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Bioc 3321 Spring 2011 Xavier Prat-Resina Univ. Minnesota Rochester Bioc 3321 Study guide Module 6: Bioenergetics and channels 1. The hydrolysis of ATP has a standard Gibbs free energy of -30.5 kJ/mol ATP4- + H2O ADP3- + P- + H+ a. Explain if the Gibbs free energy will increase, decrease or remain the same if we increase the pH of the medium. b. Will the equilibrium constant be larger, smaller or the same at this larger pH? 2. The reaction of combustion a. Sort in decreasing order of Gibbs free energy i. CH3CH2COOH ii. CH3CH2CH3 iii. CH3CH2CH2OH iv. CH3CH2CHO b. Since a combustion reaction is a redox reaction. Do the same with redox potentials 3. The E′° values for the NAD+/NADH and pyruvate/lactate conjugate redox pairs are −0.32 V and −0.19 V, respectively. a. Which pair is likely to oxidize and which to reduce in standard conditions? Why? b. Suggest conditions of concentrations in which the reaction may be reversed 4. The plasma membrane Na+-glucose symporter of an epithelial cell uses the electrochemical gradient of sodium cations to create a gradient of glucose molecules. + [glucose]out + [glucose]in [Na ]out [Na ]in a. If [Na+]out > [Na+]in. This means that (circle one) i. [glucose]out > [glucose]in ii. [glucose]out < [glucose]in Bioc 3321 Spring 2011 Xavier Prat-Resina Univ. Minnesota Rochester b. If the sodium gradient is substituted by a calcium gradient Ca2+ of the same amount. Will the ratio of glucose glucose(one side) / glucose (other side): (circle one, ignore the cell potential) i. Increase by double ii. Increase by less than double iii. Increase by more than double iv. Why? Module 7: Catabolism of Carbohydrates 5. The third step of glycolysis is a retroaldol reaction in which aldolase catalyses the conversion of fructose 1,6-biphosphate into glyceraldehyde phosphate and dihydroxiacetone phosphate: 6. 7. 8. 9. Draw the structures of glyceraldehyde phosphate and dihydroxiacetone phosphate indicating how the numbers indicated in the fructose above. At the end of this test there is a scheme of the glycolysis pathway. Just by the molecules involved in the pathway: a. Which step of the glycolysis pathway will yield a molecule of reduced NADH? b. Why does the overall glycolysis pathway yields two and not one molecule of NADH? Breaking down glycogen yields glucose-6-phosphate without spending one molecule of ATP. How many molecules of ATP will yield each molecule of glucose coming from glycogen when its converted into pyruvate? In some bacteria glucose is transformed anaerobically into ethanol. If [114C]glucose (glucose labeled at C-1 with 14C) is used as a substrate, what is the location of 14C in the product ethanol? Explain. The transformation of fumarate into succinate has the following potential: Fumarate + 2H+ + 2e– → succinate E'° = +0.031 V Explain with this information, which one will appear first in the Citric Acid Cycle. Bioc 3321 Spring 2011 Xavier Prat-Resina Univ. Minnesota Rochester Module 8: Regulation of Metabolism 10. Phosphofructokinase is one of the enzyme in the glycolysis pathway subjected to more regulation. Concentrations of ATP and ADP can change the activity of the enzyme. a. From what you know about glycolysis. Will [ADP] will be an activator or an inhibitor of the enzyme. Why? b. The graph shown below shows the activity of the enzyme (velocity) as a function of [ATP]. The different lines show the activity of the enzyme at different concentrations of the activator F-2,6-P i. 1M F-2,6-P ii. 0.1 M F-2,6-P iii. No F-2,6-P Identify what concentration of F-2,6-P each curve represents. 11. The free energy for converting malate to oxaloacetate is highly endergonic (∆G’o = 30 kJ/mol). This reaction is the last step of the citric acid cycle and it is driven forward by maintaining low concentrations of oxaloacetate. a. Explain why a low concentration of oxaloacetate may drive forward this endergonic reaction. Bioc 3321 Spring 2011 Xavier Prat-Resina Univ. Minnesota Rochester b. What is the maximum concentration of oxaloacetate that allows the reaction to go forward. Assume [malate] = 1mM, pH=7, [NADH] = 1μM and [NAD+] = 1μM, and all are in steady state. Module 9: Catabolism of Lipids 12. What is the structure of the partially oxidized fatty acyl group that is formed when oleic acid, 18:1(Δ9), has undergone three cycles of β oxidation? 13. Below is list of events that occur during fatty acid oxidation. For each fatty acid drawn below, fill in the blank with the letter corresponding to any event required for 1 cycle of -oxidation of the acyl chain. (Note: -oxidation produces acetyl-CoA and/or propionyl-CoA.) The steps do NOT have to be given in the order they occur. A letter may be used in more than one blank. Some letters may not be used. Each blank will have more than one letter. If a step is used more than once per blank, put it down only once per blank. a. A dehydrogenase transfers a hydride ion to NAD+. b. A dehydrogenase transfers a proton to NAD+. c. A dehydrogenase transfers two hydrogens to FAD. d. A dehydrogenase transfers two protons to FAD. e. A reductase reduces the fatty acyl chain. f. Propionyl CoA is formed. g. ATP is hydrolyzed to AMP + PPi. h. NADH is oxidized. i. An isomerase converts a 3=4 double bond to a 2=3 double bond. j. NADPH is oxidized. Module 10: Catabolism of Amino Acids 14. Write the hydrolysis of a peptide bond by water indicating the motion of electrons and the overall balanced reaction. 15. Explain why the skeletal muscle converts the product of transamination glutamate into alanine and not into glutamine like the rest of the tissues? Bioc 3321 Spring 2011 Xavier Prat-Resina Univ. Minnesota Rochester Additional information Useful equations DG 0 = DH 0 -TDS 0 RT lnK nF RT o Ecell = Ecell lnQ nF 𝑝𝐻 = −log[𝐻3 𝑂+ ] o E cell = DG = DG 0 + RT lnQ 𝑝𝐻 = 𝑝𝐾𝑎 + 𝑙𝑜𝑔 [𝑏𝑎𝑠𝑒] [𝑎𝑐𝑖𝑑] Metabolic pathways Glycolysis: Bioc 3321 Spring 2011 Xavier Prat-Resina Univ. Minnesota Rochester Citric Acid cycle Acetyl-CoA + 3NAD+ + FAD + GDP + Pi + 2 H2O 2CO2 +3NADH + FADH2 + GTP + CoA + 3H+ Beta-oxidation of fatty acids: From C-16 to C-14 Palmitoyl-CoA + CoA + FAD + NAD+ + H2O → myristoyl-CoA + acetyl-CoA + FADH2 + NADH + H+ Bioc 3321 Spring 2011 Xavier Prat-Resina Univ. Minnesota Rochester Amino acid catabolism and urea cycle 2 NH3 + CO2 + 3 ATP + H2O → urea + 2 ADP + 4 Pi + AMP Bioc 3321 Spring 2011 Xavier Prat-Resina Univ. Minnesota Rochester