Reading the Double Helix: DNA Transcription Quiz

Quiz Answer Key and Fun Facts

1. Transcription, or the synthesis of RNA from DNA template, needs to start somewhere. There exist certain segments of DNA that contain the necessary base-pair sequences to initiate RNA synthesis. What are these sites called?

Answer: promoter sites

Promoter sequences in prokaryotes are remarkably similar. At 35 bp upstream (-35 sequence) and at 10 bp upstream (-10 sequence) from the start site of transcription, the average sequences are TTGACA and TATAAT, respectively. These two sequences are called the consensus sequences.

The actual promoter sequences for different operons may differ from the consensus sequences, but the closer they are, the stronger the promotion sequence. As a general rule, promoter sequences that match the consensus sequences more closely invite more frequent transcription.

2. RNA synthesis is catalyzed by the large enzyme RNA polymerase, the holoenzyme of which consists of four subunits. Which of the four subunits is responsible for recognition of promoter sites?

Answer: sigma

RNA polymerase slides loosely along the template DNA while the sigma subunit searches for promoter sequences by forming transient hydrogen bonds with the DNA base pairs. The RNA polymerase does NOT engage in a trial-and-error form of search where it repeatedly binds with DNA until it finds a promoter site.

This explains the extremely high rate constant for RNA polymerase binding to promoter sites (10^10 M^-1 s^-1). Different types of sigma subunits can recognize different promoter sequences, so the sigma subunit plays a large role in determining where RNA polymerase begins transcription.

3. RNA polymerase needs to unwind and separate the DNA double helix before it can synthesize any RNA. DNA is often supercoiled. What type of supercoil facilitates the unwinding of DNA?

Answer: negative supercoil

A negative supercoil essentially "spring-loads" double-helical DNA for unwinding. Right and left-handed supercoils simply determine the overall shape of the DNA molecule. For circular, negatively supercoiled DNA, a left-handed supercoil creates a toroidal shape (donut) while a right-handed supercoil creates a twisting closed-loop double helix (on top of the double helix of the two stands of DNA).

Interestingly, the gene that codes for the enzyme that is responsible for introducing negative supercoils to DNA - topoisomerase II - is actually down-regulated by negatively supercoiled DNA.

This is a nice feedback inhibition mechanism to ensure that DNA does not become overly negatively supercoiled.

4. What is usually located at the 5' end of a newly synthesized RNA chain?

Answer: ATP or GTP

Unlike DNA, RNA can be synthesized de novo, meaning it does not require a primer. RNA synthesis still occurs in the 5'-3' direction, with RNA polymerase catalyzing nucleophilic attacks by the 3'-OH on the innermost phosphate of a (ribo)nucleoside triphosphate.

5. Which subunit of the RNA polymerase holoenzyme is not present during most of elongation?

Answer: sigma

The sigma subunit departs after RNA polymerase has synthesized about 9-10 nucleotides of RNA. RNA polymerase binds more strongly to DNA without the sigma subunit present, and will not release the template DNA until termination. The departed sigma subunit can join with another RNA polymerase to search for promoter sites.

6. The error rate of RNA synthesis is about the same as the error rate of DNA replication.

Answer: False

The error rate of RNA synthesis is about one error in every 10^4 or 10^5 nucleotides, compared to a rate of one error in every 10^6 or 10^7 nucleotides for DNA replication. The relatively high error rate is not a cause for concern because a single gene is usually transcribed multiple times.

7. Although DNA is double-stranded, RNA polymerase only uses one strand to synthesize RNA. What is this strand called?

Answer: template strand

The template strand of the DNA contains the complementary base pair sequence of the transcribed RNA. The coding strand is the other DNA strand, which contains an identical base-pair sequence to the transcribed RNA with thymine in place of uracil. While elongation is occurring, the new RNA actually forms a hybrid double helix with the template strand for about 8 nucleotides.

After this number, a structure in RNA polymerase forces the RNA and DNA to separate in opposite directions so that the template strand can reform a double helix with the coding strand behind the transcription bubble.

8. At termination, the RNA-DNA hybrid must separate, a process that is facilitated if the base-pairing between the two strands are weak. Which is the weakest of the four RNA-DNA base pairs?

Answer: rU-dA

A very simple termination signal involves the coding of a palindromic GC rich region followed by an oligo-U (repeated U nucleotides) region. The palindromic GC rich region is self-complementary, causing the new RNA strand to form hydrogen bonds with itself in that region, creating a stem-loop structure that causes RNA polymerase to stop elongation.

