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BL4010 PROBLEM SET 1 FALL 2006 1. Explain the distinguishing properties of water and their chemical basis. Water has a high dielectric constant, high specific heat, high surface tension, and is less dense in the frozen state than the liquid state. The high surface tension is a result of hydrogen bonding which is very strong in water (30% covalent). High dielectric constant is due to combination of ionization of the OH bond and phenomena of proton transfer. High specific heat is related to both these properties. The increased density of water on freezing is due to Hbonding but also to the bent configuration of the molecule enabling packing in a tetrahedral geometry. The hydrogen bonding network of this packed state and the partial covalency actually sparses the water molecules into a less compact form. 2. Explain the difference between equilibrium and steady state. At equilibrium (chemical), no net change in concentration of products and reactants occurs (closed system). At steady-state, a net change can occur but this happens at a constant rate (open system). 3. State the four laws of thermodynamics. Zeroth Law Two systems in thermal equilibrium with a third are in thermal equilibrium with each other. First Law Energy can neither be created nor destroyed. OR more accurately from its derivation in class: The quantity of energy supplied to any isolated system in the form of heat is equal to the work done by the system plus the change in internal energy of the system. (equivalency of heat and energy (enthalpy) plus an unknown). Second Law Spontaneous processes occur such that the overall disorder of the universe is increased. (entropy) Third Law By no finite series of processes is the absolute zero attainable. (When T=0 ΔG=ΔH). BL4010 PROBLEM SET 1 FALL 2006 4. A solution containing 10 mM lactic acid and 87 mM lactate has a pH = 4.80. What is the Ka? What is the pH if the concentration of lactate equal to that of lactic acid? HR →H+ + RpH = pKa + log([R-]/[HR]) 4.8 = pKa +log(0.087/0.010) pKa = 4.8 - log(.087/.01) = 4.8 - 0.94 = 3.86 Ka = 10-386 = 1.3 x 10-4 5. List the four main classes of biomolecules. Give one example molecule for each class and draw the chemical structure (pH=7). Proteins (amino acids) H3N+ CH3 O C H O ALANINE Carbohydrates (sugars) O HC HC OH HC OH HC OH CH2OH RIBOSE Nucleic acids O CH3 HN O O P O O O HO O N OH THYMIDINE MONOPHOSPHATE Lipids H3C NH2 OH OH SPHINGOSINE BL4010 PROBLEM SET 1 FALL 2006 6. Consider the ionization of lysine. Draw the structure at each ionization state. Using the following pKa values, draw the titration curve and calculate the pI. backbone amino pKa = 9.2 backbone carboxyl pKa = 2.3 side chain amino pKa = 10.5 NH3+ NH3+ NH3+ NH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 H3N+ pKa = 2.3 pKa = 9.2 pKa = 10.5 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 OH C H O CH2 O C H O CH2 O C H O H3N+ H2N H2N CH2 O C H O 10.5 pH 9.2 2.3 0 0.5 1 1.5 2 2.5 3 Equivalents OH- 7. Draw the structure of the tripeptide I-G-E (pH=10). Identify the peptide bonds. Label the alpha carbons, the N-terminus, and the C-terminus. CH3 H3C HC H2N CH2 CH2 H C H O N O O O CH2 H CH2 O N H N-terminus alpha carbons O C-terminus BL4010 PROBLEM SET 1 FALL 2006 8. What defines a state function? Give an example. A state function is independent of path. In other words, it is a property of the system that is inherent and does not depend on how the system arrived at that state. For example, the internal energy inherent in a molecule (i.e. sum potential energy of its bonds and collective electronic properties) is independent of how the molecule was formed. Other state functions include enthalpy and entropy. 9. Identify and describe the thermodynamic parameter(s) that determine(s) the spontaneity of any given process? Spontaneity is determined by the change in internal energy. If the energy of the products is less than that of the reactants (i.e. the reaction goes downhill) it is spontaneous. This is dependent on both the enthalpy (ΔH) and the entropy (ΔS) according to ΔG = ΔH - TΔS. 10. Describe the probable events involved in the evolution of living cells. Rise of organic molecules (primordial conditions - reducing atmosphere, extremes of temperature and pH in concentrated microenvironments). Coalescence of organics into larger molecules...eventually self-replicating molecules such as small RNA's. Rise of lipids and membranes...imperfect barriers at first...better barrier with crossover molecules later allowing separation of charge, control of concentration gradients and the rise of metabolism. A minimal self-replicating structure or set of structures would quickly proliferate. Inaccurate replication leads to radiation and evolution begins. OR...insert your favorite theory here. Additional problems from Voet & Voet: 3.3 In terms of thermodynamic concepts, why is it more difficult to park a car in a small space than it is to drive it out from such a space? Basically, this a simple matter of limited degrees of freedom. When the car is in the open it can go forward, backward, turn. When parking in a small space there is usually only one way in and maximal two configuration (nose in or nose out). Entropy is reduced which is a thermodynamic penalty. When driving out..there is usually one way out but many final configurations.