Bioorganic Chemistry: A Chemical Approach to Enzyme Action by Hermann Dugas

By Hermann Dugas

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Extra info for Bioorganic Chemistry: A Chemical Approach to Enzyme Action (Springer Advanced Texts in Chemistry) by Hermann Dugas (1999-08-27)

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While some of the proteins of the ribosome presumably have a catalytic function, the rest as wel1 as the ribosomal RNA (rRNA) participate in specific conformational interactions that occur during protein synthesis. Protein synthesis is a dynamic process, but again this process occurs in an ordered fashion which the sequential coupling of amino acids demands. The site to which the fMet-tRNNMet binds on the ribosome is referred to as the peptidyi site. The stage is now set for the synthesis of the peptide linkage.

The 3'- or 2'-hydroxyl of the terminal adenylic acid of the tRNA molecule then attacks the anhydride intermediate to give an aminoacyl-tRNA molecule. R-CH / COOe "'NH 3 (j) + ATP + tRNA(3'-OH) amino acid -pp. • II Mg2+ aminoacyl-tRNA synthetase .. /OH tRNA ll-AMP R", H3 N/ o II CH -C-O-tRNA aminoacyl-tRNA The ester linkage between the hydroxyl of the tRNA is a high energy bond (due to the adjacent 2'-hydroxyl and cationic amino functions) so that the overall enzyme catalyzed reaction has a free energy change close to zero.

Malonic acid KdK2 = 700 diethyl malonic acid KdK2 = 120,000 It may be noticed that in the case of malonic acid, much of the space between the two carboxyl groups is occupied by water, but in the case of the diethyl malonic acid, this space is occupied by two alkyl groups. The two ethyl groups provide a medium of low dielectric constant, so that development of a full negative charge by the first carboxyl function is strongly felt by the second carboxyl. Subsequently, a strong electrostatic repulsion will be felt upon loss of the second proton, and hence the high ratio of the two dissociation constants.

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