 5 lectures on photosynthesis. Your syllabus shouldsay what topics you will cover. Make sure that this includes some statementof what estimates you would do, what experiments you would describe andwhat calculations you would do. Try to view this with a fresh perspectiveand don’t feel the need to do anything the same way that I did. This shouldbe one paragraph or less. You are making a syllabus with bullets.(c) Experiments and photosynthesis. Give a brief description (1-paragraphmaximum) of three experiments that have shed light on the nature of pho-tosynthesis. Make sure to say the concept of the experiment, how it wasimplemented and the nature of the resulting data.NOTE: this problem will be graded by Rob.12. Respiration and Photosynthesis: A Feeling for the MacroscopicNumbers.Most of this problem was motivated by the outstanding book Guessti-mation by Lawrence Weinstein and John Adam. I highly recommend thisbook to all of you and believe strongly that even if you think estimates ofthis kind are “trivial”, they are well worth your time. Some of the mostimportant and interesting episodes in the history of science having involvedestimates. Two of the most important are: i) when Newton estimated theacceleration of the moon as it “falls” around the Earth and compared it tothe acceleration at the Earth. He found that they differed by nearly a factorof 3600, corresponding to the 60-fold difference in distance from the centerof the Earth, suggesting the inverse square law, ii) Kelvin’s estimates of theage of the Earth and the lifetime of the sun. Both of Kelvin’s estimate wereinconsistent with geology and foreshadowed the discovery of radioactivity.In problems like this, I want to see clear statements of your assumptions,the key orders of magnitude that dictate your estimates and some sort ofsummarizing statement about what the estimates mean. Further, these esti-mates should involve very little looking stuff up online.(a) The Keeling curve shows two extremely interesting features of theoverall CO2budget of the Earth. First, it is most famous for illustrating theimpact of humanity on the atmospheric composition, revealed through thetrend of increasing CO2over time. However, the second interesting feature ofthe Keeling curve is the annual variation in CO2concentrations which reflectthe summer-winter cycle of the greener northern Hemisphere. Keeling’s sonRalph has now made it his mission to make careful measurements of the timeevolution of atmospheric oxygen.Several interesting links on this stuff are:http://www.scivee.tv/node/4611http://explorations.ucsd.edu/Features/Keeling Curve/and the Scripps feature posted with this homework.2Spend a little time thinking about atmospheric oxygen by making a simpleestimate of how long it would take for the breathing of humans to use up theatmospheric oxygen if photosynthetic organisms were not around to performcarbon fixation. There are a variety of different ways to approach this. First,in class I already worked out the number of molecules in the atmosphere (andits mass) so you could figure out how much O2there is that way. Alterna-tively, you could just try to figure out how long it would take for all humansto have breathed in the whole atmosphere and by thinking about what frac-tion of the O2is combusted. For the purposes of this estimate, just imaginethat with each breath you are burning glucose (you might want to write downthe relevant reaction). Figure out the mass per breath and use that to figureout the number of breaths in the atmosphere (given the atmospheric mass).Weinstein and Adam point out that we can use CPR and sustain someonein life, so we don’t exhaust all of the oxygen with each breath. Again, youshould not have to look up very much to solve this problem.(b) Make an estimate of the amount of CO2absorbed per year by thegrowth of a new forest on one km2of land. Hint: figure out the numberof trees in a 1 km2area and average over the time from when the trees aresaplings to fully grown to figure out how much carbon was used to make thetrees.Though it is not critical to the estimate, you might enjoy taking a look atthe Earth Observatory to get a sense of the leaf area index:http://earthobservatory.nasa.gov/Observatory/Datasets/lai.modis.html.A second way to do this problem that you should also try is to figure out thearea per tree. Now, imagine that the roughly 1000 W/m2of power resultingfrom incident sunlight is used to fix carbon (with some efficiency dependingboth upon what fraction of the day the sunlight is present and the actualefficiency of light absorption and energy usage - use the geometric mean ruleby trying to make an upper and lower bound on how efficient this can be).Then use the rule of thumb that ten photons are needed for each carbonfixed. NOTE: in the solutions, we will give you the best current estimates ofthis number resulting from measurements on tree plantations.3(c) There is much discussion about deforestation and its impact on theenvironment. Make an estimate of the total CO2released into the atmo-sphere as a result of burning of forests for as long as man has used fire. Workout this number in parts per million for atmospheric CO2and compare thisto the numbers you see in the Keeling curve. In addition, make a simpleestimate of the total energy released by such burning.3. Molecular Orbitals and the HOMO-LUMO Gap.In this problem, you will work out for yourselves many of the ideas dis-cussed in class using the case study of the H2molecule, but
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