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RNA and Transcription

Tier 1 · #4 of 33 · highest yield · topic 2.2 — every high-yield fact from the book chapter, exam-ready.

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  1. Front
    By mass, what fraction of total cellular RNA is rRNA ?
    Back
    ~80%
  2. Front
    Which structural feature of ribose makes RNA more reactive and alkaline-labile than DNA?
    Back
    The 2'-hydroxyl (2'-OH) group
  3. Front
    Of the three major RNA types, which is the rarest by cellular mass?
    Back
    mRNA ( ~5% )
  4. Front
    RNA uses ______ in place of thymine ; it lacks the methyl group but pairs with adenine identically.
    Back
    uracil
  5. Front
    Which RNA type makes up ~15% of total cellular RNA?
    Back
    tRNA
  6. Front
    In eukaryotes, which rRNA molecule carries the peptidyl transferase (peptide-bond-forming) catalytic activity?
    Back
    28S rRNA
  7. Front
    In prokaryotes, which rRNA carries the peptidyl transferase activity (the equivalent of eukaryotic 28S )?
    Back
    23S rRNA
  8. Front
    Does the catalytic peptidyl transferase activity of the ribosome reside in the rRNA or the ribosomal proteins?
    Back
    The rRNA ( proteins are scaffolding, not the catalyst )
  9. Front
    Which 3' terminal sequence is present on every eukaryotic tRNA ?
    Back
    CCA
  10. Front
    Is the 3' CCA sequence of tRNA encoded in the genome or added post-transcriptionally?
    Back
    Added post-transcriptionally ( not genome-encoded ), by CCA-adding tRNA nucleotidyltransferase
  11. Front
    Through what type of bond does an amino acid attach to its tRNA ?
    Back
    An ester bond
  12. Front
    To exactly which atom of tRNA is the amino acid esterified?
    Back
    The 3'-OH of the ribose of the terminal adenosine (of the CCA )
  13. Front
    What is the eukaryotic small ribosomal subunit (by Svedberg value), and which rRNA does it contain?
    Back
    40S subunit , containing 18S rRNA
  14. Front
    What is the eukaryotic large ribosomal subunit , and which three rRNAs does it contain?
    Back
    60S subunit , containing 28S, 5.8S, and 5S rRNA
  15. Front
    Which small RNAs guide pseudouridylation and 2'-O-methylation modifications of rRNA ?
    Back
    snoRNAs ( small nucleolar RNAs )
  16. Front
    What are tRNAs that differ in sequence but carry the same amino acid called?
    Back
    Isoacceptor tRNAs
  17. Front
    List the five zones of a mature eukaryotic mRNA in 5'→3' order.
    Back
    5' cap , 5'-UTR , protein-coding region (AUG to stop), 3'-UTR , poly-A tail
  18. Front
    What DNA sequence upstream of the start site determines which strand is read as template for a given gene?
    Back
    The promoter
  19. Front
    What is the name of the DNA strand that the RNA polymerase reads (also called the antisense strand)?
    Back
    The template strand
  20. Front
    Which DNA strand has the same sequence as the RNA product (with T for U)?
    Back
    The coding strand (sense strand)
  21. Front
    Does the whole genome use one designated template strand ?
    Back
    No — different genes use different strands , depending on which strand carries that gene's promoter
  22. Front
    In eukaryotes, which core promoter element sits ~-30 bp upstream of the transcription start?
    Back
    The TATA box
  23. Front
    Which general transcription factor recognizes the TATA box ?
    Back
    TFIID
  24. Front
    TFIID is composed of which two parts?
    Back
    TATA-binding protein (TBP) plus the TBP-associated factors (TAFs)
  25. Front
    Which minimal promoter element can initiate transcription alone even without a functional TATA box ?
    Back
    The Initiator (Inr)
  26. Front
    Which eukaryotic RNA polymerase synthesizes all mRNA (and most snRNA)?
    Back
    RNA Pol II
  27. Front
    Which eukaryotic RNA polymerase makes most rRNA (28S, 18S, 5.8S)?
    Back
    RNA Pol I
  28. Front
    Which eukaryotic RNA polymerase synthesizes tRNA , 5S rRNA , and small stable RNAs?
    Back
    RNA Pol III
  29. Front
    What complex is formed by the ordered assembly of general transcription factors at the promoter before transcription begins?
