Final answer:
Proteins are typically modified post-translationally. Hydroxyproline is an example of such a modification, which occurs after the protein structure is formed. The near-universal genetic code reflects a common origin while also allowing the incorporation of unique amino acids like pyrrolysine and selenocysteine in some organisms.
Step-by-step explanation:
The modifications of uncommon proteins, aside from the special cases of pyrrolysine and selenocysteine, typically occur post-translationally, after the protein has been assembled from amino acids. One example of such a modification is the conversion of proline to hydroxyproline. These modifications can alter the protein's function, stability, or localization, and are essential for the activity of certain proteins. The amino acids such as sec and pyl, although not among the 20 standard amino acids, are referred as the natural amino acids due to their genetic encoding.
It is important to note that all living species use a nearly universal genetic code for protein synthesis, supporting the theory of a common origin. The ability to incorporate non-standard amino acids like pyrrolysine and selenocysteine, which are encoded in some genomes, demonstrates nature's complexity and adaptability. Editing by aminoacyl-tRNA synthetases (AARSs) prevents access of non-proteinogenic amino acids to the Genetic Code, making a clear distinction between proteinogenic and non-proteinogenic amino acids.