HRR: translation Flashcards
Compare and contrast the main structural components of prokaryotic versus eukaryotic mRNAs.
Prokaryotes: 70s with 50s and 30s subunits; 50s has 23 and 5s rRNAs, 30 has 16s rRNAs
Eukaryotes: 80s with 60 and 40s subunits; 60 has 28, 5, and 5.8s rRNAs, 40 has 18s rRNAs
Describe secondary and tertiary structure of the tRNA molecule and pinpoint the anticodon region and the amino acid attachment site
Secondary: a clover leaf structure; base of the clover holds the anticodon. 3’ end has CAA, and the last A attaches the amino acid.
Tertiary: an L shaped structure; the anticodon is at the base of the structure. 3’ end has CAA, and the last A attaches the amino acid.
Describe a “charged” tRNA molecule and how it is generated.
A tRNA molecule with the amino acid attached via an aminoacyl linkage. Once charged, it can go to the ribosome and deliver the amino acid.
Describe the function of aminoacyl-tRNA synthetases in implementing the genetic code.
Aminoacyl-tRNA synthetases recognize their corresponding amino acid and catalyze the reaction in which it is attached correctly to the corresponding tRNA. There is an editing function if an incorrect aminoacyl linage is formed.
Describe how aminoacyl synthetases work
They recognize the R group on an amino acid and utilize ATP to add AMP on the carboxyl group, forming an aminoacyl intermediate. It then finds the correct tRNA and switches the AMP for the tRNA (CAA end).
Explain why the genetic code is “degenerate”.
More than one codon can code for the same amino acid
What are the stop codons? Start codon?
UAG, UAA, UGA; AUG
Describe codon-anticodon base pairing and indicate the “wobble” bases.
Codons (read 5’ to 3’) are complementary to anticodons (read 3’ to 5’)
Wobble bases are the third bases of codons and the first bases of anticodons, and they are what allows for degeneracy.
Explain why inosine is a frequent base modification in the anticodon loop of tRNA.
Deamination of adenosine forms inosine; inosine base pairing maximizes the number of codons that a tRNA can read by forming non-standard base pairings.
Define the Shine-Dalgarno sequence and describe its role in translational initiation
This is how the ribosome recognizes where the start codon is in prokaryotes. The mRNA has this sequence upstream of the start codon and it functions as a marker for the recognition of the codon. The 30s subunit binds to the sequence via complementary base pairing.
Compare the initiation step of translation in prokaryotes versus eukaryotes. Describe how the mechanisms for recognition of the AUG start codon differ
Prokaryote: uses the shine-delgarno sequence
Eukaryote: uses linear scanning to find the Kozak sequence that contains the start codon
Describe initiation of translation in prokaryotes
-IF1 and IF3 bind to 30s unit
-IF2-GTP binds with the charged initiator tRNA, fMet-tRNA
-The IF1 and IF3 dissociate
-The 50s unit joins
-GTP hydrolyzes, resulting in the release of IF2-GDP
Describe initiation of translation in eukaryotes
-Formation of the ternary complex containing met-tRNA-EIF2-GTP
-The ternary complex and eukaryotic initiation factors (namely EIF3 and EIF4) bind to the 40s subunit. This forms the preinitiation complex.
-EIF-4F helps the PIC bind to the m7Gppp cap on the 5’ end of mRNA. The three main subunits are 4G, 4E 44G connects to EIF3. Associated with 4G are 4A (RNA helicase) and 4E (binds the cap)
-PIC finds start codon
-EIF5 triggers hydrolysis of EIF2-GDP, thereby releasing them from the ribosome. This enables the 60s unit to bind to form the 80s initiation complex.
Describe the modification of methionine on the initiator in bacteria
They have an enzyme that protects the amino group, because if not it can interact with other parts of the peptide. The enzyme formylates it.
Specify the roles of the following elongation factors: EF-Tu, EF-Ts, EF-G during the
elongation phase of translation. Specify their counterparts in eukaryotes.
EF-Tu: binds to charged tRNA and brings it to the A site to base pair and form peptidyl tRNA; functions in proofreading. eEF-1a in eukaryote
EF-Ts: exchanges GDP-pi for GTP to activate EF-Tu/eEF-1a; eEF-1bg in eukaryote
EF-G: catalyzes the translocation of peptidyl tRNA from the A site to the P site; eEF-2 in eukaryote
Specify two steps in the elongation phase of translation that require GTP hydrolysis.
Attaching the codon to anticodon, moving peptidyl tRNA to the P site
Name the enzyme that catalyzes peptide bond formation.
Peptidyl transferase
Describe how proofreading occurs during the elongation step of translation.
GTPase on EF-Tu will not fire off if the base-pairing is not correct. It gets kicked out before the GTPase fires off if it is not correct.
mRNA is translated in the ___ direction and that proteins are synthesized
from the ___ end to the ____
5 to 3; amino to carboxyl
Define polyribosomes and explain how they improve the efficiency of translation.
Multiple ribosomes translating a single mRNA molecule; more ribosomes per mRNA molecule leads to a higher efficiency
Describe the functions of protein chaperones
Facilitate protein folding by binding and stabilizing polypeptides; allows for proper conformational forming; there are co-translational chaperones such as heat shock proteins
Describe the mechanism by which translation is terminated.
-Stop codon moves to the A site
-Release factors are attracted and recognize the stop codon
-The RF binds to the A site and hydrolyze the tRNA from the C terminal AA of the polypeptide chain
Describe how miRNAs are generated and the mechanisms by which miRNAs regulate
gene expression
miRNAs genes are transcribed by Pol II and made inter pri-miRNA transcripts. They are processed and into small double stranded RNAs that can be recruited into RISC complexes. The RISC separates the strands and helps a strand base pair with the target strand. This allows for regulation via stopping translation or triggering degradation of the protein.
The UTR is part of the ___ (intron or exon)
exon
In prokaryotes, transcription occurs ___ translation
Simultaneously with; mRNA is not processed or spliced
What is a p-body?
Storage depots for mRNA; non-membranous cytosolic organelles
