10 Transcription

1. What percentage of eukaryotic pre-mRNAs are estimated to undergo alternative splicing or alternative 3′ cleavage?

∼10%
Nearly 100%
∼90%
∼50%

2. During transcription, how long is the transient DNA/RNA hybrid region formed within the RNA polymerase?

∼3 nucleotide pairs
The entire length of the gene
∼9 nucleotide pairs
∼25 nucleotide pairs

3. Which chemical modification is found in ribosomal RNA and is mediated by snoRNPs?

7−methylguanosine
Reverse transcription
Pseudouridine
Poly−A addition

4. How does the organization of genes in a prokaryotic mRNA typically differ from that of a eukaryotic mRNA?

Prokaryotic mRNAs contain introns that must be removed by the spliceosome.
Eukaryotic mRNAs lack untranslated regions (UTRs) at the 5′ and 3′ ends.
Prokaryotic mRNAs are monocistronic, while eukaryotic are polycistronic.
Prokaryotic mRNAs are often polycistronic, encoding multiple different proteins.

5. In the maturation of the 45S rRNA precursor, what is the role of pseudouridine?

It serves as the start codon for the ribosomal proteins.
It is a chemical modification added to the precursor.
It catalyzes the cleavage of the precursor into 18S and 28S subunits.
It acts as a signal for the spliceosome to remove introns.

6. What is the role of the TBP (TATA-binding protein) subunit within the TFIID complex?

It acts as a helicase to unwind the DNA double helix.
It recognizes and binds to the TATA box sequence in the promoter.
It adds a poly−A tail to the 3′ end of the transcript.
It catalyzes the formation of the phosphodiester bond between nucleotides.

7. Which molecule is responsible for the chemical modifications, such as pseudouridylation and methylation, of the eukaryotic 45S rRNA precursor?

miRNAs
snRNPs
snoRNPs
RNase P

8. Which DNA strand has the same sequence as the newly synthesized RNA transcript (with the exception of U replacing T)?

The leading strand
The antisense strand
The coding (non-template) strand
The template strand

9. In eukaryotes, the 45S pre−rRNA transcript is processed into three mature rRNA molecules. Which mature rRNA is NOT derived from this precursor?

5.8S rRNA
18S rRNA
5S rRNA
28S rRNA

10. What post-transcriptional modification is required at the 3′ end of all tRNAs to allow amino acid attachment?

Polyadenylation by poly-A polymerase
Addition of a 7-methylguanosine cap
Cleavage of the D loop by RNase D
Addition of a CCA sequence by tRNA nucleotidyl transferase

11. A retrovirus infects a host cell and utilizes its enzyme to integrate its genetic information. According to the notable exception to the Central Dogma, what is the first step in this information transfer?

Host DNA polymerase is used to replicate the viral RNA genome into double-stranded RNA.
The RNA genome is directly translated into proteins in the cytoplasm.
The RNA genome is copied into DNA using reverse transcriptase.
DNA serves as a template to synthesize more viral RNA genomes immediately.

12. Which type of regulatory RNA is specifically known for serving as a scaffold and regulating diverse cell processes like X-chromosome inactivation?

snRNAs
lncRNAs (long noncoding RNAs)
miRNAs
siRNAs

13. What is the approximate error rate of RNA transcription compared to DNA replication?

They have roughly the same error rate of 1 per 10^6 nucleotides.
1 error per 10^4 nucleotides for transcription vs 1 per 10^9 for replication.
Transcription is more accurate because it only copies small portions of the genome.
1 error per 10^9 nucleotides for transcription vs 1 per 10^4 for replication.

14. In the eukaryotic nucleus, which specific RNA species is responsible for guiding the chemical modification and processing of ribosomal RNAs (rRNAs)?

snoRNAs
miRNAs
piRNAs
snRNAs

15. A mutation that prevents the formation of the BRE element in a promoter would most directly affect the binding of which factor?

TFIIF
RNA Polymerase I
TFIIB
TFIID

16. In prokaryotes, the 30S pre-rRNA transcript is cleaved to produce which mature rRNA species?

5S, 16S, and 23S rRNAs
5.8S, 18S, and 28S rRNAs
5.8S, 16S, and 28S rRNAs
5S, 18S, and 23S rRNAs

17. Given a DNA template strand with the sequence 3′−GCTA−5′, what will be the sequence of the resulting RNA transcript?

3′−CGAU−5′
5′−GCUA−3′
5′−CGAU−3′
5′−CGAT−3′

18. Considering the speed of biological processes, how does the rate of RNA transcription compare to DNA replication in a cell?

