We have modeled how the charged levels of different tRNAs, that carry the same amino acid (isoacceptors), respond when this amino acid becomes growth limiting. The charged levels will approach zero for some isoacceptors (e.g. ) and remain high for others (e.g. ), as determined by the concentrations of isoacceptors and how often their codons occur in protein synthesis. The theory accounts for which (synonymous) codons for the same amino acid that are used in ribosome mediated transcriptional attenuation, the choices of synonymous codons in trans-translating tmRNA and the over representation of rare codons in mRNAs for amino acid biosynthetic enzymes.