I do not understand how to solve for part a of question 1, I

| October 22, 2018

1 of 6Biological Sciences 103Spring, 2015K. HiltHomework #3Know:a) the components and their functions in the electron transport chain of mitochondriab) how ATP synthase worksc) the components and their functions in photosynthesis; the concepts of the Calvin cycled) the reactions for biosynthesis of palmitic acidAssigned problems in Biochemical Calculations (Segel):Oxidation and reduction:read pages 172 174examples 3-12, 3-13, and 3-14 on pages 175 – 179View the following two animations:1) ATPase Scene 2 which shows ATP synthase as a molecular motor, synthesizing ATP.www.evolusie.co.za/anim_ATPase3_flv.htm2) Powering the Cell: Mitochondria at http://multimedia.mcb.harvard.edu/ which illustrates severalthings, including ATP synthase and translocation of ATP and ADP across the inner mitochondrialmembrane.Note: both animations will require either Apple Quicktime Player and/or Flash MacromediaPlugin. Both may be downloaded for free from the web.1.A student has 35 ml of a crude extract of pig heart. They want to determine how many total I.U.s ofmalate dehydrogenase they have in the extract. They take 0.1 ml of the extract and add it to 400 µl of 20 mMMOPS, pH 7.4 (dilution A). After mixing gently, they take 400 µl of dilution A and add it to 800 µl of 20 mMMOPS, pH 7.4 (dilution B). They then run the assay that is listed below:400 μl10 μl10 μl30 μl20 mM MOPS, pH 7.410 mM NADH (in H2O)25 mM oxaloacetate (in H2O)of dilution B of their MDH solution, in 20 mM MOPS, pH 7.4They mix everything gently together and then measure the ΔA340/Δ time. Their measured ΔA340/20 sec.was -0.065.a) How many total I.U.s of MDH were in the crude extract?b) Why did you mix gently?c) Which of the above enzyme assay components should be kept on ice? Why? Which componentsshould not be kept on ice? Why?2 of 6Read the following blog from Nova (http://www.pbs.org/wgbh/nova/blogs/physics/2014/03/quantum-life/)concerning excitons in photosynthesis.QUANTUM PHYSICSQuantum Biology: Better Living Through Quantum MechanicsBy Seth Lloyd on Mon, 10 Mar 2014A quantum computer is a serious piece of hardware. My colleagues and I build quantum computers fromsuperconducting systems, quantum dots, lasers operating on nonlinear crystals, and the like. Although the part of aquantum computer that actually performs the calculation is too small to be seen even under a microscope, theapparatus used to address and control the quantum computer typically takes up an entire laboratory full ofequipment. In order to keep their sensitive components shielded from the environment, many quantum computershave to operate at very low temperatures, sometimes a few thousandths of a degree above absolute zero.So in the spring of 2007 when the New York Times reported that green sulphur-breathing bacteria were performingquantum computations during photosynthesis, my colleagues and I laughed. We thought it was the most crackpotidea we had heard in a long time. Closer examination of the paper, published in Nature, however, showed thatsomething decidedly non-crackpot was going on.It’s not easy being quantum. Credit: wagaboodlemum/Flickr, under a Creative Commons license.3 of 6Photosynthesis converts light from the Sun into chemically useful energy inside cells. In photosynthesis, particles oflight called photons are absorbed by light-sensitive molecules called chromophores (light carriers in ancientGreek), which are arranged in a tightly bound structure called an antenna photocomplex. When a photon isabsorbed, a quantum particle of energy called an exciton is generated. (An exciton isnt a particle in the traditionalsense, but it acts enough like a particle that physicists find it useful to treat it as one. Such mathematical likenessesare called quasi-particles.) The exciton hops from chromophore to chromophore inside the photocomplex until itarrives at the reaction center, an agglomeration of molecules that take in the exciton and transform its energy into aform that the living system can put to use to perform cellular metabolism, grow, and reproduce. The great majorityof the energy used by living systems once came from photosynthesis: Every calorie that you consume came originallyfrom excitons that hopped through the antenna photocomplex of a photosynthetic organism.By zapping complexes of photosynthetic molecules with lasers, the authors of the paper were able to show that theexcitons use quantum mechanics to make their journey through the photocomplex more efficient. The experimentalevidence was strong and compelling. The authors also speculated that the excitons were performing a particularquantum computation algorithm called a quantum search, in which the wave-like nature of propagation allows theexcitons to zero in on their target. As it turns out, the excitons were performing a different kind of quantumalgorithm called a quantum walk, but the crackpot fact remained: Quantum computation was helping the bacteriamove energy from point A to point B.How could tiny bacteria be performing the kind of sophisticated quantum manipulations that it takes human beingsa room