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BIOL200 > RR11: Translation 1 > Flashcards

RR11: Translation 1 Flashcards

1
Q

what removes the nuclear proteins associated with mRNA once it is on the cytoplasmic side?

A

helicase activity associated with cytoplasmic filaments on the cytoplasmic site

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2
Q

what are 2 proteins that bind to the mRNA once it is on the cytoplasmic side?

A

cap binding complex eIF4E
protein that binds to the poly A tail, PABPC (c for cytoplasmic)

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3
Q

what happens to PABPN?

A

sent back to the nucleus

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4
Q

what happens when RNA is decorated with all the important proteins?

A

ready to be translated

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5
Q

how do all 3 classes of RNAs play an essential role in translation?

A

tRNAs are required to bring in the AAs and read the codons on the mRNA
rRNAs are there for assembling the giant protein synthesis machinery that enables the complex to read the mRNA and summon the correct tRNAs and AAs
the mRNA is the sequence of codons

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6
Q

what proportion of the RNA in cells does rRNA make up?

A

transcribed at a very high rate, makes up 80% of the RNA in cells, by far the most abundant

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7
Q

what is the composition of the large ribosomal subunit in bacteria?

A

23S RNA+ 5S RNA + 31 proteins = 50S large subunit

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8
Q

what is the composition of the small ribosomal subunit in bacteria?

A

15S RNA+ 21 proteins = 30 S small subunit

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9
Q

what is the size of the bacterial ribosome?

A

70S

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10
Q

what is the composition of the large ribosomal subunit in eukaryotes?

A

28S rRNA+5.8S RNA+ 5SRNA+ 50 proteins = 60S large subunit

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11
Q

what is the composition of the small ribosomal subunit in eukaryotes?

A

18S rRNA + 33 proteins = 40S small subunit

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12
Q

what is the size of the eukaryotic ribosome?

A

80S

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13
Q

what is an important property of the rRNA?

A

across organisms sequence is highly similar, there are fluctuations
the secondary structures that those sequences generate are highly conserved in almost all organisms
forms a highly complex structure with many stem loops
the way in which RNA folds is related to its function

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14
Q

what shape does tRNA fold into?

A

an upside down L

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15
Q

where is the anticodon positioned on the tRNA?

A

at the top of the L

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16
Q

where will tRNA attack aminoacyl-tRNA synthethase?

A

at the extremity of the base, the 3’ end

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17
Q

what does aminoacyl tRNA synthethase do?

A

ensures that the appropriate AA is bound to a tRNA

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18
Q

what are the two important sites present on aminoacyl tRNA synthetase?

A

there is a substrate binding site on the enzyme, and then a site for the appropriate interaction with the correct tRNA that would encode for the particular amino acid

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19
Q

what ensures that the correct AA is linked to the tRNA?

A

interactions with the anticodon loop and sometimes other regions within the tRNA per se

20
Q

how does aminoacyl tRNA synthetase create the bond between the AA and tRNA?

A

use ATP to link that amino acid to the 3’ end of the tRNA to generate a high energy ester bond
* This AA is now linked to that particular tRNA

21
Q

what makes the genetic code degenerate?

A

a single aminoacyl tRNA synthétase can bind to more than one unique tRNA and a single tRNA can bind to more than one single codon

22
Q

how come multiple codons can code for the same amino acid?

A
  • When the ribosome is reading on a codon, it creates a very special environment
  • The 3’ nucleotide of the codon and the 5’ nucleotide of the anticodon can sometimes interact in NON Watson crick base pairing manners, so there is a little bit of flexibility (wobble pairing)
23
Q

what are some amino acids that are coded for by different codons?

A

leucine, serine, arginie

24
Q

what are some amino acids coded for by only one codon?

A

tryptophan (UGG) and methionine (AUG)

25
Q

why is methionine always the first AA coded for during protein synthesis?

A

The tRNA that is bound to methionine comes in two forms (true in bacteria and eukaryotes)

26
Q

what are the two forms of the methionine tRNA and what do they do?

A

One of the forms is the kind of tRNA that will bind to Met and be used whenever an AUG codon arises within the mRNA sequence during elongation
* the other is called the initiation tRNA methionine (tRNAi Met) and that tRNA is structurally distinct or it is distinguished
* In bacteria, it is because it’s formulated
* The tRNAi MET in bacteria and in eukaryotes is the tRNA that will bring in methionine as the first amino acid at the N terminus of a poly peptide chain

27
Q

why is tRNAi MET distinct from the other tRNA?

A

because it can interact with a critical site in the small ribosomal subunit called the P site

28
Q

what are the three steps in protein synthesis?

A

initiation, elongation, termination

29
Q

how is the pre-initiation complex formed?

