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4.4 RNA Processing ā Test 1
Q1. The 5' cap of mRNA is required for:ā Stability, splicing, transport and translation initiation of the mRNA
Q2. The immediate product of eukaryotic transcription (by Pol II) is:ā A pre-mRNA (primary transcript)
Q3. Cryptic splice sites are sequences that:ā Resemble consensus splice signals but are not normally used as true sites
Q4. RNA molecules that catalyse biochemical reactions are called:ā Ribozymes
Q5. Which is NOT a part of the prokaryotic transcription process?ā Polyadenylation (eukaryotic-style)
Q6. A bacterial (operonic) mRNA characteristically:ā Has multiple ORFs/stop codons (polycistronic)
Q7. A gene with promoter, 280 bp 5'UTR, three exons (1.2 + 2 + 4 kb) and two introns, 170 bp 3'UTR ā the mature mRNA size is approximately:ā 7.65 kb (ā7.2 kb exons + UTRs)
Q8. A signal peptide typically contains:ā A positively charged N-terminal region followed by ~10ā15 hydrophobic residues
Q9. Apolipoprotein B is 100 kD in liver but 48 kD in intestine from the same gene because of:ā RNA editing (CāU creating a stop codon)
Q10. Berk-Sharp (S1 nuclease) mapping is used to analyse:ā Intron-exon junctions / transcript structure
Q11. During splicing, which snRNP binds the branch-site sequence in the intron?ā U2
Q12. Which snRNP binds the 5' splice site of pre-mRNA?ā U1
Q13. The 5' cap structure consists of:ā A 7-methylguanosine joined by a 5'-5' triphosphate linkage to the first nucleotide
Q14. Which statement about the 5' cap is INCORRECT?ā It protects the transcript from RNase III-family enzymes
Q15. RNA editing is best defined as:ā Alteration of the nucleotide sequence of an RNA after transcription
Q16. Following reverse transcription, which element is absent from the double-stranded cDNA?ā Intron sequences
Q17. Guide-RNA-dependent uridylate insertion (kinetoplastid editing) requires all the following EXCEPT:ā 3'-U-exonuclease (for insertion)
Q18. Group I and group II self-splicing introns: which statements are correct? A) Group I self-splice by transesterification; C) some group I/II introns contain ORFs translated into protein; D) group II introns can move by RNA-mediated (retro) mechanisms.ā A, C, D
4.4 RNA Processing ā Test 2
Q19. Events occurring in the cytoplasm include:ā Protein synthesis (translation)
Q20. Heterogeneous nuclear RNA (hnRNA = pre-mRNA) is transcribed by:ā RNA Pol II
Q21. In Leishmania/trypanosomes, minicircles of kinetoplast DNA encode:ā Guide RNAs (gRNA) for editing maxicircle cryptogene transcripts
Q22. In the RNAi pathway, Dicer cleaves:ā Long double-stranded RNA into short (~21ā23 nt) duplexes
Q23. In trypanosomes, joining a 35-base spliced-leader to many transcripts occurs by:ā Trans-splicing
Q24. Nonsense-mediated mRNA decay (NMD) initiation involves the:ā Exon junction complex (EJC)
Q25. Initiation of translation from most eukaryotic mRNAs requires:ā The 5' cap (and poly-A tail for efficiency)
Q26. Intron removal from pre-mRNA is carried out by the:ā Spliceosome
Q27. In some protozoan parasites, a leader transcribed elsewhere is joined to many transcripts by:ā Trans-splicing
Q28. Multiple self-splicing introns nested within one another are called:ā Twintrons
Q29. An internal ribosome entry site (IRES) in an mRNA:ā Promotes cap-independent translation (e.g. under stress)
Q30. Which event is NOT involved in eukaryotic mRNA splicing?ā Coupling each phosphodiester bond to ATP hydrolysis (chemistry is via transesterification)
Q31. Ribozymes splice introns by:ā Transesterification
Q32. RNA editing by guide RNA ā which statement is NOT true?ā gRNA is mainly for chemical modification of tRNA
Q33. Self-splicing RNAs are examples of:ā Ribozymes
Q34. The spliceosome (snRNA + protein + pre-mRNA) is found in:ā Eukaryotic cells
Q35. Intron splicing chemistry occurs by:ā Trans-esterification
Q36. Which nucleotide in the intron is critical for lariat formation?ā Adenine (the branch-point A)
4.4 RNA Processing ā Test 3
Q37. Scientists find it hard to map the exact transcription termination site in eukaryotes because:ā The 3' end is generated by cleavage prior to actual termination, then polyadenylated
Q38. Which is a POST-TRANSLATIONAL modification?ā Protein folding/glycosylation
Q39. Which statement about siRNA is NOT true?ā It cannot act at the transcriptional level
Q40. Components of the mammalian polyadenylation machinery include:ā CPSF, CstF, CF I/II, poly(A) polymerase, PABII and symplekin
Q41. Poly(A) polymerase (PAP) adds the poly-A tail by:ā Template-independently adding AMP from ATP to the 3' end
Q42. The polyadenylation signal recognised by CPSF is:ā AAUAAA
Q43. Venkatraman Ramakrishnan's Nobel Prize was for work on the:ā Structure and function of the ribosome
Q44. A disease arising from aberrant splicing is:ā Ī²-thalassaemia (splice-site mutations)
Q45. The chicken ovalbumin primary transcript (7700 nt) is much larger than the mature mRNA mainly due to:ā mRNA splicing (intron removal)
Q46. RNA editing that involves a cytidine deaminase is:ā Substitution editing (CāU, as in apoB)
Q47. Protein splicing refers to:ā Removing intervening protein sequences (inteins) from a translated protein
