Genomics #5 RNA types.txt

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Genomics #5 RNA types.txt
2012-02-10 11:41:44

genomics RNA types
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  1. T/F: the information flow dogma of DNA->RNA->Proteins, holds true for eukaryotes, virusis and extremophile microorganism.
    False, confirmed only in eukaryotes
  2. T/F: There is limited evidence that suggests that DNA was a precursor of RNA.
    False, opposite
  3. Name some of the different functional types of RNA.
    • Protein synthesis RNA,
    • Post-transcriptional modification of RNA,
    • Regulatory RNA,
    • Prokaryotic-unique RNA
  4. RNA cans perform many ___________ of DNA and proteins because of the ________ of functions.
    functions, diversity
  5. What are the functions of mRNA, rRNA, and tRNA?
    • mRNA- encodes for protein sequence,
    • rRNA- provides the structural mechanism for protein assembly to occur,
    • tRNA- aligns correct AA in protein sequence based on the appropriate DNA nucleotide sequence, these are all considered Protein Synthetic RNA
  6. What is the full name of snRNA, its function, and class?
    • Small Nuclear Ribonucleic Acid (RNA),
    • Maturation of initial mRNA transcripts,
    • a Post-Transcriptional Modification RNA
  7. What is the full name of snoRNA, its function, and class?
    • Small Nucleolar RNA,
    • Modification of RNA nucleotides,
    • a Post-transcriptional Modification RNA
  8. What is the full name of RNase P, its function, and class?
    • Ribonuclease P,
    • tRNA maturation [H1-RNA plus proteins],
    • a Post-transcriptional Modification RNA
  9. What is the full name of Rnase MRP, its function,and class?
    • Ribonuclease Mitochondrial RNA Processing,
    • rRNA maturation , mitochondrial DNA replication, and mRNA degradation,
    • a Post-transcriptional Modification RNA
  10. What is the full name of Y RNA, its function, and class?
    • Y RNA,
    • tRNA maturation & DNA replicationand maintenance,
    • a Post-transcriptional Modification RNA
  11. What is the full name of aRNA, its function, and its class?
    • Antisense RNA,
    • attenuate transcription or block translation,
    • enhance mRNA degradation and destabilize mRNA,
    • Regulatory RNA
  12. What is the function of Cis-natural antisense transcript and its class?
    • Regulate transcriptional events, RNAi (RNA interference), alternative splicing
    • Regulatory RNA
  13. What is the full name of Long ncRNA, its function, and class?
    • Long noncoding RNA,
    • Modulate interaction of transcription factors and repressors with promoters,
    • Regulatory RNA
  14. What is the full name of miRNA, its function, and its class?
    • MicroRNA,
    • Gene regulation,
    • Regulatory RNA
  15. What is the function of Telomerase RNA?
    • Telomere synthesis
    • maintains telomere ends
  16. What are some of the functions of Post-transcription Modification RNA?
    • Processing/regualting mRNA transcription.
    • Processing, breaking-down, blocking translation of RNA. Processing and modifing rRNA for appropriate methylation pattern.
    • Also includes RNAs used for DNA replication and maintenance. (Y-RNA)
  17. What is the full name of piRNA, the function, and the class?
    • Piwi-interacting RNA,
    • Prevent transposon insertion into DNA,
    • Regulatory RNA
  18. What is the full name of siRNA, the function, and the class?
    • Small interfering RNA,
    • Gene regulation,
    • Regulatory RNA
  19. Ribozyme, AKA____________ is a ribonucleic acid enzyme that can___________________. Name the 5 major classes.
    • Catalytic RNA, can catalyze a reaction
    • Tetrahymena group one intron,
    • RNase P,
    • Hammerhead ribozyme,
    • Hairpin ribozyme,
    • Hepatitis delta virus ribozyme
  20. Antisense provides________ and _______, it is the ____________ sequence of a linear array of nucleotides to target specific locations within a long polymer of nucleotides.
    • specificity
    • targeting,
    • complementary
  21. What is the antisense ribozyme that binds the RNA sequence then cleaves the phosphodiester bond. What is the classification of the enzyme activity?
    • RNase P,
    • Endoribonuclease
  22. Name the antisense ribozyme that is used to cleave the 5' leader RNA from the precursor-tRNA to form active tRNA.
    RNase P,
  23. Rnase P must bind to other ___________ to form the _________ complex in order to work. This complex has the specificity to _____________________________.
    • Proteins,
    • Cleavage complex,
    • clip the 5' end leading to the maturation of the tRNA
  24. What is the ribozyme that influences mitochondrial DNA replication and pre-rRNA processing?
    RNase MRP
  25. What is the ribozyme that cleaves mRNA at the 5'UTR region to prevent translation and decrease expression of proteins?
    RNase MRP
  26. What is the ribozyme that will maximize activity of the ribosomal RNAs by methylation and uridation? What does this allow to happen?
