Rna structure

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Luis Alvarez
Biomoleculas II
Dr. Alvarez Salas

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Rna structure

  1. 1. RNA Structure
  2. 2. THE FLOW OF GENETIC INFORMATION DNA mRNA PROTEIN DNA 1 2 3 1. REPLICATION (DNA SYNTHESIS) 2. TRANSCRIPTION (RNA SYNTHESIS) 3. TRANSLATION (PROTEIN SYNTHESIS) 4. REVERSE TRANSCRIPTION (DNA SYNTHESIS) 4
  3. 3. This is fine but: The human genome project revealed that we have only about 10,000 protein-coding genes (about 1.5% of the genome) Most mRNAs contain UTRs (5’, 3’) and introns Most of the genome is transcribed Carninci et al. 2005. Science, 309:1556 Venter et al. 2001. Science, 291:1304
  4. 4. Atomic numbering scheme and definition of torsion angles for a polyribonucleotide chain
  5. 5. Average Torsion Angles for Nucleic Acid Helices (in °) Structure Type Alpha Beta Gamma Delta Epsilon Zeta Chi A-DNA (fibres) -50 172 41 79 -146 -78 -154 GGCCGGCC -75 185 56 91 -166 -75 -149 B-DNA (fibres) -41 136 38 139 -133 -157 -102 CGCGAATTCGCG -63 171 54 123 -169 -108 -117 Z-DNA (C residues) -137 -139 56 138 -95 80 -159 Z-DNA (G residues) 47 179 -169 99 -104 -69 68 DNA-RNA decamer -69 175 55 82 -151 -75 -162 A-RNA -68 178 54 82 -153 -71 -158
  6. 6. Movements of bases in sequence-dependent structures (tip, inclination, opening, propeller, buckle, twist, roll, tilt, slide, rise, shift and tilt).
  7. 7. Secondary Structures of RNA Chastain, M. and Tinoco Jr., I., (1991) Prog. Nucleic Acid Res. Mol. Biol. 41, 131-177.
  8. 8. Types of ncRNAs Short ncRNAs Size Functions miRNAs 19-24bp Targeting of mRNAs piRNAs 26-31bp Transposon repression, DNA methylation tiRNAs 17-18bp Regulation of transcription? snoRNAs 60-300bp rRNA modifications PASRs 22-200bp Unknonwn TSSa-RNAs 20-90bp Maintenance of transcription? PROMPTs <200bp Activation of transcription? Long ncRNAs lincRNAs >200bp Scaffold DNA-chromatin complexes T-UCRs >200bp Regulation of miRNA and mRNA levels? Other >200bp Several miRNA = microRNAs piRNAs = PIWI RNAs tiRNAs = trancription initiation RNAs snoRNAs= small nucleolar RNAs PASRs = promoter associated small RNAs TSSa-RNAs = TSS associated RNAs PROMPTs = promoter upstream transcripts lincRNAs = large intergenic RNAs T-UCRs = transcribed unltraconserved regions
  9. 9. RNA Structure a). Chemistry of RNA i). Bases found in RNA ii). Ribose sugar iii). RNA polynucleotide chain iv). Secondary and tertiary structure b). Characteristics of prokaryotic RNA i). Classes of prokaryotic RNA ii). Structure of prokaryotic messenger RNA c). Transcription initiation in prokaryotes i). Transcription ii). Promoter structure iii). Prokaryotic RNA polymerase structure iv). Initiation of transcription and the sigma cycle d). Regulation of the lactose operon i). Function of the lactose operon ii). Negative control: Lac repressor and inducer iii). Postive control: CAP and cAMP
  10. 10. The major bases found in DNA and RNA DNA RNA Adenine Adenine Cytosine Cytosine Guanine Guanine Thymine Uracil (U) uracil-adenine base pairthymine-adenine base pair
  11. 11. Examples of modified bases found in RNA Dihydrouridine Pseudouridine 1-methylguanosine 7-methylguanosine 1-methyladenosine 2-thiocytidine 5-methylcytidine Ribothymine
  12. 12. RNA polynucleotide chain • 2’ -OH makes 3’, 5’ phosphodiester bond unstable DNA polynucleotide chain
  13. 13. Tertiary structure Secondary structure
