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RNA

RNA. History. mRNA and tRNA worked out in the 1960s Purification of RNA lead to 23S, 16S, and 4S species and accounted for 85% of all RNA tRNA accounted for about 15% of all RNA Hybridization experiments did not match DNA mRNA accounts for only 1-4% of RNA. Types of RNA. mRNA tRNA

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RNA

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  1. RNA

  2. History • mRNA and tRNA worked out in the 1960s • Purification of RNA lead to 23S, 16S, and 4S species and accounted for 85% of all RNA • tRNA accounted for about 15% of all RNA • Hybridization experiments did not match DNA • mRNA accounts for only 1-4% of RNA

  3. Types of RNA • mRNA • tRNA • rRNA • snRNA • snoRNA • siRNA • microRNA

  4. Primary RNA • mRNA (messenger RNA) • Transcribed from DNA • Is then translated into protein • rRNA(ribosomal RNA) • Necessary for helping ribosomes make protein (catalysis) • tRNA (transfer RNA) • Mediates amino acid recognition with codons

  5. Other RNA • snRNA – small nuclear • snoRNA – small nucleolar • microRNA – micro • siRNA – short interfering These RNA species have a variety of functions and not all of them have been worked out yet.

  6. RNA and Rfam • Pfam is a database we discussed to determine groups of proteins • Rfam is a similar database for families of RNA • www.rfam.sanger.ac.uk

  7. tRNA and folding • tRNA have a unique fold • There are multiple websites to determine RNA folding • http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi

  8. Ribosomal RNA • Has a structural and functional role in ribosomes • Prokaryotes: 70S which is 30S & 50S, which is 16S, 23S, 5S • Eukaryotes: 80S which is 45S which is 18S, 28S, and 5.8S

  9. snRNA • Found in nucleus • Involved with splicing and telomer maintenance • 5 classes U1, U2, U4, U5, U6

  10. snoRNA • Modify both rRNA and snRNA • 2 Classes • C/D Box – methylate rRNA • H/ACA Box – convert uridine to peudouridine in rRNA

  11. miRNA • Recent discovery • Small approximately 22 nucleotides • Function to down regulate protein expression. • http://www.mirbase.org/search.shtml

  12. RNAi (siRNA) • Double stranded RNA • Small, artificial • Degradation by RISC and Dicer • Protective mechanism for plants and animals

  13. mRNA • Coding RNA • Central Dogma “one gene – one protein” • No longer valid • Alternative splicing, regulation, introns, etc. • Altered expression by: • Region, development, environment, disease, gene activity

  14. mRNA • Key research areas • mRNA expression database • There is a DNA database, but is an mRNA database equally good? • Potential problems with and mRNA database • How to measure mRNA expression

  15. mRNA expression • Steady-state mRNA (polyA isolation) • Transcriptional control • RNA processing control • RNA export control • RNA surveillance control

  16. est database • How to study mRNA • Highly unstable, need to make cDNA • Turn mRNA into DNA with reverse transcriptase • Clone into a vector • Sequnce (this is called an express sequence tag EST) • ESTs can be isolated from specific cells at specific times under specific conditions. • This can aid in finding when types of proteins MAY be expressed

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