RNA Structure

• What is the secondary structure of tRNAs?

  Cloverleaf shape, “CAA” acceptor stem, 4 distinct loops
• What is the “CAA” acceptor stem?

  Amino acid attachment point; added post-synthesis
• What are the 4 loops in the secondary structure of tRNAs?

  D loop, Anticodon loop, Variable loop, TΨC loop
• What does the D loop contain?

  Abundant dihydrouridine
• What does the anticodon loop contain?

  Specific trinucleotide sequence (corresponding to an amino acid)
• What does the TΨC loop contain?

  T, Ψ, C nucleotides (invariant)
• What is the tertiary structure of a tRNA?

  L-shape
• What are the base-pairing interaction that form the tertiary structure of a tRNA?

  D loop with variable and TΨC loops
• What interactions occur within a tRNA molecule?

  Watson-Crick base pairs, Non-Watson-Crick base pairs, triple base pairs, Metal ion/polyamine binding
• What is the purpose of metal ions/polyamines in RNA structure?

  Shield negatively charged phosphate groups, stabilize tertiary structure
• What are some examples of divalent metal ions/polyamines?

  Mg2+ and Spermine (contains amine, NH2 groups)
• What is the purpose of rRNAs?

  Provide structural foundation for ribosomal proteins
• What modified nucleotides are found in rRNAs?

  Ribothymidine (T) and Pseudouridine (Ψ)
• How are different rRNA species classified?

  Via sedimentation coefficients (prokaryotic ribosome → 70S; consists of 50S and 30S rRNA strands)
• What is the structure of rRNAs?

  Complex secondary and tertiary structures, extremely varied sequences, structures nearly homologous
• How can RNA molecules play a role in catalysis?

  Via hydrolytic or transesterification reactions
• What processes the 5’-ends of a tRNA molecule?

  RNAse P (type of ribonuclease)
• What is a ribozyme?

  A piece of RNA that is catalytic and uses either itself or another piece of RNA to cleave something
• What is the spliceosome and what does it do?

  Multiple ribozymes; carries out splicing of introns from pre-mRNA
• What are riboswitches?

  Regulatory segments found in ssRNA
• What do riboswitches do?

  Turn RNAs on or off through small molecule binding
• What do ligands bind to in riboswitches and what does that cause?

  Ligands bind to an aptamer domain leading to RNA structural changes
• What are the two forms of regulation that riboswitches are involved in?

  Regulation of transcription and translation
• What are aptamers?

  Sequences that form 3D structures that can be used to identify specific types of biomarkers on certain cells
• What can ribozymes cleave?

  Self (phosphate backbone) or other pieces of RNA