RNA structure Reading Chapter 6 from Neidle Handout of Chapter 6 from Blackburn & Gait Know the 3 major forms of RNA and their characteristics - mRNA, tRNA, rRNA Know hydrolysis of RNA reaction Know the structures ssRNA can form - hairpins, bulges, loops, duplexes Know the base pairing of the modified G•U tRNA - know some of the modifies nucleotides found in tRNA Know the tetraloop structure Know how pseudoknots form Be able to calculate the lowest energy structure of a small RNA when I give you a table

of the G values

RNA3 major classes:

mRNA 2-5%tRNA 10-15%rRNA 80-85%

mRNA - number of different mRNAs in a cell can range from 100s to 1000s & sizes can differ from 100s to 1000s nucleotidesIn bacteria, mRNA synthesized, utilized and degraded continually so constant turnover, t1/2 of mRNA ~2 min

tRNA - most cells have 60-70 different tRNAs (74-95 nts)

rRNA - E.Coli ribosomes have: 5S (120 nt), 16S (1542 nt), 23S (2904 nt) Eukaryotic ribosomes have: 5S (145 nt), 18S (1869 nt), 28S (5025 nt), 5.8S (157 nt) In eukaryotes, mitochondria & chloroplasts contain DNA and ribosomes, so euks can have > 1 different sets of mRNAs, tRNAs and rRNAs

Other (non-coding) ncRNAs:snRNA (small nuclear) - involved in mRNA synthesis, removal of intervening seq and polyadenylationsnoRNA (small nucleolar) - process rRNA precursors in euk nuclei7S RNA - in cytoplasmic RNP, involved in transport of proteins through membranesiRNA (small interfering) - 20-25 nt double-stranded RNA molecules that play a variety of roles in biology, most notably in RNA interference (RNAi) piRNA (piwi interacting) - 29-30 nt RNA molecules expressed in mammalian testes; forms RNA-protein complexes with Piwi proteins; complex linked to transcriptional gene silencing of retrotransposons and other genetic elements in germ line cellsgRNA (guide) - RNA that guides the insertion of uridines into mRNAs in trypanosomes in a process known as RNA editingRiboswitches - RNA elements found in non-coding regions of mRNA molecules, gene expression is modulated when metabolite binds directly to the RNA. Many riboswitches, once liganded, repress expression of nearby genes involved in the synthesis of the metabolite, providing an efficient feedback mechanism of genetic controlAlso other catalytic RNA molecules - RNA molecules capable of self-splicing and self-cleavage

Nucleotides & Nucleic AcidsHydrolysis of RNA

Nucleotides & Nucleic Acids

RNA structure

Single-stranded (ss) RNAs

Nucleotides & Nucleic Acids

RNA structure - M1 RNA from RNase P

Nucleotides & Nucleic Acids

RNA structure - rRNA

Nucleotides & Nucleic Acids

RNA structure - tRNA

Nucleotides & Nucleic Acids

RNA structure - tRNA = pseudouridineI = inosineT = ribothymineD = 5,6-dihydrouridinem1I = 1-methylinosinem1G = 1-methylguanosinem2G = 2-methylguanosinePu = purinePy = pyrimidineG* = 2’-O-methylguanylate

Bulge loop

Interior loop

Bulge loop

Interior loop

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