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BIOL200 > RR11: Translation I > Flashcards

RR11: Translation I Flashcards

1
Q

What’s the role of tRNAs?

A

Bring amino acids and help read the codons of mRNA.

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2
Q

What’s the role of rRNA?

A

Assembling the synthesis machinery that will be able to read the mRNA and summon the correct tRNAs and amino acids.
It plays a role in the function of the ribosome.

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3
Q

Which type of RNA is involved in protein synthesis?

A

All 3 of them.
mRNA
tRNA
rRNA

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4
Q

What’s the % of rRNA in the total cellular RNA?

A

rRNA accounts for 80% of the total cellular RNA.
It’s transcribed at high rates

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5
Q

The ribosome is constituted of 2 subunits. What are they?

A

Bacteria: 50S subunit and 30S subunit. Gives the 70S ribosome

Eukaryotes: 60S subunit and 40S subunit. Gives 80S ribosome.

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6
Q

What is the 50S subunit of bacteria ribosome composed of?

A

23S rRNA and 5S rRNA
31 proteins

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7
Q

What is the 30S subunit of bacteria ribosome made of?

A

16S rRNA
21 proteins

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8
Q

What is the 60S subunit of eukaryotic ribosome made of?

A

28S attached with a 5.8 S rRNA
5S rRNA
50 proteins

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9
Q

What is the 40S subunit of eukaryotic ribosome made of?

A

18S rRNA
33 proteins

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10
Q

Are rRNA folds conserved?

A

Yes, those are highly conserved structures.
They form these stem-loop secondary structures.

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11
Q

Are the subunit of ribosome active structures?

A

No. Only the assembled ribosome is the active structure.

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11
Q

Are the sequences of rRNA conserved?

A

Not necessarily. Only the secondary stem-loop structures that the sequences generate are conserved.

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12
Q

What are the modifications done to pre-tRNAs to make them into mature tRNAs?

A
  • 5’ end sequence is removed
  • a short segment is removed
  • CCA is added on the 3’ end
  • more modifications of internal bases
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13
Q

What is the sequence of tRNA that gets attached to aminoacyl tRNA synthetase?

A

The CCA sequence on the 3’ end.

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14
Q

What does the aminoacyl tRNA synthetase do?

A

They are specific to an amino acid.
Ensure that the appropriate amino acid is bound to the correct tRNA for the protein synthesis reaction.e

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15
Q

How does aminoacyl tRNA synthetase link the amino acid to the right tRNA and interacts with the codon?

A
  1. Recognize and bind to their corresponding tRNA
  2. Binding of the amino acid
  3. ATP used to link the amino acid to the 3’ end of the tRNA to generate high energy ester bond
  4. The tRNA linked to the amino acid binds to the complementary codon.
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16
Q

Why would the genetic code be considered degenerate?

A

Because it’s not perfectly ordered. An aminoacyl tRNA synthetase can bind to more than one unique tRNA and a single tRNA can bind to more than one single codon. Different codons can give the same amino acid, so aminoacyl tRNA synthetase have to be able to bind to different tRNA without too much specificity.

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17
Q

How can we differentiate the 2 tRNAs for methionine?

A

methionine tRNA used for initiation is structurally different from the tRNA used for methionine during elongation.
It has a structure that allows it to interact with the P site on the ribosomal subunit.

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18
Q

What’s different about the tRNA of methionine during initiation in bacteria?

A

Bacterial tRNA of methionine is modified by adding a formyl group.

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19
Q

Can tRNA of methionine used for initiation be also used for methionine during elongation?

A

No. The tRNA used for methionine during initiation is exclusively used for initiation and same goes for tRNA of Met druing elongation.

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20
Q

How does the assembly of the pre-initiation complex work in translation?

A
  1. eIF 1, eIF3 and eIF1A are bound to the small ribosomal subunit
  2. eIF2 in its GTP-bound form interacts with tRNA Met
  3. Formation of a complex that can interact with the small ribosomal subunit
  4. When everything is bound together, it forms the 43S pre-initiation complex
21
Q

What is eIF2?

A

eukaryotic Initiation Factor 2.
It’s an initiation factor that interacts with tRNA Met for initiation.
It’s a GTP binding protein.

22
Q

Is the 43S pre-initiation complex necessary in translation?

A

Yes. It’s a highly regulated step and if the pre-initiation complex is not done properly, protein synthesis can’t occur.

23
Q

What does the cell do if it realizes that it doesn’t have the right conditions to survive?

A

It will shut down protein synthesis by phosphorylating eIF2, so it can never bind to GTP.
Since eIF2 can’t be in its GTP-bound form, it won’t be able to interact with tRNA Met for initiation, so the 43S pre-initiation complex can’t form.

24
Q

Where does the cap go for efficient translational initiation of eukaryotic mRNA?

A

A cap goes on the 5’ end of the mRNA to allow the initiation of the protein synthesis reaction.

25
Q

Why are mRNA transcripts of class 2 (RNA pol 2) the only ones that are capped?

A

Because the dimeric guanylyltransferase binds to the phosphorylated C-terminal domain (CTD) of RNA pol2.

26
Q

Are transcripts by RNA pol 1 and 3 efficiently transcribed?

