• protect RNA from nucleases
• act as an attractant for many translation initiation factor binding

1. sees cleavage signal (AAUAAA)
2. cleavage via specific endonucleases downstream of cleavage signal
3. add tail via polyA polymerase

• protection from degradation from nucleases
• stabilize translation initiation complexes in protein-RNA interactions

During transcription, the mRNA will form, and the DNA coding strand will loop out, forming a intervening sequence.

SEQUENCE DEPENDENT LOOPING

1. snRNA (snRPs) binds to conserved sequences in splice sites
2. this will occur at a 5' splice site (within intron is GU), 3' splice site (within intron is AG), and a branch point (usually an A within intron) (each site has different snRP's)
3. this will line up multiple snRP subunits (at least five snRP's)
4. they will fold up to form a catalytic splicesome
5. lariat forms by phosphate at 5' donor site attacking the 2' OH group on A that represents branch point
6. there is attack of OH by phosphate at acceptor site at separate exon (Exon 2)
7. two exon join and lariat structure forms

Function of various sequences within intron

• apoB48 found in intestines (form chylomicrons)
• apoB100 found in liver (LDL/lipid trafficking)

• 5 mg cap
• 5' UTS (non translated)
• AUG (start codon)
• exons in open reading frame
• UAA/UAG/UGA (stop codons)
• 3' UTS (non translated)
• 3' polyA tail

half life of mRNA in euk. and prok.

• prok.- minutes
• euk.- anythin btw minutes and years

• target for:
  • processing
  • storage
  • degredation

• stability vs. RNase (can take out RNA)
• protein bind based on structgure
• oocyte mRNA stability

• sequence INDEPENDENT hydrolysis of RNA phosphodiester backbone
• general degredation of all RNA molecules
• extracellular defense against RNA viruses

End product- cleave bond to produce nucleoside after phosphate leaves.

Role of IFN in mRNA degredation

1. activates 2'-5' polyA synthetase
2. binds to RNase-L (sensitive to induction, so mostly inactive)
3. once RNase-L on, it chews up mRNA

1. binds protein kinase that will bind ATP
2. become activated
3. phosphorylate various proteins
4. block protein synthesis

1. fos/jun turn on myc
2. myc recruit ras/src
3. all this leads to increase in mRNA population

1. transcription forms specific secondary structures
2. Drosha processing of specific conserved structure sequences
3. exported to cytosol via exportin
4. Dicer sepearates two strands of specific secondary structure
5. results in a mature miRNA binding within RISC complex
6. leads to blocking of mRNA transcription or cut the mRNA at a specific sequence
   1. cutting = mRNA silencing

• 5'- RNase P(prok) and Maturase (euk)
• 3'- RNase D(prok) and exonuclease editing (euk)

Polymerase that transcribes tRNA

Relation of tRNA gene location to other genes

Mechanism of action of processing of large rRNA (45s rRNA)

• EXTENSIVE post transcriptional modifications via autocatalytic splicing 
• multicopy rRNA gene clusters in nucleolus
  • one ORF codes for three 45S [re-rRNA's
• flanked by tandem repeats and BAMHI islands (restriction sites)
  • within one gene, you could have many ORF's

Polymerase that transcribes "large" rRNA

1. GTP binds to 5' end of intron
2. G attach to intron causing it to separate from exons
3. OH on one of the exons undergoes nucleophilic attack on 3' end of intron
4. allows exons to be spliced together

All this happens within active site of catalytic riboswitches.

• one gene produces one molecule of 5S rRNA
• it is highly conserved via very simple construction
• multiple copies flanked by tandem repeats

NO post transcriptional modification of the final product.

Importance of tRNA post transcriptional modifications

• autocatalytic processing of intervening sequenced that are spliced out adjacent to anticodons
• profound structure, fucntion relation
  • changes are associated with with differentation and neoplastic progression