2. In order to understand the mechanism of cyclooxygenase, the two derivatives of arachidonic acid shown below (A and B) have been prepared. These derivatives are selectively deuterated (i.e. the H atoms at these doubly allylic positions have been replaced with deuterium atoms. This is a very common strategy to elucidate reaction mechanisms. Please predict where the deuterium atoms would end up in the product of the cyclization reaction catalyzed by the enzyme. Assume that the reaction is initiated by a tyrosyl radical by the enzyme, as usual. A OH O= B OH

5. Consider the decarboxylation of dimethyloxaloacetate 7 to 3-methyl-2-oxobutyrate 8 shown below H3CO cat. Cu²+ & CO2 CH3OH (aq) cat. Cu²+ no reaction CH3OH (aq) 9 a. Provide a mechanism to account for the fact that Cu2+ catalyzes this reaction. b. In one sentence explain why Cu2+ does not similarly catalyze the decarboxylation of 9.

22) answer the following question.. Refer to the kinetic scheme for competitive inhibition and the structures shown below to E+S ES E +P -co- CO- 1 2 EI Compound 1 was determined to act as a competitive inhibitor through standard inhibition studies. Structural studies did not show any resemblance to the transition state. Compound 2 was also determined to act as a competitive inhibitor. Structural studies showed that it does resemble the transition-state. The K, constant is used to assess relative affinity of inhibitors for enzymes. That is, each compound has its own K, value. We can interpret K, the same way we do with Ka values. True or False: K, > Kµ2. Briefly explain your answer.

1. Shown below is the intermediate in the aldolase mechanism, after dissociation of the first product (GA-3P). Draw resonance structure of this intermediate showing the carbanion species AND the arrow movement that associated with formation of this resonance structure. CH₂OPO²- H 1 Lys-N-C || -B-H :A- H-B Covalent enzyme- enamine intermediate

1) Sketch out the schematic diagram for the enzymatic mechanism of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) Please provide the structure of the functional groups of the substrate and enzyme involved in the reaction at each step (rest of the structure can be indicated as R) Indicate clearly the flow of the electrons at each step Indicate in short form the cofactor involved and the acid or basic groups of the enzyme involved

3. The succinate dehydrogenase reaction in the direction it proceeds within the CAC is shown below (left to right): FAD FADH, H-C-H H-C-H coo- succinate dehydrogenase Succinate Fumarate AG" - O kl/mol a) Calculate the standard reduction potential for the overall reaction above. b) Based on the reduction potential, calculate and compare your standard transformed free energy change to the textbook value (above), and venture to explain any discrepancies. c) Assuming the temperature of the cell is 37 °C, calculate the equilibrium ratio of oxidized to reduced cofactor when the ratio of oxidized product to reduced substrate is 1.2. .

1.The diagram below shows an outline of the aminotransferase mechanism that skips the specific steps that show how electrons flow when a Schiff base is formed or is hydrolyzed. Using the mechanistic details given below A. Draw the mechanism for Enzyme- PLP Schiff base formation using pyridoxal and the lysine amine group using arrow to indicate electron flow. B. Draw the mechanism for hydrolysis of the Schiff base to form the a-keto acid, which is the reverse of the first reaction. Stage 1 Lys residue 2-O,PO- Enz Amino acid Lys residue (CH2)4 (CH₂2)4 H R-C-COO R- NH₂ NH₂ R-C-COO *NH₂ H H- 2-0,PO- 2-0,PO- A. show how this forms Stage 1 Lys residue Enz (CH2)4 HO 2-O,PO Enzyme-PLP Schiff base OH Amino acid-PLP Schiff base (aldimine) LOH 2-0₂PO- OH 20,PO- a-Keto acid COO Ketimine a-Keto acid 2-0,PO- R-C- NH₂ B. show how the a-keto acid forms a-Keto acid H Enzyme-PLP Schiff base الرواية وطري Ketimine Pyridoxine (vitamin B6) Pyridoxal phosphate (PLP) Pyridoxamine phosphate Stage 2 Amino acid…

1. Calculate the pH of a 0.05 M solution of HCl. 2. Calculate the pH of a 0.1 M solution of NaOH. 3. Calculate the pH of an acetic acid solution in which [CH3COO - ] = 0.037 M and [CH3COOH] = 0.044 M. (pKa = 4.76) 4. You are conducting a biochemical experiment with an enzyme that has optimal activity at pH = 10.00. You decide to use carbonate (pKa1 = 6.38, pKa2 = 10.30) as the buffer to keep the pH stable throughout the enzymatic reaction. (Recall that the formula for carbonic acid is H2CO3.) You prepare a 0.5 M solution of carbonate buffer at pH = 10.00. Calculate the concentrations of the major carbonate species in your solution. 5. Calculate the pH of the buffer solution in which [H3PO4] = 0.038 M and [H2PO4 - ] = 0.046 M (pKa1 = 2.12, pKa2 = 7.21, pKa3 = 12.32). 6. Add 5.0 mL of 0.1 M NaOH to 80 mL of buffer from question 5 and calculate the pH.

the two derivatives of arachidonic acid shown below (A and B) have been prepared. These derivatives are selectively deuterated (i.e. the H atoms at these doubly allylic positions have been replaced with deuterium atoms. This is a very common strategy to elucidate reaction mechanisms. Please predict where the deuterium atoms would end up in the product of the cyclization reaction catalyzed by the enzyme. initiated by a tyrosyl radical by the enzyme Im stuck on it

2. ( Labeling molecules with isotopes has long been used to trace and characterize metabolic pathways. Upon oxidation in the mammalian liver of L- glutamate labeled as shown on the right, write the metabolic reactions that lead to the products as shown below using structure formulas. No need to include the enzymes. (a) succinate [ (1-14C)-succinate ] (b) (c) (d) citrulline [ 15NH2-CO-NH-(CH2)3-CH (NH3)-COO-] H COO- 15,1 + 14 [ H-NC-H urea [ 15NH₂-CO-15NH₂] aspartate [ (1-14C,2-15N)-L-aspartate and (4-¹4C,2-¹5N)-L- aspartate ] H CH₂ L CH₂ COO- (2-14C, 15N)-L-glutamate