Philip James Farabaugh
Professor · Tenured
Department of Biological Sciences
College of Natural and Mathematical Sciences
He/Him/His/Himself
About
I earned a B.A. in Biology (UC San Diego, 1972), a Ph.D. in Biochemistry (Harvard University, 1978) and trained as a postdoctoral fellow in Genetics (Cornell University, 1978-1981). I use molecular genetics, mainly, to study how cells (yeast, bacteria or mammalian cells) avoid mistakes in translating RNA into protein. In translating a gene into a protein three nucleotide words (“codons”) are interpreted into amino acids; since there are multiple frames in which genes can be read, errors can result from losing register with the gene (“frameshifting”). Other errors result from incorrectly decoding a codon (“misreading”). These errors can have dire effects on cellular health and, in humans, lead to neurodegeneration and cancer, among other outcomes.Research interests
Our laboratory has been concerned with odd events that occur during protein synthesis. We originally discovered programmed +1 translational frameshifting in the Ty family of retrotransposons about 30 years ago and spent many years thoroughly exploring its mechanism. At the end of that work, we discovered we had been studying how the Ty elements manipulated the translation system to drastically increase the frequency of translational errors by forcing decoding by an "incorrect" tRNA—one that makes fewer than three base pairs with the mRNA. We became intrigued with the associated issue of "misreading", where incorrect tRNAs are occasionally accepted into the ribosome resulting in an incorrect protein being produced. Our work has identified a general mechanism responsible for these errors in which non-Watson/Crick base pairs mimic the structure of the standard A•U and G•C pairs, forcing errors that cause specific misreading errors at high frequency. We continue to explore the mechanism(s) underlying these errors and the ways the cell ensures that their frequency doesn't get out of hand.Teaching interests
As a molecular geneticist, I have taught a range of courses from the introductory level (BIOL 100 Concepts of Biology, BIOL 302 Molecular and General Genetics), advanced (BIOL 414/614 Eukaryotic Molecular Genetics, BIOL 426/626 Approaches to Molecular Biology) and graduate seminars (BIOL 770 - Graduate Seminar in Molecular Biology).Education
- Postdoc, Genetics — Cornell University (1981)
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Ph D, Biochemistry
— Harvard University (1978) The lacI gene: sequence of the gene and mutational hotspots
- BA, Biology — University of California San Diego (1972)