8.3 - Translation Flashcards
How do ribosomes recognize the translation start site?
By complementarity between the end of the 16S rRNA and a specific sequence on the mRNA called the Shine Dalgarno sequence
Where is the Shine Dalgarno sequence located?
Upstream of the translation start codon
What is the translation start codon on mRNA
AUG or in some cases GUG
What does AUG normall code for?
Methionine
What does AUG code for in bacteria?
The AUG start codon encodes for a modified version of methionine called formyl-methionyl tRNA (fMet tRNA).
When does addition of C=O group occur?
After the charging the tRNA with regular methionine.
What happens when protein synthesis finishes?
fMet is, for some reason, removed by a ribosomal protein
What do immune cells respond to?
To fMet and fMet-peptides.
Immune cells can also respond to LPS, lipoproteins, flagellin protein, lipopolysaccharides, etc
What chaperones help with protein folding?
DnaK and DnaJ
What happens if the protein is not properly folded?
The protein can be fed to GroEL for refolding
What happens if the protein is still not properly folded after it is passed to GroEL
The protein may be passed to a protease for degradation
How does GroEL work?
(1) An unfolded protein substrate binds to GroEL
(2) ATP binds to ring protein twists and elevates to meet the GroEL cap
(3) Denatured protein renatures inside special protected environment
(4) Isolate proteins and can sponteanously renature themselves
Name two proteases
ClpY ATPase and ClpQ protease
What family of proteins fo ClpY and ClpQ belong to?
AAA+
What happens if you have broken RNA during translation?
This means the protein will not get built fully but also ribosome will get stuck since termination codon will not be reached on broken mRNA.
How can you unstick ribosomes and remove proteins?
With tmRNA
What is another name for tmRNA?
SsrA
What is tmRNA?
A bacterial RNA molecule with a dual tRNA-like domain (TLD) and mRNA-like domain (MLD).
What do tmRNAs do?
(1) They restore protein synthesis (by freeing the ribosomes).
(2) They eject the truncated mRNA from the staled ribosomes.
(3) They tag the incomplete protein for immediate destruction by proteases.
What happens while the stuck peptide is in the P-site?
tmRNA will bind to the empty A site of the ribosome. The ribosome will then move from the 3’ end of the truncated mRNA onto the “resume codon” of mRNA-like domain (MLD).
How long will translation of MLD occur?
Until the in-frame tmRNA stop codon is encountered
What is the incomplete peptide tagged with?
A specific sequence by the tmRNA itself. This tag sequence is recognized by another enzyme called SspB.
What does SspB do?
It will enhance the recognition of the tag sequence by ClpXP proteins.
What are ClpXP proteins?
Chaperons that are part of the AAA+ family.
How does ClpXP work?
It uses energy from ATP hydrolysis to degrade the tagged proteins. The amino acids are then recycled.
Is tmRNA stable or unstable?
mRNA is unstable but tRNA is stable so tmRNA is stable
What happens to bacteria if you delete a component of tmRNA?
Cells either get sick or they die
When is it most advantageous to have tmRNA?
When nutrients are rich and cells are growing fast (i.e. when cells are doing a lot of things at once)
Finish the sentence:
Toxic proteins have tags recognized by special ____
Special AAA+ unfolding proteins and special cognate adapters
Between prokaryotes and eukaryotes which has higher protein synthesis rate?
Bacteria have 10x higher protein synthesis
What is the number of IF’s in prokaryotes?
3
What is the number of IF’s in eukaryotes
10
Between prokaryotes and eukaryotes which has smaller ribosomes?
Prokaryotes
