Translation in Prokaryotes/Eukaryotes Flashcards
Where is the 16s rRNA found?
Small ribosomal subunit in prokaryotes
What are the three ribosomal sites in prokaryotes?
A, P, and E
What are the three functional centers of the ribosome?
1) Decoding center
2) Peptidyl transferase center
3) GTPase associated region (GAR)
What is the decoding center?
Center at the A side where tRNA and mRNA pair
- 3 highly conserved bases in the rRNA at this site
What is the PTC?
peptide bond forms here
in large subunit
5 conserved bases in rRNA that bind 3’ end of aminoacyl tRNA and peptidyl tRNA
What is the GTPase associated region?
Binding site in 50S, made of 23S rRNA
translation factors with GTPase activity interact with GAR causing GTP hydrolysis
Conformation change in the protein alters translation
What does peptidyl transferase do?
Catalyzes formation of peptide bonds
Between amino group of new amino acid and carbonyl of existing peptide chain
What are IFs?
Initiation factors
How many initiation factors are required in prokaryotes?
3
Called IF1, IF2, IF3
Where do IF1 and IF3 bind?
small subunit of ribosome
How does translation start?
Small 30S subunit binds mRNA
What is the Shine-Dalgarno sequence?
Purine rich sequence in mRNA upstream of AUG complementary sequence on 16S rRNA
Aligns initiation in P site
Only important in prokaryotes
Each gene in a polycistronic mRNA has a Shine-Dalgarno sequence
What does IF2 do?
It’s a GTPase
binds initiation tRNA (in prokaryotes, formyl-methionine)
facilitates initiation tRNA into the P site
also, to end the initiation phase, IF2 interacts with GAR (remember, what is GAR?) on 50S subunit, triggering GTP hydrolysis
causes conformation change, and the two ribosomal subunits associate
IFs fall off
What are the steps of elongation in prokaryotes?
1) New aminoacyl-tRNA binds in the A site
2) Peptide bond forms
3) translocate
How many elongation factors are there?
3
EF-Tu, EF-Ts, EF-G
What does EF-Tu do?
Binds aminoacyl tRNAs
positions them in A site, so anticodon binds codon w/ hydrogen bonding
(if the wrong tRNA is put in, EF-Tu falls off with the tRNA still attached)
Interacts with GAR–hydrolysis of GTP results in release of EF-Tu
What is EF-Ts?
Catalyzes the exchange of GTP for GDP so EF-Tu can bind another aminoacyl-tRNA
What is EF-G?
Another GTPase required for translocation
binds ribosome, GTP is hydrolyzed
conformation of protein changes and moves it along mRNA
What facilitates translation termination?
Release factors
What are the release factors in prokaryotes?
RF1, RF2, RF3
How do RF1 and 2 work?
Look like tRNAs and recognize stop codons in A site
changes conformation in the PTC, transforming the peptidyl transferase to an esterase
How does RF3 work?
Another GTPase–promotes binding of RF1 and RF2 to ribosome
What are trapped ribosomes?
If there is a mutated or damaged mRNA that has no stop codon,
translation goes all the way to the 3’ end and the ribosome is trapped
(RRF doesn’t bind to release)
What is a tmRNA?
tmRNA – an RNA that has features of tRNA and mRNA
- charged with an alanine
- binds EF-Tu and SmpB – protein mimicking small arm
of tRNA
tmRNA enters the A site
- Ala incorporated into the peptide
How are trapped ribosomes released?
the mRNA part of tmRNA is used as a template for translation
encodes 10 AAs and has a stop codon
this provides normal termination
How does initiation occur in eukaryotes?
Ribosome scans mRNA until it finds a start codon
No Shine-Delgarno sequences!
What is included in the pre-initiation complex in eukaryotes?
40s subunit and multiple eIFs (eukaryotic initation factors)
What is eIF3?
Blocks ribosomal assembly and facilitates mRNA binding
What is eIF2?
GTPase
binds charged Met-tRNA
What is the cap binding complex?
Binds to most mRNA before they can bind pre-initiation complex
What are the major proteins in the cap binding complex?
eIF4E = cap binding protein, binds 5’ cap–rate limiting stem in initiation
eIF4A = helicase (ATP dependent)