full of equipment to perform? Natural selection is a powerful force. Photosynthetic bacteria have beenaround for more than a billion years, and during that time, if a little quantum hanky panky allowed some bacteria toprocess energy and reproduce more efficiently than other bacteria, then quantum hanky panky stuck around for thenext generation. Nature is also the great nanotechnologist. Living systems operate on the basis of molecularmechanisms, where atoms and energy are channeled systematically through molecular complexes within the cell.The molecules in turn are assembled using the laws of quantum mechanicsquantum weirdness is always lurkingjust around the chemical corner. These quantum changes can either help or hinder energy transport. Naturalselection ensures that the role of quantum weirdness in cellular energy transport is a beneficial one.How can quantum weirdness assist in energy transport? The answer lies in a phenomenon called wave-particleduality. Wave-particle duality means that waveslight and soundare at bottom composed of particlesphotonsand phonons. Conversely, things that we think of as particles, such as electrons, atoms, or for that matter soccerballs, have waves associated with them.The quantum wave of a soccer ball is about the same size as the ball itself, and doesnt extend halfway down thesoccer field (although the ball can sometimes seem to be on Lionel Messis left and right foot at the same time). Butthe wave corresponding to a particle can be much larger than the particle itself. While a single exciton consists of anexcited electron within a chromophore, the wave corresponding to a propagating exciton can extend over manychromophores.4 of 6Does that make sense? Of course not! Quantum mechanics is fundamentally strange and counterintuitive: Quantumparticles dont behave like soccer balls.To see how the wavelike nature of excitons can assist in their propagation, first visualize a classical kind of excitondynamics. Imagine that each chromophore is a lilypad, and the exciton is a frog hopping randomly betweenneighboring lilypads. The frog starts at the edge of the circular lilypond. How long does it take to get to the pondscenter? Because the frog is hopping from lilypad to lilypad at random, it sometimes moves towards the center of thepond, but it is equally likely to move to the left or right, or even backward. The frog will land on a substantial fractionof all the lilypads in the pond on its way to the center. The number of hops the frog has to take to get to the center isproportional to the number of lilypads in the pond.Now consider a quantum frog. The frogs initial wave is circularly symmetric at the edge of the lilypond andpropagates inward, like a backward version of the wave created when you drop a stone in the center of a pond. Thetime it takes for the wave to travel from the shore to the center of the pond is proportional to the radius of thelilypond. But the radius of the lilypond goes as the square root of the number of lilypads in the pond, because thenumber of lilypads is proportional to the area of the pond, i.e., the radius squared. The wavelike nature ofpropagation in quantum mechanicsthe quantum hophas the potential to get the frog to the center of the pondmuch more quickly than the classical hop. So, for example, if the frog hops once a minute, and a classical frog takes100 minutes to get to the center, then the quantum frog takes only 10 minutes.In green sulphur-breathing bacteria, the antenna photocomplex through which the excitons propagate is like thelilypond for the quantum frog: The waves corresponding to the excitons are spread out over many chromophores,and wavelike propagation allows excitons to move more quickly from chromophore to chromophore than classicalhopping would allow.Together with Alan Aspuru-Guzik and Patrick Rebentrost at Harvard, my MIT colleague Masoud Mohseni and Iconstructed a general theory of how quantum walks in photosynthesis can use the wavelike nature of quantummechanics to attain maximum efficiency. It turns out that wavelike transport is not always the best strategy. Tounderstand why, suppose that the lilypond is full of rocks sticking up out of the water. As the wave moves throughthe pond, it scatters off the rocks. As a result, the wave never reaches the middle of the pond, which remains calmand protected. This is a phenomenon called destructive interference. Although the wave can propagate a shortdistance, eventually the random waves scattered off the rocks interfere with the overall waves propagation,effectively stopping it in its tracks. The quantum frog becomes completely stuck: A classical hopping strategy wouldhave been more efficient. In the antenna photocomplex, the rocks are microscopic irregularities and moleculardisorder that scatter the quantum wave as it tries to pass through.By constructing detailed quantum mechanical models, my collaborators and I were able to identify the optimalstrategy for the interplay between wavelike propagation and classical hopping in photosynthesis. Over shortdistances, the wavelike propagation is more effective than random hopping. The exciton travels