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

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…

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

5.1

5) In an experiment to investigate the inhibition of the enzyme-glucosidase the following data for the rates of reaction with glucopyranoside for various substrate concentrations was obtained. By constructing a Leaver-Burk plot, determine the value of the Michaelis constant. [S]/ (10-6 mol dm-3) v/ (10-3 mol dm-3 s-1) 1.00 2.00 3.00 4.00 16.7 33.3 41.1 49.8

8

In humans, the biosynthesis of L-glutamine is catalyzed by the L-glutamine synthetase. The global reaction can be written as follows: ATP + glutamate + NH3 ADP + phosphate + glutamine The A,Gº' value for this reaction is -16.3 kJ.mol-1 (from left to right). 1- Explain the significance this information. 2- This reaction can be considered as the sum of two component reactions which are exergonic and endergonic, respectively, under standard conditions. Write these two component reactions and evaluate A,Gº of the endergonic reaction. Data: A,Gº of ATP hydrolysis = -30.4 kJ mol-¹