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ID: 806735 • Letter: T
Question
There are four blanks. I need help filling them in. The options to fill them are after the blanks.
Nucleophilic catalysis is important in the reaction mechanism that thrombin employs for the hydrolysis of proteins. In the first step of the catalytic mechanism, the_________ [Choose one]--> (hydrogen) (nitrogen) (oxygen) (sulfur) atom of a(n) _________Choose one option -->(Asp residue, Cys residue, His residue, Ser residue, Thr residue, water molecule) acts as a nucleophile to attack a peptide bond in the substrate. In a subsequent step of the mechanism, the_________[Choose one]--> (hydrogen) (nitrogen) (oxygen) (sulfur) atom of a(n) _________Choose one option -->(Asp residue, Cys residue, His residue, Ser residue, Thr residue, water molecule) acts as a nucleophile to cleave a bond, producing the final leaving group in the reaction.
Explanation / Answer
The polypeptide substrate binds to the surface of the serine protease enzyme such that the scissile bond is inserted into the active site of the enzyme, with the carbonyl carbon of this bond positioned near the nucleophilic serine. The serine -OH attacks the carbonyl carbon, and the nitrogen of the histidine accepts the hydrogen from the -OH of the [serine] and a pair of electrons from the double bond of the carbonyl oxygen moves to the oxygen. As a result, a tetrahedral intermediate is generated. The bond joining the nitrogen and the carbon in the peptide bond is now broken. The covalent electrons creating this bond move to attack the hydrogen of the histidine, breaking the connection. The electrons that previously moved from the carbonyl oxygen double bond move back from the negative oxygen to recreate the bond, generating an acyl-enzyme intermediate. Now, water comes in to the reaction. Water replaces the N-terminus of the cleaved peptide, and attacks the carbonyl carbon. Once again, the electrons from the double bond move to the oxygen making it negative, as the bond between the oxygen of the water and the carbon is formed. This is coordinated by the nitrogen of the histidine, which accepts a proton from the water. Overall, this generates another tetrahedral intermediate. In a final reaction, the bond formed in the first step between the serine and the carbonyl carbon moves to attack the hydrogen that the histidine just acquired. The now electron-deficient carbonyl carbon re-forms the double bond with the oxygen. As a result, the C-terminus of the peptide is now ejected.
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