  14. 14. Secondary Structures of RNA Chastain, M. and Tinoco Jr., I., (1991) Prog. Nucleic Acid Res. Mol. Biol. 41, 131-177.
  15. 15. 5’ 3’ promoter region exons (filled and unfilled boxed regions) introns (between exons) transcribed region translated region mRNA structure +1 Gene structure
  16. 16. • ribosomal RNA (rRNA) 16S (small ribosomal subunit) 23S (large ribosomal subunit) 5S (large ribosomal subunit) • transfer RNA (tRNA) • messenger RNA (mRNA) Structure of prokaryotic messenger RNA 5’ 3’ PuPuPuPuPuPuPuPu AUG Shine-Dalgarno sequence initiation The Shine-Dalgarno (SD) sequence base-pairs with a pyrimidine-rich sequence in 16S rRNA to facilitate the initiation of protein synthesis Classes of prokaryotic RNA AAU termination translated region
  17. 17. Transcription RNA polymerase closed promoter complex open promoter complex initiation elongation termination RNA product
  18. 18. Classes of eukaryotic cellular RNAs • ribosomal RNA (rRNA) 18S (small subunit) 28S (large subunit) 5.8S (large subunit) 5S (large subunit) • transfer RNA (tRNA) • messenger RNA (mRNA) • heterogeneous nuclear RNA (hnRNA) (precursors of mRNA) • small nuclear RNA (snRNA) U1, U2, U3, U4, U5, U6, U7, U8, U9, U10... • small cytoplasmic RNA (scRNA) 7SL RNA What are the enzymes responsible for the synthesis of these RNAs?
  19. 19. The human RNA polymerases Polymerase Location Product RNA polymerase I nucleolus 18S, 28S, 5.8S rRNA RNA polymerase II nucleoplasm hnRNA/mRNA, U1, U2, U4, U5 snRNA RNA polymerase III nucleoplasm tRNA, 5S RNA, U6 snRNA, 7SL RNA mitochondrial RNA polymerase mitochondrion all mitochondrial RNA _________________________________________________________________ Sensitivity of the nuclear RNA polymerases to a-amanitin1 RNA pol I resistant RNA pol II high sensitivity (binds with K = 10-8 M) RNA pol III low sensitivity (binds with K = 10-6 M) 1 cyclic octapeptide from the poisonous mushroom Amanita phalloides
  20. 20. Structure of eukaryotic mRNA 7mGppp Cap 5’ 5’ untranslated region AUG initiation translated region (A)~200 poly(A) tail 3’ untranslated region UGA termination 3’AAUAAA polyadenylation signal • all mRNAs have a 5’ cap and all mRNAs (with the exception of the histone mRNAs) contain a poly(A) tail • the 5’ cap and 3’ poly(A) tail prevent mRNA degradation • loss of the cap and poly(A) tail results in mRNA degradation
  21. 21. Structure of the 5’ cap 7mG = 7-methyl guanosine Triphosphate linkage 2’ ribose methylations
  22. 22. What is non-coding RNA? The term non-coding RNA (ncRNA) refers to those transcripts that are not translated into proteins.
  23. 23. A little bit of history: heteronuclear RNA (hnRNA) Warner et al. 1966. J. Mol. Biol.19:349. Salditt-Georgieff et al. 1981. Mol. Cell. Biol. 1:179. small nuclear RNA (snRNA) involved in splicing regulation Weinberg & Penman, 1968. J. Mol. Biol. 38:289. small nucleolar RNA (snoRNA) in ribosome biogenesis Zieve & Penman. 1976. Cell. 8:19. H19 expressed in early mouse embryogenesis but no ORF or protein product Pachnis et al. 1988. EMBO J. 7: 673. Brannan et al. 1990. Mol. Cell. Biol. 10: 28. XIST required for X inactivation in mammals Brown et al. 1991. Nature. 349: 38. Penny et al. 1996. Nature .379: 131. miRNAs and siRNAs as a part of the RNAi mechanism of mRNA regulation
  24. 24. DNA RNA mRNA PROTEIN Catalytic RNAs Long ncRNAs (>200nt) rRNA Short ncRNAs (<200nt) tRNA Riboswitches UTRs Introns siRNAs

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