Molecular Biology week 10 quiz (Chapter 11)
Match the details about features of the mRNA used for bacterial translation initiation to the name of the feature.
***A bacterial mRNA molecule that is polycistronic means that = each open reading frame has its own initiation and termination codons ***Shine-Dalgarno sequence = A polypurine tract thatis located 6-8 nt of the AUG initiation codon ***anti-Shine-Dalgarno sequence = Polypyrimidine tract in the 3' end of the 16S rRNA in the small ribosomal subunit. ***Purpose of Shine-Dalgarno sequence = To guide the small ribosomal subunit so that it's P site is surrounding the AUG start site
If there is incorrect codon/anticodon matching in the ribosome P site, what happens? Put the below steps in chronological order
***A conformational change in the ribosome is triggered ***More mis-incorporations occur due to mismatching ***Premature termination ***The polypeptide is degraded by cellular peptidases and proteases
Match the following facts to each question about translation elongation
***After the very first initiator tRNA-Met is loaded into the P site - where is the the next charged tRNA loaded? = The A site ***Elongation factor Tu in bacteria or elongation factor eEF1A in eukaryotes = Loads the aminoacyl-tRNAs onto the ribosome ***GTP hydrolysis = Source of energy that EF Tu uses for loading charged tRNAs onto the ribosome ***Site where peptidyl bond formation occurs = Attached to the amino acid attached to the tRNA in the A site ***Process where the tRNA in the A site moves to the P site and the one in the P site moves to the E site = translocation ***Factor that promotes translocation = EFG in bacteria; eEF2 in eukaryotes ***Recognizes stop codons = Class 1 release factors ***Additional GTPase involved in translation termination = Class 2 release factors ***Process by which the large and small ribosomal subunits dissociate from each other thereby releasing the final tRNA and mRNA = ribosome recycling
During translation termination, the polypeptide is released from the ribosome. Ribosome recycling occurs next. Match the features of bacterial versus eukaryotic ribosome recycling.
***Bacteria Step 1: Which two factors bind in the ribosome A site? = RRF and EGF-GTP ***Bacteria Step 2 = Disassociation of the 2 ribosomal subunits ***Bacteria Step 3 = IF3 binds to the small ribosomal subunit and the peptidyl tRNA disassociates wit the P site. ***Eukaryotes: Step 1 = eRF1 is still in the A site and ABCE1 interacts with it there where ATP hydrolysis occurs ***Eukaryotes : Step 2 = eIF2D allows ejection of the mRNA and the deacylated tRNA ***Eukaryotes: Step 3 = eIF1 + eIF1A + eIF3 stabilize the dissociated state of the ribosomal subunits by binding to the small subunit
Match features of eukaryotic versus bacterial initiator tRNAs
***Bacteria: Type of methionine on the initiator tRNA = formylated methionine ***Eukaryotes: Type of methionine on the initiator tRNA = methionine ***Bacteria: Unusual base pairs at the top of the acceptor stem = C-A ***Eukaryotes: Base pairs at the top of the acceptor stem = A-U at 1st position and C-G at 3rd position ***Base pairs in common at anticodon stem between bacteria and eukaryotes = 3 consecutive G-C base pairs
Put the below steps of eukaryotic non-stop or no-go decay allowing mRNA decay and ribosomal rescue in chronological order.
***Ribosome encounters long string of A's with no stop codon in it ***Ribosomes stall and stack up ***An endonuclease known as Cue2 cleaves the mRNA in the A site of stalled or stacked ribosomes ***Termination factors Pelota and Hbs1 associate with the ribosome A site ***ABCE1-GTP is recruited by Pelota and Hbs1 ***ABCE1's GTPase activity provides energy for dissociation of the ribosomal subunits and release of the tRNA with bound polypeptide and the mRNA and termination factors
Put the following steps of tmRNA:SmpB mediated ribosomal rescue from truncated mRNAs in bacteria in chronological order
***SmpB partner protein binds in ribosome A site because there is no mRNA in the A site ***Alanine from acceptor arm of tmRNA is peptide bonded to the truncated polypeptide ***template mRNA is released and subsequently degraded by RNases ***Short ORF on tmRNA is translated to 10 amino acids added onto the polypeptide ***Translation meets stop codon on tmRNA ***Free ribosomes are liberated and tagged polypeptide is degraded by proteases
Put the steps of the eukaryotic RQC (Ribosomal Quality Control) pathway to degrade incomplete proteins into chronological order.