like a wave right up5 of 6to the distance at which destructive interference causes it to get stuck. At this point, the fact that living systems arehot, wet environments comes into play: The environment effectively gives the exciton a whack that gets it unstuckand makes it perform a classical hop, which frees up the exciton to propagate again. (The technical term for thiswhack is decoherence.) Then the process repeats. The wave propagates until it gets stuck; the environment gives ita whack; the exciton hops. Eventually, the exciton reaches the reaction center in the minimum possible time.Expressed in terms of our quantum frog, the rule is simple: Wave until you get stuck, then hop.The birds, the bees, and the fruit fliesPhotosynthetic plants and bacteria are masters of the minutiae of quantum mechanics, manipulating quantumcoherence and decoherence to attain almost 100% energy transport efficiency. If quantum hanky panky is soeffective, are there other living beings that take advantage of quantum effects to live better and have more offspring?Only in the case of photosynthesis have scientists actually found the smoking gun (or maybe the smoking photon).However, there are several other organisms in which quantum mechanisms apparently play an important role.European robins are sensitive to the Earths magnetic field, which helps them during migration. Do they have a tinycompass in their heads, a piece of magnetite that swivels back and forth to point out magnetic north? Apparentlynot. Instead the evidence suggests another light-activated quantum mechanism. A photon excites an electron, whichswivels around in the Earths magnetic field; the rate at which the electron decays from its excited state depends onhow far it has swiveled. Since the robins need light to detect magnetic north, the next time you see a flock of themstumbling around at night, you know what is going on.I smell a quantumQuantum mechanics may also be involved in the sense of smell. Scientists have long believed that smell operates viaa lock and key mechanism, an idea Linus Pauling first proposed more than 50 years ago. The molecule to besniffedthe odorantlocks into a receptor in the olfactory apparatus that can only fit that particular key. Thereceptor then unlocks or changes its configuration, leading to a flow of ions sufficiently large to trigger a neuron tofire.The problem with this model is that olfactory receptors are not very specific: They can be unlocked by many differentkeys. This has led some researchers to propose that the receptors are sensitive not only to the shape of the odorantmolecule, but to its vibrational frequenciesthat is, its sound. The combination of shape and sound provides aunique signature for the molecule. For the vibrational theory of smell to hold, however, the underlying dynamics ofthe molecule in the receptor must be intrinsically quantum mechanical: The receptor must respond to individualphononsquasi-particles of soundgenerated by the molecule. Experiments show that fruit flies are indeedsensitive to vibrational frequencies of molecules, supporting the hypothesis of quantum smell. When trained tosense a molecule with a particular vibrational frequency they are attracted to it like flies tophonons.6 of 6Who is quantum?Where else might quantum mechanics play a role in life? Because light is made up of photons, interactions betweenliving systems and light represent a good place to look. Our eyes are capable of detecting single photons by a highlyquantum mechanical mechanism: A molecule in the retina absorbs a single photon, and uses its energy to release theflow of tens of thousands of ions, stimulating a neural response. Neural impulses in the brain are probably toocoarse and classical to support the wave-like quantum dynamics that hold sway in photosynthesis, but at the level ofindividual synapses, the neurotransmitter binding mechanism might well benefit from the same types of quantumdynamics that apparently enhance smell.As scientists delve deeper into the details of molecular dynamics in living systems, they are likely to see moreexamples of quantum mechanics at work. We dont yet know exactly what aspects of biology benefit from quantummechanics. But we do know one thing: The unquantized life is not worth living.Go DeeperEditors picks for further readingNature: Physics of life: The dawn of quantum biologyIn this Nature news feature, asks whether quantum biology should be treated as a new scientific discipline.World Science Festival: Quantum BiologyIn this 90-minute webcast, Seth Lloyd, Thorsten Ritz, and Paul Davies discuss the intersection of biology andquantum mechanics.Tell us what you think on Twitter, Facebook, or email.Seth LloydSeth Lloyd was the first person to develop a realizable model for quantum computation and is working with a varietyof groups to construct and operate quantum computers and quantum communication systems. Dr. Lloyd is theauthor of over a hundred and fifty scientific papers, and of "Programming the Universe" (Knopf, 2004). He iscurrently professor of quantum-mechanical engineering at MIT.

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