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Information and EntropySwinging in the Tree of LifeDating the Major Events of LifeSTUDY QUESTIONS 2/1/08Lecture 2: ThermodynamicsWrite the First Law of Thermodynamics in the form of an equation, and then describe it in words. Do the same for the Second Law of Thermodynamics.The first law states that energy cannot be created or destroyed, but only transferred or transformed. ∆H = H(products) – H(reactants)The second law says that entropy is always increasing in an isolated system.What are the consequences of the First Law for energy transformations in an organism?Need to transform available energy into useful forms at the right place and at the right time. When ∆H (enthalpy/energy in a system) is negative heat is given off and it’s exothermic, when it’s positive then it’s endothermic.What are the consequences of the Second Law for metabolic energy transformations in an organism?Explosions, entropy ∆S always increases in an isolated system, positive, disorder increasesDescribe the role of catalysts in biological reactions.Speed up reactions but doesn’t affect ∆GTake a look at the examples of chemical equations from lecture 2. How can you determine whether entropy is increasing or decreasing? How can you determine if enthalpy is increasing ordecreasing?Now put the two together: if entropy increases, does the Gibb’s free energy go up or down? What if enthalpy increases? What expectations do you have for entropy and enthalpy for a spontaneous reaction?Lecture 3: DiffusionWrite Fick’s First Law and describe its basic properties.How does the molecule weight of a molecule affect its rate of diffusion? What other factors affect a molecule’s ability to diffuse across a membrane?Does the rate of diffusion increase or decrease as the area of the membrane increases? Does the rate of diffusion increase or decrease as the thickness of the membrane increases?Relate lecture 2 to diffusion: how does diffusion change entropy? Enthalpy? Using the time-to-diffuse equation, calculate how long it takes for glucose (D = 7.0 x 10-6 cm2/sec) to diffuse the length of a peripheral neuron 0.5 m (= 50 cm) in length.If a cell needs a lot of gas, should it be large or small? Explain. How could an organism exploit diffusion to do biological work?BSCI 207: Sample exams questions from Bill from the Thermodynamics and Diffusion lectures.1. During the construction of the new Biosciences Research Building, a team of biologists from the College of Chemical and Life Sciences discovered a new species of bacterium thriving underground. The scientists cannot seem to find any organic molecules in the soil, so they are puzzled as to the energy source being utilized by this organism. 1. Suggest one possible inorganic molecule or type of inorganic molecule that could provide the energy source for these creatures:_______________________________________2. What is the important feature or characteristic of this molecule that allows it to serve as an energy source? _________________________________________#2. ****Questions a through i refer to this reaction:6CO2 + 6H2O  C6H12O6 +6 O2 a. CO2 is A. oxidized or E. reducedb. H is A. positive or E. negativec. S is A. increasing or E. decreasingd. S is A. positive or E. negativee. G is A. positive or E. negativef. ATP is A. required or E. generatedg. the reaction is A. catabolic or E. anabolich. the reaction is A. exergonic or E. endergonici. the reaction is A. exothermic or E. endothermic3. What may you surmise about the oil/water partition coefficient of solute molecule X if it enters cells by simple diffusion ?A. LargeB. SmallC. negativeD. larger than 1.0E. X does not have one4. Which of the following would increase the rate of simple diffusion of a solute into a cell:A. decreased surface areaB. increased oil/water partition coefficient C. adding OH groups to the solute moleculeD. decreased temperatureE. thicker membrane5. Which of the following molecules would NOT be a likely source of high energy electronsfor a unicellular organism living in the hydrothermal vents? Explain!A. H2SB. H2C. CO2D. NH3E. CH46. If solute Q has a D = 4.2 x 10-5 cm2/sec, how long will it take solute Q to diffuse 60 mm isan aqueous solution? (Tricky one here! Note the units of distance!)Information and Entropy1. Define stability, fidelity, entropy and redundancy in respect to information theory in cells.2. What is the difference between periodic and aperiodic information? Which contains more information in a message of the same size? Explain.3. What are the benefits and drawbacks for an organism to have inorganic crystals to store its’ genetic code? How is this different for an organism with nucleic acid crystals? (Keep in mind the context from number 1.)4. Why don’t organisms use silicon instead of carbon crystals?5. Why is it important for RNA to be autocatalytic? How does this relate to the RNA world?6. Describe and draw a phospholipid. Why is the structure of a phospholipid important for organisms? Where does one find phospholipids?7. Explain what is meant by “spontaneous biological order at the expense of universal disorder” in the context of phospholipids. Does this increase or decrease entropy? (Keep in mind what is the closed system.)Swinging in the Tree of Life1. Why is it important for DNA to not be completely stable? What would (or would not) happen if DNA did not change over time?2. What is natural selection? Why is it important for understanding phylogenies?3. Are all phylogenies accurate? Why or why not?4. Define primitive, convergent and derived similarity. Give an example of each.5. Define homologous and analogous structure. Give an example of each.6. How is time shown on a cladistic phylogenetic tree?7. What are the two types of homologous traits? Define them.8. What is a synapomorphy? Give an example.9. How can you tell which species are more closely-related to one another on a cladogram? Can you tell which species are older using a cladogram?10.What is another name for a monophyletic group?11.What is the difference between an outgroup criterion and an ontogenetic criterion? Why are they useful? Can they both be used in the same tree?Dating the Major Events of Life1. What is the difference between relative and absolute dating? Does a cladogram give relative or absolute times of speciation?2. What is catastrophism? How would it


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UMD BSCI 207 - Study Guide

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