RNA Processing and Splicing Questions and Answers

Q: RNAs that catalyze biochemical reactions such as self-splicing nitrous are known as :

Catalytic RNAs are known as ribozymes.Thomas Cech showed in the early 1980s that the group I intron of Tetrahymena rRNA splices itself out with no protein enzyme, and Sidney Altman showed that the RNA of RNase P cuts tRNA precursors; they shared the 1989 Nobel Prize in Chemistry. The peptidyl transferase that forms peptide bonds in the ribosome is also an RNA, so ribozymes are central to life. (The paper's 'self-splicing nitrous' means self-splicing introns.)Spliceosomes are complexes of RNA and protein that splice nuclear pre-mRNA. Mature RNAs are processed transcripts in general, and lariats are the looped introns released by splicing, not the catalysts.

Q: In Leishmania it was shown that the minicircles :

The minicircles encode guide RNA (gRNA) molecules involved in the RNA editing of maxicircle cryptogene.The mitochondrial DNA (kinetoplast DNA) of Leishmania and trypanosomes is a network of a few dozen maxicircles and thousands of minicircles. Maxicircles carry the mitochondrial genes, but many are 'cryptogenes' whose transcripts cannot be translated until uridines are inserted or deleted by RNA editing. The short guide RNAs that template this editing are encoded mostly by the minicircles.Minicircles carry no cryptogenes of their own to edit, which rules out option B, and their products are guide RNAs, not microRNAs or unspecified noncoding RNA.

Q: Which of the following sn RNAs pair to form the catalytic active site during pre-mRNA splicing ?

The pair is U6-U2.During spliceosome activation, U4 snRNA, which holds U6 in an inactive base-paired form, is released. U6 then pairs with U2, which is itself paired with the branch-point region of the intron. The U2-U6 structure, with bound metal ions, forms the catalytic core that carries out both transesterification steps of splicing; the spliceosome is therefore a ribozyme.U1 pairs with the 5' splice site early on and leaves before catalysis, and U6-U4 is the inactive pre-catalytic pair. U5 holds the exons in place but does not pair with U4 in the active site.

Q: A transcription unit is 8000 nucleotides long. If only 15% of this unit is exon, calculate the approximate molecular weight of the protein encoded :

The protein is about 44 kDa.Only the exons are translated. Three nucleotides code for one amino acid, and an average amino acid residue weighs about 110 Da:\[ \begin{aligned} \text{exon} &= 0.15 \times 8000 = 1200 \text{ nt} \\ \text{residues} &= 1200 / 3 = 400 \\ \text{mass} &= 400 \times 110 = 44000 \text{ Da} \end{aligned} \]1200 kDa mistakes the number of nucleotides for kilodaltons. 40 kDa uses 100 Da per residue, and 100 kDa ignores the fact that only 15% of the unit is exon.

Q: The nucleotides from the 5'end of the bacterial tRNA precursor are cleaved during the maturation process. Which enzyme is involved in this process ?

The 5' leader of a tRNA precursor is removed by RNase P.RNase P is an endonuclease that cuts the precursor to leave the mature 5' end of the tRNA. It is a ribonucleoprotein, and in bacteria its RNA subunit (M1 RNA in E. coli) is itself the catalyst: Sidney Altman's work on it was one of the discoveries of ribozymes, recognised by the 1989 Nobel Prize.RNase Z processes the other end, cutting off the 3' trailer. tRNA nucleotidyltransferase adds the CCA sequence to the 3' end. S1 nuclease is a fungal enzyme that degrades single-stranded nucleic acids and is used as a laboratory tool, not in tRNA maturation.

Q: The disease which arises because of aberrant splicing is :

The disease arising from aberrant splicing is thalassemia.Many β-thalassemia alleles are splicing mutations. Changes at the GT or AG splice sites abolish normal splicing, and others create new cryptic splice sites within the introns of the β-globin gene, so the mRNA is processed wrongly and little or no functional β-globin is made. It is the classic textbook example of disease caused by defective splicing.Huntington's disease is caused by an expanded CAG repeat. Sickle cell anemia is a single missense mutation (Glu6Val) in β-globin. Cystic fibrosis is most often due to the ΔF508 deletion in CFTR, a protein-folding defect.

Q: Which of the following type of RNA functions as components of RNA splicing machinery ?

The splicing machinery uses small nuclear RNA (snRNA).The spliceosome is built from small nuclear ribonucleoproteins, each containing an snRNA: U1, U2, U4, U5 and U6. These RNAs base-pair with the 5' splice site, the branch point and each other, and help catalyse the removal of introns from pre-mRNA.tRNA carries amino acids to the ribosome during translation. siRNA and microRNA silence genes after transcription by guiding mRNA cleavage or translational repression; they are not part of the spliceosome.

RNAs that catalyze biochemical reactions such as self-splicing nitrous are known as :

A.Spliceosomes
B.Mature RNAs
C.Ribozymes
D.Lariats

Exam Year(s)

MH SET - 2018, SET Exam - 2018,

Answer: C

Catalytic RNAs are known as ribozymes.

Thomas Cech showed in the early 1980s that the group I intron of Tetrahymena rRNA splices itself out with no protein enzyme, and Sidney Altman showed that the RNA of RNase P cuts tRNA precursors; they shared the 1989 Nobel Prize in Chemistry. The peptidyl transferase that forms peptide bonds in the ribosome is also an RNA, so ribozymes are central to life. (The paper's 'self-splicing nitrous' means self-splicing introns.)

