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) rRNA (ribosomal 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

7. tRNA and folding tRNA have a unique fold
There are multiple websites to determine RNA folding

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.

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No longer valid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