11 Protein Synthesis

1. Approximately how much of an actively growing bacterium’s energy is dedicated to protein synthesis?

2. What happens to the polypeptide chain during the translation process as it moves through the ribosome?

It stays in the P-site until the entire protein is finished.
It is immediately spliced to remove non-coding protein segments.
It passes through a channel in the large subunit called the exit tunnel.
It is degraded by proteases in the exit tunnel.

3. What is the specific orientation and base-pairing relationship between a codon and an anticodon?

They bind in an antiparallel fashion via hydrogen bonds.
They bind in a parallel fashion via covalent acyl linkages.
The 5′ end of the codon pairs with the 5′ end of the anticodon.
They associate through hydrophobic stacking of the unusual bases.

4. All tRNA molecules share a common sequence at their 3′ terminus where the amino acid is attached. What is this sequence?

5′-GGC-3′
5′-AUG-3′
5′-CCA-3′
5′-UAA-3′

5. Which feature of tRNA is responsible for recognizing and binding to the mRNA codon?

The acceptor stem
The T loop
The anticodon loop
The D loop

6. How many dedicated aminoacyl-tRNA synthetases are typically found in most organisms?

3, one for each site in the ribosome.
61, one for each sense codon.
20, one for each amino acid.
64, one for every possible triplet combination.

7. Which statement accurately describes a polycistronic mRNA?

It is typical of eukaryotic transcripts and codes for one protein.
It is an mRNA that has been modified with a poly-A tail.
It is an mRNA that contains introns and requires splicing.
It contains multiple open reading frames, each coding for a different protein.

8. In the transcription of DNA to RNA, a ‘T’ (Thymine) in the DNA template strand specifies which base in the resulting RNA?

G (Guanine)
A (Adenine)
C (Cytosine)
U (Uracil)

9. A mutation results in the insertion of two nucleotides into the middle of an exon. What is the most likely consequence for the resulting protein?

A frameshift mutation that alters all subsequent amino acids.
No change, as the code is non-punctuated.
A silent mutation because the genetic code is degenerate.
A missense mutation affecting only the two inserted bases.

10. What defines an ‘Open Reading Frame’ (ORF) in the context of genetic sequences?

A series of three nucleotides that codes for a single amino acid.
Any sequence of DNA that can be transcribed into RNA.
The entire mRNA sequence from the 5′ cap to the poly-A tail.
A sequence of at least 50 codons uninterrupted by a stop codon.

11. An amino acid is encoded by multiple codons that differ only at the third nucleotide position. Which property of the genetic code best describes this phenomenon?

The code is degenerate.
The code is non-overlapping.
The code is specific.
The code is universal.

12. What happens to a tRNA molecule after its amino acid has been incorporated into the growing peptide chain at the ribosome?

It is degraded by the peptidyl transferase center.
It is covalently linked to the next incoming aminoacyl-tRNA.
It remains permanently attached to the mRNA to prevent degradation.
It moves to the E site and is then released for recharging.

13. In prokaryotes, which of the following codons can occasionally serve as an initiator codon, in addition to AUG?

5′-CCC-3′
5′-GUG-3′
5′-UAA-3′
5′-UAG-3′

14. A researcher identifies a sequence of mRNA that contains 150 nucleotides without a termination codon. According to the standard definition, what has the researcher found?

A Shine-Dalgarno sequence.
A polycistronic transcript.
A Kozak sequence.
An Open Reading Frame (ORF).

15. The eukaryotic 5′ cap is joined to the mRNA through which unusual chemical linkage?

An acyl linkage similar to tRNA charging.
A 3′−3′ phosphodiester bond.
A 5′−5′ triphosphate bridge.
A peptide bond between the guanine and a 7-methyl group

16. Which specific property of the genetic code ensures that a single codon does not represent more than one amino acid?

The code is degenerate.
The code is non-overlapping.
The code is specific.
The code is universal.

17. Which ribosomal component contains the ‘decoding center’ where charged tRNAs read the mRNA codons?

The exit tunnel
The large subunit
The small subunit
The aminoacyl-tRNA synthetase

18. During the process of tRNA charging, what is the first chemical step catalyzed by the aminoacyl-tRNA synthetase?

Hydrolysis of the PPi from the 3′ CCA tail.
Adenylylation of the amino acid.
Decarboxylation of the amino acid.
Formation of an acyl linkage with the 3′ hydroxyl group.

19. Which of the following describes a key difference between prokaryotic and eukaryotic mRNA transcripts?

Eukaryotic mRNA uses a different set of 64 codons for its genetic code.
Eukaryotic mRNA is translated in the 3′→5′ direction.
Prokaryotic mRNA can be polycistronic, while eukaryotic mRNA is typically monocistronic.
Prokaryotic mRNA lacks start and stop codons.

