Biologically uninformed science idiot: Self-defense (1)

Fig. 1. Coding events in the ribosomal cycle of protein biosynthesis. Proteins, which play an essential role in cellular metabolism, are composed of 20 (+2) natural amino acids. These are generally activated by 20 different aminoacyl-tRNA synthetases (aaRS) and loaded onto tRNA adaptors, which decode the genetic program using a triplet code and thus translating the genetic information into functional polymers that fold into 3D structures. Once the protein is folded, it should become functional to sustain cellular life. Upper part: A simplified scheme of the ribosomally mediated translation of genes into proteins. In the operational RNA code (Schimmel et al., 1993), the 3′-terminus of the acceptor part of the tRNA has to be aminoacylated appropriately. For each tRNA, the 3′-terminus codon composition and its 3D structure shape should be placed in a very specific way to enable the interaction between their acceptor tails and its cognate aaRS. In this process, tRNA is not just a ‘passive’ adaptor but it actively participates in binding to elongation factor (EF) Tu (charge code) and the accommodation step in the ribosomal elongation cycle (Dale and Uhlenbeck, 2005). The ‘anticodon’ or triplet code, which is based on codon-anticodon interactions, is degenerate, ‘wobbled’ and non-overlapping (Crick, 1968). The conformational specificity of the protein core is a stereochemical (or folding) code (Rose and Wolfenden, 1993) that enables proper folding into functionally active protein structures. Post-translational modifications (PTMs), occur on nearly all proteins also having their own “code” (Lothrop et al., 2013). Lower part right: General framework of identity elements in the context of the cloverleaf model of tRNA’s secondary structure with marked nucleotides that are present in nearly all tRNA species (Mukai et al., 2017). For example U33 is essential for translocation in ribosome while N73 is the so-call “discriminatory base” (Shi and Schimmel, 1991). Lower part left: a generalized translation scheme focusing on codon-anticodon interactions.

Simply put, the codon-anticodon interactions only occur in the context of natural selection for food energy-dependent biophysically constrained viral latency and the physiology of pheromone-controlled reproduction, which links RNA-mediated DNA repair to healthy longevity via control of the virus-driven degradation of messenger RNA, which links mutations to all pathology.