RNA Structure

Three main classic types of RNA:

• tRNA, or transfer RNA. In the older literature it is also called sRNA for soluble RNA, since its small size makes it more soluble than other types.
  • The classic example is yeast phenylalanine tRNA, tRNA^Phe:
    • tRNA^Phe has 76 bases arranged into a "clover leaf" (in two-dimensional representations, (tRNA^Phetext Fig 27-16, p 1080) secondary structure characterized by extensive hydrogen bonding interactions, analogous to secondary structures in proteins.
    • 42 of the 76 bases are involved in base pairs to create
      • a "stem" where the amino acid is carried esterified to the 3' hydroxyl group of the terminal adenine (tRNA's always have a CCA sequence at their 3' ends), and three arms, clockwise from the stem,
      • the TC arm named for the conserved sequence of thymine-pseudouridine-cytosine in the open loop,
      • the anticodon arm named for the anticodon sequence in the loop which recognizes the codon in the mRNA,
      • the D arm named for the conserved dihydrouridine in its loop.
      • There is also a variable arm between the TC arm and the anticodon arm, so called because it varies considerably (3-21 bases) between different varieties of tRNA.
    • Yeast tRNA^Phe has a complex folded, tertiary structure analogous to the tertiary structures of proteins, to give an "L" shaped molecule (text Fig 27-18, p 1080).
      • The tertiary structure is held together by non-Watson-Crick base parings between the arms and stacking interactions between bases within and between the stems of the arms (text Fig 8-25a, p 286).
      • The bases involved in the tertiary base pairings are mostly invariant, indicating a common tertiary folding pattern for all tRNAs.
      • The overall folded tRNA is compact, with most of the bases, with the exception of the -CCA end and the anticodon, inaccessible to solvent.
  • tRNAs have 15 invariant positions, including the seven noted above, and eight position which are specified as to base type (purine or pyrimidine).
  • tRNAs have many modified bases (up to 25%). (text Fig 27-17, p 1080)
    • As in proteins, tRNAs are made from a standard set of monomers, this time the four bases, A, U, C, G. These bases may then be modified post transcriptionally.
    • Nearly 80 modified bases are known, which have been found at over 60 positions in the tRNA molecule.
• mRNA, or messenger RNA. (text Fig 8-22, p 284)
  • mRNA is of quite variable length, with no necessary or common secondary or tertiary structures. (Wouldn't expect secondary structures, since the important function is to pass on information to code proteins, and the probability that a protein structure with a 20 letter code giving a given structure will also give a particular structure for a 4 letter code is pretty much a chance affair.
  • mRNA is largely unmodified, with the exception of the addition of polyA strings on the end.
  • Some large and small nuclear RNAs are the result of the initial manufacture of messenger in exon-intron form, and the subsequent removal of small RNA exons for degradation.
• Last main classic type of RNA:
  • rRNA or ribosomal RNA.
    • rRNA, like tRNA has a definite secondary structure due to hydrogen bonding interactions between bases to make double helical stems.
    • This structure is quite complex due to the large size of rRNA, as shown for the proposed structure of the smaller, 16s, rRNA of E. coli, as seen in (text Figure 27-14, p 1079).
    • The overall three-dimensional structure of rRNA is more complex because it is accomplished as a supramolecular ribonucleoprotein structure. In this case the actual 3-D structure results from the interaction of the RNA core and a large group of proteins. (text Figure 27-13, p 1077)
    • The eukaryotic ribosome is significantly larger , though similar to the prokaryotic ribosome. (text Figure 27-15, p 1079)
    • Because of the complexity of this structure, and the fundamental importance of ribosomes for life, the rRNA sequence is quite evolutionarily stable, and has found a great deal of use in determining the relationships of organisms at the most fundamental levels: Eubacteria vs. Archbacteria vs. Eukaryotes.

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Last modified 29 March 2009