20. In the context of the Wobble Hypothesis, which position of the mRNA codon is subject to modified base-pairing rules?

The 5th position of the tRNA.
The 1st position (5′ end of the codon).
The 2nd position.
The 3rd position (3′ end of the codon).

21. A mutation results in the insertion of a single nucleotide into the coding sequence. What is the most likely outcome for the resulting protein?

The protein will be identical because the code is degenerate.
A silent mutation with no change in amino acid sequence.
A missense mutation affecting only that specific codon.
A frameshift mutation that alters all subsequent amino acids.

22. Which ribosomal site is responsible for holding the tRNA that is linked to the growing polypeptide chain?

The A site.
The E site.
The decoding center.
The P site.

23. What is the role of the ‘decoding center’ in the small ribosomal subunit?

It catalyzes the formation of the peptide bond.
It ensures the correct base-pairing between the mRNA codon and tRNA anticodon.
It attaches the 7-methylguanosine cap to eukaryotic mRNA.
It identifies the Shine-Dalgarno sequence in eukaryotes.

24. Which mutation type involves a base substitution that results in the premature termination of a polypeptide chain?

Frameshift mutation
Missense mutation
Nonsense mutation
Silent mutation

25. The Kozak sequence in eukaryotes is significant because it:

Acts as the binding site for the 5′ methyl-guanosine cap.
Interacts with the 16S rRNA to align the ribosome.
Increases translation efficiency by interacting with initiator tRNA.
Signals the end of the mRNA transcript.

26. How does the ribosome in prokaryotes correctly identify the start codon within a polycistronic mRNA?

Interaction with the poly-A tail via initiation factors.
Base-pairing between the 16S rRNA and the Shine-Dalgarno sequence.
Scanning from the 5′ cap until the first AUG is encountered.
Recognition of a 5′−5′ triphosphate bridge.

27. Which amino acids are unique because they are each encoded by only a single codon?

Serine and Leucine
Lysine and Arginine
Methionine and Tryptophan
Alanine and Glycine

28. In prokaryotic translation, which sequence is responsible for recruiting the small ribosomal subunit by base-pairing with the 16S rRNA?

Shine-Dalgarno sequence
Poly-A tail
Kozak sequence
The 5′ cap

29. How many dedicated aminoacyl-tRNA synthetases are typically found in most organisms?

30. A mutation changes a codon from UCA (Ser) to UAA. Which type of mutation and functional consequence has occurred?

Missense mutation causing an amino acid substitution.
Nonsense mutation leading to premature termination.
Frameshift mutation altering the entire downstream sequence.
Silent mutation with no change in the primary structure.

31. What percentage of a cell’s energy is dedicated to protein synthesis in actively growing bacteria?

Approximately 10%
Less than 1%
Over 95%
Up to 50%

32. The eukaryotic 5′ cap is uniquely characterized by which type of chemical linkage?

2′ -to-3′ acyl linkage
High-energy thioester bond
3′-to-5′ phosphodiester bond
5′-to-5′ triphosphate bridge

33. The property of the genetic code known as ‘degeneracy’ refers to:

The absence of punctuation between codons in an ORF.
The fact that the code is identical across all known life forms.
The ability of one amino acid to be encoded by more than one codon.
The degradation of mRNA after translation is complete.

34. The ‘wobble’ position in translation allows for unconventional base-pairing. Where specifically are these modified rules applied?

The 2′ position of the mRNA codon and the 2′ position of the tRNA anticodon.
The 3′ position of the mRNA codon and the 1′ position of the tRNA anticodon.
The 5′ end of the 16S rRNA and the Shine-Dalgarno sequence.
The 1′ position of the mRNA codon and the 3′ position of the tRNA anticodon.

35. In the context of the cloverleaf structure of tRNA, where is the anticodon located relative to the amino acid attachment site?

Inside the exit tunnel of the small subunit.
In a loop directly opposite the acceptor stem.
Within the D loop.
On the same end as the 3′ CCA sequence.

36. What is the primary role of the aminoacyl-tRNA synthetase during the ‘charging’ process?

Transcribing tRNA molecules from DNA templates.
Matching the anticodon to the mRNA codon in the decoding center.
Attaching the correct amino acid to its corresponding tRNA.
Catalyzing the formation of peptide bonds between amino acids.

