Deck 14: The Mechanism of Translation

Question 1

Which component is not directly involved in the process known as translation?

A) mRNA
B) tRNA
C) rRNA
D) DNA

Answer 1

DNA

Question 2

Which statement is not true about the nucleolus?

A) The nucleolus is the site of rRNA synthesis.
B) The nucleolus is a membrane-bound organelle within the nucleus.
C) The nucleolus is the site of ribosome subunit assembly.
D) The nucleolus is composed of a fibrillar center, dense fibrillar component, and granularcomponent.

Answer 2

The nucleolus is a membrane-bound organelle within the nucleus.

Question 3

Ribosomes carry out the process of protein synthesis in the ____________ after assembly in
The _____________ within a special compartment called the ______________.

A) cytoplasm, cytoplasm, nucleolus
B) nucleus, cytoplasm, nucleolus
C) nucleolus, cytoplasm, nucleus
D) cytoplasm, nucleus, nucleolus

Answer 3

cytoplasm, nucleus, nucleolus

Question 4

Which component of mammalian ribosomes accounts for 60% of the mass?

A) ribosomal RNA
B) ribosomal protein
C) messenger RNA
D) transfer RNA

Question 5

In eukaryotes, ribosomal RNAs are transcribed by

A) RNA polymerase I
B) RNA polymerase II
C) RNA polymerase III
D) RNA polymerase IV

Question 6

What is an anticodon?

A) The base sequence of an mRNA that signals the termination of translation.
B) The base sequence of an mRNA that binds to a complementary codon in tRNA.
C) The base sequence of a tRNA that binds to a complementary codon in mRNA.
D) The base sequence of a tRNA that accepts an amino acid, via a reaction catalyzed by aminoacyl-tRNA synthetase

Question 7

Aminoacyl-tRNA synthetases are enzymes that

A) catalyze loading of an anticodon onto the 3? end of a tRNA.
B) catalyze loading of an amino acid onto the 3? end of a tRNA.
C) catalyze loading of an amino acid onto the anticodon loop of a tRNA.
D) act as chaperones to fold tRNA into its functional L-shaped tertiary structure.

Question 8

Transfer RNAs couple to amino acids by

A) a high-energy ester bond
B) a redox-sensitive disulfide bond
C) hydrogen bonding interactions that mimic base-pairing
D) a hydrogen bond between the tRNA 3' OH and the amino group of the amino acid

Question 9

Which statement is not true about ribosomes:

A) There are three tRNA binding sites on the ribosome, the A site, the P site, and the E site.
B) Ribosomal subunits are assembled in the nucleolus of the cell.
C) Peptide bond formation is catalyzed by a ribosomal protein.
D) Eukaryotic ribosomes are composed of a 40S and 60S subunit.

Question 10

GTP hydrolysis is required for

A) joining of the 40S and 60S subunits.
B) peptide bond formation.
C) start codon recognition and initiation factor release.
D) A and C

Question 11

Hydrolysis of ATP indirectly fuels protein synthesis by

A) generating a high energy bond between the amino acid and tRNA.
B) loading the ternary complex onto the 40S subunit.
C) triggering translocation of the mRNA within the ribosome during elongation.
D) triggering dissociation of the large and small ribosomal subunits at termination so they can be recycled.

Question 12

Which is not a member of the eukaryotic "ternary complex" of translation initiation?

A) Met-tRNA
B) eIF2
C) mRNA
D) GTP

Question 13

Below is a simplified diagram of several components of the translation machinery. The ribosome is moving from left to right in this figure. The arrow points to the:

A) 3'end of the Mrna
B) 5' end of the mRNA
C) 3' end of the rRNA
D) 5' end of the rRNA

Question 14

The start codon for translation in eukaryotes is

A) UUG
B) GUG
C) AUG
D) all of the above

Question 15

Which of the following is/are required as an energy source for translation?

A) GTP only
B) ATP only
C) GTP and ATP
D) No energy source is required.

Question 16

Transfer RNAs are thought to improve the fidelity of mRNA translation by

A) preventing translocation if an incorrect amino acid is present in the peptidyl transferase center.
B) increasing the rate of GTP hydrolysis by EF-Tu upon accurate codon-anticodon pairing.
C) activating proofreading activity of eEF2.
D) linking codon-anticodon mispairing in the P site to translation termination.

Question 17

The stop codon is recognized by

A) a special aminoacyl tRNA
B) eRF1 and eRF2
C) GTP
D) a molecular chaperone

Question 18

Which of the following does not need to occur for translation to terminate?

A) cleavage of the polypeptide from the tRNA in the P-site
B) recognition of the stop codon by a release factor
C) translocation by eEF2
D) binding of a tRNA to the A-site

Question 19

Nascent polypeptides exit the ribosome via

A) the E (exit) site
B) the mRNA exit channel
C) a long tunnel
D) a large cavity that allows protein folding before its release

Question 20

The crystal structure of the ribosome provided key new evidence that

A) the mechanism of translation is fundamentally different among the three branches of life.
B) the mRNA is situated in a tunnel in the small ribosomal subunit.
C) ribosomal proteins facilitate structural transitions during translocation.
D) ribosomal RNAs catalyze peptide bond formation.

Question 21

Which step of translation requires mRNA decoding by a protein?

A) Initiation
B) Elongation
C) Termination
D) A and C

Question 22

The signal recognition particle (SRP) is a ribonucleoprotein complex that binds to ribosomes translating polypeptides that bear a signal sequence for targeting to

A) the endoplasmic reticulum.
B) the nucleus.
C) the mitochondria.
D) the cytoplasm.

Question 23

What is a molecular chaperone?

