RNA and Protein Synthesis Flashcards
Where is rRNA made
Nucleolus
Where is mRNA made
Nucleoplasm
Where is tRNA made
Nucleoplasm
What are the mRNA stop codons
UGA
UAA
UAG
What is the TATA box
25 nt upstream, Promoter region for TF binding
What is the -10 Pribnow box
TATAAT, 10 nt upstream. Promoter region
What is the -75 CCAAT box
Promoter region
What happens to transcription when there’s a promoter mutation
Large decrease in level of gene transcription
What is the silencer region
Site where repressors bind
What are the helix-loop-helix and helix-turn-helix
Structure in DNA that allows protein to interact with DNA
What is the zinc finger motif
A structure in DNA that contains a zinc atom and allows protein to bind with DNA
What transcribes DNA template into RNA molecule
RNA polymerase
What is action of RNA polymerase I
Makes rRNA in eukaryotes
What is action of RNA polymerase II
Makes mRNA in eukaryotes
What is the action of RNA polymerase III
Makes tRNA in eukaryotes
What is the smallest RNA
tRNA
What is the largest RNA
mRNA
What is the most abundant RNA
rRNA (r=rampant)
What is the action of alpha amanitin
A mushroom toxin that inhibits RNA polymerase II
What are the RNA’s in prokaryotes
Just 1 RNA polymerase
What antibiotic inhibits prokaryotic RNA polymerase
Rifampin
How do prokaryotes terminate transcription
- Rho factor - RNA dependent ATPase in Ecoli - knocks RNA polymerase off template
- Rho-independent - GC rich region, makes strong H bonds that makes a hairpin structure and RNA breaks off
What is hnRNA
The initial transcription - heterogenous nuclear RNA
It is RNA that is hot off the presses
How does RNA leave the nucleus
It has to be processed - 3 things have to happen
What are the 3 things you have to do to make mRNA from hnRNA?
- Cap on 5’ end
- Polyadenylation of 3’ end
- Splice out introns
What is the 5’ cap
7-methyl-guanosine
What provides 5’ cap
SAM: S-adenosyl-methionine
What provides the polyadenylation of the 3’ end
Poly-A polymerase - adds 200-250 adenines to 3’ end
What signal gets poly-A polymerase started
AAUAAA
What splices the introns before mRNA can leave the nucleus?
Spliceosome
What amino acid frequently has more coding sequences in the mRNA than are represented in the peptide that is created from it?
Methionine (More AUG codons than methionine)
How is transcription of the lac operon regulated?
- CAP - allows RNA pol to bind DNA and start transcription of beta galactosidase gene; won’t bind DNA if glucose present
- Lac repressor - prevents RNA pol from binding DNA
What is aminoacyl tRNA
tRNA that is charged with an amino acid
What enzyme charges tRNA with amino acids
Aminoacyl tRNA synthetase
What is the hydroxyl end of the tRNA
3’ end, always ends CCA
At what end of tRNA does aminoacyl tRNA synthetase work
3’ end
Where are ribosomes synthesized?
Nucleus, transported to cytoplasm
What are the subunits of a eukaryotic ribosome
60S and 40S –> 80S
What starts initiation in protein synthesis
Initiation factors (IFs)
What is the role of IFs
Help assemble smaller ribosomal subunit with the initiator tRNA (always start with f-met tRNA in prokaryotes)
What does IF-2 do in prokaryotic translation
First binds 30S, then binds fmet tRNA
What allows 50S to attach to 30S?
Hydrolyzes GTP on IF, releases energy and allows attachment –> 70S
What is the A site
Where incoming aminoacyl tRNA binds
What is the P site
Where polypeptide tRNA binds (chain)
What is the E site
Where free tRNA located
Where does first fMet RNA bind
P site
What is required to bind an incoming aminoacyl-tRNA to A site
Elongation factor EF
What part of ribosome has peptidyltransferase activity
50S (23S rRNA in prokaryotes)
What is elongation factor G
Required for translocation in prokaryotes
What is required for translocation in eukaryotes
EF-2
What toxins inhibit EF-2
Diphtheria Exotoxin A (pseudomonas)
What is the release factor
Binds stop codon on mRNA and hydrolyzes GTP, releases new polypeptide at T site.
Mechanism of aminoglycoside antibiotics
Bind 30S subunit early so can’t pair with starter tRNA
Mechanism of linezolid
Binds 50S subunit so can’t start initiation
What antibiotics affect initiation of protein synthesis
Aminoglycosides
Linezolid
Mechanism of tetracyclines
Bind 30S subunit later, prevent aminoacyl tRNA from getting to A site
What classes of antibiotics work at 30S subunit
Aminoglycosides
Tetracyclines
Mechanism of chloramphenicol
Inhibits peptidyltransferase part of 50S subunit (23S rRNA)
Mechanism of macrolides
Bind 50S and inhibit translocation
Mechanism of clindamycin
Binds 50S and inhibits translocation
Antibiotics that affect 50S subunit
Chloramphenicol Linezolid Macrolides Clindamycin Streptogramins
What happens in postranslational modification of trimming
N or C terminal are trimmed
What cells are notable for making extracellular proteins?
Fibroblasts - collagen, fibrilin, elastin
Hepatocytes - albumin, transport proteins, ferritin, coagulation factors
Plasma cells - Ig’s
What enzyme matches amino acids to tRNA?
Aminoacyl-tRNA synthetase
What antibiotics are inhibitors of prokaryotic protein synthesis at 30S subunit?
Tetracycline
Aminoglycoside
“Buy AT 30, CCELL at 50”
What antibiotics are inhibitors of prokaryotic protein synthesis at 50S subunit?
"Buy at 30, CCELL at 50" Chloramphenicol Clindamycin Erythromycin (macrolides) Linezolid Lincomycin