37. What is the result of the second step of the tRNA charging reaction?

Binding of the tRNA to the mRNA codon.
Transfer of the amino acid to the tRNA and release of AMP.
Release of the polypeptide chain from the ribosome.
Formation of ATP from AMP and PPi

38. Why are β-sheets unable to form within the exit tunnel of the large ribosomal subunit?

The exit tunnel is composed entirely of proteins that repel hydrophobic regions.
Tertiary interactions are required before any secondary structures can form.
The narrow width of the tunnel limits the physical conformation of the polypeptide.
The tunnel contains peptidyl transferase which breaks β-sheet hydrogen bonds.

39. Which of the following correctly describes the ‘non-overlapping’ nature of the genetic code?

The ribosome cannot translate two different mRNAs at the same time.
There are no gaps or punctuation between the codons.
The same codon cannot be used for two different amino acids.
Each nucleotide is read as part of only one triplet codon in a series.

40. During the first step of tRNA charging, known as adenylylation, the amino acid reacts with which molecule?

GTP
Pyrophosphate (PPi)
AMP
ATP

41. Which ribosomal site is the last to be occupied by a tRNA before it leaves the ribosome?

The A site
The Kozak site
The P site
The E site

42. What is the specific linkage formed between an amino acid and its tRNA during the charging process?

A phosphodiester bond between the amino acid and the 5′ end of the tRNA.
A peptide bond between the amino acid and the tRNA synthetase protein.
A hydrogen bond between the amino acid's R-group and the anticodon loop.
A high-energy acyl linkage to the 2′ or 3′ hydroxyl group of adenosine.

43. During tRNA charging, what is the fate of the adenosine monophosphate (AMP) molecule?

It base-pairs with the anticodon to stabilize the structure.
It remains covalently attached to the 3′ end of the tRNA.
It is converted back into ATP using the energy of the acyl linkage.
It is released after the amino acid is transferred to the tRNA.

44. Which site within the ribosome is specifically responsible for holding the tRNA that carries the growing polypeptide chain?

The P site
The A site
The decoding center
The E site

45. Why does the wobble position allow for fewer than 61 distinct tRNAs to be required for translation?

Because stop codons do not require tRNAs.
Because the genetic code is non-overlapping.
Because amino acids can be directly attached to the ribosome.
Because one tRNA anticodon can pair with multiple different mRNA codons.

46. In eukaryotic translation, what is the significance of the Kozak sequence?

It provides the 5′ cap necessary for ribosomal recruitment.
It is the sequence that encodes the poly-A tail at the 3′ end.
It increases translation efficiency by interacting with the initiator tRNA.
It serves as the binding site for the 16S rRNA to begin assembly.

47. What is the result of a ‘silent’ mutation in the coding sequence of a gene?

The creation of a stop codon that halts translation early.
A deletion that is 'silenced' by a subsequent insertion.
A mutation that prevents the ribosome from binding to the mRNA.
A change in the nucleotide sequence that does not alter the amino acid sequence.

48. The width of the exit tunnel in the large ribosomal subunit imposes what constraint on the newly synthesized protein?

It prevents the formation of any secondary structures.
It limits the polypeptide length to 50 amino acids.
It allows for the formation of α-helices but generally precludes β-sheets.
It forces the protein into its final tertiary 3D conformation.

49. What is the mass composition of a typical ribosome?

Two thirds rRNA and one third protein.
Equal parts RNA and protein.
One third rRNA and two thirds protein.
Mostly lipid with some protein.

50. Which component of the ribosome is primarily responsible for the catalytic activity of peptide bond formation?

Aminoacyl-tRNA synthetase within the A site.
Ribosomal proteins in the small subunit.
Ribosomal RNA (rRNA) in the large subunit.
The 5′ cap structure on the mRNA template.

51. Which component of the ribosome is responsible for catalyzing the formation of peptide bonds?

The rRNA of the small subunit.
The proteins of the small subunit.
Aminoacyl-tRNA synthetase.
The rRNA of the large subunit.

52. A codon table displays the code as it appears in which molecule?

The protein sequence
The tRNA anticodon
The mRNA
The template strand of DNA

53. Which of the following best describes the structural composition of a functional ribosome?

It is primarily composed of DNA and proteins found in the nucleolus.
It is composed of roughly two-thirds rRNA and one-third protein by mass.
It is a protein-dominated complex with rRNA acting only as a scaffold.
It consists of equal parts of tRNA, mRNA, and rRNA.

54. In eukaryotes, the process by which the ribosome moves along the mRNA from the 5′ cap to find the first start codon is known as:

Transition
Scanning
Transformation
Translocation

55. Which of the following is NOT one of the three ‘nonsense’ codons?

56. If a template strand of DNA reads 3′−TAC GGG TTT−5′, what will be the corresponding amino acid sequence after transcription and translation?

Tyr-Gly-Phe
Met-Pro-Lys
Met-Gly-Phe
Ile-Pro-Asn