RNA Flashcards
RNA subtypes
mRNA: Largest
tRNA: transfers mRNA info to aa chain; smallest
rRNA: part of ribosome, binds aa together; most abundant
hnRNA: heterogeneous nuclear RNA
Sites of RNA synthesis
Nucleoplasm: mRNA, tRNA
Nucleolus: rRNA
Start codon
AUG – methionine
prokaryotes –formyl-methionine
Stop codons
UGA
UAA
UAG
Operon
Structural genes transcribed (coding region) + promoter region + all regulatory regions (enhancers and repressors)
Transcription factors
Bind to promoter region (-75 CCAAT box, -25 Hogness/TATA box, and -10 Pribnow/TATAAT box) in order for transcription to take place
Operator region
Binds repressor (stops transcription) or inducer (starts transcription), located between promoter and start site
Response elements
Enhancer region and repressor region
Increase or decrease rate of transcription when bound by protein factors
Location may be close to, far from, or within the promoter region
Common structural motifs
Helix-loop-helix
Helix-turn-helix
Zinc finger
Leucine zipper
Lac operon
Excess glucose and excess lactose: operon OFF, CAP not bound
- lactose binds to lac repressor, changes shape and causes it to dissociate from DNA
- if lactose absent, lac repressor is bound
Excess glucose, absent lactose: Operon OFF both – lac repressor bound and CAP not bound
Absent glucose causes CAP to bind
Absent glucose, absent lactose: Operon OFF, lac repressor bound
Absent glucose, excess lactose: Operon ON, RNA polymerase binds and RNA transcribed
CAP: catabolite activating protein – TF
Termination of prokaryotic RNA transcription
Rho factor of E coli – RNA-dependent ATPase) – energy of ATP knocks RNA poly off template
GC-rich DNA -> GC same strand binding forms stem-loop (hairpin) in RNA -> pause in RNA poly-> weak RNA bonds -> separation of RNA poly
RNA processing and splicing
Allows it to leave nucleus
Cap 5’ end: 7-methyl-guanosine by SAM (s-adenosyl-methionine)
Poly-A 3’ end – by poly-A polymerase (signal AAUAAA)
Remove interons – euk: splicosomes remove interons, spice together exons
Eukaryotic RNA polymerases
RNA poly 1: rRNA
RNA poly 2: mRNA
RNA poly 3: tRNA
(order of use)
Alpha-amantin
Mushroom toxin inhibits RNA poly II
Causes hepatotoxicity, liver failure
Prokaryotic RNA polymerase
Single RNA poly
Inhibited by rifampin
Rifamin – 4 Rs
Rifampin
RNA poly inhibitor
Red secretions
Revs up CYP450
Protein translation
mRNA -> ribosome -> protein and rRNA
Ribosomal subunits
Euk: 60S + 40S = 80S (Even)
PrOk: 50s (has 23 rRNA molecule) + 30s = 70S (Odd)
Initiation of protein synthesis in prokaryote
Initiation factors IF-1, -2, -3
Assist in assembly of small ribosomal subunits (30S) to first tRNA – fMET
IF2 binds 30S then fMET tRNA binds at the P site (subsequent bind at the A site)
50S hydrolyses GTP on IF2 -> energy release
-50S attaches to 30S = 70S prok ribosome
Linezolid action
Binds 50S, inhibits initiation of prok ribosome
Tetracycline action
Late – prevents tRNA from binding A site
Elongation
2nd step of protein synthesis
EF (elongation factors) required for subsequent tRNA to bind A site
Energy from GTP
50 S has peptidyl transferase activity – transfers aa from P site to aa on A site
-in 23 s rRNA in prok
Translocation – ribosome complex moves down mRNA 3 nt
- > tRNA shift to next site: A-> P, P->E, E-> out to be recharged
- requires EFG in prok and EF2 in euk
Stop codon : UGA, UAA, UAG terminates
Chloramphenicol action
Inhibits 23S rRNA – blocking peptidyl transferase activity
Antibiotics inhibiting 50S translocation step
Streptogramins
Lincomycin
Clindamycin
Macrolides
Termination
3rd step of protein synthesis
don’t match tRNA release factor binds to mRNA -hydrolyses GTP -releases polypeptide from ribosome -subunits/complex disassociates
Post translational modification possibilities
C- or N- terminal trimed
Covalent modifications: add molecule
-glycosylation, hydroxylation, phosphorylation
disulfide bonds
protein folding
- primary structure aa sequence
- secondary structure – alpha helix/beta pleated sheet
- tertiary/quaternary structure- folding
