For over a billion years, the central dogma of biology has been limited largely to 20 canonical amino acids, and their sequence within proteins defined by triplet nucleotide codons. Only recently have researchers developed the ability to rationally alter these two basic tenets of biology. The ability to rationally add new building blocks to the genetic code has enabled the site-specific incorporation of hundreds of noncanonical amino acids (ncAAs) with novel properties into proteins in living organisms. Recent technological advances have enabled high level mammalian expression of proteins containing ncAAs, the use of unique codons to direct ncAA incorporation, extension of this methodology to a range of eukaryotic organisms, and the ability to encode building blocks beyond α-amino acids. These ncAAs have been used to study and control proteins in their native cellular context and to engineer enzymes and biotherapeutics with improved or novel properties. Similarly, researchers have leveraged advances in DNA synthesis to recode entire genomes, enabling the generation of organisms with enhanced userdefined properties, such as highly efficient incorporation of ncAAs. The work described in this thesis details efforts to develop tools to genetically encode novel ncAAs, including backbone modified and redox active amino acids; applications of an expanded genetic code for enzyme engineering and human therapeutics; and initial progress towards recoding the yeast mitochondrial genome.