6. Describe the active site of the enzyme, which is the place where the reaction occurs. In yourdescription, identify the interaction of ADP, nitrate, Mg2+, and substrate arginine with importantamino acids.The active site of the enzyme is composed of a very dense network of interactions. Theseinteractions are what hold the substrates in place. The concentration contains five arginines and

The active site is the region of an enzyme where substrate molecules bind and undergo a chemical…

Answered: 6. Describe the active site of 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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1. If a molecule is interating with its side chains of an enzymes active site but it is not the substrate of the enzyme what kind of enzyme regulation is this? 2. What is the change in thetype of bond between Ser 80 -> Arg. 3. Will this change cause the complex to be more or less stable. Explain
2. (Part A) Coenzyme-dependent enzymes can catalyze the general transformations shown below. What would be the best coenzymes to use for the two steps in the scheme, and why? R CO₂H A R SCOA B R R
о 6. What is the catalytic triad and what particular protein family would you find this? What is the general role of the catalytic triad? Predict what would happen if Asp were mutated to Gly. ructure formation of alpha heli
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)
4. The urea cycle was the first metabolic cycle to be discovered, predating the description of the citric acid cycle by 5 years. Hans Krebs along with Kurt Henseleit used their Warburg manometer (pictured) to monitor the use of carbon dioxide and ammonia in the synthesis of urea. In the presence of a slice of liver, urea could be produced, but the reaction require ornithine and citrulline. Since citrulline is not consumed during the course of the enzymatic cycle, but is rather regenerated, Krebs described 2N citrulline as a "catalyst" of the process. ОН ÑH2 (a) What do initiation of the urea cycle and initiation of gluconeogenesis have in common? What is the first committed step of the urea cycle, what reactants are used, what product is (b) produced, where does it take place, how is it allosterically regulated, and how is the allosteric regulator produced?
5. Shown below are the first steps in the mechanism of a cysteine protease, which catalyses amide bond hydrolysis in a similar manner as serine proteases. (a) Complete this mechanisms, and (b) sketch the approximate reaction coordinate diagram for this catalyzed reaction relative to the uncatalyzed proteolysis. HN N HN cysteine protease
2. “Most enzymes are gene-encoded proteins." Using this lens, explain: A) effects of increased temperature on the rate of enzymatic reactions, and B) effects of decreased temperature on enzymatic reactions, and C) importance of optimal pH and ionic strength on enzymatic reactions.
2. What is the chemical reaction that lactase catalyzes? Write it below in word form as well as in its chemical equation.
4. An enzyme-substrate complex has a Kd = 100 nM. A competitive inhibitor with which of the following Ki values will be most effective at inhibiting this enzyme? A) K₁ = 10 nM B) K₁ = 100 nM C) K₁ = 1000 nM D) None of the above - only the KM is important Briefly explain:
3. At what substrate concentration would an enzyme with a keat of 25.0 s¹ and a KM of 3.5 mM operate at 25% of its maximal rate? How many reactions would the enzyme catalyze in 45 seconds when it is fully saturated with substate, assuming the enzyme has one active site?
3. Enzyme specificity. To determine the specificity of substrate binding for a particular enzyme/protein, structurally related compounds may be used as potential substrates and Km values may be calculated. However, many compounds structurally related to the substrate may bind to the active site but cannot be converted to product. In these instances, the substrate analogs are used as potential competitive inhibitors of substrate binding. Low K, values indicate high affinity of the enzyme for the inhibitor, whereas high K,values indicate low binding affinity. Consider the enzyme xanthine oxidase, which catalyzes the formation of uric acid from the purine bases hypoxanthine or xanthine in humans. The Km for hypoxanthine is 15.0 μM and for xanthine it is 45.0 μM. A few compounds used as competitive inhibitors of the normal substrate hypoxanthine are listed in the table below with their K; values. Comparing the structures of hypoxanthine with the listed substrate analogs, what can you…
8.Choose the False statement about enzyme binding sites Binding at an allosteric site ca affect binding and catalysis at the Ortho steric site. In addition to ortho steric sites , some enzymes have other sites where catalysis can be conducted. They are called , allosteric sites, from “allo,” the other. In principle, allosteric ligands can have structures that do not resemble those of substrates. Ligand binding at an allosteric site can cause a conformational change of an enzyme. Enzyme can be inhibited by an allosteric ligand that does not complete with substrate.

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6. Describe the active site of the enzyme, which is the place where the reaction occurs. In your description, identify the interaction of ADP, nitrate, Mg2+, and substrate arginine with important amino acids.