A
  • Initiation is very complex and is under very strict controls
  • in order for initiation to happen, a small ribosomal subunit that might have dissociated from an mRNA is kept separate from the large ribosomal subunit by virtue of association with initiation factors (IF1, 3, 1A)
  • Make sure small subunit cannot interact with the big one unless conditions are met
  • tRNAi MET will interact with another initiation factor called eIF2 (eukaryotic) , which is a GTP binding protein
  • When eIF2 in its GTP bound form interacts with the tRNAi MET they form this complex and at that point can interact with the small ribosomal subunit that is already bound to eIF3, 1 and 1A
  • When all this comes together they form the 43S pre initiation complex
30
Q

how can this process be stopped and in under what conditions?

A

If the cell recognizes that its in poor growing conditions doesn’t have the appropriate nutrients, eIF2 will be phosphorylated, and then it cannot bind GTP, and so it will not interact with tRNAi MET and never form a complex and stop protein synthesis

31
Q

what is required for the efficient translation of mRNA?

A

a 5’ cap
only class 2 transcripts have this cap structure, only class 2 mRNAs are officially translated

32
Q

how was the importance of the 5’ cap showed?

A
  • hypothesis that critical proteins interact with the 5’ cap (7mGDP) and they are essential to trigger the protein synthesis reaction
  • used affinity chromatography and covalently linked the 7mGDP structure to sepharose beads and ran cytoplasmic extracts over that
  • Purified protein that is the cap binding protein
  • Show that by adding a bit of that protein could greatly enhance the translation of mRNAs that are capped
  • If same with uncapped viral transcripts there was no effect
  • Evidence that some protein that binds to the cap is critical for enhancing protein synthesis in cells
33
Q

what is in fact the name of that cap binding protein and what other proteins are in that complex?

A
  • EIF4E is that cap binding protein that was isolated
  • part of a complex called the eIF4 complex: eIF4E, 4A, B and G
34
Q

what does the eIF4 complex do?

A

binds to the 5’ end of the mRNA to be translated, and the mRNA is then activated

35
Q

what is a particularity about eIF4E?

A
  • EIF4E is limiting: if you add extra, the cells undergo uncontrolled growth and division, which leads to the formation of tumors
  • Regulation of those proteins is very important
36
Q

what does eIF4 complex do?

A
  • EIF4E interacts with the 5’ end, positions the other subunits to carry out their functions
  • EIF4G recruits the 43S pre initiation complex through an interaction with eIF3
  • Protein protein interaction, and you combine the 43S pre initiation complex (small subunit) and the 5’ end of the mRNA to be translated
  • Somehow, the polyA tail is interacting with eIF4G
  • It was found that eIF4G interacts directly with PABPC
  • This suggests that while PABPC is bound to the poly A tail it interacts with the subunit of eIF4 at the 5’ end of mRNA thus forming a LOOP of mRNA
37
Q

what is a property of the RNA loop?

A

the ribosomes go around the loop,
* The ribosomes go around the loop, drop off and reinitiate
* This makes it highly efficient because the ribosomes are never too far from where they have to restart translation

38
Q

what happens once the eIF4 complex has assembled on the 5’ end?

A

another critical enzymatic activity present with eIF4 becomes activated and it is activated through interaction with one of the other subunits
* eIF4A is an ATP dependent helicase that gets activated by its neighboring subunit eIF4B
* EIF4A unwinds RNA and the whole complex starts to scan, pulling everything along the mRNA
* This scanning is important to remove secondary structure and take that complex to the initiator codon AUG

39
Q

when does that scanning of the mRNA stop?

A

till tRNAi MET will recognize that AUG and then initiate a number of changes important for later reactions

40
Q

what does the 5’ end of the mRNA do when the complex is scanning the mRNA?

A

follows along the complex and forms another loop

41
Q

what happens when the complex reaches the AUG codon?

A
  • the P site of the small subunit is situated right over the AUG codon
  • Gives rise to conformation changes, eIF5 is a GAP protein and that accelerates the GTP-are function associated with eIF2 which leads to a major conformational change
42
Q

what are the function of the different protein in eIF4 complex?

A

eIF4E: cap
eIF4G: binds eIF3 and PABPC
eIF4A: RNA helicase
eIF4B: enhances eIF4A activity

43
Q

what causes the initiation factors to dissociate?

A
  • Once the tRNA i MET interacts with AUG that is a conformational change triggered by GTP-are activity present in eIF2, and those initiation factors dissociate
44
Q

what are left with once the initiation factors leave?

A

the small subunit bound to a AUG codon recognized by the large subunit, the formation of a functional 80S ribosomal complex*
The complex has a free A site and a free E site, P site is occupied by tRNAi MET

45
Q

what does the A site correspond to?

A
  • A site corresponds to the aminoacyl site, called the acceptor site
  • The A site is free and ready to accept any incoming tRNAs
46
Q

what does the P site correspond to?

A
  • The P side corresponds to the peptidal transfer site
47
Q

what does the E site correspond to?

A
  • The E site is the exit site

BIOL200 (29 decks)

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