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The following diagram shows part of the degradation pathway of the amino acid, Lys. Answer the question associated with each letter in the diagram.   Is the substrate oxidized, reduced, or neither oxidized nor reduced?   What is the required cofactor for this reaction?   Is TPP required for this decarboxylation reaction?   Is Lys classified as a glucogenic or a ketogenic amino acid?

Upload your answers to these questions. a.) Outline the reactions required to release a molecule of stored glucose from liver glycogen into the bloodstream. You may use acceptable abbreviations for the names of compounds–structures are not necessary. Include enzyme names or general type of enzymatic reaction for each step. (3 pts.) b.) Again in the liver, outline the series of reactions required to store a molecule of glucose as glycogen. You may use acceptable abbreviations for the names of compounds-–structures are not necessary. Include enzyme names or general type of enzymatic reaction for each step.  (3 pts.) c.) Briefly explain what provides the free energy required for the reactions outlined in part b.  (2 pts.)

Electron Transport Chain and Oxidative Phosphorylation  Write out the missing compound, cofactor, name, element, or ion for each of the 24 points (numbered circles) on this diagram of the electron transport chain.    1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19.   20. 21. 22. 23. 24.

Upload your answers to these questions. a.) Draw out the synthesis of the ketone body, acetoacetate, which forms in the liver under fasting conditions. It is formed in three steps.  (4 pts.) b) For the the last step in the synthesis of acetoacetate, include the arrow pushing mechanism for the reaction and identify which reaction in glycolysis it is parallel to. (3 pts.) c.) Draw out the reactions that converts acetoacetate into the other two ketone bodies. Show the structures the three ketone bodies and label each with an acceptable name.  (2 pts.) d.) Ketone bodies are exported from the liver and utilized as an energy source by the extra-hepatic tissues. The brain, which normally utilizes glucose as its energy source, can, under fasting conditions, partially convert to using ketone bodies over the course of a few days. Show how a molecule of the ketone body, 

Identify the eight following cofactors and coenzymes and, from the metabolic reactions we have encountered, name a reaction that requires the cofactor. Name or acceptable abbreviation is ok. (1 pt. each)   Name:                                      Rection:   c.         Name:                                     Reaction: d. By NEUROtiker – Own work, Public Domain, https://commons.wikimedia.org/w/index.php?curid=1555660 Name:                                    Reaction:

Upload an image of your answer to this question. Both pyruvate decarboxylase (an enzyme associated with alcoholic fermentation) and one of the enzymes in the pyruvate dehydrogenase complex (E1) require thiamine pyrophosphate (TPP).  In fact, the substrate goes through common carbanion intermediate in both of these enzymatic reactions. a. Outline the mechanism for the formation of this common resonance stabilized carbanion intermediate starting with pyruvate and show how this carbanion intermediate is resonance stabilized.  For TPP, you only have to show the structural part that is involved in the reaction (the business end of the cofactor).  (3 pts.) b). Beginning with the common stabilized carbanion anion intermediate, show how acetaldehyde is formed as the product of pyruvate decarboxylase in alcoholic fermentation and how a covalent S-acetyl dihydrolipoyl (the 2-C piece attached to the lipoic acid) intermediate is formed in the pyruvate dehydrogenase complex.  For TPP and lipoic acid, you only have to show the ring structural part that is involved in the reaction (the business end of the cofactor).  (3 pts.)

Upload an image of your answer to these questions. Write out all of the reactions in which ATP participates either as a reactant or as a product in glycolysis. Include the structures of all the substrates and products, compound names, enzyme names, and include any necessary cofactors. (12 pts.) NOTE: Acceptable abbreviations for compound names and cofactors are ok, but you need to write out the names of the enzymes. 

This figure shows the fraction or percent of myoglobin or hemoglobin O2 binding sites occupied on the y-axis as a function of O2 partial pressure shot on the x-axis. The middle Hb blue curve is for normal Hb. The right-hand red Hb curve reflects the shift in the bonding affinity of Hb in response to a drop in pH, whereas the left-hand green Hb curve reflects the change in response to an increase in pH.     Diagram citation Wikimedia Commons (Public Domain)  Image Description  Graph depicting hemoglobin oxygen saturation percentage against oxygen partial pressure (mmHg). Three curves represent different pH levels: green for pH 7.8 (alkalosis hypocapnia), blue for pH 7.4 (normal), and red for pH 7.0 (acidosis hypercapnia). The y-axis ranges from 0 to 100%, indicating hemoglobin oxygen saturation, while the x-axis ranges from 0 to 120 mmHg, indicating oxygen partial pressure. The curves show the relationship between oxygen binding and blood pH. Which of these curves shows the greatest affinity for O2? (1 pt.) Which one of the two shifted Hb curves, right or left, would result in the release of the most O2 to the cells, if the lung pO2 decreases from 100 torr to 60 torr and the pO2 of the tissues remains the same at 27 torr? Briefly justify your answer. (2 pts.)

Upload an image of your answers to this question. Splenda is a sugar substitute that can be used in cooking, whereas Nutrasweet cannot (It is a dipeptide and is thermally unstable). Splenda is made from D-sucrose by substitution of some of the hydroxyl groups with chlorine atoms. Draw the structure of Splenda given the following information about the hydroxyl groups that have been replaced by chlorine atoms. The hydroxyl groups at carbons 1 and 6 of the sugar in the furanose form and the hydroxyl group at carbon 4 of the sugar in the pyranose form have been replaced by chlorine atoms. The sugar in the pyranose form has the same stereochemical configuration as galactose.   For your interest: A foreign post-doctoral student in Great Britain first prepared Splenda. He misunderstood the word “test” and thought the supervisor said “taste,” so he did (not good chemical practice).  It turned out that this chlorinated derivative of sucrose is 600 times sweeter than sucrose itself.

In the following procedure, the protein of interest, CA, is initially concentrated by precipitation from a 30% saturated ammonium sulfate solution. If you were interested in using ammonium sulfate precipitation to isolate a highly charged peptide, would you expect the peptide to precipitate from a low or high concentration ammonium sulfate in solution? Briefly justify your answer.   Procedure from the reference cited below: “Briefly, cells expressing the wild-type CA protein were lysed through a microfluidizer. Soluble CA protein in the clarified lysate was concentrated by precipitation from 30% saturated ammonium sulfate. CA protein was redissolved in 50 mM Tris (pH 8.0) and functionally purified by the addition of sodium chloride to a final concentration of 2.5 M. After two rounds of functional purification, the wild-type CA protein was resuspended in 50 mM sodium phosphate buffer (pH 7.5) and dialyzed against the same buffer. The dialyzed sample was further purified by a subtractive anion exchange chromatography step using a Q-HP HiTrap column (catalog no. 17-1154-01, GE Healthcare, Piscataway, NJ). Purification of 2Mut and 4Mut CA mutants followed the same protocol that was used for wild-type CA except that 200 mM β-mercaptoethanol was included in all buffers throughout the process. The functionally purified capsid mutant proteins were redissolved in 50 mM Tris (pH 7.5) and 40 mM β-mercaptoethanol prior to dialysis in the same buffer, and a subsequent purification with subtractive anion exchange chromatography was performed.” Tsiang, M., Niedziela-Majka, A., Hung, M., Jin, D., Hu, E., Yant, S., Samuel, D., Liu, X., & Sakowicz, R. (2012). A Trimer of Dimers Is the Basic Building Block for Human Immunodeficiency Virus-1 Capsid Assembly. Biochemistry, 51(22), 4416-4428.