Transcription is faster than DNA replication but slower than protein translation.
Both processes occur at approximately the same speed of 800 nucleotides/sec.
Transcription is the fastest process to allow for rapid gene expression.
Transcription is much slower than DNA replication.

19. Which snRNA molecules form the core of the spliceosome?

U2,U4,U5,U6,U7
U1,U2,U3,U4,U5
U1,U2,U4,U5,U6
U1,U2,U3,U5,U6

20. Which of the following is a key functional difference between RNA Polymerase and DNA Polymerase during nucleic acid synthesis?

RNA Polymerase has a higher degree of accuracy than DNA Polymerase.
RNA Polymerase produces a product that remains permanently base-paired to the template.
RNA Polymerase synthesis is significantly faster than DNA Polymerase.
RNA Polymerase does not require a primer to initiate synthesis.

21. The active site of RNA polymerase contains which specific metal ion required for the catalytic addition of nucleotides?

Zn2+
Mg2+
Ca2+
Fe2+

22. Which of the following is a key property of RNA polymerase that distinguishes it from DNA polymerase?

RNA polymerase does not require a primer to initiate synthesis.
RNA polymerase uses deoxyribonucleotides as substrates.
RNA polymerase synthesizes in the 3′ to 5′ direction.
RNA products remain permanently base-paired to the DNA template.

23. Which eukaryotic RNA Polymerase is uniquely responsible for transcribing the 5S rRNA gene?

RNA Polymerase II
The single prokaryotic-like RNA Polymerase
RNA Polymerase III
RNA Polymerase I

24. What is the sedimentation coefficient (S value) of the large ribosomal subunit in a eukaryotic cell?

40S
80S
60S
50S

25. The BRE element in a eukaryotic promoter is recognized by which transcription factor?

TFIIB
TBP
TFIIE
TFIID

26. During the initiation of transcription, which General Transcription Factor (GTF) is responsible for phosphorylating the CTD (C-terminal domain) of RNA Polymerase II to release it from the promoter?

TFIIE
TFIIH
TFIID
TFIIB

27. Which of the following is true regarding the template strand choice for transcription?

The choice of template strand is determined by the promoter sequence of the individual gene.
The bottom strand is always used as the template for every gene on a chromosome.
RNA polymerase randomly selects a strand to transcribe during every initiation event.
Both strands are transcribed simultaneously to produce double-stranded RNA.

28. Which enzyme is responsible for the notable exception to the standard flow of genetic information in retroviruses?

DNA Polymerase δ
RNA-dependent RNA polymerase
Reverse transcriptase
Integrase

29. What is the primary function of miRNA (MicroRNA) in the cell?

They help to process and chemically modify rRNAs.
They regulate gene expression by blocking translation and causing mRNA degradation.
They act as adaptors between mRNA and amino acids.
They protect the germ line from transposable elements.

30. What structural feature of eukaryotic mRNAs facilitates their export from the nucleus and protects them from degradation at the 3′ end?

The removal of exons during alternative splicing.
The addition of a CCA sequence by tRNA nucleotidyl transferase.
A tail of approximately 250 adenine nucleotides.
A 7−methylguanosine cap attached via a 5′−to−5′ bridge.

31. What happens to the pre−mRNA sequence located between the CA cleavage site and the GU−rich region during 3′ end processing?

It becomes the scaffold for the 7−methylguanosine cap.
It is degraded in the nucleus after cleavage.
It is spliced to the next exon to form a functional domain.
It remains attached and serves as a signal for ribosomal binding.

32. In terms of catalytic speed, how does RNA polymerase compare to DNA polymerase and the ribosome?

It operates at roughly the same speed as DNA polymerase.
It is faster than both DNA polymerase and the ribosome.
It is slower than DNA polymerase but faster than the ribosome.
It is the slowest of the three molecular machines.

33. Approximately what percentage of the total RNA in a cell is comprised of ribosomal RNA (rRNA)?

3−5%
15%
95%
80%

34. In the process of pre−mRNA splicing, what specific chemical structure is formed when the 2′−OH of an adenine in the intron attacks the 5′ splice site?

