(a) Fill in the blank regarding the mechanism of chymotrypsin below.(1) Polypeptide substrate binds non covalently in the enzyme active site. The catalyticTriad includes a reactiveNucleophile that attacks the electrophilic amide Catom.(2) The resulting tetrahedral- Is stabilized by H-bonding interactions with thehole.(Note: this is the same word repeated)(3) Collapse of the tetrahedral intermediate and H * Transfer from-Lead to theCleavage of the C-N bond. The N-terminal peptide is bound through acyl linkage to serine.(4) AMolecule then binds to the active site and attacks the acyl ester car-bonyl.(5) The resulting tetrahedralTions with theSame word repeated).(6) The second peptide fragment is released, and the enzyme returns to its initial state.Intermediate is stabilized via enthalpic interac-hole. (Note: this is the same answer as (2), and is again the(b) Trypsin and chymotrypsin are two closely related proteases; however, trypsin cleaves afterpositively charged residues (i.e.ArgandLys) while chymotrypsin cleaves after aromaticresidues (i.e.Phe.TyrandTrp). Suggest how this specificity is achieved?

Serine proteases are protein cleaving enzymes that have Serine, Histidine and Aspartate (the…

Answered: (a) Fill in the blank regarding the…

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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You are studying the kinetics of a novel competitive inhibitor of ATP-citrate lyase that can be used to prevent obesity. What is likely true about this inhibitor? (A) This inhibitor lowers the Vmax of ATP-citrate lyase. (B) The inhibitor likely looks structurally similar to acetyl CoA. (C) The inhibitor binds to an allosteric region on ATP-citrate lyase and prevents catalysis. (D) You can distinguish between an uninhibited and inhibited enzyme by comparing the x-intercepts on a Lineweaver-Burk plot. (E) This inhibitor lowers the KM of ATP-citrate lyase. Related to this question, you should also be able to: • explain the function of ATP-citrate lyase and why inhibition would prevent obesity • interpret Michaelis-Menten & Lineweaver-Burk plots related to this question • explain the differences between a competitive and non-competitive inhibitor
How will a graph of reaction rate (V) vs. [substrate] for an allosteric enzyme differ from the hyperbolic plot characteristic of enzymes having Michaelis-Menten kinetics?
PLP is a cofactor for a number of enzymes involved in amino acid metabolism. Give an example of reaction in which PLP participates in cleavage of the a, b, and c bonds of an amino acid, as diagrammed in shown Fig.
(b) The values of kinetic parameters for a variety of synthetic ester and peptide substrates ofa- chymotrypsin are compared for the reaction scheme below where ES is the Michaelis complex, ES' E+S Substrate K₁ N-Ac-Trp–OC₂H5 N-Ac-Phe-OC2H5 N-Ac-Leu-OC2H5 N-Ac-Phe-CONH2 N-Ac-Tyr-p-nitro-anilide ES K₂ 3.5 13.0 3.2 1.7 K-₁ is the acylenzyme, P₁ is the first product to be released, P2 is the second product, k2 is the acylation rate constant, k3 is the deacylation rate constant, and kcat = k2 k3/( k2 + k³). In the table below, N- Ac = N-acetyl; -CONH₂ = carboxamide; -OC₂H5 = ethyl ester; p-nitroanilide = −NH-C6H4-NO2 simulating a peptide group. ES' K2 (S-¹) K3 (S-1) 0.84 2.2 0.19 P₁ K3 0.073 H → E+ P2 Kcat (S-1) 0.82 1.9 0.18 0.070 0.038 KM (MM) 0.08 1.3 4.2 24.0 0.35 1 Kcat/ KM (mM-¹ s¯¹) 10.3 1.5 0.04 0.003 0.11 The value of kcat for N-Ac-Phe-OC2H5 is two-fold greater than that for the L-tryptophanyl analog and more than 10-fold greater than the value of kcat for the ester substrate…
What is the catalytic triad on chymotrypsin? Detail its importance.
(b) Biotin is a coenzyme required for a key step in gluconeogenesis. (i) To which enzyme is biotin linked and what is the nature of the bond? (ii) What properties do the biotin and the linkage have that enable biotin to interact with two distinct active sites in this enzyme? (iii) What chemical steps take place at each of these active sites (no need to specify the complete reactions)?
This is a conjectural question: If the reactive part of coenzyme A is the thioester, why is the molecule socomplicated?
1. In a catabolic pathway, metabolite X gets converted into metabolite Y, metabolite X 0 J mol-¹ and AG' is <0 J mol-¹ for this reaction. a) At standard states, is this reaction favorable? b) Is the reaction favorable or unfavorable at cellular condition? c) Is this an endergonic or exergonic reaction in the cell? d) Would you describe this as a thermodynamically downhill or uphill reaction in the cell?
What if C-1 of the oxaloacetate were labeled instead, when would the label be released as CO2?
Drug D reversibly binds to enzyme E and inhibits its activity toward substrate S. D binds equally well whether or not S is bound. Sketch a graph of the expected 1/v vs. 1/[S] relationship for: A) The enzyme reacting with S in the absence of drug D, B) The enzyme reacting with S in the presence of a small amount of drug D, and C) The enzyme reacting with S in the presence of a large amount of drug D.
Which of the following statements is correct for the reaction catalyzed by chymotrypsin? ○ The substrate carbon atom bonded to Ser195 in the acyl enzyme intermediate has a tetrahedral geometry ○ The Ser195 hydroxyl oxygen atom is the catalytic nucleophile for the deacylation phase of the overall reaction mechanism ○ The oxyanion hole accelerates the reaction by tightly binding the substrate carbonyl oxygen at the peptide bond that is cleaved ○ Asp102 stabilizes the tautomeric state of the catalytic histidine ○ The first reaction product contains a proton derived from an active-site water molecule
We want to measure the activity of alanine aminotransferase (ALAT) present in a serum. The reaction catalyzed by the enzyme is: Reaction 1: I- *H₂N- glutamate H - C-COO CH₂ CH₂ COO 0.1 M phosphate buffer pH 7.4 : 550 μL 1.2 M alanine: 100 μL CH3 pyruvate CH3 C time (min) A340 CIO O COO The enzyme reaction is alized in the following conditions: In a 1 cm-cuvette are added: COO™ pyruvate lactate dehydrogenase* (LDH, 300 µμg.mL-¹): 50 μL 1.5 mM NADH : 200 μL 0.04 M a-ketoglutarate: 500 µL serum containing ALAT: 600 μµL ALAT NADH + H+ 0 0.915 a-cétoglutarate COO LDH * Lactate dehydrogenase (LDH) reduces pyruvate into lactate, with the concomitant oxydation of NADH. This allows to indirectly measure the amount of product formed. с=0 CH₂ 1 0.741 Reaction 2: NAD+ CH₂ COO™ H-C CH3 OH COO™ lactate alanine H + *H3N-C The reaction is performed at 25 °C and the absorbance at 340 nm is monitored every minute, for 5 min. The absorbance values are given in the table below: Data: ENADH at 340 nm =…

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