Spliceosomes are complexes of RNA and protein that splice nuclear pre-mRNA. Mature RNAs are processed transcripts in general, and lariats are the looped introns released by splicing, not the catalysts.

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In Leishmania it was shown that the minicircles :

A.Encode guide RNA (gRNA) molecules involved in the RNA editing of maxicircle cryptogene
B.Encode guide RNA (gRNA) molecules involved in the RNA editing of minicircle cryptogene
C.Encode micro RNA
D.Encode noncoding RNA

Exam Year(s)

MH SET - 2019, SET Exam - 2019,

Answer: A

The minicircles encode guide RNA (gRNA) molecules involved in the RNA editing of maxicircle cryptogene.

The mitochondrial DNA (kinetoplast DNA) of Leishmania and trypanosomes is a network of a few dozen maxicircles and thousands of minicircles. Maxicircles carry the mitochondrial genes, but many are 'cryptogenes' whose transcripts cannot be translated until uridines are inserted or deleted by RNA editing. The short guide RNAs that template this editing are encoded mostly by the minicircles.

Minicircles carry no cryptogenes of their own to edit, which rules out option B, and their products are guide RNAs, not microRNAs or unspecified noncoding RNA.

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Which of the following sn RNAs pair to form the catalytic active site during pre-mRNA splicing ?

A.U6-U2
B.U1-U2
C.U6-U4
D.U5-U4

Exam Year(s)

MH SET - 2019, SET Exam - 2019,

Answer: A

The pair is U6-U2.

During spliceosome activation, U4 snRNA, which holds U6 in an inactive base-paired form, is released. U6 then pairs with U2, which is itself paired with the branch-point region of the intron. The U2-U6 structure, with bound metal ions, forms the catalytic core that carries out both transesterification steps of splicing; the spliceosome is therefore a ribozyme.

U1 pairs with the 5' splice site early on and leaves before catalysis, and U6-U4 is the inactive pre-catalytic pair. U5 holds the exons in place but does not pair with U4 in the active site.

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A transcription unit is 8000 nucleotides long. If only 15% of this unit is exon, calculate the approximate molecular weight of the protein encoded :

A.40 kDa
B.1200 kDa
C.44 kDa
D.100 kDa

Exam Year(s)

MH SET - 2020, SET Exam - 2020,

Answer: C

The protein is about 44 kDa.

Only the exons are translated. Three nucleotides code for one amino acid, and an average amino acid residue weighs about 110 Da:

\[ \begin{aligned} \text{exon} &= 0.15 \times 8000 = 1200 \text{ nt} \\ \text{residues} &= 1200 / 3 = 400 \\ \text{mass} &= 400 \times 110 = 44000 \text{ Da} \end{aligned} \]

1200 kDa mistakes the number of nucleotides for kilodaltons. 40 kDa uses 100 Da per residue, and 100 kDa ignores the fact that only 15% of the unit is exon.

Discuss in Forum

The nucleotides from the 5'end of the bacterial tRNA precursor are cleaved during the maturation process. Which enzyme is involved in this process ?

A.RNase P
B.RNase Z
C.t-RNA nucleotidyl transferase
D.\(S_{1}\) nuclease

Exam Year(s)

MH SET - 2023, SET Exam - 2023,

Answer: A

The 5' leader of a tRNA precursor is removed by RNase P.

RNase P is an endonuclease that cuts the precursor to leave the mature 5' end of the tRNA. It is a ribonucleoprotein, and in bacteria its RNA subunit (M1 RNA in E. coli) is itself the catalyst: Sidney Altman's work on it was one of the discoveries of ribozymes, recognised by the 1989 Nobel Prize.

RNase Z processes the other end, cutting off the 3' trailer. tRNA nucleotidyltransferase adds the CCA sequence to the 3' end. S1 nuclease is a fungal enzyme that degrades single-stranded nucleic acids and is used as a laboratory tool, not in tRNA maturation.

Discuss in Forum

The disease which arises because of aberrant splicing is :

A.Huntington's disease
B.Cystic fibrosis
C.Sickle cell anemia
D.Thalassemia

Exam Year(s)

MH SET - 2024, SET Exam - 2024,

Answer: D

The disease arising from aberrant splicing is thalassemia.

Many β-thalassemia alleles are splicing mutations. Changes at the GT or AG splice sites abolish normal splicing, and others create new cryptic splice sites within the introns of the β-globin gene, so the mRNA is processed wrongly and little or no functional β-globin is made. It is the classic textbook example of disease caused by defective splicing.

Huntington's disease is caused by an expanded CAG repeat. Sickle cell anemia is a single missense mutation (Glu6Val) in β-globin. Cystic fibrosis is most often due to the ΔF508 deletion in CFTR, a protein-folding defect.

Discuss in Forum

Which of the following type of RNA functions as components of RNA splicing machinery ?

A.t-RNA
B.Small nuclear RNA (Sn RNA)
C.Small interfering RNA (Si RNA)
D.Micro RNA

Exam Year(s)

MH SET - 2025, SET Exam - 2025,

Answer: B

The splicing machinery uses small nuclear RNA (snRNA).

The spliceosome is built from small nuclear ribonucleoproteins, each containing an snRNA: U1, U2, U4, U5 and U6. These RNAs base-pair with the 5' splice site, the branch point and each other, and help catalyse the removal of introns from pre-mRNA.

tRNA carries amino acids to the ribosome during translation. siRNA and microRNA silence genes after transcription by guiding mRNA cleavage or translational repression; they are not part of the spliceosome.

Discuss in Forum

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