Nature uses 20 amino acids to make diverse proteins. However, since the diversity from 20 amino acid — Physical Chemistry — Kinetics Chemistry Question
Post–translational modification
Nature uses 20 amino acids to make diverse proteins. However, since the diversity from 20 amino acids sometimes is not enough, chemical modifications are carried out mostly at the side chains of amino acids to generate more diverse functional groups by many natural enzymes. Many types of these post–translational modifications are important in recognition of protein–protein, protein–DNA, protein–RNA molecules. These modifications are used as turn–on (off) switches, transferring messages, known as signal transduction in living cells. Recently, methylation was found to be as important as other known post–translational modifications, such as phosphorylation and glycosylation. Like other modifications, there is a reverse reaction, demethylation. The two processes work oppositely, turning signals on and off (off and on), like phosphorylation and glycosylation. However, processes of methylation and demethylation in nature are quite different. In other words, the mechanisms of the two facilitating enzymes are not the reverse of each other.
Considering the functional groups of side chains existing in 20 amino acids, what kind of functionality is suitable for generating more diversity owing to methylation and demethylation? Name two amino acids.
Model Answer
Lys (K) and Arg (R) provide plausible methylation sites at their side chains, because they can accept more than one methyl groups. Other amino acids side chains with oxygen nucleophile can hold only one methylation.
In methylation of an amino acid side chain, S–adenosylmethionine (SAM) is used as a cofactor. SAM is made from methionine and ATP. Deduce the structure of SAM.
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Model Answer
Triphosphate group is a good leaving group and sulfur is a good nucleophile. Sulfur of methionine undergoes SN2 type reaction with ATP with triphosphate as the leaving group to form SAM.
Propose a mechanism of amino acid methylation with SAM.
Model Answer
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Two steps make up the proposed mechanism for demethylation. The enzyme uses FAD as a cofactor for the first step. Propose plausible mechanisms for demethylation.
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Model Answer
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