Question

In eukaryotic transcription by RNA polymerase II, formation of a preinitiation complex A. begins with the binding of a protein (TBP) to the TATA box of the promoter. B. involves the ordered addition of several transcription factors and the RNA polymerase. C. allows an ATP-dependent opening of the two strands of DNA. D. requires that the C-terminal domain of RNA polymerase II not be phosphorylated. E. all of the above.

Short answer

A: Binding of TBP to the TATA box of the promoter B: Ordered addition of transcription factors and RNA polymerase C: ATP-dependent opening of the DNA strands D: Requirements of the C-terminal domain of RNA polymerase II E: All of the above Answer: A, B, and C

Step-by-step solution

Statement A: Binding of TBP to the TATA box of the promoter

This statement is correct. Transcription initiation in eukaryotes begins with the binding of a protein called TATA-binding protein (TBP) to the TATA box of the promoter region. The TATA box is a conserved DNA sequence that helps position RNA polymerase II for correct transcription initiation.

Statement B: Ordered addition of transcription factors and RNA polymerase

This statement is correct as well. Following the binding of TBP, different transcription factors are recruited to the promoter region in an ordered manner, which in turn helps to recruit RNA polymerase II to the promoter.

Statement C: ATP-dependent opening of the DNA strands

This statement is correct. The ATP-dependent helicase activity of the transcription factors opens the DNA double helix, making the DNA template strand accessible for RNA polymerase II.

Statement D: Requirements of the C-terminal domain of RNA polymerase II

This statement is not entirely correct. The C-terminal domain (CTD) of RNA polymerase II undergoes a process of phosphorylation and dephosphorylation, regulating its activity during transcription; however, the presence or absence of phosphorylation does not solely define the formation of a preinitiation complex.

Statement E: All of the above

Since Statement D is not entirely correct, it is not appropriate to choose "all of the above" as the correct answer. So, based on our analysis, the correct statements describing the formation of a preinitiation complex during eukaryotic transcription by RNA polymerase II are A, B, and C.

Key concepts

RNA Polymerase II

Understanding the role of RNA polymerase II in eukaryotic transcription is crucial for grasping the fundamental processes of gene expression.
The enzyme RNA polymerase II (Pol II) is responsible for synthesizing messenger RNA (mRNA) from a DNA template, a process known as transcription. This complex enzyme not only catalyzes the formation of the mRNA strand but also plays a pivotal role in the capping, elongation, and processing of the pre-mRNA.

During transcription initiation, the C-terminal domain (CTD) of Pol II is particularly important. The CTD, which comprises repeating units of a seven-amino acid sequence, undergoes phosphorylation and dephosphorylation events, regulating the interaction of Pol II with the transcription machinery and the newly synthesized RNA. Although phosphorylation of the CTD is not required for the assembly of the preinitiation complex, as alluded to in the textbook exercise, it is crucial for the subsequent stages of transcription, particularly the transition from initiation to elongation phase, where Pol II travels along the DNA to transcribe the genetic code into RNA.

TATA Box

The TATA box is a critical component of gene regulation and a fundamental concept in the study of eukaryotic transcription. This DNA sequence, typically found approximately 25-35 base pairs upstream of the transcription start site, acts as a core promoter element that is recognized and bound by transcription factors.

One of the first factors to interact with the TATA box is the TATA-binding protein (TBP), a subunit of the transcription factor TFIID. Binding of TBP to the TATA box causes slight bending of the DNA helix, facilitating the assembly of additional components of the transcription machinery. This initial interaction is pivotal for the positioning and recruitment of RNA polymerase II, setting the stage for transcription initiation. As the question from the textbook exercise highlights, the binding of TBP to the TATA box is integral to the formation of the preinitiation complex, a process highly conserved across eukaryotic organisms.

Transcription Factors

Transcription factors are proteins that perform a key function in the regulation of gene expression. They serve as the bridge between the DNA sequences of gene promoters and the transcriptional machinery, which includes RNA polymerase II.

The assembly of the transcription preinitiation complex involves the sequential addition of various transcription factors to the promoter DNA. This orchestrated process begins after the TATA box has been bound by TBP. Subsequent factors such as TFIIA, TFIIB, TFIIE, TFIIF, and TFIIH join the complex, each with a unique role to maintain the correct assembly, stability, and activity of RNA polymerase II.

TFIIH, for instance, possesses helicase and kinase activities which are important for unwinding the DNA helix (an ATP-dependent process) and phosphorylating the CTD of RNA polymerase II, as indicated in the exercise. These steps are essential for the transition from transcription initiation to elongation, highlighting the choreographed nature of transcription factor action and their indispensable role in accurate transcription.