5. Shown below are the first steps in the mechanism of a cysteine protease, which catalyses amide bond hydrolysisin a similar manner as serine proteases. (a) Complete this mechanisms, and (b) sketch the approximate reactioncoordinate diagram for this catalyzed reaction relative to the uncatalyzed proteolysis.HNNHNcysteine protease

Cysteine proteases are known for their ability to cleave proteins in a highly specific manner and…

Answered: 5. Shown below are the first steps in…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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1. Hydrolysis of 1 M glucose 6-phosphate catalyzed by glucose 6-phosphatase is 99% complete at equilibrium (i.e., 1% of the substrate remains). Which of the following statements is most nearly correct? (R= 8.315 J/mol-K; T = 298 K) A AG" is-11 kl/mol. B) AG" is +5 kJ/mol. C) AG" is 0 kJ/mol. DAG" is +11 kJ/mol. E) AG" cannot be determined from the information given. Explain your choice in one line: -2.16x298 (2) - 11386.15 -> 11.4 КТ 5 The high state conculto alle My negative and st" positive (either for D) then onditions, one
3. Prostaglandins (5) are derived from the 20-carbon fatty acid arachidonic acid in a reaction catalyzed by the enzyme prostaglandin endoperoxide synthase. This enzyme, a cyclooxygenase, uses oxygen to convert arachidonic acid () to PGG2 (G2), the immediate precursor of many different prostaglandins. a) The kinetic data given below are for the reaction catalyzed by prostaglandin endoperoxide synthase. Focusing here on the first two columns, determine the Vmax and Km of the enzyme (note, ¤¯↑¤Ð 的单位) [Arachidonic Rate of formation acid] of PGG₂ (MM) (mm/min) 0.5 1.0 1.5 2.5 3.5 23.5 32.2 36.9 41.8 44.0 Rate of formation of PGG₂ with 10 mg/mL ibuprofen (mm/min) 16.67 25.25 30.49 37.04 38.91 b) Ibuprofen () is an inhibitor of prostaglandin endoperoxide synthase. By inhibiting the synthesis of prostaglandins, ibuprofen reduces inflammation and pain. You have learned the three mechanisms() for enzyme inhibition, what they are and how Vmax and Km changed? (you can illustrate as a table) c)…
3. (a) Wakil's pioneering studies on fatty acid synthesis included the crucial observation that bicarbonate is required for the synthesis of palmitoyl-CoA. He was surprised to find that very low levels of bicarbonate could sustain palmitate synthesis; that is, there was no correlation between the amount of bicarbonate required and the amount of palmitate produced. Later he also observed that 14C-labeled bicarbonate is not incorporated into palmitate. Explain these observation (b) The condensation reaction catalyzed by B-ketoacyl-ACP synthase generates a 4-carbon unit by combining a 2-carbon unit with a 3-carbon unit and loss of CO2. Write with structural formulas how this occurs. What is the thermodynamic advantage of this way of generating the 4-carbon unit over combining two 2-carbon units as occurs fatty acid oxidation or ketone body reactions" (c) Decide where labeled carbon atoms will be found in palmitate if (i) (3-1“C)malonyl-SCOA or (ii) (2- 14C)malonyl-SCOA are used.
6. Examine the plot of the enzyme-catalyzed reaction below: Wheat-germ acid phosphatase shows Michaelis-Menten kinetics when acting on para-nitrophenol phosphate 16 14 12 10 8 4 2 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 (S] / mM a) Is this reaction better characterized by Michaelis-Menten kinetics or simple mass action? b) What is the approximate value of Vmax? Km? c) Assuming that this plot was made at 100 nM enzyme, draw the curve, including axis labels, for 300 nM enzyme. d) Imagine that this enzyme is inhibited by a competitive inhibitor with Ki (for inhibitor) = Km (for substrate). Note that v = (kcat [E] tot [S]/Km) / (1 + [S]/Km + [I]/Ki). Draw the curve of reaction velocity (v) versus [S] for [I] = 1 mM. e) Now consider an experiment where you simultaneously introduce substrate and competitive inhibitor at equal concentrations. Make a plot of v versus concentration of [S] = [I], i.e. the X-axis should be the concentration of both I and S, which are equal. v/ uM min-