Q48. Which RNA functions as a component of the splicing machinery?ā Small nuclear RNA (snRNA)
Q49. Which snRNAs pair to form the catalytic core of the spliceosome?ā U6 and U2
Q50. Alternative splicing is best described as:ā Producing multiple distinct mRNAs/proteins from a single gene by joining different exon combinations
Q51. Which is a ribonucleoprotein enzyme whose catalytic activity resides in its RNA component?ā RNase P
Q52. hnRNA-binding proteins ā which statement is INCORRECT?ā They are core catalytic subunits of the ribosome
Q53. Which one of these does NOT use RNA sequencing as the core method?ā Mammalian epigenome (DNA methylation) sequencing
Q54. The 'wrong' statement about mRNA among these is:ā Poly(A) is added to the 5' end
4.4 RNA Processing ā Test 4
Q55. Which statement about eukaryotic RNA processing is INCORRECT?ā Capping occurs at the 3' end
Q56. Which statement about mRNA processing is INCORRECT?ā mRNAs lacking an in-frame stop codon are stabilized and efficiently translated
Q57. Which process can make one gene encode two or more related proteins?ā Alternative RNA splicing
Q58. For designing a eukaryotic expression microarray with unique probes, the best region to target is:ā The 3' region of the coding sequence and 3' UTR (more gene-specific)
Q59. In trypanosomes, the Y-shaped (branched) intermediate replacing a lariat is generated during:ā Trans-splicing
Q60. The poly-A tail and its binding protein (PABP) function to:ā Enhance mRNA stability and translation (closed-loop with the cap)
Q61. The branch-point adenosine's role in splicing is to:ā Provide the 2'-OH that attacks the 5' splice site (first transesterification)
Q62. Capping enzymes are recruited to the transcript via:ā The phosphorylated CTD (Ser5) of RNA Pol II
Q63. AāI (adenosine-to-inosine) RNA editing is carried out by:ā ADAR (adenosine deaminase acting on RNA)
Q64. The exon junction complex (EJC) is deposited:ā Upstream of exon-exon junctions after splicing
Q65. Group I intron self-splicing is initiated by:ā A free guanosine (G) cofactor whose 3'-OH attacks the 5' splice site
Q66. Which describes the cap-binding complex's role?ā Binds the 5' cap to aid splicing, export and translation initiation
Q67. tRNA splicing differs from pre-mRNA splicing in that it:ā Uses protein enzymes (endonuclease + ligase), not snRNPs
Q68. Nonsense-mediated decay (NMD) targets mRNAs that:ā Contain a premature termination codon (upstream of an EJC)
Q69. Which best describes co-transcriptional processing?ā Capping, splicing and 3' processing occur while the transcript is still being made, coordinated by the Pol II CTD
Q70. miRNAs regulate gene expression mainly by:ā Base-pairing (often imperfectly) with target mRNA 3'UTRs to repress translation or destabilize mRNA
Q71. The closed-loop model of mRNA describes interaction between:ā The 5' cap (via eIF4G) and the 3' poly-A tail (via PABP)
Q72. Which modification protects the mRNA 3' end and signals maturity?ā Poly-A tail
4.4 RNA Processing ā Test 5
Q73. Ī²-position Ā³Ā²P-labelled ATP is used during mRNA synthesis/processing. Where does the label most likely end up in mature mRNA?ā Retained at the 5' cap region (the Ī²-phosphate becomes part of the 5'-5' cap triphosphate)
Q74. Group II introns are notable because they:ā Self-splice via a branch-point adenosine (lariat), resembling spliceosomal splicing
Q75. Which RNA type guides chemical modification (e.g. 2'-O-methylation, pseudouridylation) of rRNA?ā snoRNA
Q76. The processing of the eukaryotic 45S pre-rRNA yields:ā 18S, 5.8S and 28S rRNAs
Q77. Which best describes pre-mRNA capping timing?ā Co-transcriptionally, soon after the first ~25 nt are made
Q78. The spliceosome assembly order begins with:ā U1 binding the 5' splice site, then U2 at the branch point
Q79. ADAR-mediated AāI editing can:ā Recode codons, create/destroy splice sites, and alter miRNA targeting
Q80. Which enzyme removes introns from nuclear pre-mRNA?ā The spliceosome (snRNP-based ribozyme machinery)
Q81. Deadenylation (poly-A tail shortening) generally leads to:ā mRNA decay (decapping and degradation)
Q82. Which best describes trans-splicing?ā Joining exons from two separate RNA molecules
Q83. Which feature distinguishes mature eukaryotic mRNA from pre-mRNA?ā A 5' cap, removal of introns, and a 3' poly-A tail
Q84. The 'spliced leader' added in trans-splicing provides:ā A capped 5' end and common leader to many mRNAs
Q85. Which is true of the catalytic mechanism of the spliceosome?ā It is RNA-catalysed (U6/U2 form the active site) ā a ribozyme
Q86. Which describes the role of CstF in 3' processing?ā Binds the downstream GU/U-rich element to help define the cleavage site
Q87. AāI and CāU editing are examples of which broad type of editing?ā Substitution (base-modification) editing
Q88. Which RNA is the catalytic component of the ribosome (peptidyl transferase)?ā rRNA (the large-subunit rRNA)
Q89. The first chemical step of pre-mRNA splicing is:ā The branch-point A 2'-OH attacking the 5' splice site (lariat formation)
Q90. Which best describes the relationship of group II introns to the spliceosome?ā Mechanistically similar (branch-A, lariat) and possibly evolutionarily related