Nonsense Mediated Decay Mechanism

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Questions and Answers

What role does Upf3 play in the process of nonsense-mediated decay?

It assists in the phosphorylation of UPF1.

It displaces EJC during translation.

It promotes the splicing of mRNAs.

It triggers mRNA decay if retained. (correct)

What happens to normal transcripts during the translation process?

There is no interaction between EJC and ribosomes.

EJC remains attached, leading to mRNA decay.

The ribosome displaces EJC, allowing normal protein production. (correct)

Ribosomes displace the EJC and protein production halts.

What is the outcome for transcripts that contain premature stop codons (PTCs)?

They continue to be associated with Upf3 without triggering decay.

They are subject to degradation via the NMD pathway. (correct)

They are successfully translated into functional proteins.

They undergo additional splicing to remove the stop codon.

Which factor is involved in associating with mRNA during its export and monitoring for premature stop codons?

Upf3 Signup and view all the answers

What happens to the mRNA if Upf3 is not displaced by the ribosome during translation?

It triggers mRNA decay due to EJC retention. Signup and view all the answers

What is the primary function of tRNAs in protein synthesis?

They transport amino acids to the ribosome. Signup and view all the answers

Which step involves the formation of a high-energy ester bond?

Linkage of an amino acid to a tRNA. Signup and view all the answers

What role does ATP play in the linkage of an amino acid to tRNA?

It supplies energy for the linkage reaction. Signup and view all the answers

How does the tRNA-mRNA interaction contribute to protein synthesis?

It ensures that the correct amino acid is matched to the codon. Signup and view all the answers

What is produced as a byproduct when an amino acid is linked to tRNA?

AMP and PPi Signup and view all the answers

What is the significance of the 3' CCA linkage in tRNA?

It links the tRNA to its specific synthetase. Signup and view all the answers

Which enzyme is responsible for linking phenylalanine to its specific tRNA?

Aminoacyl-tRNA synthetase Signup and view all the answers

What type of bond is formed between the amino acid and the tRNA?

High-energy ester bond Signup and view all the answers

What initiates the binding of the tRNA to the mRNA during translation?

Formation of the Phe-tRNA Phe complex Signup and view all the answers

What is the net result of the tRNA-mRNA interaction during protein synthesis?

The accurate translation of the genetic code into a polypeptide chain is facilitated. Signup and view all the answers

What is the primary function of tRNAiMet in bacteria?

To initiate the formation of a polypeptide chain Signup and view all the answers

Which ribosome binding site does tRNAMet interact with during translation?

80S ribosome A site Signup and view all the answers

How does tRNAiMet differ from tRNAMet in terms of methionine modification?

tRNAiMet has a formyl group, while tRNAMet is unmodified Signup and view all the answers

Which enzyme is responsible for charging both tRNAiMet and tRNAMet?

Aminoacyl tRNA synthetase Signup and view all the answers

What common characteristic do both tRNAiMet and tRNAMet share?

They are charged by the same aminoacyl tRNA synthetase Signup and view all the answers

What complex is formed when eIF2-GTP interacts with tRNA-Met(i)?

43S PIC Signup and view all the answers

Which factors are bound to the 40S ribosomal subunit during the initiation of translation?

eIF1, eIF1A, eIF3 Signup and view all the answers

What is the significance of eIF5 in the translation initiation process?

It forms the 43S PIC by interacting with other initiation factors. Signup and view all the answers

What does 'Met' refer to in the context of translation initiation?

Methionine Signup and view all the answers

Which function does GTP serve during the translation initiation process?

It provides energy for the binding of eIF2 to tRNA. Signup and view all the answers

What is the initial recognition point for the translation initiation process?

5' cap of mRNA Signup and view all the answers

Which factor is primarily responsible for the recruitment of the 43S preinitiation complex?

elF4G Signup and view all the answers

What activity does elF4A perform during the scanning process in translation initiation?

RNA helicase activity Signup and view all the answers

Which molecular component is necessary for the attachment of the 43S PIC to mRNA?

AUG sequence Signup and view all the answers

What is the role of PABPC in translation initiation?

Interaction with the elF4G protein Signup and view all the answers

In the context of mRNA activation, what do the factors within the elF4 complex facilitate?

Interaction with the mRNA structure Signup and view all the answers

Which of the following sequences is essential for initiating protein synthesis?

AUG codon Signup and view all the answers

What type of molecular activity is required for the 43S PIC to proceed with translation initiation?

Helicase activity Signup and view all the answers

What is the function of eIF4 during the translation initiation process?