A 45S precursor rRNA
A 5′−to−5′ triphosphate bridge
A lariat structure
A cloverleaf secondary structure

35. Which structural loop of the tRNA contains the specific sequence that base pairs with the mRNA codon?

D loop
Anticodon loop
T loop
Acceptor stem

36. Which eukaryotic RNA polymerase is responsible for the transcription of the 5S rRNA gene?

RNA Polymerase I
RNA Polymerase IV
RNA Polymerase III
RNA Polymerase II

37. In the cloverleaf secondary structure of tRNA, which loop contains the sequence that base-pairs with the mRNA codon?

D loop
Acceptor stem
Anticodon loop
T loop

38. The ENCODE project suggests that as many as 90% of human pre−mRNAs can undergo alternative splicing. What is the primary biological advantage of this process?

It allows prokaryotic cells to produce monocistronic mRNAs.
It ensures that every gene is transcribed at exactly the same rate.
It significantly increases the diversity of proteins that can be encoded by a single gene.
It prevents RNA polymerase from making errors during transcription.

39. Based on the prevalence of different RNA types, which class makes up the vast majority (approximately 80%) of the total RNA in a cell?

snRNAs
rRNAs
mRNAs
tRNAs

40. During the initiation of eukaryotic transcription, which general transcription factor contains the TBP subunit that recognizes the TATA box?

TFIIH
TFIID
TFIIB
TFIIF

41. True or False: In eukaryotic cells, transcription and translation are tightly coupled so that the 5′ end of mRNA is translated while the 3′ end is still being synthesized.

False
True

42. Which component of the spliceosome is responsible for recognizing the specific sequences required for intron removal?

Reverse Transcriptase
snRNPs (small nuclear ribonucleoproteins)
tRNA nucleotidyl transferase
miRNAs

43. What is the role of TFIIF in the eukaryotic transcription initiation complex?

It adds chemical modifications like pseudouridine to the transcript.
It recognizes the DPE (downstream promoter element).
It stabilizes the polymerase interaction with TBP and TFIIB and helps attract other factors.
It triggers the cleavage of the pre−mRNA at the termination site.

44. What is the specific catalytic role of TFIIH during the transition from transcription initiation to elongation?

It phosphorylates the C-terminal domain (CTD) of RNA polymerase II.
It catalyzes the formation of the first phosphodiester bond.
It adds the 7-methylguanosine cap to the 5′ end of the transcript.
It recruits the poly-A polymerase to the 3′ end of the gene.

45. What happens to the region of the 3′ end of a pre-mRNA that is located downstream of the cleavage site?

It is spliced back into the coding sequence.
It is incorporated into the poly-A tail.
It is degraded in the nucleus.
It serves as a template for reverse transcriptase.

46. In prokaryotes, transcription and translation are described as ‘tightly coupled.’ What does this imply about the structure and processing of prokaryotic mRNA?

Prokaryotic mRNAs must be exported to the cytoplasm before translation can occur.
Splicing must occur to remove introns before ribosomes can bind.
Translation of the 5′ end of the mRNA begins while the 3′ end is still being synthesized.
The mRNA is modified with a 7−methylguanosine cap to facilitate ribosome binding.

47. Which of the following describes a key difference between the 5′ cap and the poly-A tail of eukaryotic mRNAs?

The 5′ cap uses an unusual 5′ to 5′ triphosphate bridge.
The poly-A tail is added before splicing, while the cap is added after.
The poly-A tail is encoded in the DNA template, while the cap is not.
The cap consists of a string of approximately 250 adenines.

48. How many copies of rRNA genes are typically found per haploid genome in humans?

Thousands of copies
Approximately 200 copies
Varies by cell type
One single copy

49. Which of the following describes a unique characteristic of prokaryotic mRNA compared to eukaryotic mRNA?

It is often polycistronic, containing instructions for several different proteins.
It contains exons that are spliced together in the nucleolus.
It contains 5′ and 3′ untranslated regions (UTRs).
It is heavily modified with a poly−A tail at the 3′ end.

50. In the context of pre-mRNA splicing, what defines the structure known as a ‘lariat’?

A linear sequence of exons joined together.
A loop formed by a 2′ to 5′ phosphodiester bond at the branch point 'A'.
The complex of snRNAs and proteins that performs the splicing.
The 3′ end of the mRNA after it has been cleaved but before polyadenylation.

51. Which enzyme is responsible for processing the 5′ end of a tRNA precursor?

RNase D
RNase P
RNA Polymerase III
tRNA nucleotidyl transferase

52. During the maturation of tRNA, which enzyme is responsible for adding the 3′ terminal sequence required for amino acid attachment?

RNAse D
RNA Polymerase III
tRNA nucleotidyl transferase
RNAse P