decoding box Flashcards
what two things must ribosomes do as part of codon-anticodon recognition?
1- generate a water free zone
2- monitor codon-anticodon pairs using a decoding site
what advantage is there of having an acceptable error frequency?
ensures there is a balance, considering both need and cost of accuracy
why will the entire ternary complex not fit into the A site?
contains EF-Tu, a protein of 400 amino acids
what are the two steps for decoding?
1 - aa-tRNA-Tu-GTP binds in A/T site, GTP hydrolysis and dissociation of Tu-GDP
2- rotation of the cognate tRNA into the A/A site
how is the energy for accommodation provided?
there is strain on the tRNA when it is in the A/T site, GTP hydrolysis and dissociation from EF-Tu causes the tRNA to relax, providing energy of accomodation
what is the structure of the decoding box?
largely made up of 16S RNA from the small ribosomal subunit, folded into 46 helical stems. the three conserved residues G530, A1492 and A1493 are located on helices 18 and 44 respectively. there is also the protein S12
what is the function of ribosomal protein S12?
present on the periphery of the decoding box, associated with accuracy of translation
why is hydrolysis of GTP required for domain closure?
the tRNA anticodon loop pairs with the mRNA that is also in the A site, the 3’ end of the tRNA is buried within the 3 folded domains of EF-Tu, hydrolysis and subsequent dissociation of Tu-GDP is required
when does domain closure occur?
when the ribosome senses that a tRNA has come into the A site, as it occurs, the ternary complex is squeezed
what is the role of the bases G530, A1492 and A1493?
feel for codon-anticodon interactions, with one edge of each base pair in the major groove of the helix
how are A-U and G-C differentiated from each other in the major groove?
the arrangement of H-bond acceptors is different in the major groove but identical in the minor groove
why does the ribosome inspect the minor groove?
to identify if the base-pair obeys Watson-crick complementary pairing
what does A1493 monitor?
pairing between codon position 1 and anticodon position 3
what happens when a cognate or near cognate tRNA approaches the decoding box?
both fit into A/T site, GTP hydrolysis and base flipping occurs
only the cognate tRNA will rotate into the A/site
why is there wastage of energy when a near-cognate tRNA approaches the decoding box, but not a non-cognate tRNA?
a near-cognate tRNA fits into A/T triggering domain closure, but does not fit into A/A
a non-cognate tRNA does not fit into A/T at all
