RNA Translation and Controlling Gene Expression Flashcards
tRNA: what is the anticodon?
a sequence of 3 nucleotides which is complementary to the mRNA codon the tRNA translates
the anticodon is responsible for recognizing the mRNA codon to be translated
tRNA: where is the AA acceptor site?
it’s at the 3’ end of the tRNA molecule and is opposite of the anticodon. This is where the AA attaches to the tRNA
How is the tRNA for Valine named when it is unloaded and loaded with an AA
unloaded = tRNAVal
loaded = Val-tRNAVal
What is the wobble base hypothesis
refers to that some codons pair with >1 anticodon/tRNA
the 1st 2 codon-anticodon pairs obey normal base pairing rulse, but the 3rd position is more flexible
What are the common wobble base pairings
G-U (and vice versa), I-U, I-A, and I-C
I = modified inosine base (inosine is derived from adenine)
Mneumonic: wobbly bases like GUAC (as in guacamole)
In tRNA loading, how is an AA activated so it can be loaded onto a tRNA to create an aminoacyl tRNA?
AA + ATP → AA-AMP + PPi
AA-AMP + tRNA → aminoacyl tRNA + AMP
the _____ of AA and tRNA will power peptide bond formation
hydrolysis
What are aminoacyl-tRNA synthetases?
enzymes that ensure the correct AA is paired w/ its correlating tRNA
What is the prok. and euk. ribosome numbers?
prok. = 70S (30S small subunit and 50S large subunit) with a 23S ribozyme
euk. = 80S (40S small subunit and 80S large subunit) with a 28S ribozyme
mneumonic:
prok. are odd little creatures. euk are even.
Of the E, P, and A sites on the ribosome, what is the order in which tRNA molecules move through these sites?
A → P → E
Does prokaryotic translation always have to occur at the 5’ site of the mRNA? Why or why not?
No, because prok mRNA is polycistronic
What is the Shine-Dalgarno sequence?
the prok mRNA binding site where the ribosome attaches to start translation
What are the basic steps in the initation of prok. translation?
1) 30S (small subunit) binds to proteins IF1 and IF3; this complex then binds to the mRNA transscript
2) the 1st aminioacyl-tRNA (aka initiator tRNA) and IF2 joins; IF2 is bound to GTP
3) 50S (large subunit) joins and completes the complex
- process is powered by 1 GTP
- initiator tRNA = met-tRNAmet
Will all AUG on prok mRNA signify a start codon?
No. in order for AUG to be a start codon, it needs to be preceeded by a Shine Dalgarno sequence
In the elongation step of prok. translation, _____ transferase catalyzes the formation between fMet & the 2nd AA
peptidyl transferase
In the elongation step of prok. translation, when peptidyl transferase catalyzes the formatio between fMet & the 2nd AA, what is considered the nucleophile, the electrophile, and the leaving group?
The carboxylic C on fMet is the electrophile and the N on the 2nd AA is the nucleophile (because the N attacks the C), while the tRNA is the leaving group
In the elongation step of prok. translation, what occurs during translocation?
tRNA in the P site moves to the E site, and the tRNA in the A site moves to the P site; then, the next codone followed by its anticodon moves into the A site. This process is repeated until a stop codon is reached.
Termination in prok. translation:
1) occurs when a stop codon appears in the ___ site of the ribosome, which signals a realse factor (not tRNA) to enter the ____ site.
2) _____ transferase hydrolyzses the bond between the last tRNA and the completed polypeptide.
3) the _____ separates and release both the mRNA and polypeptide
1) A, A
2) peptidyl
3) ribosome
It takes ___ high energy bonds to make a peptide chain
4n
n = # AA in the chain
What sequence functions in starting euk translation?
5’UTR sequences (i.e. Kozak sequence)
these are usually situated a few nucleotides before the start codon
Describe what happens during the initiation step in euk translation
Initation complex located the 5’ cap and scans for the start codon: 40S, Met-tRNAMet, and several eukaryotic initiation factors proteins (eIFs) binds to the 5’ cap; additional proteins are recruited, and then the whole complex scans for the start codon
1) the amount of eIF proteins present can either increase or decrease _____ rates
2) eIFs are controlled by _______ modification i.e. phosphorylation, which couples translation to upstream signaling pathways
1) translation
2) post-translational
Eukaryotes have 2 main elongation factor proteins: eEF-1 and eEF-2. What are the primary roles of each?
eEF-1: helps load aminoacyl-tRNA into the A site & catalyzes release of GDP
eEF-2: is a translocase
In euk translation, what are the main roles of release factors eRF1 & eRF3 during termination?
eRF1: recognizes all 3 termination codons
eRF3 is a GTPase that helps eRF1 release the completed protein