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CORE Block 2 > Translation Regulation > Flashcards

Translation Regulation Flashcards

1
Q

Define no-go mRNA decay

A

Decay of mRNAs bound by stalled ribosomes due to extensive secondary structures

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2
Q

Why is mRNA decay important?

A

It protects the cell from accumulation and aggregation of abberant proteins and potentially toxic proteins.

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3
Q

Describe the mechanism of nonsense-mediated mRNA decay.

A
  • ribosome reaches a stop codon during the pioneering (first) round of translation but eIF4A bound to UPF2 and UPF3 is sitting at the EJC, downstream of where ribosome is stalled
  • SURF complex containing SMG proteins and UPF1 is bound to the ribosome, and the two complexes join to form the DECID complex, phosphorylating UPF1 and activating its ATPase
  • UPF1 then inhibits the CBD and mRNA is degraded
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4
Q

What processes mediate nonsense mediated decay?

A
  • translational repression
  • dissociation of mRNA from ribosome
  • targeted inhibition of splicing
  • degradation of nascent polypeptide
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5
Q

When is eIF2 phosphorylated and inhibited?

A
  • amino acid starvation
  • heme deficiency
  • ER stress
  • double stranded RNA
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6
Q

Describe the mechanism of global translation regulation by eIF2 phosphorylation.

A
  • guanine exchange factor eIF2b only acts on eIF2 when it is not phosphorylated
  • when phosphorylated, eIF2 holds tightly to eIF2b so it cannot go on to remove GDP from other eIF2 molecules
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7
Q

What are three forms of global translation regulation?

A
  • eIF2 hosphorylation
  • mTOR and eIF4E
  • EF-2 regulation
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8
Q

What is mTOR and what does it do in the cell?

A

Mechanistic Target of Rapamycin. Regulates cell growth by:

  • controlling mRNA translation
  • ribosome biogenesis
  • autophagy
  • metabolism
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9
Q

How is mTORc1 activated? Inhibited?

A

Activated by things that are good for the cell. Inhibited by things that are harmful to the cell.

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10
Q

Where are the factors found that act on mTOR?

A

Sitting on the lysosome.

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11
Q

How is eIF4E activity regulated by mTOR?

A
  • mTOR phosphorylates 4E-BP which binds eIF4E and inhibits it. Phosphorylation allows eIF4E to be released and to interact with other factors such as eIF4G
  • 4E-BP can be dephosphorylated by protein phosphatase 2A
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12
Q

Describe global translation regulation by EF-2.

A
  • EF-2 is phosphorylated by the mTOR pathway (good)
  • diptheria toxin or pseudomonas toxin causes ADP ribosylation of EF-2 (bad)
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13
Q

Describe cytoplasmic polyadenylation.

A

In order or an mRNA to be cytoplasmically polyadenylated it must have:

  • cytoplasmic polyadenylation element (CPE) in 3’ UTR
  • CPE-binding protein (CPEB)
  • nucleation of proteins by CPEB to regulate polyadenylation and translation
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14
Q

In what processes is cytoplasmic polyadenylation invovled?

A
  • germ-cell development
  • cell division and senescence
  • synaptic plasticity, learning, and memory
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15
Q

How is cyoplasmic polyadenylation regulated by CPEB?

A
  • When CPEB is unphosphorylated, it binds CPE and forms complex with PARN and Gld2. Poly-A specific ribonuclease works faster than the Gld2 polymerase, and the polyA tail is degraded, keeping the mRNA static.
  • a kinase phosphorylates CPEB so that PARN is released and Gldn2 adds A’s to the polyA tail, allowing it to be translated.
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16
Q

How is eIF4E affected by cytoplasmic polyadenylation?

A

When the mRNA is held static, PABP cannot bind, thus eIF4E cannot interact with eIF4G and translation cannot occur.

17
Q

Why might mRNAs be localized to different parts of the cell for translation?

A

The protein product may be needed in that region of the cell.

18
Q

Describe subcellular targeting of mRNAs.

A
  • cis-acting elements specify RNA targeting
  • trans-acting factors recognize cis-elements and bind them to form larger RNP particles
  • molecular motors transport RNP particles to different parts of the cell.
  • mRNAs are translationally dormant while en route
19
Q

How is iron stored in cells and how does it enter cells?

A

In ferritin. It is brought to the cell by transferrin and enters through transferritin receptors.

20
Q

How are proteins involved in iron storage and metabolism regulated?

A
  • ferritin mRNA has IRE in 5’ UTR that are not bound by IRE-BP under high Fe, so the storage protein continues to be made.
  • under low Fe, IRE-BP is active and binds IRE, blocking ribosomal scanning so no ferritin is made.
  • TfR mRNA has IREs in 3’ UTR that have less stable AU regions, so no binding by IRE-BP under high Fe causes the transcript to be degraded
  • when Fe is low, IRE-BP bind IRE and stabilize the transcript so that iron can be brought into the cell
21
Q

How does eIF2 control translation through delayed re-initiation of specific mRNAs?

A
  • under low stress, eIF2 has GTP and can reinitiate translation rather quickly after recycling, more chance to stay in same ORF and translate next start site.
  • under high stress, eIF2 is phosphorylated and does not quickly reinitiate translation, so it may start in another ORF and translate mRNA for stress-related transcription factors
22
Q

What is an IRES and how does it take place of a capping structure in viruses?

A

Internal ribosome entry site:

-secondary structure in 5’ UTR directly recruits eIF4G to 5’ end without eIF4E

23
Q

Why might IRES be used by viruses?

A

So it can shut down translation of capped (host) mRNAs and only express its own proteins.

24
Q

What is a common virus that uses IRES?

A

HepC

25
Q

How else can viruses trick the translational machinery using seconary structures?

A

It can use mRNA to mimic tRNA sitting in P site to trick ribosome to start at codon other than AUG.

26
Q

How does the ribosome coordinate translation and protein folding based on availability of amino acids?

A
  • if amino acids or tRNAs are scarse, it will slow down translation. conversely, it will speed up
  • fast translation may prevent aggregation or hydrophobic regions from being exposed too long
  • slow translation may allow for slower and more coordinated folding of important domains
27
Q

How can the ribosome control the fate of nascent polypeptides?

A

It is covered in many factors not involved in translation that help with proper folding (chaperones) or detect improper folding (degradation).

28
Q

How does puromycin inhibit translation?

A

-mimics charged tRNA and binds A site, forming bond with C-term of previous aa and terminating translation early.

(prok and euk)

29
Q

How does cycloheximide inhibit translation?

A

Inhibits peptidyl transferase in 60S (euk) so elongation does not continue.

Do not treat human with this!

30
Q

How does streptomycin inhibit translation?

A

Prevents binding of formylated methioning tRNA to P site by binding 30S ribosome (prok)

-misreading of codons at low concentrations

31
Q

How does streptomycin resistance arise

A

Mutations to 12S of 30S small subunit

32
Q

How does tetracycline inhibit translation?

A

Binds A site of 30S small subunit (prok) so tRNA cannot bind.

33
Q

How does chloramphenicol inhibit translation?

A

Inhibits peptidyltransferase in prok and mito (can be toxic to euk bc of this!).

34
Q

How does erythromycin inhibit translation?

A

Binds 23S rRNA of 50S large subunit (prok) and blocks peptide release tunnel.

CORE Block 2 (9 decks)

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