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  • Q1: Explain the role of eicosanoids formed as a result of metabolism of n-3and n-6 fatty acids in human physiological processes. In your answer consider data from relevant observational (epidemiological) studies alongside explanation of mechanism of action of these eicosanoids.2.See Answer
  • Q2:Calculate the plasma osmolality and comment on its significance. See Answer
  • Q3:Explain the pathophysiology of the different types of Diabetes Mellitus. See Answer
  • Q4:Consider the enzyme-catalyzed reaction AB. You determine experimentally that the maximal initial velocity. Vmax for the amount of enzyme you have added is 50 mM of B appearing per minute. You also determine that the Michaelis constant, K. for this enzyme is 20 mM of A. What concentration of A will give an initial velocity of 25 mM of B appearing per minute?See Answer
  • Q5: Short Answer 1. A study on rat metabolism is being conducted. There are 3 different groups of rats involved. Group 1 Diet rich in fat but normal in carbohydrates and protein Group 2 Diet rich in protein but normal in carbohydrates and fat Group 3 Diet rich in carbohydrates and normal protein and fat a. The three groups are kept in identical environments with opportunities for physical activity. Write a hypothesis, predicting the expected energy levels for each group for the first 4 days of the experiment. Please explain your predictions. (A-4, 2-C) 3 Scanned with CamScanner b. You run the experiment for 20 days and then analyze the results. How do you expect the three groups to compare in terms of body size/mass and general health? (A-4, 2-C) de toutes 2. Track athletes often say that the 400m sprint is much more exhausting and harder on the legs than the 100m sprint. What type of respiration would a 400m sprinter rely mostly on as they reach the end of the race? Explain. (A-4, 2-C) 3. Several anti-nuclear war protesters claim that inhabitants of the earth did not perish from nuclear bombs or the radiation afterwards, that the people would slowly succumb to changes brought on during the "nuclear winter". During a "nuclear winter", a lot of dust would be drifting in the atmosphere causing the blockages of the sun's electromagnetic spectrum. Based on your knowledge of photosynthesis, what impact would this have on humans that are still alive and why? (A-4, 2-C) Scanned with CamScannerSee Answer
  • Q6:a) Briefly describe the overall tertiary structure of MHETase. (Approach this as in Problem 1.) How many and what kind of domains does the polypeptide have (e.g., what class)? Even if you think that there is a single domain, would there be a way to divide it into 2 sub-domains? Specify which parts of the polypeptide below to each domain or sub- domain (unless you think that there is only 1 domain and no sub-domains).See Answer
  • Q7:b) MHETase is believed to use a catalytic triad to hydrolyze the ester linkage in MHET, just like the catalytic triad in the serine proteases. Examine the structure of MHETase complexed with the analog and identify the 3 residues in the catalytic triad. For each one, find the most important distance between that residue and its partner in the mechanism and fill out the chart, identifying the 2 atoms used and the distance between them. Also identify the secondary structure in which it is found (e.g., a-helix, ß-strand, tight turn, or loop). Residue (name & #) Ser His Asp Identify the most relevant inter-atomic distance and identify the atom name (click on it in PyMOL) (e.g., "CB" or "C4" or "OG") Atom in Ser: Atom in substrate analog: Atom in His: Atom in Ser: Atom in Asp: Atom in His: distance between atoms (Å) 2° structural context/nWhat other residues in the enzyme are important for binding MHET? Identify at least 4 that seem to play an important role. Residue (chain, name & #) Atom of the residue and the substrate analog? distance Type(s) of interaction (e.g., H-bond, between charge-charge, coordination bond, van der Waals) atoms (Å) 2⁰ structural context Which, if any, of these residues might explain why MHET is a good substrate, but BHET is not? And how would it explain the substrate specificity?See Answer
  • Q8:c) The enzyme contains 5 disulfide bonds. Given that this is a secreted enzyme, is this expected or surprising? List the 5 disulfide bonds below (e.g., "Cys41 - Cys142") and circle the one that you would expect to be most important for enzyme activity.See Answer
  • Q9:d) Going back to the first question, briefly discuss the roles of the 2 (sub)domains in the mechanism of MHET hydrolysis. Broadly speaking, what role does each one play?See Answer
  • Q10:Assigned topic- Alcoholic Liver Disease Assigned Section- Treatments and Conclusion |See Answer
  • Q11:Consider the reaction mechanism shown below for this question: CH₂ CH₂ NH₂ CH₂ CH₂ Lyase O Ligase 6 Oxidoreductase Transferase O Hydrolase CH₂₂ CH₂ 0,PO 5 CH CH₂ What class of enzyme does this belong to? O Translocase CH₂ 20,P H₂C CH₂ CH₂ 2 CH₂ 20,PO CH₂ 20,PO Net₂See Answer
  • Q12:Bonus: Determine the primary sequence of the following peptide. (10 Pts) A. Trypsin treatment generated the following fragments: (LFVCYMGFR) (HDITNAATYR) (AEK) (CPS) (K) (QIVAAR) (LWVANK) B. Chymotrypsin treatment generated the following fragments: (AEKL) (F) (VCY) (MGF) (RHDITNAATY) (RL) (W) (VANKKQIVAARCPS) C. Thermolysin treatment generated the following fragments: (LF) (VCY) (MGFRHD) (ITNAATYR) (AEK) (LW) (VANKKQ) (1) (V) (AARCPS) Legend: Trypsin = Lys & Arginine (R.) Chymotrypsin = Tyr, Trp, Phe, Leu (R.) Thermolysin = Leu, Val, lle, Met (R₂)See Answer
  • Q13:1. Why does EDTA (structure shown below) quench DNA polymerization reactions at physiological pH? Show the mechanism involving the atoms in EDTA that may be responsible (3 points) میری HO HO OH OHSee Answer
