Exam 11: Transcription in Eukaryotes

Which of the following factors plays a role in RNA cleavage during polymerase backtracking?

RNA polymerase has a single active site that switches between RNA synthesis and cleavage. Describe a model for this "tunable" RNA polymerase active site. How does this compare with the structure and function of DNA polymerase active sites?

Compare and contrast four different classes of DNA-binding domains found in eukaryotic transcription factors.

Describe X-ray crystallographic evidence for a four step cycle of RNA synthesis during RNA polymerase II transcription.

Which of the following is involved in transcription in prokaryotes, but not in eukaryotic transcription?

Define the "histone code" hypothesis and discuss evidence for and against it.

Draw a rough sketch of the structure of a nuclear pore complex.

What shape does TBP have? What is the geometry of the interaction between TBP, the TATA box, and the DNA double helix? Does TBP interact with the major or minor groove?

List the major types of RNA polymerases in eukaryotes and the types of genes they are responsible for transcribing.

Explain how fluorescence recovery after photobleaching (FRAP) experiments may differentially support either the "hit and run" model or the "enhanceosome" models of transcriptional activation.

Explain how the same type of chemical modification of nucleosomes,

Eukaryotic core promoter elements have all of the following characteristics, except:

Describe four different ways in which chromatin structure can be altered by chromatin remodeling complexes. What role does chromatin remodeling play in activation and repression of gene transcription?

Explain the underlying genetic defect leading to Hutchinson-Gilford progeria.

Diagram the structure of a "typical" eukaryotic protein-coding gene, including all potential regulatory regions. Indicate where the RNA polymerase II preinitiation complex interacts.

Describe the structure and function of the homeodomain. What other protein domain does it most resemble?

Draw a detailed diagram of a basic leucine zipper (bZIP). Illustrate the interaction of this motif with another polypeptide and with DNA. Point out the leucine zipper and the basic DNA-binding domain.

You create a chimeric protein that contains the DNA binding domain of the Fork head transcription factor and the transactivation domain of the Sp1 transcription factor. Which of the following predictions would you make concerning the activity of your chimeric protein?

Discuss the role of the variant linker histone H1b in muscle progenitor cell differentiation.

Which is recruited first to a gene, the preinitiation complex, histone acetyltransferases (HATs), or SWI/SNF? Explain your answer.