A

No, only the transcripts made by RNA pol 2 can be efficiently transcribed because of the 5’ end cap.

27
Q

What is the 5’ end cap put on mRNAs called?

A

7-methylguanylate

28
Q

What is the dimeric guanylyltransferase?

A

It’s a capping enzyme that catalyzes the formation of the 5’ end cap.
Without it, the cap can’t be put on the mRNA.

29
Q

What happens when we add the eIF4E to an mRNA that doesn’t have a cap on?

A

It doesn’t do anything.

30
Q

What happens when we add the eIF4E to an mRNA that does have a cap on?

A

It catalyzes the reaction of the cap on the mRNA and enhances protein synthesis in cells.

31
Q

What does eIF4E do?

A

It’s part of a complex called eIF4 that binds to the 5’ end of the mRNA after cytoplasmic remodelling, in the cytoplasm.
It’s the cap-binding protein

32
Q

What does the multi-subunit protein complex eIF4 is composed of?

A

eIF4E
eIF4A
eIF4G
eIF4B
together, they bind to the 5’ end of an mRNA to be translated

33
Q

What happens when the eIF4 complex binds to the 5’ end of the mRNA to be translated?

A

The mRNA is activated.

34
Q

Why is eIF4E under tight regulations inside the cell?

A

Because if we add more copies of eIF4E into the cell, the cell undergoes uncontrolled growth and division, and it can give rise to tumors.

35
Q

What’s the position of the proteins in the eIF4 complex on the 5’ end of the mRNA and what do they do?

A

eIF4 complex: eIF4E, eIF4G, eIF4B, eIF4A bind to the 5’ end of mRNA
eIF4G: Interacts with PABPC (3’ end) creating a loop of mRNA.
eIF4G: recruits 43S pre-initiation complex by interacting with eIF3.
eIF3: on the small ribosomal subunit (40S)
eIF4A: RNA-helicase in the eIF4 complex, gets activated by ATP. Carries the complex on the mRNA.
eIF4B: enhances eIF4A activity
Ready for translation

36
Q

Why is the position of the protein in the eIF4 complex so important?

A

Because eIF4E needs to interact with the 5’ end, and that positions the other subunits to carry their own function.

37
Q

What does the mRNA loop do in translation?

A

mRNA is in a loop during translation, so the ribosomes would just go around the loop and fall off to reinitiate.
It makes the structure highly efficient because the ribosomes are never too far to restart another translation cycle.

38
Q

When we say that translation is efficient, what does it mean for mRNA?

A

It means mRNA is most likely stable.

39
Q

What is the role of eIF4A in the eIF4 complex?

A

It’s an RNA helicase that removes any secondary structure in the 5’ region of the mRNA.
ATP-dependent.
Carries the complex and the other proteins on the mRNA during translation.
Acts like a motor.

40
Q

What’s the role of the entire eIF4 complex?

A

It scans the mRNA to get to the AUG codon.
When tRNA Met initiation recognizes the codon, then it changes the reaction to get to initiation and then elongation of the protein.

41
Q

Where would eIF4E go during the scanning process, when eIF4A starts carrying the complex along the mRNA?

A

It’s still debatable, but eIF4E would still be associated with the complex eIF4 complex and form a loop during the entire translation.

42
Q

What’s the direction of translation?

A

5’ to 3’.
Starts where the eIF4 complex is, on the 5’ end, to the 3’ end poly A tail.

43
Q

What happens when the tRNA Met associates with the AUG start codon?

A

Conformational changes in the complex caused by eIF5.
When the scanning complex associates with the AUG start codon, eIF2-GTP is hydrolyzed by eIF5 (GAP protein) to eIF2-GDP.
- initiation factors dissociate
We’re only left with the small 40S subunit.

44
Q

What are the sites on the small 40S ribosomal subunit?

A

E (exit)
P (peptidyl)
A (aminoacyl) : Accepts new tRNA

45
Q

On which site is situated the tRNA Met Initiation when it meets AUG start codon?

A

It’s on the P site.
P site + tRNA Met Initiation + AUG start codon = all interacting

46
Q

When does the large 60S ribosomal subunit come in?

A

The large 60S ribosomal subunit recognizes the small 40S ribosomal subunit bound to the AUG start codon after all the initiation factors leave because of eIF5.

47
Q

What do we call the structure formed by the small and large ribosomal subunits?

A

ADS ribosomal complex.
It’s a functional complex.
80S ribosome.

48
Q

When the ADS functional ribosomal complex is formed, what is the only occupied site?

A

The P site is occupied by tRNA Met initiation. The A and E sites are free.

49
Q

Does having a longer Poly A tail make a difference?

A

Yes. When the mRNA has a longer Poly A tail, it means the mRNA is more stable, so we have a more efficient translation.
More Poly A, more PABPC protein to interact with the poly A tail.
More Poly A means more protein to bind to the 5’ end and create the loop.
It all contributes to the stabilization of mRNA to have more efficient translation.

50
Q

What’s the role of PABPC protein?

A

It binds to the Poly A tail of mRNA to protect it. It blocks the ability of RNAase to chew the molecule from the 3’ end to the 5’ end.

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