  • Q14:2. A DNA polymerase is isolated and found to have an error rate of 1 in 106. (6 points, 3 each) A. Suppose that the error rate is determined solely by the relative stabilities of incorrect and correct base pairs. What would the difference in free energy between correct and incorrect nucleotides incorporated by the polymerase have to be in order to explain the error rate? B. Solution studies of isolated oligonucleotides indicate that the energetic difference is actually -1.2 kJ.mol-1. What is the equilibrium constant of correct-incorrect base pair discrimination based on these solution studies?See Answer
  • Q15:3. The direction of RNA synthesis was determined by growing bacteria for a short period of time with trinucleotides labeled with tritium (³H) on their bases. The structure of RNA looks like : 5' pppNpNpNpNp...N-OH 3' (N = nucleosides; p = phosphates). Cleavage of RNA by a base occurs after the 3' phosphate. (8 points, 2 each) A. What products are produced if RNA is digested with a base? B. The products obtained in Part A can be distinguished by thin layer chromatography. Which of the products would you expect to be differentially labeled if new nucleotides are added at the 5' end (i.e., synthesis is in the 3' to 5' direction)?/nC. Which products would be differentially labeled if RNA is synthesized from the 5' to 3' direction? D. When the experiment was done the tritium label was found in the spot containing N-OH? In which direction is RNA synthesized.See Answer
  • Q16:4. Reto is an aspiring medicinal chemist whose project involves screening a library of compounds to find molecules that bind with high affinity to the opioid receptor (a membrane protein). Based on our discussion of the thermodynamics of binding, answer the following questions (10 points) A. Reto titrated a candidate compound C (fluorescently tagged) against the purified receptor and obtained the isotherm below. Reto concluded that he found a high affinity specific binder. Is Reto's conclusion correct? Why or Why not? What is missing from the experiment? (2) 1/Fluorescence polarization 450 400 350 300 250 200 150 100 50 0 0 10 20 30 40 [Ligand] (n) 50 60 70/nB. After performing the required controls, Reto obtained the following binding isotherm (left) and the associated Scratchard plot (right). What is the value of K, for the interaction between C and the receptor? What is the total protein concentration used in this experiment? (2) Binding isotherm Scratchard plot 1/Fluorescence anisotropy 300 250 200 150 100 50 0 0 10 20 30 40 [Ligand] (nM) 50 60 [bound ligand]/[free ligand] 0.6 0.5 0.4 0.3 0.2 0.1 0 1 2 3 4 bound ligand [L]bound (nM) in 6/nC. Next, Reto performed the affinity measurements on mammalian cells that express the opioid receptor. He is surprised to find that the K, from these measurements is over 10-fold higher than what he measured with the purified protein. Can you speculate a possible reason that could explain this observation? D. Given the poor affinity of the compound C, Reto modified the library, rescreened and found a candidate molecule R that binds the opioid receptor with a K, of 2nM. A high throughput measurement of binding isotherms of R and other receptors revealed that R also binds to the glucagon receptor with a K₁ of 5 μM. Based on this data, what should be the concentration of R that Reto should recommend for further testing of the compound R in vivo (i.e. in a living human body)? (2)/nE. In an in vitro experiment with R and the opioid receptor, what is the fractional saturation of the receptor, when the concentration of R is 200 nM? (2)See Answer
  • Q17:5. p53 is activated under cellular stress, and turns on genes involved in stress response. In the absence of stress its levels are kept low by proteasomal degradation through interactions with MDM2 ubiquitin ligase that marks it for degradation. (17 pts) A. Identify at least three hydrogen bonding interactions that stabilize the p53-MDM2 complex? (3 pts)/nB. Use the secondary structure prediction web server Proteus (http://www.proteus2.ca/proteus2/) and underline the residues that will participate in helix formation (2 pts): SQETFSDLWKLLPEN SQETFSDLWKLLAEN C. Based on Borcherds et al, which residue in the peptide can be mutated to increase the helical structure of the peptide? Is this in line with the prediction from (2) above (2 pts)? D. How does the Kd between p53 and MDM2 change upon mutating Pro27 to Ala (3 pts)?/nE. What assay was used by Boercherd's et al to determine the effect of Pro27Ala mutation on DNA replication post DNA damage (3 pts)? F. What is the effect of Pro27Ala mutant on cell cycle progression post DNA damage? Based on this result what is the mechanism by which p53 regulates cell fate after DNA damage? (4 pts)See Answer
  • Q18:Q6. The World Health Organization (WHO) has conducted worldwide clinical trial for the usage of potential SARS-CoV-2 main protease inhibitors as COVID therapeutics. (14 pts) A. Briefly explain (in 1-2 sentences) why viral proteases are important in the replication cycles of viruses like HIV and SARS-CoV-2. (3 pts)/nB. IC50 values were measured for new compounds designed as inhibitors for SARS-CoV-2 main protease, as shown below: P3 P3 cythe highe 14b 11r P2 13b P1 H₂N Compound 11r 13b 14b IC50 (μM) 0.18 0.67 >50 Based on this data, what type(s) of modifications are NOT tolerated by the main protease at the "P3" functional group of the inhibitor? Provide a brief hypothesis for how the P3 site interacts with the protease. (5 pts) (from Zhang et al., Science 2020, 368, 409.)/nC. You synthesize an analog of one of the compounds from part B called 15L and discover that it binds SARS-CoV-2 main protease with a KD of 250 nM. What concentration of 15L would result in ~50% saturation of the main protease? Briefly explain your answer. (4 pts) D. What enzyme that violates the central dogma can be used in an assay to measure SARS-COV2 RNA levels? (2 pts)See Answer

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