Ribosomal Elongation Cycle

This chapter provides a brief review of the reactions of the elongation cycle, and discusses recent data that clarify and explain some points of the divergent aspects of the current models of the elongation cycle. It shows that the location and the features of the deacylated tRNA in either the P or E site are extremely sensitive to the buffer conditions applied. These data explain the discrepancies of the current models of the elongation cycle and the controversy about the features and importance of the E site. It shows that the striking differences can be traced back to differences in the buffer systems used by the two groups. It presents contact patterns of deacylated tRNA with the ribosomal subunits and the P/E hybrid site, and contact patterns of tRNAs in the ribosomal pre and post states. Escherichia coli cells grow happily in D2O instead of H2O, thus replacing all the protons with deuterons. The crystal structure of the ternary complex has demonstrated that EF-Tu is more than 50 A from the anticodon. The central enzymatic activity of the ribosome is the formation of the peptide bond that is formed at an active center on the large ribosomal subunit, the PTF center. Different affinity-labeling approaches were applied to identify components at or near the peptidyltransferase (PTF) center. As a topographical method, affinity labeling cannot directly identify the component actually involved in the enzymatic activity.