To bind and activate the mRNA. Signup and view all the answers

Which step in translation initiation involves the formation of the 48S initiation complex?

Recognition of AUG codon by initiator tRNA. Signup and view all the answers

What is the result of eIF2-bound GTP hydrolysis during translation initiation?

Release of GDP and addition of the large ribosomal subunit. Signup and view all the answers

Which component is primarily responsible for the recognition of the AUG start codon during translation initiation?

Initiator tRNA (tRNA-Met). Signup and view all the answers

What function does GTP serve in the translation initiation process?

To energize the eIFs and assist in complex formation. Signup and view all the answers

Which step is primarily responsible for the release of initiation factors during translation initiation?

Hydrolysis of elF5B-bound GTP Signup and view all the answers

What role does GTP play during the translation initiation process?

It is involved in the formation of the initiation complex Signup and view all the answers

Which of the following is NOT a component of the 80S ribosome complex during translation initiation?

PABPC Signup and view all the answers

Which factor is essential for the binding of initiator tRNA to the small ribosomal subunit?

elF1A and elF5B Signup and view all the answers

What is the correct order of events starting from the binding of the initiator tRNA to the assembly of the 80S ribosome?

Initiator tRNA binding, mRNA binding, conformational change, GTP hydrolysis Signup and view all the answers

What is the primary role of the A site in the ribosome during elongation?

To facilitate the binding of incoming amino acids Signup and view all the answers

Which molecule is crucial for the entry of tRNA into the A site?

Elongation factor EF1α Signup and view all the answers

What occurs immediately after a peptide bond is formed during the elongation process?

The ribosome moves one codon down the mRNA Signup and view all the answers

In the context of the elongation phase, what is the fate of the tRNA once it enters the E site?

It is released from the ribosome Signup and view all the answers

Which step in the translation elongation process emphasizes the importance of codon-anticodon pairing?

Entry of the tRNA into the A site Signup and view all the answers

What triggers the hydrolysis of EF1α-GTP during translation elongation?

Base-pairing of the anticodon-codon Signup and view all the answers

During which stage does the molecule EF1α release GDP and Pi?

Stage 2, after codon-anticodon pairing Signup and view all the answers

What is the primary effect of EF1α hydrolysis during translation elongation?

It brings amino acids in the P and A sites closer together. Signup and view all the answers

What structural change occurs in the ribosome due to the hydrolysis of EF1α-GTP?

It causes a conformational change. Signup and view all the answers

What molecule binds to the A site of the ribosome in the first stage of translation elongation?

EF1α-GTP Signup and view all the answers

What is the role of the hydrolysis of EF1alpha-GTP in the translation elongation process?

It triggers conformational changes that promote peptide bond formation. Signup and view all the answers

Which statement accurately describes the function of the ribosome's A site during translation elongation?

It accepts incoming aminoacyl-tRNAs for peptide bond formation. Signup and view all the answers

In the context of elongation, what effect does the proximity of amino acids in the P and A sites have?

It enables the ribozyme to catalyze peptide bonding. Signup and view all the answers

What is the primary function of the E site during translation elongation?

To allow the exit of deacylated tRNA. Signup and view all the answers

What occurs immediately after the formation of a peptide bond during translation elongation?

The ribosome translocates to the next codon on the mRNA. Signup and view all the answers

What is the primary action that occurs during ribosome translocation?

The ribosome moves one codon downstream along the mRNA. Signup and view all the answers

Which site in the ribosome is responsible for holding the tRNA that carries the growing polypeptide chain?

P site Signup and view all the answers

What drives the process of ribosome translocation during translation elongation?

Hydrolysis of EF2-GTP Signup and view all the answers

What occurs to the tRNA in the A site after the ribosome translocates?

It moves to the P site. Signup and view all the answers

Which statement correctly describes the role of EF2 during ribosome translocation?

EF2-GTP hydrolysis facilitates the movement of the ribosome. Signup and view all the answers

What is the primary function of the A site in the ribosome during translation elongation?

To bind tRNA carrying the next amino acid Signup and view all the answers

What happens to EF1α after GTP hydrolysis occurs during translation elongation?

It releases GDP and Pi Signup and view all the answers

Which of the following statements describes the role of GTP in the elongation process?

It drives the conformational change of the ribosome after tRNA binding Signup and view all the answers

What is the significance of the conformational change in the ribosome during translation elongation?

It positions the tRNA for peptide bond formation Signup and view all the answers

Which site on the ribosome is primarily associated with the exit of tRNA after it has donated its amino acid?

E site Signup and view all the answers

What role does eRF3-GTP play during translation termination?