    Back
    The pre-initiation complex (PIC)
  30. Front
    Which proteins, bound to enhancers , are required to accelerate inefficient PIC formation into productive transcription?
    Back
    Activator proteins
  31. Front
    What is the in vivo Pol II elongation rate?
    Back
    ~2,000 nucleotides per minute
  32. Front
    What is the in vitro elongation rate when polymerase is stripped of elongation factors ?
    Back
    ~300 nucleotides per minute
  33. Front
    Which is the longest known human gene, and roughly how long does it take to transcribe?
    Back
    The dystrophin gene (2,400,000 bp); up to ~20 hours
  34. Front
    Eukaryotic transcription termination is coupled to which process?
    Back
    Cleavage and polyadenylation
  35. Front
    Histone acetylation by HATs neutralizes the positive charge of which residue on histone tails?
    Back
    Lysine
  36. Front
    What is the effect of histone acetylation on chromatin and transcription?
    Back
    Opens chromatin (euchromatin) → transcription ON
  37. Front
    What do HDACs (histone deacetylases) do to chromatin and transcription?
    Back
    Restore the positive charge → compact chromatin (heterochromatin) → transcription OFF
  38. Front
    What effect does DNA methylation at CpG sites have on transcription?
    Back
    Represses transcription
  39. Front
    By what mechanism do distant enhancers and silencers contact the promoter from hundreds of bp away?
    Back
    DNA looping
  40. Front
    What are positive regulatory elements that bind activators called, versus negative ones that bind repressors ?
    Back
    Enhancers ( positive ) vs. silencers/NREs ( negative )
  41. Front
    What is the initial unprocessed Pol II transcript called (heterogeneous nuclear RNA)?
    Back
    pre-mRNA / hnRNA
  42. Front
    What molecule is added as the 5' cap of eukaryotic mRNA ?
    Back
    7-methylguanosine (m7G)
  43. Front
    What unusual linkage joins the 5' cap to the mRNA — the only such bond in a normal RNA chain?
    Back
    A 5'-to-5' triphosphate linkage
  44. Front
    Which translation initiation factor recognizes the 5' cap to recruit ribosomes?
    Back
    eIF4E
  45. Front
    Name the three simultaneous functions of the 5' cap .
    Back
    Protects the 5' end from exonucleases , signals nuclear export , and is recognized by translation initiation factors
  46. Front
    How many adenosine residues are in a typical poly-A tail ?
    Back
    100-250 adenosines
  47. Front
    What is the polyadenylation signal sequence at which the pre-mRNA is cleaved?
    Back
    AAUAAA
  48. Front
    What are the two main functions of the poly-A tail ?
    Back
    Stabilizes the mRNA and facilitates nuclear export
  49. Front
    What are intron -derived sequences (transcribed but absent from mature mRNA) versus the retained sequences called?
    Back
    Introns (removed) vs. exons (retained)
  50. Front
    What ribonucleoprotein complex catalyzes splicing?
    Back
    The spliceosome
  51. Front
    Which five snRNAs make up the spliceosome ?
    Back
    U1, U2, U4, U5, U6
  52. Front
    Virtually all spliceable eukaryotic introns begin with ______ and end with ______ (the GU-AG rule).
    Back
    GU (5' end); AG (3' end)
  53. Front
    In splicing, which group of the branch-point adenosine attacks the 5' splice site to form the lariat?
    Back
    Its 2'-OH (2'-hydroxyl)
  54. Front
    After the lariat forms, which group of the upstream exon attacks the 3' splice site to join the exons?
    Back
    Its free 3'-OH
  55. Front
    What happens to an intron -containing pre-mRNA that fails to be spliced?
    Back
    It is retained in the nucleus and degraded ( splicing is not optional )
  56. Front
    What process joins exons of one pre-mRNA in different combinations to make multiple protein isoforms?
    Back
    Alternative splicing
  57. Front
    Alternative splicing is the primary reason ~20,000 genes can produce roughly how many proteins?
    Back
    >100,000 proteins
  58. Front
    Which is the most common mechanism of alternative splicing ?
    Back
    Exon skipping
  59. Front
    Which proteins generally promote splicing at nearby sites, versus those that generally suppress it?
    Back
    SR proteins ( promote ) vs. hnRNPs ( suppress )
  60. Front
    Which polymerases are used for in vitro transcription of vaccine mRNA ?
