RNA Splicing

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Questions and Answers

What type of elements can act on any different splice site on the genome?

Trans acting elements (correct)

Spliceosome proteins

Cis elements

snRNPs

Which type of proteins bind to sequences in exons and recruit components of the core splicing machinery?

heterogeneous nuclear ribonucleoproteins (hnRNPs)

SR Proteins (correct)

Splicing repressors

Splicing activators

What is the function of the exon junction complex (EJC)?

To remove the first round of translation

To recycle back into the nucleus

To deposit 24 nucleotides upstream of spliced junctions during splicing (correct)

To stabilize the complex

What is the outcome of Alternative splicing?

Increases the complexity of the protein that can be generated from the available genomic coding sequences Signup and view all the answers

What is the function of nonsense-mediated mRNA decay (NMD)?

To eliminate transcripts with premature termination codons Signup and view all the answers

Which type of RNAs are involved in post-transcriptional control?

Non-coding RNAs Signup and view all the answers

What type of splicing involves splicing between two pre-mRNA molecules?

Trans splicing Signup and view all the answers

What is the function of heterogeneous nuclear ribonucleoproteins (hnRNPs)?

To bind to sequences in exons or introns and interfere with binding of core splicing machinery Signup and view all the answers

What is the primary mode of action of regulatory RNAs?

Scaffolding to recruit proteins, DNA, and/or RNA Signup and view all the answers

What is the main function of molecular chaperones?

To recognize and correct misfolded proteins Signup and view all the answers

What is the primary function of heat shock proteins HSP60 and HSP70?

To act as molecular chaperones Signup and view all the answers

What is the purpose of ubiquitination?

To mark proteins for degradation Signup and view all the answers

During co-translational folding, where does protein compaction occur?

Within the polypeptide exit tunnel and at the surface of the ribosome Signup and view all the answers

What is the function of the chaperonin HSP60?

To act as a barrel-shaped isolation chamber for protein refolding Signup and view all the answers

What is the characteristic of regulatory RNAs that reflects their function?

Their ability to bind proteins Signup and view all the answers

What is the purpose of ATP hydrolysis in the HSP70 chaperone cycle?

To provide energy for protein folding Signup and view all the answers

Study Notes

Splicing

RNA molecules, in complex with proteins, perform key steps in splicing, rather than proteins alone.
Cis elements involved in splicing include:
5' splice site (donor site)
3' splice site (acceptor site)
Branch point
Polypyrimidine tract
Trans-acting elements can act on any different splice site in the genome.

Alternative Splicing

Increases the complexity of the protein that can be generated from available genomic coding sequences.
Regulated by cis-acting elements, trans-acting factors, transcription, and chromatin structure.
Alternative splicing is a key regulatory mechanism.

Splicing Activators and Repressors

SR Proteins:
Have extensive repeats of serine and arginine.
Are RNA binding proteins.
Bind to sequences in exons, recruiting components of the core splicing machinery and activating splicing.
hnRNPs (heterogeneous nuclear ribonucleoproteins):
Are RNA binding proteins.
Bind to sequences in exons or introns.
Interfere with the binding of core splicing machinery, repressing splicing.

Trans Splicing

Involves splicing between two pre-mRNA molecules.
Involves the same signals and components as cis splicing.
Occurs in a variety of organisms, including Drosophila and C. elegans.
In mammalian cells, can be associated with cancer.

Nonsense-Mediated mRNA Decay (NMD)

Is a RNA quality control mechanism.
Eliminates transcripts with premature termination codons (PTCs).
Premature stop codons can arise from mutations, defects in splicing or transcription.
Is a gene regulatory mechanism that also targets non-mutant transcripts.

Exon Junction Complex (EJC)

Is deposited 24 nucleotides upstream of spliced junctions during splicing.
Is removed by the first round of translation and recycled back into the nucleus.
The core consists of 4 proteins: eIF4A3, MAGOH, RBM8A, and BTZ.

Post-transcriptional Control by Non-coding RNAs

Non-coding RNAs include:
"House-keeping" RNAs (e.g., rRNAs and tRNAs)
Regulatory RNAs, including small ncRNAs (200 nucleotides)
Main mode of action: scaffold to recruit proteins, DNA, and/or RNA.

Post-translational Control

Protein folding involves:
Polypeptide chain folding into a unique 3D conformation.
Final secondary structures, including α-helices and β-sheets.
Most hydrophobic residues are hidden in the interior core.
Co-translational folding occurs within the polypeptide exit tunnel and at the surface of the ribosome.

Molecular Chaperones

Molecular chaperones recognize incorrect configurations due to the exposure of hydrophobic surfaces.
Heat shock proteins (HSP60 and HSP70) are molecular chaperones.
HSP70:
Functions early, sufficient for many proteins.
ATP-bound HSP70 binds to exposed, short stretches of hydrophobic amino acids and hydrolyses ATP to ADP.
Provides opportunity to fold correctly, prevents mis-folding, and formation of aggregates.
Releases the protein when ATP has been exchanged for ADP.
HSP60 (chaperonin):
Acts later, provides a barrel-shaped isolation chamber.
Substrate captured via hydrophobic entrance (helps with unfolding).
Binding of ATP and sealing with cap releases protein into chamber.
Protein re-folding in isolation.
ATP hydrolysis weakens binding of cap.
Binding of new ATP ejects cap and releases protein.

Marking Proteins for Degradation - Ubiquitination

Ubiquitin is a small, 76 amino acid protein.
Ubiquitin is heat-stable and highly evolutionarily conserved.
Ubiquitin is expressed in all eukaryotic cells.
Glycine 76 binds to a lysine residue on the substrate.

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Description

RNA splicing is a process where RNA molecules, in complex with proteins, perform key steps. This quiz covers the cis and trans elements, spliceosome proteins, and alternative splicing. Test your understanding of this crucial biological process.