ABSTRACT
This chapter discusses the differing views of codon context and also discusses in support of the idea that interactions between adjacent transfer ribonucleic acid (tRNA) molecules at the aminoacyl- and peptidyl-sites of a translating ribosome affect translational step-times and are a major contributor to codon context bias. It presents and also discusses the evidence that codon pair utilization patterns are highly biased, biases in protein coding sequences, and that they differ between organisms. This observation fulfills a prediction of the notion that tRNA-tRNA interactions at adjacent codons influence translational step-times. The chapter suggests that translational step-times in Escherichia coli are related, perhaps in a predictable way, to the species-specific patterns of codon pair utilization and explains the possible functional and practical significance of these observations. The possibility that biases in codon usage can influence polypeptide elongation rates has been widely discussed and, although direct effects of codon choice on translation rates are difficult to demonstrate.