2. Regarding the glycolysis metabolic pathways covered in class: A. In the EMP metabolic pathway, what chemical is catabolized to form pyruvate? (1 step away) B. There are two products of step 4 in the EMP pathway. If they were not phosphorylated, how would you describe these as monosaccharides (for example, an aldohexose and a ketopentose)? C. In the TCA Cycle, what chemical is produced by catabolism of isocitrate? (1 step away) D. Describe the major differences between primary, secondary and partial oxidation metabolism in terms of cell growth rate, (ii) oxygen consumption rate, and (iii) products formed.
Draw two reaction coordinate diagrams (DG vs reaction coordinate) that compare the uncatalyzed process of lipid flipping (lipid out à lipid in ) from outer to inner leaflet to the flippase-catalyzed process.
3. (a) In Bakers yeast there are two variants of cytochrome c, a heme containing protein of 108 amino acid residues that catalyzes electron transfer reactions in mitochondria. The two forms of cyto- chrome c known as iso-1 and iso-2 cytochrome c differ in 17 of the 108 amino acids. The content of proton dissociable side chains for the two cytochromes c is given in the table below: Side chain pka iso-1 cytochrome c Ziso-1 iso-2 cytochrome c 12.5 3 4.0 4 8.0 4.0 6.0 10.0 9.0 7.0 4.0 Arginine Aspartate Cysteine Glutamate Histidine Lysine Tyrosine -NH3Ⓡ -COOH 1 4 4 16 5 1 1 What is the overall electrostatic charge on each cytochrome at pH 8? (b) To the right is a diagram of the chemical groups in carboxymethyl-cellulose and DEAE-cellulose that are used for ion exchange chromatography to purify proteins. At pH 8 which chromatographic resin has to be used to separate iso-1-cytochrome c from iso-2-cytochrome c from a lysate of yeast cells? If the proteins are separated by application of a…
7. An enzyme-catalyzed reaction proceeds by the mechanism below: E+S1ES --2E+P E+A 3 EA EA+S4→ EAS --5→ EA + P E+I6 → EI EAS +17→ EAIS -8 EIS + P A. B. C. E = enzyme, S = substrate, I = inhibitor, P = product and A = activator Rate constants (k's) for the forward reactions are: K1, K2, k3, K4, k5, k6, k7, and k8 Rate constants (k's) for the reverse reactions are: k-1, k-3, K.4, k.6, and k.7 Write the enzyme balance for this mechanism. How many total equations will result from applying the RAPID EQUILIBRIUM ASSUMPTION? Using any concentrations of species in the mechanism and any of the rate constants (k's), write ONE of the equations that would result from applying the QUASI STEADY STATE ASSUMPTION. (ONLY ONE EQUATION; ANY OF THEM ARE FINE)
Predict the effect of each of the following amino acid substitutions on the KM and kcat of the enzyme-catalyzed reactions
5. Suppose an enzyme needed a cysteine thiol (sulfhydryl) group for its catalytic activity, and catalysis required the Cys thiol to act as a nucleophile at the beginning of the catalytic cycle. That would mean the Cys residue had to be in its UNPROTONATED (conjugate base) form. If that particular Cys residue in that protein had a pKą of 7.5, what fraction (percent, or proportion) of the total enzyme molecules would have the Cys R group in its ACTIVE form at pH 7.0?
3. (а) 0.0050 M operate at one-quarter of its maximum rate? At what substrate concentration would an enzyme with a kcat of 30.0 s-1 and a Km of (b) trations [So]: ½ Km, 2 KM, and 10 KM. Determine the fraction of Vmax that would be obtained at the following substrate concen- (c) ( 1 (HIV-1) has been the object of innumerable studies to develop effective chemotherapeutic agents. It has been shown that p6* known as the late assembly protein is an inhibitor of HIV protease. An assay was developed using an artificial polypeptide substrate containing a p-nitrophenylalanine residue at the cleavage point that undergoes a small change in absorption at 295 nm upon bond hydrolysis that could be followed spectrophotometrically. The cleavage of the peptide bond is shown schematically on the right. Results of the assay are given in the table below. The protease of the human immunodeficiency virus- Lys NH2 Ala Nle Arg Ala Val-Nle-NH-CH- C-NH-Glu CH2 Lys NH2 Ala NO2 Nle H2OH NHIV-1 protease Ala Vo…
(a) What is the role of Glu 270 in catalysis? (b) What is the role of Arg 145 in catalysis?

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