***Stalled ribosome subunit dissociation recruits NEMF and Ltn1 ***NEMF replaces 40S small ribosomal subunit and interacts with the 60S large ribosomal subunit ***NEMF adds alanine and threonine amino acids to the C terminus of the polypeptide ***Ltn1 ubiquitinates the incomplete protein ***Incomplete protein is degraded by the proteasome
Put the 3 broad steps of translation initiation in chronological order
***The small ribosomal subunit identifies the initiation codon within the mRNA ***A methionyl-tRNA is loaded into the P site of the ribosome where it base pairs with the initiation codon ***The large ribosomal subunit must join the small subunit
Which of the below components have been found to be important in examples of incorporation of non-standard amino acids into proteins with specialized functions?
A. mRNA elements such as stem-loops C. specialized tRNA D. dedicated aminoacyl-tRNA synthetase
-- associates with the A site; -- associates with the E site, and -- is a GTPase that helps to direct f-Met-tRNAfMet to the AUG in the -- site.
B. IF1; IF3; IF2; P site
How are premature stop codons recognized in the mRNAs of higher eukaryotes?
B. Ribosomes encounter a stop codon upstream of a exon junction complex tag the mRNA transcript and trigger recruitment of Upfs 1, 2, 3, eRF1, and eRF3-GTP to degrade the mRNA and protein
GAPs (GTPase-activating proteins) and GEFs (Guanine-nucleotide exchange factors) both play roles in GTP hydrolysis during translation. Interestingly, it is documented that the ribosome itself can act as a _____ in its interaction with EFTu to allow full acceptance of the aminoacyl-tRNA into the A site and release of EFTu-GDP
GAP
Conformational changes of the G530, A1492, A1493 amino acids in the 16S rRNA A site of the bacterial ribosome rearrange when a cognate tRNA anticodon-mRNA codon interaction occurs. These structural changes are thought to be critical for triggering ______ activation by EFTu and for accommodation of the cognate tRNA in the A site.
GTPase
What is the name of the elongation factor that is a GTPase and promotes structural rearrangements of the ribosome during translocation?
D. EFG in bacteria (eEF2 in eukaryotes)
When any of the 3 normal stop codons are misread by aminoacyl-tRNA species (often due to specific sequence elements in the mRNA) such that termination of translation fails to occur, this is called:
D. Nonsense suppression
During translation initiation, initiation factors load the -- site of the -- subunit of the ribosome with methionine-loaded --.
D. P; small; initiator tRNA-Met
Why is the +1 frameshifting that can occur during translation to produce bacterial termination factor RF2 called a programmed frameshifting event?
D. This frameshifting only occurs when RF2 concentrations are low, which slows down termination, allowing the frameshift to occur which allows continued translation to produce more RF2.
Large non-cognate amino acids are rejected from the -- site of the tRNA based on size exclusion. Smaller non-cognate amino acids are occasionally initially accepted and activated and moved to the editing site, but then rejected pre-transfer to the tRNA and --. If a non-cognate amino acid gets activated and charged onto the tRNA in the amino-acylation site, it can be hydrolyzed post-transfer from the tRNA in the -- site.