A) A protein that binds to ribosomes at the rough ER membrane.
B) A protein that post-translationally modifies a nascent polypeptide by adding or removing a phosphate group.
C) A protein component of the large ribosomal subunit that helps with correct peptide bond formation.
D) A protein that helps a nascent polypeptide chain to adopt its correct three-dimensional fold.

Question 24

When the translation initiation factor eIF2 is phosphorylated in response to a sudden temperature increase or viral infection, translation can be greatly inhibited. In this case, phosphorylated eIF2 is under _______________ control, and the phosphorylation of eIF2 leads to global (general or widespread) _____________ control.

A) translational; post-translational
B) post-translational; translational
C) post-translational; transcriptional
D) translational; transcriptional

Question 25

In response to unfavorable conditions such as hypoxia or osmotic shock, translation can be globally repressed by

A) modification of mRNA 7-methylguanosine caps
B) ribosome stalling via a conformation change in eEF2
C) phosphorylation of eI $\alpha$
D) puromycin synthesis

Question 26

Give a brief explanation of the role of the following RNAs during protein synthesis:
mRNA
tRNA
rRNA

Question 27

Draw a rough sketch of a ribosome, showing the location of the large and small subunits and the E, P, and A sites.

Question 28

Why do you suppose eukaryotes evolved a specialized subnuclear structure for ribosome biogenesis?

Question 29

Eukaryotic ribosomes misincorporate one amino acid for every 1,000-10,000, whereas the eukaryotic replication machinery misincorporates one nucleotide for every ~1x10⁷, a number which goes down to ~1x10⁹ following activity of the mismatch repair machinery. (a) Why can the cell tolerate a higher rate of error in translation than in replication? (b) Besides errors that occur in the ribosome, what is another potential source of error in protein synthesis?

Question 30

Mammalian ribosomes are composed of a 60S and a 40S subunit. What is "S"?

Question 31

Which component of the nucleolus is thought to be the location of active ribosomal genes?

Question 32

An active ribosomal RNA gene has a "Christmas tree" structure as visualized by electron microscopy. What are the "branches" and what is the "trunk"?

Question 33

Diagram the pathway for assembly in the nucleolus, maturation, and nuclear export of ribosomal subunits in yeast.

Question 34

Diagram the two steps of aminoacyl-tRNA charging.

Question 35

Describe an in vitro assay to demonstrate that aminoacylation of tRNA_CUA with pyrrolysine requires a novel archael aminoacyl synthetase, PylS.

Question 36

Aminoacyl-tRNAs display high fidelity, even for amino acids such as threonine and serine that have very similar side chains. Present a model for the proofreading activity of aminoacyl- tRNA synthetases based on recent X-ray crystallographic evidence.

Question 37

Draw a diagram to summarize the process of translation initiation in eukaryotes. Indicate at what points ATP or GTP hydrolysis are required.

Question 38

In eukaryotes, the mRNA to be translated is most likely folded into secondary and tertiary structures and coated with protective RNA-binding proteins. Discuss the importance of the 5′ cap and poly(A) tail for loading of the mRNA onto the 43S complex.

Question 39

In order to recycle into its active form to bind another initiator Met-tRNA, eIF2-GDP must be converted to eIF2-GTP. Describe how this occurs and explain how this process differs from GTP hydrolysis.

Question 40

The younger sibling of a friend of yours has been diagnosed with a rare disease called leukoencephalopathy with vanishing white matter. Explain the genetic basis of this disease.

Question 41

Explain (or draw a clearly labeled diagram) the sequence of events that occurs during translation in eukaryotic cells as a protein elongates by one amino acid. At each step, specify what is happening in the ribosome's A site, P site, and E site. Indicate at what points GTP hydrolysis is required.

Question 42

Do stop codons always specify termination? Explain your answer.

Question 43

tRNA was originally thought to be a static "adaptor" during protein synthesis. Discuss recent evidence suggesting that tRNA plays an active role in initial selection and proofreading during translation.

Question 44

Draw the bond forming between the growing polypeptide chain and the amino acid attached to the tRNA in the A site. Name the bond.

Question 45

What is the function of and where is the "peptidyl transferase" region of the ribosome? Of what is this region primarily composed?

Question 46

Diagram the cotranslation translocation pathway mediated by the signal recognition particle (SRP) from the ribosome to the endoplasmic reticulum.

Question 47

The E. coli trigger factor has been described as hunching over the exit of the ribosome tunnel "like a crouching dragon." What is it doing?

Question 48

Does a special tRNA bind to the stop codon in the mRNA during termination?

Question 49

Diagram the mechanism of translational control by phosphorylation of eukaryotic initiation factor 2 (eIF2), starting with activation of protein kinase RNA (PKR).

Question 50

Imagine you have treated reticulocytes from a heme-regulated inhibitor kinase (HRI) knockout mouse with hemin. Predict the effect of this treatment on eIF2 phosphorylation state and globin synthesis. Describe an experiment to test your predictions. Shown sample positive results.

Question 51

Describe a toeprint assay involving mammalian ribosomal subunits and a mRNA in a cell-free extract that contains all the factors necessary for translation.
(a) What results would you expect to see with 40S ribosomal subunits alone?
(b) With 60S subunits alone?
(c) With both subunits and all amino acids except serine, which is required in the 15^th position of the polypeptide?

Question 52

What would be the effect on the function of eIF2 of inhibiting its guanine exchange factor?
Would the outcome be different if eIF2 were phosphorylated?

Question 53

You are investigating a tRNA whose charging specificity appears to be affected by a U11:G24 to U11:A24 base pair in the D stem. Design an experiment using an in vitro reaction to show that changing this base-pair changes the charging specificity of the tRNA.

Question 54

A skeptic thinks that only proteins can be enzymes. Provide X-ray crystallographic and biochemical evidence in support of the view that the ribosome is a ribozyme.