So the researchers tested the ribosomes' ability to use their normal starting materials: actual amino acids attached to their correct RNA tag. Much to the researchers' surprise, the mutant ribosomes performed perfectly.

"The key difference between puromycin and the real amino acids used in this reaction is that puromycin lacks the RNA tag," says Green. "Researchers use puromycin all the time to study ribosome function, for many good reasons. But now we know ribosomes don't always treat this molecule as they would real amino acids."

As a result, she says, scientists should carefully evaluate whether the use of puromycin could have skewed interpretation of their experiments.

Amino acids' RNA tags, called transfer RNA or tRNA, help the ribosome identify the right amino acid to add to the protein, since it matches itself to the genetic instructions (messenger RNA) the ribosome is reading. But the tRNA also acts as a handle for the small amino acid: Specific parts of the tRNA are "held" by other evolutionarily unchanged nucleotides in the ribosome as the amino acid is added onto the protein. Green points out that these nucleotides quite likely position the amino acid properly to catalyze what is already a pretty easy reaction.

The scientists were funded by the National Institute of General Medical Sciences and the Howard Hughes Medical Institute. Authors on the paper are Biochemistry and Molecular Biology graduate student Youngman, Green, laboratory technician Julie Brunelle and undergraduate student Anna Kochaniak, all of Johns Hopkins.

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