translation: decoding and peptide bond formation Flashcards
what are the 4 phases in the elongation phase of translation?
1: decoding
A charged tRNA enters the ribosome
Base pairing between the mRNA codon and tRNA anticodon
Release of elongation factor
2: accommodation:
Movement of amino acid end of the tRNA into peptidyl transferase center
3: peptide bond formation
4: translocation
EF-G or eEF2
what are the elongation factors?
Bacteria:
EFTu - G protein
EFTs
EFG - G protein
Eukaryotes:
eEF1A - G protein
eEF1Ba
eEF2 - G protein
what is entry to the irbosome based on?
trial and error
describe the decoding step:
EFTu oreEF1A delivers the aminoacyl-tRNA to the ribosome where the anticodon will be matched against the mRNA codon in the A site. The matching process determines whether the correct charged tRNA stays in place or not
The ribosome doesnt select a specific aminoacyl-tRNA but it can select for whatever aminoacyl-tRNA has an anticodon that best matches the mRNA codon
describe what helps decoding in bacteria;
Conserved nucleotides in the 16S region respond to the formation of the short double helix and select amino acids change configuration and stably interact with the minor groove of the codon-anticodon helix
A1492, A1493 and G530 help stabilize the A site via hydrogen bonding in bacteria
describe what helps decoding in eukaryotes;
In eukaryotes conserved nucleotides in the 18S center change confirmation the same way
A1824, A1825 and G626 help stabilize.
describe factor release;
If the codon-anticodon is good the the tRNA willbe released by EF. this depends on hydrolysis of GTP also carried by the EF
EF-Tu (GTP) will bind aa-tRNA
Ef-Tu (GDP) will NOT bind aa-tRNA
Conformational changes in the ribosome occur and the latent GTPase activity of EFTu/eEF1A is activated
The ribosome L7/L12 proteins act as a GAP on the latent GTPase activity and once activated will released the aa-tRNA.
Accommodation will now be able to proceed
describe the recycling of EFTu/eEF1A;
Has a higher affinity for GDP than GTP so a new molecule of GTP won’t displace it
A guanine nucleotide exchange factor is needed (GNEF) - EFTs/eEF1Ba
describe accomidation;
Once the elongation factors are released, the 3’ end of the tRNA bearing the amino acid must travel into the peptidyl transferase center through a process called accommodation
describe peptide bond formation;
Involves transfer of the polypeptide chain from the tRNA in the P site to the aa-tRNA in the A site by which aa-tRNA ends up getting pulled to the P site
The peptidyl transferase active site has highly conserved rRNA elements which position both the aa-tRNA in the A site and the peptidyl tRNA in the P site for catalysis
The 2’ OH of peptidyl-tRNA facilitates the nucleophilic displacement reaction by attracting a proton front the terminal amino group
why is proline an exception to smooth protein synthesis?
Incorporated way slower
An N-alkyl-amino acid
Has just 1 single proton available
who discovered EFP/eIF5A?
Glick and Ganoza
what is the purpose if EFP/eIF5A?
Essential to alleviate the ribosome stalling that occurs with proteins containing 3 or more consecutive prolines
EF-P (eIF5A) - position itself between the E and P sites and stimulates peptide bond formation
When the new peptide is formed, the chain is transferred from the tRNA in the P site to the aa-tRNA in the A site at the same time the 3’ end of the aa-tRNA ratchets into the P site
describe translocation;
The mRNA bound to the aa-tRNA finishes ratcheting through the ribosome which opens the A site to begin again
The tRNA in the E site is positioned to leave the ribosome
EFG/eEF2 binds in the A site and promotes the structural rearrangements - is a latent GTPase - activity activated by the GAP center
what factor contains diphthamide?
eEF2