    • snoRNA,
    • proteins bind appropriately (form snoRNP) and allow the translation process
  27. There are (2) target sites for snoRNA, what are they and what does the snoRNA do to the site?
    • C/D box: targets rRNA sites for methylation (~115 O-methylations),
    • H/ACA box: targets rRNA sites for pseudouridinylation [isomerization of uridine to pseudouridine](~96 pseudouridines)
  28. The snRNA provides recognition of the ____ and the ____ intronic sequences.
    5' and 3' intronic sequences
  29. _________combines with proteins to form snRNP.
  30. snRNPs combine with ________ to process introns from the nascent transcript.
  31. The spliceosome is made from which two RNAs?
    snRNP and pre-mRNA
  32. T/F: snRNPs take pre-mRNA transcript, target introns for excission and are involved in alternative splicing of protiens.
  33. How do transposons promote evolution of the DNA of an organism?
    they move parts of the DNA around on the genome
  34. What is a Transposon?
    A DNA sequence that moves from one location on the genome to another
  35. What is the largest class of small RNA molicules in animal cells? What is the estimated number of copies in a spermatocyte or spermatid?
    • Piwi-Interacting RNA,
    • Prevent transposon insertion into DNA (silencer), 1 million
  36. Where does the highest level of transposon silencing take place by piRNA?
    • in the spermatocyte or spermatid and
    • only in the testes (gametes).
  37. ___________ is sythesized from a long single stranded non-coding precursor RNA.
  38. After the primary piRNA binds to its complementary target which allows for the recruitment of proteins to form a __________.
    cleavage assembly
  39. Ping Pong Mechanism is the theory that __________ piRNA gets modified by _________ for more complete cleavage of the transposon.
    • primary,
    • secondary piRNA
  40. Name the 2 classes of RNA interference (RNAi) made from dsRNA duplexes:
    • MicroRNA (miRNA)
    • small interfering RNA (siRNA)
  41. Considered a defense against viral infections, ________ ,uses dsRNA and is a highly conserved process of regulating gene expression.
    RNAi(<25 nt)
  42. Which of the RNAi is derived from longer RNA hairpin transcripts with stems forming _________ stems.
    • miRNA,
    • imperfect
  43. Which of the RNAi is derived from double strand percursors with ________ Watson-Crick base pairing, generally of viral origin?
    siRNA, complete
  44. Which RNAs both will form protein complexes with a family of proteins called Argonaute that assemble into RNA-induced silencing complex (RISC)
    siRNA and miRNA
  45. What is the full name of RISC? What components are needed to form it? What does it do?
    • RNA-induced silencing complex (RISC),
    • family of proteins called Argonaute with miRNA or siRNA.
    • Cleave and silence mRNA
  46. miRNA generally binds to the _____ end of the target _______ transcript, forming _________ base pairing to block translation.
    • 3'UTR,
    • mRNA,
    • incomplete
  47. siRNA can bind ___________on the mRNA forming _______ base pairing leading to the cleavage of the target mRNA.
    • anywhere,
    • complete
  48. _______ is a small non-coding, single stranded RNA of 21-24 nucleotides long, but can target ~200 mRNAs each.
  49. by binding to 3' (some 5' UTR) segments of mRNA, _________ influences the stability of mRNA and also decreases translation ability.
  50. What % of gene expression is regulated by miRNAs?
  51. How does miRNA block translation?
    binding to the 3' UTR sterically blocks the loading into the ribosome for translation.
  52. T/F: miRNA can only regulate a specific mRNA.
    False, it has multiple targets
  53. MicroRNAs produced from double stranded RNA that is processed by the ____________.
    Dicer endonuclease
  54. Dysregulation of microRNA synthesis may lead to ________ formation
  55. Drosha-DG-CR8 is a rna protein complex that converts____________ giving it the hair-pin-loop.
    converts the primary miRNA to a pre miRNA in the nucleus
  56. What transports the pre-miRNA from the nucleus to the cytosol?
    Exportin 5
  57. What cleaves the hair-pin-loop off the pre-miRNA? Where? What is left?
    • Dicer endonuclease
    • in the cytoso
    • dsRNA
  58. After cleavage of the hair-pin-loop what happens to the dsRNA? Why?
    • it unwinds,
    • reduced thermal stability by losing the head
  59. What are the 2 ways that siRNAs can control gene expression?
    • Transcriptional gene silencing (TGS),
    • Posttranscriptional gene silencing (PTGS)
  60. When does PTGS happen? What is the result?
    • After the formation of a RISC
    • cleavage of the target mRNA to silence it
  61. T/F: Dicer trims dsRNA which binds to Argonaute to form the RISC complex which is used to cleave and silence the mRNA.
  62. T/F: siRNA can induce methylation of histones resulting in wide repression of gene expression.