Question 1

What is the TATA box and where is it located in the promoter?

Accepted Answer

The TATA box is a conserved DNA sequence, typically T-A-T-A-A-A, found in eukaryotic promoters. It is usually positioned 25 nucleotides upstream from the transcription start site. The TATA box serves as the recognition site where the TATA-binding protein initiates assembly of the transcription machinery for RNA Polymerase II.

Question 2

How do general transcription factors guide RNA Polymerase II to the promoter?

Accepted Answer

General transcription factors, specifically TFII variants A through H, sequentially bind to the promoter to recruit and position RNA Polymerase II. TFIID first recognizes the TATA box, then TFIIA and TFIIB build a platform for RNA Polymerase assembly with TFIIF. Finally, TFIIE and TFIIH complete the initiation complex, enabling transcription to begin.

Question 3

What role does TFIIH play in starting transcription?

Accepted Answer

TFIIH performs two critical functions in transcription initiation. It unwinds the DNA duplex around the start site and phosphorylates the C-terminal domain of RNA Polymerase II. This phosphorylation changes the polymerase's conformation, allowing it to release from the initiation complex and begin synthesizing the RNA transcript.

Question 4

Why do eukaryotes require transcription factors while prokaryotes do not?

Accepted Answer

Eukaryotic transcription requires additional proteins called transcription factors to first bind the promoter region and recruit RNA Polymerase, enabling tight regulation of gene expression. Prokaryotic RNA Polymerase can directly bind template DNA and initiate transcription without these accessory proteins. This difference reflects the greater complexity of eukaryotic gene regulation through activators and repressors.

Question 5

What happens to general transcription factors after RNA Polymerase II begins elongation?

Accepted Answer

Once RNA Polymerase II starts synthesizing the RNA transcript and enters the elongation phase, most general transcription factors are released from the DNA. This release allows the polymerase to continue transcription independently and permits another round of transcription initiation with a new RNA polymerase molecule at the same promoter.

Question 6

How does the pre-initiation complex regulate transcription rates?

Accepted Answer

The pre-initiation complex, formed by transcription factors assembling with RNA Polymerase at the promoter, has inherently low transcription activity. Regulatory proteins called activators and repressors can enhance or decrease the transcription rate of the pre-initiation complex, providing cells with precise control over gene expression levels.

Question 7

Is the TATA box present in all eukaryotic genes?

Accepted Answer

No, the TATA box is only present in 10-15% of mammalian genes, despite being the most widely studied core promoter sequence. While the TATA box provides a well-characterized platform for assembling transcription factors and recruiting RNA Polymerase, many eukaryotic genes use alternative core promoter sequences for transcription initiation.

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