D. amino-acylation site; hydrolyzed; editing
Match the following protein factors and RNA sequences with their functions
***binds to the 5' cap = eIF4E ***Binds to the poly(A) tail = PABPs ***eIF4G = Binds to both PABPs and eIF4E which allows the mRNA to form a closed loop structure ***Pre-initiation complex = The small 40S ribosomal subunit bound with several translation initiation factors ***Kozak = Sequence in the 5' UTR that surrounds the first AUG; the PIC scans from the 5' end of the mRNA to this sequence to locate the translation start codon ***Recognition of AUG initiator start codon by the PIC causes = Release of eIF1 and Pi and Eif2 ***eIF5B-GTP hydrolysis = Ribosome subunit joining occurs and release of additional initiation factors from the complex
There are ______ amino acids that are encoded by ___________ codons that base pair with the anticodons of _______ tRNAs. The reason that there can be fewer tRNAs than codons is due to _______ pairing where there is promiscuity in the reading of the 3rd RNA codon position by the first position of the anticodon of the tRNAs.
20, 61, 40, wobble
Class I release factors bind in the _______ site of the ribosome upon recognizing a stop codon, and facilitate release of the polypeptide from the peptidyl tRNA. Class II release factors are types of enzymes called _______ and promote different facets of the termination process in bacteria and eukaryotes.
A, GTPases
Although tRNAs are often drawn as a cloverleaf shaped structure, in actuality, they form a -- shaped structure. The 5' and 3' ends of the tRNA together form the -- stem, at the 3' end of which is the --. The 3 nucleotides of the anticodon are typically stacked on one another in a structure known as a --.
A. L; acceptor; 3' CCA tail; U-turn
There are typically -- aminoacyl tRNA synthetases, one for each amino acid. One given aminoacyl tRNA synthetase can add its amino acid onto more than one tRNA, these sets of tRNAs that get charged with the same amino acid are called --. This reaction requires energy provided by the release of pyrophosphate from --. The AMP bound amino acid is then transferred to the 2' or 3' OH of the ribose of the -- of the 3' CCA tail of the tRNA.
C. 20; isoacceptors; ATP; adenosine
How do erythromycin and streptomycin antibiotics work?
C. Block the exit channel of the ribosome for the polypeptide; cause shape changes to the small subunit so near-cognate tRNAs are accepted and leading to incorrect proteins
Which of the below statements is NOT accurate?
C. It is the protein part of snRNPs that are involved in processing of introns in mRNA processing
According to the hybrid states model, during translocation, after peptide bond formation, the tRNA first moves spontaneously with respect to the -- subunit. There is then a global rotation of the -- subunit. EFG then promotes movement of the anticodon and -- domain of the ribosome (connected to the polypeptide). During the final step, the ribosome ratchets back to its unrotated conformation.
C. large; small; elbow
Match the following features of Class I versus Class II aminoacyl-tRNA synthetases
Class I: Where does the synthetase recognize the acceptor stem of the tRNA? = minor groove Class II: Where does the synthetase recognize the acceptor stem of the tRNA? = major groove Class I- where does the synthetase attach the amino acid to the ribose of the adenosine? = 2' OH Class II- where does the synthetase attach the amino acid to the ribose of the adenosine? = 3' OH
Define the following translation related terms
Codon = sequence of 3 nucleotides in an mRNA that code for an amino acid Anticodon = A region in the tRNA that base pairs with the codon of mRNA Aminoacyl-tRNA synthetases = Enzymes that attach the appropriate amino acid to the various tRNAs tRNA = RNAs that decode mRNA and participate in the synthesis of polypeptides ribosome = A large molecular machine composed of RNA and protein and performs protein synthesis ribosome small subunit = Subunit of ribosome that deciphers the mRNA ribosome large subunit = Subunit of ribosome that mediates the formation of peptide bonds between amino acids
Put the 3 broad steps of ribosome rescue (occurs if ribosome pausing or arrest occurs) in chronological order
The mRNA is targeted for decay The truncated protein is targeted for proteolysis The ribosomes are recycled
Match the following features to the large or small ribosomal subunits
The subunit where interactions between mRNA and tRNA take place = small subunit The subunit where peptide bond formation takes place = large subunit Large subunit = Location of the exit tunnel for the polypeptide How many antibiotics work = blocking the exit tunnel