chapter 31 protein synthesis Flashcards
which error frequency is intolerable
10^-2
the error frequency must not exceed 10^-4 to effectively produce large proteins
10^-4
where are amino acids attached in tRNAs
to 3’ end to 3’ hydroxyl group of an adenosin
why are certain bases unusually methylated in tRNAs
so that they don’t form base pairs and to be accessible for other interaction.
The methylations also give a hydrophobic character that can be used when interacting with certain proteins
about ….. of the bases are paired in tRNAs
50 %
tRNA which form of helix does it have
A form
Components of tRNA
5-phosphorylated terminus DHU loop (dihydrouracil) anticodon loop extra arm variable loop Tpsi C loop (ribothymine pseudouracil-cystosine) CCA arm
what is I in anticodons
purine base inosin
How is inosin formed
deamination of adenosine after the synthesis of the primary transcript
what checks if the codon-anticodon duplex is correct in bacteria
the 30s subunit with 16s that form hydrogen bonds with the first two correct nucleotides in the anticodon but not with the wrong ones
why must aminoacids be activated
because peptide formation between free aminoacids is not thermodynamically favourable
where are ATPs consumed when activating aminoacids
the first one is in the formation of ester bond in aminoacyl-tRNA and the other is considered in driving the reaction forward
how do aminacyl-tRNA synthetases correctly remove or accept the correct amino acid?
through acylation sites rejecting ones that are larger than the correct one
hydrolytic sites
cleaving ones that are smaller than wanted
Which parts of tRNAs interact extensively with amino-acyl synthetase
acceptor stem and anticodon loop
How many classes of synthetases and the differences?
1- CCA is helical in II and hair pin in I
2- I 2’ and II 3’
3- bind ATP in different conformations
4- I monomeric and II dimeric
which subunit is mRNA being translated bound to in bacteria ? what about tRNA?
30s subunit
in contact with both
30s and 50s
the consensus of shine dalgarno sequence in prokaryotes
AGGAGG
Factors determining the start of protein synthesis
pairing of 3’ of 16s to initiation sites
pairing of anticodon to codon
initiation codons for bacteria
AUG GUG UUG
which tRNA initiates protein synthesis in bacteria
tRNAf with N-formylmethionine
when is N-formylmethionine removed
when 10 aminoacids have been synthesized
What enzyme formylates methionin
transformylase
what is the rate limiting step in protein synthesis in bacteria
the formation of 70s initiation complex
what is the highly conserved site that interacts with EF-TU in subunit 50s is called? function?
sarcin ricin loop interacts with EF-Tu complex and causes the hydrolysis of its GTP releasing EF-Tu-GDP
what is accomodation in protein synthesis in bacteria
when structural changes happen moving the aminoacyl-tRNA closer to p-site in subunit 50s
which factor recognises and interacts with tRNAf
IF2
polyribosome /polysome
Multiple ribosomes translating an mRNA simultaneously
tRNAs and stop codons?
They don’t exist
what recognises stop codons
RFs
RF1 and RF2 and RF3
RF 1 : UAA UAG
RF2 : UAA UGA
RF3: removes the other ones when the protein synthesized is released
what does RFs interact with and how?
The peptidyl transferase center on the 50s subunit using a highly conserved loop containing GGQ with glutamine being methylated
promoting water molecule attacks on the ester linkage between tRNA and the polypeptide chain
How is the 70s complex entirely dissociated
through the hydrolysiss of GTP by binding to EF-G and RRF (ribosome release factor)
the initiation factor in eukaryotes?
eIFs
when are internal ribosome entry sites are used? The function ?
when there are no 5’caps. They faciltate the association of subunit 40s to mRNA
the eukaryotic counterparts of elongation factors in eukaryotes
EF-G
release factors
EF1alpha
EF1Betagamme EF1By
EF2
eRF1 and eRF3 to accelerate the activity of eRF1
antibiotics that inhibit protein synthesis in eukaryotes?
and how do they operate and what do they affect?
ricin a-sarcin and diptheria
they all inhibit elongation
ricin and a-sarcin covalently modify rRNA and diptheria covalently modify the elongation factor EF2
secretory pathway
cotranslation of a protein directed towards the endoplasmic reticulum
a ribosome in eukaryotes remain free in …… unless directed to the …..ER
cytoplasm, ER
the components of translocation across endoplasmic reticulum
1- signal sequence
2- signal recognition particle (SRP)
3- SRP receptor (SR)
4- Translocon
