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BIOL3612.MERGED.202610 Activity Questions from the Literature 2B: Preparing tRNAs and synthesizing protein

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In the original publication of the 4V42 ribosome structure (Yusupov et al., 2001), the researchers included an image of all three tRNAs as well as the mRNA (much like you did, though perhaps from a different angle). The authors say, regarding this image, that "the simultaneous reading of the two codons is accommodated by a kink in the mRNA backbone of about 45o between the A and P codons":   They also say something that is more difficult to see in this image, so think back to what you yourself observed as well as you were creating your own image: "The A- and P-tRNA backbones are closest at the acceptor stems, which approach within 5 Angstroms of each other.... The CCA tails of the A- and P-tRNAs converge, as expected, at their 3' ends in the peptidyl transferase site of the [large] subunit." Meanwhile they note that the anticodons of the A- and P-tRNAs are approximately 10 Angstroms apart.   Your own experience manipulating the 4V42 structure file plus this description above should make it clear why it is difficult to show translation in the ribosome as a series of flat 2D representations: it's a highly 3D process.   As a review, if the 4V42 structure file (and corresponding experiment) had been able to contain tRNAs with amino acids attached, where would they be? Let's assume that only two codons have been read so far. Choose the best answer below.   The amino acids would be attached to the tRNAs that are in the:  

Options
A.E site and P site; in the figure above they would be at the back and obscured from view
B.P site and A site; in the figure above they would be at the back and obscured from view
C.E site and P site; in the figure above they would be at the bottom in contact with the mRNA
D.P site and A site; in the figure above they would be at the bottom in contact with the mRNA
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To approach this question, I’ll break down what the scenario asks and then evaluate each answer in turn. Option 1: "E site and P site; in the figure above they would be at the back and obscured from view". This option pairs E site with P site, but the scenario specifies two codons have been read and focuses on where the amino acids would be attached. The E site is where deacylated tRNAs exit, not where aminoacyl-tRNAs carrying amino acids would be located for peptidyl transfer. Additionally, describing their position as at the back and obscured from view doesn’t align with the described visibility o......Login to view full explanation

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