    Back
    Phage RNA polymerases ( T7, T3, or Sp6 )
  61. Front
    In the Pfizer/BioNTech COVID-19 vaccine, every uridine was replaced with which modified base?
    Back
    N1-methylpseudouridine (m1ψ)
  62. Front
    What two effects does N1-methylpseudouridine substitution have on vaccine mRNA ?
    Back
    Reduces immunogenicity and increases translation efficiency
  63. Front
    In what are vaccine mRNAs packaged for protection from RNases and cellular uptake?
    Back
    Lipid nanoparticles (LNPs)
  64. Front
    Which two cellular mRNA features must be enzymatically added to vaccine mRNA to prevent rapid degradation?
    Back
    A m7G 5' cap and a poly-A tail
  65. Front
    What is the complete set of RNA molecules transcribed from a genome (coding and non-coding) called?
    Back
    The transcriptome
  66. Front
    What two post-synthesis modifications do snoRNAs guide on rRNA ?
    Back
    Pseudouridylation and 2'-O-methylation of ribose
  67. Front
    Why can RNA fold back on itself to form secondary structure (hairpin loops, bulges, internal loops) while DNA does not?
    Back
    Because RNA is single-stranded , so complementary sequences within the same strand can base-pair
  68. Front
    Name the three secondary-structure motifs RNA forms by intramolecular base-pairing.
    Back
    Hairpin loops, bulges, and internal loops
  69. Front
    Complete the central principle of RNA biology: "______ determines fold, fold determines ______."
    Back
    Sequence ; function
  70. Front
    tRNA folds from which secondary structure into which tertiary shape?
    Back
    From a cloverleaf (secondary) into an L-shape (tertiary)
  71. Front
    In rRNA , what is the structural role of its hairpin/secondary structure?
    Back
    The hairpins scaffold (build the structural framework of) the ribosome
  72. Front
    When an mRNA hairpin is encountered mid-elongation, what happens to the polymerase, and what counteracts it?
    Back
    The hairpin can stall/pause the polymerase ; elongation factors push it through
  73. Front
    Mechanistically, WHY does the cell need elongation factors during transcription?
    Back
    To prevent the polymerase from pausing/stalling at hairpin-forming sequences in the template
  74. Front
    Give the consensus sequence of the eukaryotic TATA box .
    Back
    5'-GNGTATA(A/T)A(A/T)-3'
  75. Front
    Name the four elongation factors that prevent RNA Pol II from pausing at hairpins.
    Back
    TFIIF, CSB, ELL, and elongin
  76. Front
    In transcription, define "upstream": which direction and which number sign?
    Back
    Toward the 5' end of the coding strand ; assigned negative numbers from the start site
  77. Front
    In transcription, define "downstream": which direction and which number sign?
    Back
    Toward the 3' end of the coding strand ; assigned positive numbers from the start site
  78. Front
    What is the consensus sequence of the Initiator (Inr) element in humans?
    Back
    YYANWYY
  79. Front
    After TFIID binds the TATA box , which general transcription factors assemble (in order) to complete the pre-initiation complex ?
    Back
    TFIIA, TFIIB , then Pol II with TFIIF , then TFIIE and TFIIH
  80. Front
    Which general transcription factor binds the TATA box FIRST and bends the DNA to nucleate the pre-initiation complex ?
    Back
    TFIID
  81. Front
    Mutations at GU/AG splice-site boundaries or branch points cause what general consequence?
    Back
    Disease (a classic exam scenario) — by disrupting splicing
  82. Front
    To which cis-elements do SR proteins and hnRNPs bind to control alternative splicing?
    Back
    Exonic splicing enhancers (ESEs) or silencers
  83. Front
    What family of enzymes charges each tRNA with its correct amino acid?
    Back
    Aminoacyl-tRNA synthetases
  84. Front
    Besides structural stability, what is the essential functional role of the modified nucleotides (e.g. pseudouridine, dihydrouridine) in tRNA ?
    Back
    Precise recognition of the tRNA by its aminoacyl-tRNA synthetase
  85. Front
    Pseudouridylation is the isomerization of ______ to pseudouridine , which changes the hydrogen-bond geometry.
    Back
    uridine
  86. Front
    In the nucleus , DNA is wound around what protein structure to form a nucleosome?
    Back
    A histone octamer
  87. Front
    Which spliceosome snRNA recognizes and binds the 5' splice site (the GU) of an intron ?
    Back
    U1 snRNA

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