**Educational Content: Mechanism of Peptide-Bond Cleavage by Metalloproteases**Protease enzymes are specialized in cleaving proteins by hydrolyzing peptide bonds. The initial strategy for each type of metalloprotease involves the generation of a nucleophile that targets and attacks the peptide bond specifically at the carbonyl group.**Understanding the Mechanism:****Diagram Explanation:**The diagram depicts a molecular structure involved in the cleavage of a peptide bond catalyzed by a metalloprotease. It features:- **R1 and R2:** Represent side chains attached to the peptide backbone.- **HN:** Indicates the amine group of the peptide bond.- **Zn²⁺ Ion:** Central metal ion crucial for the enzyme's catalytic activity, facilitating nucleophilic attack.- **Enz:** Represents the enzyme, shown interacting with hydrogen (H) atoms.- **Curved Arrows (Illustration Purpose):** Use these to show the movement of electrons during the reaction. These arrows depict the nucleophilic attack and bond breakage stages needed for the cleavage process.**Activity Instructions:**Students are prompted to draw curved arrows on the pre-drawn structures to illustrate the metalloprotease mechanism. Here's how to proceed:1. **Select the Draw Tool:** Use the drawing tool to visualize the electron movement.2. **Show Mechanism Steps:** Indicate the electron shifts from the nucleophile towards the peptide carbonyl group to initiate bond cleavage.3. **Resetting the Drawing:** If adjustments are needed, click 'More' followed by 'Reset Drawing' to clear and restart.This exercise is designed to deepen understanding of enzyme-catalyzed reactions at the molecular level, emphasizing the role of the zinc ion in lowering the energy barrier for the reaction.

Protein digestion and regulation are greatly aided by proteases, sometimes referred to as peptidases…

Answered: Protease enzymes cleave proteins by…

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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E Threonine 6. You have identified some intermediates in threonine synthesis: A, B, C, D and E. You grow a few of your mutants in the presence of these different intermediates to determine the order in which the gene products act. Below are your results. A (+) means growth and a (-) means no growth. Given these data, draw the best possible pathway for the synthesis of threonine. The diagram should use arrows to indicate one intermediate being changed to another intermediate. Indicate which gene produces the product responsible for the conversion by listing the mutant in that gene above the arrow. Mt1 Mt2 Mt4 Mt7
6
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. Phospholipases (PL) are enzymes that hydrolyzes PLA1 phospholipids into fatty acids and other lipophilic substances. Different class of phospholipase cleaves different bond in a phospholipid molecule. Shown on the right are the cleavage sites of four classes of PL: PLA1, PLA2, PLC, and PLD. R1 R2 -O-P-'·O-R3 (a) Write down the reaction of phosphatidylcholine (PC) cleaved by PLA2. Suppose the two acyl groups are R1 and R2 as shown in the figure. Make sure the chiral carbons in the reactions have the right stereochemistry (i.e., use wedge-dash notation), and the charges on the atoms reflect the molecule in neutral pH. PLA2 PLC PLD (b) Which PL is needed in order to release choline for salvage? (c) What is the structure and name of the remaining molecule after cleaving PC by the PL in (b) and releasing choline. No need to use wedge-dash notation. (d) The molecule in (c) can be used to synthesize triacylglycerol. Write down the reactions, including the enzymes and cofactors. Assume the…
4A. Write out the chemical equations (structures are not necessary) for the two steps in the reaction catalyzed by aminoacyl tRNA transferase. Include all products and reactants. Step 1: amino acid activation Step 2: aminoacyl transfer to the tRNA 4B. Write the chemical equation for the net reaction catalyzed by aminoacyl transferase. This can be determined by taking the sum of the two reactions above.
a. Suppose that you have the peptide Ala-Gly-Tyr-His-Leu and you treat it with FDNB and then 6M HCl. Draw the structures of all the products that you will have in solution (assume all reactions to go to completion).
Small molecules are used as inhibitors of protein action - as drugs. They most often do this by blocking the active site within the protein. Potential drugs can be screened computationally to determine if they are strongly bound to the protein. Figure 1 shows a possible conformation of a candidate drug molecule, 4-bromo-2- carboxymethylamide-pyrrole (abbreviation: BCMAP) at the active site of a protein (abbreviation: PR). Figure 2 shows the full protein structure whilst figure 3 shows a known inhibitor of the protein at the site, overlayed with another calculated conformer of BCMAP. (a) Explain what types of interactions, both intermolecular and intramolecular, that a molecular mechanics forcefield must be able to describe in order to be able to accurately determine the geometry of BCMAP in the protein. Identify which interactions will be the most important to describe accurately. Figure 1.4-bromo-2-carboxymethylamide-pyrrole (BCMAP) (C, N, O, and Br atoms in yellow, blue, red, and…
what does the Hexa protein domain depict? (in relation with tay sachs disease)
Macmillan Learning The graphs show a titration curve for the amino acid histidine. Label the fist curve with the major histidine species at each position. One histidine species will not be used. Label the second curve with the pKå values for the histidine functional groups and the isoelectric point (pI) of histidine. 14 12 10 pH 6 8 4 His²+ 2 His+ 0 0.0 0.5 1.0 Incorrect Answer His²- [His²+] = [His*] 1.5 [OH-] (equivalents) Hisº His [His]=[His] 2.0 2.5 3.0 Answer Bank [His+] = [His]
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