1. ARTIFICIAL AMINO ACIDS Louie iselin

2. amino acid n. An organic compound containing an amino group (NH 2 ), a carboxylic acid group (COOH), and any of various side groups, especially any of the 20 compounds that have the basic formula NH 2 CHRCOOH, and that link together by peptide bonds to form proteins or that function as chemical messengers and as intermediates in metabolism.

3. Amino Acids Central carbon Amino group Carboxylic acid group R (variable group) This is what can be changed to alter the structure and function of the amino acid. To create new amino acids new ‘R’ branches have to be developed

4. Current Capacity for amino acids

5. What are artificial amino acids? ◦ They are amino acids that are not naturally occurring ◦ They can be formed by using stop codons and assigning an amino acid or by using an entirely new code made up of 4 letters instead of 3 ◦ They can be used for various things, including marking proteins so that they can be easily studied

6. CAGE method for replacing stop codons

7. Using the amber stop codon… The amber suppressor is the tRNA most commonly used. It is the tRNA that binds to the amber stop codon and so is its anticodon. It usually carries tyrosine so a mutation library of aminoacylases can be built from tyrosine aminoayclase. The most efficient aminoacylase can then be paired with the tRNA and the AARS, which attaches the artificial amino acid onto the tRNA. Many different AARS and tRNA/ tRNA aminoacylase pairs can be created to form new UAAs.

8. Using the amber stop codon… This diagram shows the orthogonal nature of the AARS and the attachment of an artificial amino acid (x) to a stop codon tRNA.

9. Quadruplet codons ◦ Quadruplet codons offer the opportunity of another 200 amino acids serving various functions ◦ For the UAAs to be translated, orthogonal ribosomes are required that cannot translate endogenous mRNA ◦ These can only be incorporated into regular proteins posttranslationally because they require a separate ribosome

10. Orthogonal ribosomes ◦ Ribosomes are evolved through saturation mutagenesis ◦ Ribo-X was used as the starting point because it already decoded the amber stop codon ◦ Ribo-Q was found to be the most efficient

11. Functions of UAAs ◦ Metal chelating – They can be used to store or remove metals from the body ◦ Posttranslational modifications – Modifications can be made to proteins after translation by amino acid insertion ◦ Protein evolution – UAAs can cause proteins to become more efficient or give them new functions that make them outcompete natural equivalents ◦ Photo reactive probes – Protiens and pathways can be tracked and better understood through the use of UAAs that respond to light ◦ Fluorescent markers – Scientists can track proteins’ movement through markers