The consequence of the oligo-U region is that the RNA will be loosely bound to the template DNA strand (since rU-dA base pairs are the weakest), and the two strands will easily separate.

9. The remaining questions pertain to transcription as it occurs in eukaryotes. Transcription in eukaryotes is similar to, albeit more complex than, the process in prokaryotes. What polymerase is responsible for the synthesis of pre-mRNA in eukaryotes?

Answer: RNA polymerase II

RNA polymerase II synthesizes pre-mRNAs, snRNAs, and microRNAs. RNA polymerase I is very specific, only synthesizing pre-rRNA 45S. RNA polymerase III synthesizes the tRNAs, and rRNA 5S. RNA polymerase IV is only found in plants and makes siRNAs. There are more classes of RNA polymerases, including RNA pol V (also only found in plants) and others in the mitochondria and chloroplast.

10. Just like prokaryotic DNA, eukaryotic DNA contains sequences close to the transcriptional start site that serve as promoters for transcription. These sequences are classified into a certain class of promoter elements. What is the name for this class?

Answer: cis-acting elements

The name comes from the fact that the sequences are found on the same molecule of DNA as and close to the gene being transcribed (cis in Latin means "on the same side"). Promoter elements not located on the DNA template are called trans-acting elements (trans = "on the other side").

These elements include a class of protein complexes called general transcription factors (GTFs). The need for GTFs and other trans-acting elements stems from the fact that eukaryotic DNA is packaged into chromatin, making the DNA itself (and therefore the cis-acting elements) normally inaccessible to RNA polymerases.

11. A common class of GTPs is the TFII class, which is involved in promoters containing the so-called "TATA box" -25 promoter sequence, a highly conserved sequence found in most eukaryotic cells. Which TFII protein complex is responsible for binding to the TATA box?

Answer: TFIID

TFIID contains a protein subunit called the TATA box binding protein (TBP) that directly binds to the TATA box sequence. Only after TFIID has bound to DNA will the other TFII transcription factors and RNA pol II bind to the initiation site.

12. TBP binds to the major-groove side of DNA.

Answer: False

Unlike most DNA-binding proteins, TBP does not bind to the major-groove side of DNA (which contains more information about base-pair sequences). Because of this, TBP will actually distort the DNA double helix to force open the minor-groove side so that it can successfully bind to the DNA. In the process, the DNA double-strand is bent at over a 90-degree angle.

13. The transcription factor TFIIH has which of the following activities? I. kinase II. isomerase III. helicase

Answer: I and III

TFIIH phosphorylates the C-terminus tail of RNA pol II and also melts the template DNA, allowing RNA pol II to begin synthesizing RNA, marking the transition from initiation to elongation.

14. Which of the TFII transcription factors is most closely related to the sigma subunit of the RNA polymerase holoenzyme in prokaryotes?

Answer: TFIIF

Interestingly, it is not TFIID that is most closely related to the prokaryotic sigma subunit, even though both TFIID and the sigma subunit share similar roles in binding to their respective promoter sequences. TFIIF actually enters the pre-initiation complex already attached to RNA pol II.

15. In addition to core promoters like the TATA box that are located near the transcription start site, eukaryotic chromosomes also contain what are called regulatory or activation sequences (enhancers) farther away from the transcription start site that help initiate transcription. True or false: these enhancers can be located more than 1 million base pairs apart from the transcriptional start site.

Answer: True

One example of a gene with extremely distant enhancers is the sonic hedgehog (shh) gene. (Yes, if you're wondering, it's named after Sonic the Hedgehog. No, I'm not kidding...seriously...I couldn't make this stuff up.) The gene actually belongs to an entire family of genes involved in the so-called "hedgehog signaling pathway". I don't really know where the name comes from, since the genes are in no way limited to hedgehogs (humans have them, and they were first discovered in fruit flies). Anyway, the reason why these enhancers still function is that DNA is more or less flexible and can be bent in such a way that sequences far apart from each other in terms of base pairs are close to each other spatially (i.e. the DNA strand can essentially make a U-turn).

Therefore, different proteins that bind to the sequences can interact with one another.

Source: Author aznricepuff

This quiz was reviewed by FunTrivia editor crisw before going online.
Any errors found in FunTrivia content are routinely corrected through our feedback system.

My third and final DNA quiz. The subject is DNA transcription. Questions 1-8 are about transcription in prokaryotes, and questions 9-15 are about the process in eukaryotes.

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