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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.

This figure shows the results of a two-dimensional gel that was run to separate the proteins found in a snake toxin. Locate the prominent dark spot in the upper right-hand quadrant on the two-dimensional gel and answer these questions.  Name one thing that you can infer about the amino acid composition of this major spot from the isoelectric focusing direction of the gel?  What is one thing that you can infer from the PAGE direction of this gel about this protein? Image Source: Hatakeyama, D. M., de Morais-Zani, K., Serino-Silva, C., Grego, K. F., Sant’Anna, S. S., Fernandes, W., Aniz, P. A. E. A., Torquato, R. J. S., Tanaka, A. S., Sanz, L., Calvete, J. J., & Tanaka-Azevedo, A. M. (2018). Examination of biochemical and biological activities of Bothrops jararaca (Serpentes: Viperidae; Wied-Neuwied 1824) snake venom after up to 54 years of storage. Toxicon (141), 34–42. Image Description  A two-dimensional Electrophoresis (2-DE) gel showing the separation of proteins. The x-axis represents the pH range from 3 to 10, and the y-axis represents molecular weight from 15 kDa to 250 kDa. Multiple protein spots are visible, indicating their isoelectric points and molecular weights. The label A marks a significant area of interest on the gel. The gradient shading reflects the concentration of proteins, with darker spots representing higher protein abundance.

The Gly and Pro, as well as modified prolines that have a hydroxy group on the Pro ring or (Hyp), are the principal amino acids comprising collagen. Consider this excerpt from this article: Destabilization of osteogenesis imperfecta collagen-like model peptides correlates with the identity of the residue replacing glycineKonrad Beck, Virginia C. Chan, Nigel Shenoy, Alan Kirkpatrick, John A. M. Ramshaw, and Barbara BrodskyPNAS April 11, 2000 97 (8) 4273-4278; https://doi.org/10.1073/pnas.070050097 “Gly-Pro-Hyp is the most common, as well as the most stabilizing, triplet in collagen (5). The presence of Gly at every third residue is considered essential….” a. If there is a genetic mutation that interrupts this pattern of Gly at every third position, bones do not develop properly. They are characteristically brittle, resulting in a genetic disease known as osteogenesis imperfecta. Why are repeating Gly residues essential to the formation of a proper and strong collagen structure?  (1 pts.) b. Vitamin C is required for the biochemical reaction that puts the modifying OH group on a Pro in collagen. How does the presence of this group affect the relative overall strength of the collagen? (1 pts.)

The calcitonin gene can encode either the hormone calcitonin or a protein called calcitonin-gene-related peptide depending on which 3′ cleavage site is used. In the thyroid gland, cleavage and polyadenylation occur after the fourth exon leading to calcitonin production. However, in the brain, the exact same transcript is cleaved after the sixth exon yielding calcitonin-gene-related peptide. This is possible because of a process known as:

Scientists have developed novel techniques that allow them to visualize the process of DNA replication in vitro. What conclusions can you draw about the DNA replication process shown below?

In the procedure above, they mentioned that the purified protein was alkylated. Briefly explain why it might be desirable to treat the reduced protein with iodoacetic acid (ICH2CO2H) before it is subjected to further purification by HPLC.