Much of what is known about SecM stalling comes from biochemicalexperiments, in which every amino acid in SecM's sequence has beenmutated and the resulting effects measured. These experiments revealedfew residues as critical, although one stands out in every species asinvariable: arginine 163 (R163, see Fig. 13 below). However, untilrecently, little was known about the precise mechanisms at work. Acryo-EM map of a SecM-stalled ribosome revealed a shifted linkage in thePTC between the P-site tRNA and the SecM peptide. Although the shift wasonly 0.2 nm, it was hypothesized to be sufficient to inhibit peptide-bondformation, preventing synthesis of the remainder of SecM.
Each codon is a step in the process.
In order for a cell to make proteins, only the relevant instructions for those proteins are accessed in the DNA nucleotide sequence.
A model of polypeptide synthesis - YouTube
Certain nascent peptide chains are able to regulate ribosome functionwhile they are still being synthesized, i.e., when they are still insidethe ribosomal exit tunnel. One of the classical examples is TnaC, aleader peptide of the tryptophanase operon in . At highconcentrations of tryptophan, TnaC stalls the ribosome, inhibitingtermination of its synthesis. Through an intricate gene regulatorymechanism, stalling ultimately leads to the expression of genesresponsible for degrading tryptophan.