2.15.07 - 2.15.2007 o Made it through initiation, now we...

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2.15.2007 o Made it through initiation, now we are on elongation Where is IF1, we didn’t discuss it in initiation, but it exists we just don’t really know the function of it o Don’t need to know but it may help you remember something later: the function of IF1 is most thought to be that it is sitting on the A site during initiation so that no tRNA could come in and bind here during initiation so its thought that its function might be to guide the first tRNA to the P site where the start codon is, since the function hasn’t been established won’t be asked to know this Elongation o How subsequent amino acids are added on o P site is the peptidylsite o A site is the amino acyl site o A new amino acid is brought into the Amino acyl site and the growing chain of polypeptides so far assembled is at the peptidylsite o Every amino acid except the first one functions in this way, the Fmet is brought in to the P site (partial P site, what is going to be the P site) Only in initiation is where the tRNA brings an amino acid into the P site o the tRNA is not in the right shape to bind to the A site, it has to be a part of a larger complex in order to be the right shape but this complex won’t have an initiation factor because we are not in initiation any more, the complex is Elongation Factor Tu, GTP, amino acid, and tRNA EF-Tu is not in the right shape to bind to tRNA unless it is attached to GTP, once again GTP affects the shape of other molecules In the example the next codon is GGA and so a glycine tRNA comes into the A site, but how does the tRNA sense that it is GGA so that it knows to bring in glycine? Diffusion brings it in, which means that its not specific, it could bring any transfer RNA in but there must be a check to see if it is the right amino acid – (diffusion is a fast process in a molecular level) Complex comes in, say it is the right tRNA with the right amino acid, so that the tRNA has an anticodon that will form lots of hydrogen bonds with the codon in the A site all the H bonds forming here pull on the anticodon loop and deform the tRNA into a slightly different shape, this triggers GTP to cleave, the one that came in on the EF-tu GTP has been cleaved to GDP, EF-tu bound to GDP is in the wrong shape to attach to the tRNA so EF-tu is then released from the ribosomal area EF-tu was physically in the way of the peptide bond formation, it blocked the formation between the new amino acid and the chain that has been built thus far – now a peptide bonds forms (reason is because it is the correct amino acid) What if it is the wrong tRNA that comes into the A site It may form some H-bonds with the codon in the A site but it will also have other places where it is repelling some nucleotides, there is not enough association to pull on the anticodon loop and form the shape of the tRNA needed to cleave GTP and thus EF-Tu is not removed and the amino acid (wrong one) cannot be added onto the chain o Peptidyl tranferase was named before it was identified
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2.15.07 - 2.15.2007 o Made it through initiation, now we...

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