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Chapter 5: Problem 15

Proteases such as trypsin and chymotrypsin cleave proteins at different sites, but both use the same reaction mechanism. Based on your knowledge of organic chemistry, suggest a "universal" protease reaction mechanism for hydrolysis of the peptide bond.

Short Answer

Expert verified
A universal protease reaction mechanism involves formation of an acyl-enzyme intermediate through a nucleophilic attack on the peptide bond, followed by hydrolysis of this intermediate, leading to release of the remaining part of the protein and regeneration of the enzyme.

Step by step solution

01

Understand the Protease Function

Proteases are enzymes that carry out the process of proteolysis, which involves the breakdown of proteins into smaller polypeptides or single amino acids. Proteases do this by hydrolyzing peptide bonds, which are the links between amino acids in a protein. This process is a hydrolysis reaction, meaning it involves the addition of a water molecule.
02

Identify the Common Mechanism

Both trypsin and chymotrypsin use a very similar mechanism for hydrolyzing peptide bonds despite having different specificity for the type of peptide bonds they hydrolyze. The first part of the mechanism involves the formation of an acyl-enzyme intermediate, a reaction in which the peptide bond is broken by the protease. This intermediate formation is then followed by deacylation, during which water is used to release the second product from the enzyme, restoring it to its original state.
03

Describe the Universal Mechanism

A 'universal' protease reaction mechanism, irrespective of whether it is trypsin or chymotrypsin performing the reaction, would thus generally consist of two key steps. First is the nucleophilic attack on the peptide bond leading to formation of an acyl-enzyme intermediate and release of one part of the original protein. Second is the hydrolysis of this intermediate to release the other part of the original protein and regenerate the enzyme. The protease creates a favorable environment for these reactions, and its catalytic triad is crucial for facilitating both the nucleophilic attack and the subsequent hydrolysis.

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Most popular questions from this chapter

Phosphoproteins are formed when a phosphate group is esterified to an - OH group of a Ser, Thr, or Tyr side chain. At typical cellular \(\mathrm{pH}\) values, this phosphate group bears two negative charges \(-\mathrm{OPO}_{3}^{2-} .\) Compare this side-chain modification to the 20 side chains of the common amino acids found in proteins and comment on the novel properties that it introduces into side-chain possibilities.

Amino acid analysis of a decapeptide revealed the presence of the following products: \(\begin{array}{lllll}\mathrm{NH}_{4}^{+} & \text {Asp } & \text { Glu } & \text { Tyr } & \text { Arg } \\ \text { Met } & \text { Pro } & \text { Lys } & \text { Ser } & \text { Phe }\end{array}\) The following facts were observed: a. Neither carboxypeptidase \(A\) or \(B\) treatment of the decapeptide had any effect. b. Trypsin treatment yielded two tetrapeptides and free Lys. c. Clostripain treatment yielded a tetrapeptide and a hexapeptide. d. Cyanogen bromide treatment yielded an octapeptide and a dipeptide of sequence NP (using the one-letter codes). e. Chymotrypsin treatment yielded two tripeptides and a tetrapeptide. The N-terminal chymotryptic peptide had a net charge of -1 at neutral \(\mathrm{pH}\) and a net charge of -3 at pH 12 f. One cycle of Edman degradation gave the PTH derivative What is the amino acid sequence of this decapeptide?

Amino acid analysis of an oligopeptide 7 residues long gave \(\begin{array}{lllll}\text { Asp } & \text { Leu } & \text { Lys } & \text { Met } & \text { Phe } & \text { Tyr }\end{array}\) The following facts were observed: a. Trypsin treatment had no apparent effect. b. The phenylthiohydantoin released by Edman degradation was c. Brief chymotrypsin treatment yielded several products, including a dipeptide and a tetrapeptide. The amino acid composition of the tetrapeptide was Leu, Lys, and Met. d. Cyanogen bromide treatment yielded a dipeptide, a tetrapeptide, and free Lys. What is the amino acid sequence of this heptapeptide?

The human insulin receptor substrate- 1 (IRS-1) is designated protein \(\mathrm{P} 35568\) in the protein knowledge base on the ExPASy Web site (http://us.expasy.org/). Go to the PeptideMass tool on this Web site and use it to see the results of trypsin digestion of IRS-1. How many amino acids does IRS-1 have? What is the average molecular mass of IRS-1? What is the amino acid sequence of the tryptic peptide of IRS-1 that has a mass of \(1741.9629 ?\)

A quantitative study of the interaction of a protein with its ligand yielded the following results: Ligand concentration \(1 \quad 2 \quad 3 \quad 4 \quad 5 \quad 6 \quad 9 \quad 12\) \((m M)\) \(\nu\) (moles of ligand \(\begin{array}{lllllll}0.28 & 0.45 & 0.56 & 0.60 & 0.71 & 0.75 & 0.79 & 0.83\end{array}\) bound per mole of protein Plot a graph of [L] versus \(\nu .\) Determine \(K_{\mathrm{D}},\) the dissociation constant for the interaction between the protein and its ligand, from the graph.
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