Quiz 6 Flashcards
(32 cards)
RNA 5’ cap and 3’ poly-A-tail
- find ss
cap = prevent degradation + translation
tail = export + translation
What does a lin-14 mutant and lin-4 mutant do to a normal
lin-4 = longer
lin-14 = shorter (under developed)
Draw the lin-14 expression chart
find ss
What is the relationship between lin-4 and lin-14?
lin-4 is reverse compliment of lin-14
- base pair complimentation
- not negative regulation*
3 different lengths of micro-RNA
- name
- length
primary miRNA (>500 nucleotides)
precurser miRNA (60-120 nucleotides)
mature miRNA (20-22 nucleotides)
How is miRNA made?
- transcribed in the nucleus (RNA polymerase II)
- primary miRNA - Drosha + DCR8 (cleaving)
- precursor miRNA - Exportin (3’ end recognized)
- Dicer (cleave)
- mature miRNA duplex - argonaute 2 (AGO 2) + 1 strand**
- RNA-induced silencing complex (RISC) - bind multiple sites within 3’-UTR
- repress gene target (end result)
AGO proteins
- info
4 domains
- amino terminal
- PAZ domain (bind 3’)
- middle domain (bind 5’)
- PIWI domain
What part of the middle domain of AGO proteins is crucial for mRNA recognition?
SEED, 2-8 nucleotides
miRNA mechanisms of gene expression (3)
- partial deadenylation
- enzyme chew up poly-A sequence - maximal deadenylation + translation inhibition
- enzyme chew up 5’ cap - mRNA decapping + degradation (irreversible)
- exonucleases cut/chew
Draw the two pathways from mRNA to polysome and P body
find ss
How is a polysome formed? What enzymes are needed?
G3BP1 (bind together) + TIA1 (bind RNA)
- stress sensed by TIA1
- translation stalls
- bond by miRNA
= RNA storage
How is a p-body formed? What enzymes are needed?
XRN1(exonucleases)
- complete translation
- miRNA/RISC bound
- error
= degrade RNA
Most amount of non-coding RNA by mass
rRNA
Most amount of non-coding RNA by # of molecules
tRNA
3 types of long non-coding RNA (lncRNA)
- guide = binding
- decoy = inhibit miRNA/ transcription factor
- scaffold = build + create complex
Self-cleaving ribozymes
- A base deprotonates the C2’-OH
- O then attacks the C5’ phosphate creating a cyclic phosphate
What keeps the ribozyme maintained in the correct protonated state?
- metal ion stabilizes the oxyanion
- change in pKa microenvironment
- need for specific tertiery structure enforces correct state
Hairpin ribozymes
substrate => TS => product
- stabilization of TS by G8 promotes protonation of A38 which makes sure of proper cleaving
substrate
- chemical modicifcation between C2’-O and OH from water
TS
- replace PO4- to stabilize bond
product
- cyclic phosphate
Group 1 introns
- large regions of conserved RNA secondary structures = core ribozyme
- cofactor to initiate splicing
2 important regions for splicing
G-site = exogenous + coenzyme
3’omega G = last guanosine
Self-splicing vs self-cleaving
splice = put back together
cleave = break forever
Self-splicing ribozymes
- 5’exon-intron cleaved by G-site
- conformational change
- 3’omega G replace
- align with 5’-3’ exon - 5’exon attack 3’exon
- exon ligation
- intron removed
Key to backsbone splicing
3 - Mg2+
- neutralize - charge
- adjust pKa to help
nu - bind 3 site + hold in place
Steps of HIV
- bind to CD4 receptor on T-cell
- fusion with host + release
- ssRNA -> dsDNA by reverse transcriptase (nucleus)
- integration of DNA in genome via integrase
- RNA copies = new virus or HIV protein
- long polypeptide cut (HIV protease is before proline)
- release
