This invention relates, in part, to newly identified polynucleotides, polypeptides, variants and derivatives thereof; processes for making the polynucleotides and the polypeptides, and their variants and derivatives; and uses of the polynucleotides, polypeptides, variants and derivatives. The invention also relates to compositions of orthogonal aminoacyl-tRNA synthetases, and pairs of orthogonal aminoacyl-tRNA synthetases, and orthogonal tRNAs that incorporate fluorinated amino acids into proteins in response to selector codons. The present invention also includes translation biochemistry methods for site-specific incorporation of fluorinated amino acids, for example, 18F- or 19F-labelled amino acids, into proteins or peptides. Such amino acids may be used as an NMR probe for characterizing protein structure, dynamics, and reactivity or for radionuclide imaging (e.g., PET). Fluorinated amino acids may also be used to stabilize proteins or peptides.