It assists eRF1 in recognizing the STOP codon. Signup and view all the answers

What immediately occurs after eRF3 is hydrolyzed?

The ribosome complex undergoes dissociation. Signup and view all the answers

Which component is primarily involved in the binding process to the A site during translation termination?

eRF1 Signup and view all the answers

What is the significance of the conformational change that occurs during translation termination?

It facilitates the cleavage of the peptide from the ribosome. Signup and view all the answers

What occurs to the ribosome complex after the peptide chain is cleaved during termination?

It disassociates completely into its subunits. Signup and view all the answers

What is the first step in the 5' → 3' degradation pathway of mRNA decay?

Decapping by Dcp1/2 Signup and view all the answers

Which enzyme is responsible for degrading RNA from the 3' end towards the 5' end?

Exosome complex Signup and view all the answers

What happens to the Poly(A) tail during the deadenylation-mediated decay process?

It is shortened until it can no longer bind to PABPC Signup and view all the answers

Which component is crucial for initiating the decapping process before mRNA degradation?

7-methylguanosine cap Signup and view all the answers

Which complex is essential for the further degradation of mRNA fragments generated during 3' → 5' degradation?

Exosome complex Signup and view all the answers

What is the role of DCP2 in the RNA decay process?

It is involved in the decapping process. Signup and view all the answers

How does the decapping process influence XRN1 activity?

It stimulates XRN1 exonuclease activity. Signup and view all the answers

Which component is not directly associated with the decapping process?

Rps28B Signup and view all the answers

What initiates the RNA degradation from the 5' end in the Deadenylation Independent pathway?

Decapping of the m7G cap. Signup and view all the answers

Which of the following statements about the components involved in RNA decay is incorrect?

AAAA is critical for the initiation of the decapping process. Signup and view all the answers

What is the primary function of endonucleases in RNA decay?

To cut the RNA at specific internal points Signup and view all the answers

Which component is involved in the degradation pathway known as 3' → 5' decay?

Exosome Signup and view all the answers

What marks the beginning of an RNA molecule during the 5' → 3' decay pathway?

Modified guanosine cap (m⁷G) Signup and view all the answers

Which of the following statements is true regarding the roles of exonucleases in RNA decay?

Exonucleases operate following the internal cleavage by endonucleases. Signup and view all the answers

How does the RISC complex regulate mRNA translation?

By promoting the degradation of mRNA Signup and view all the answers

What is the primary role of microRNAs (miRNAs) in gene expression?

To repress translation and induce degradation of target mRNAs Signup and view all the answers

What percentage of protein-coding genes is affected by microRNAs?

60% Signup and view all the answers

In which cellular process are miRNAs critical?

Metabolism and developmental timing Signup and view all the answers

Which of the following accurately describes the structure of miRNAs?

Short double-stranded RNA molecules that imperfectly bind to target mRNAs Signup and view all the answers

Study Notes

Nonsense Mediated Decay (NMD)

Improperly spliced messenger RNA (mRNA) molecules often contain premature stop codons (PTC) which occur before the last splice junction.
This process, NMD, targets such mRNAs for degradation via a surveillance pathway.
Premature stop codons are found before the last splice junction.

Mechanism of NMD

Exon Junction Complex (EJC) deposition:
- The Exon Junction Complex (EJC) is deposited at exon-exon junctions during mRNA splicing.
Upf3 association:
- Upf3 proteins associate with mRNA during mRNA export.
Ribosomal displacement:
- During translation, the ribosome moves along the mRNA.
- If the ribosome encounters a stop codon upstream of the EJC, Upf3 is usually displaced, and translation proceeds.
NMD activation/mRNA decay:
- If Upf3 is not displaced by the ribosome due to a premature stop codon before the last splice junction, its presence triggers mRNA degradation. This can involve phosphorylation of UPF1, a subunit of the NMD machinery, and the involvement of SMG1 and UPF2.
  -The EJC is retained in the transcript with a premature stop codon (PTC), and this leads to activation of the NMD pathway and subsequent mRNA decay. -In a normal transcript, the EJC is released from the message by the ribosome. No NMD is activated.
- mRNA decay involves the degradation of the mRNA.
- mRNA degradation typically occurs fragmenting the message into smaller pieces which are either removed or destroyed.

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Description

This quiz covers the process of Nonsense Mediated Decay (NMD) and its importance in regulating improperly spliced mRNA. It includes details on the roles of the Exon Junction Complex, Upf3 proteins, and the activation of NMD leading to mRNA degradation. Test your understanding of these molecular mechanisms.