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Autonomous Mobile Robots in Nature: Transfer RNAs in Escherichia coli Bacteria

Piros, Sandor
A Master of Science Thesis in Mechatronics Submitted by Sandor Piros Entitled, "Autonomous Mobile Robots in Nature: Transfer RNAs in Escherichia coli Bacteria" May 2008. Available are both Soft and Hard Copies of the Thesis.
Transfer RNAs (tRNAs) are the smallest autonomous robots on earth. They can recognize a specific amino acid from the possible pool of 20 different amino acids. They are able to transport these protein building blocks to the ribosome, the site of amino acid assembly into protein chains. Accurate and rapid selection of tRNAs by the ribosome is critical for cell viability. There is no description in literature about their movement in the cytoplasm, but there is extensive research about tRNA recognition, selection and their relative movements into or inside the ribosome. The aim of this master thesis is to develop a model of tRNA molecular movement in bacterial cytoplasm. One of the main criteria for protein synthesis is the availability of the necessary amino acid in the vicinity of the ribosome, according to the sequence coded by a gene. The theme of this master thesis is the spatial movement/placement of aminoacylated tRNAs in the cytoplasm - viewed from the perspective of that particular aminoacylated tRNA (charged with a specific amino acid). A kinetic model of the messenger RNA - ribosome - tRNA system was developed and a computerized simulation was built to visualize different scenarios. The purpose of the simulation is to show the conditions necessary for the tRNA to deliver the particular amino acid to the ribosome within a similar timeframe to what happens in vivo. Simulations results show that it is very unlikely that tRNAs are able to get to the ribosome by random movement, and there should be a certain mechanism to preselect the cognate tRNAs. Three hypotheses were developed to give possible explanations to this process, and provide a useful guide to future research and simulations in biology and microbiology.
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