PHA 6852 University of Florida Process of Transcription in Bacteria Questions

• Discuss the process of transcription in bacteria; what is the function of the RNA polymerase holoenzyme in this process? [3 pts]
• What is a transcription bubble? [2 pts]

• What is a consensus nucleotide sequence? [2 pts]

• Outline the general differences between RNA polymerase I, RNA polymerase II, and RNA polymermase III in eukaryotic nuclei in regards to the different genes they transcribe. [3 pts]

• What are the two main differences between bacterial polymerase and eukaryotic RNA polymerase II function? [3 pts]

• Discuss the events involved in transcription initiation for eukaryotic mRNA synthesis [3 pts]

• What structural change takes place on polymerase II promoters during preinitiation complex formation [4 pts]

• What is the role of the generalized transcription factors TBP and TFIIH in the process of promoter recognition and transcription initiation by RNA Pol II? What further role does the CTD of Pol II play in transcription initiation and elongation? [10 pts]

• Briefly explain why both ends of eukaryotic mRNAs must be modified [2 points]
• A key step in transcription initiation by RNA polymerase II is the phosphorylation of the RNA polymerase II tail (or the C-terminal domain). What does this phosphorylation provide? [2 points]

• Describe how RNA capping of eukaryotic pre-mRNAs occur [4 points]

• Why is RNA splicing necessary? [2 points]

• Describe the differences between hnRNAs, snRNAs, and snoRNAs [3 points]

• What are the mechanistic similarities between Group II intron self splicing, and spliceosomal splicing [3 points]

• How is the 3’ end of eukaryotic mRNAs generated? What are CstF and CPSF and why are they important? [4 points]

• Describe how transcription termination by RNA polymerase II is coupled to polyadenylation [3 points]

• Some genes encode proteins that act rapidly to protect other genes from harsh conditions. Describe the mechanism that regulates the expression of heat shock genes [3 points]

• What are nuclear pores complexes and why are they important in regards to mRNA? How has the export of mRNA-protein complexes been observed? [4 points]

• What is the nucleolus? What macromolecules can be found there? [2 points]

• Find a journal article of your choice that reviews one of the following organelles used in RNA processing: nuclear pore complex, nucleolus, or Cajal bodies. Briefuly discuss the article, be sure to include your reference and explain how the authors were able to visualize the organelle you choose so that they could study it. [8 points]

• Briefly discuss the role of tRNA in protein synthesis in eukaryotes [2]
• Locate and read the following article: Kaufman RJ. (2004). Regulation of mRNA translation by protein folding in the endoplasmic reticulum. Trends in Biochem Sci, 29(3): 152-158.

a). What exactly is the unfolded protein response (UPR) as characterized by the author? [2]

b). Upon accumulation of unfolded proteins in the ER, what must occur for the cell to survive? [2]

• Explain in detail what is meant by antibiotic resistance. Why is this an important aspect of healthcare today? [4]

• Using online resources and/or texts, research the effect of diphtheria toxin and briefly describe its relationship to translation. [2]

• Locate and read the following article: Brooks DA. (1997) Protein processing: a role in the pathophysiology of genetic disease. FEBS Lett, 409(2): 115-120.

a). Identify one of the genetic diseases discussed in the article, and briefly describe how post-translational modification mediates the disease. [4]

b). To which family of proteins does the BiP/Glucose regulated protein 78? [1]

What characteristic differentiates it from other members of this protein family? [1]

What activity is this particular protein demonstrated carrying out in Figure 1? [1]

• What are polyribosomes? How are they used in both bacteria and eukaryotes? Why would they be more common in prokaryotes than eukaryotes? [4]
• What is a Shine-Delgarno sequence? [2]
• There are various mechanisms of translational control; choose one of the mechanisms and describe how it works in bacteria. [3]
• Antisense RNA regulates translation of transposase mRNA in bacteria. Why and how might researchers adapt the antisense model for experimental inhibition of gene expression in eukaryotic cells? [2]

1. Describe what positive and negative controls are in regards to gene regulation. [2 pts]
2. Describe the regulation of the E. coli lac operon [4 pts]
3. What is transcription synergy? [2 pts]
4. Describe in detail what the gene control region consists of for a typical eukaryotic gene. Be sure to include the TATA box as well as the mediator portion. Are all of the components the same for all TNA polymerase II-transcribed genes? If not, what may differ? [4 pts]
5. What cofactor provides the methyl group transferred to cytosine by methyltransferases? [2 pts]
6. Locate and read the following article: Panning B, Dausman J, Jaenisch R. (1997). X chromosome inactivation is mediated by Xist RNA stabilization. Cell, 90: 907-916.
   a. After differentiation, Xist is expressed at high levels only from the _______ X chromosome. [2 pts]

b. What technique did researchers use in order to determine the number of X chromosomes in the individual cell masses? [2 pts]
c. Authors indicate that the precise localization of factors that stabilize Xist RNA may be accomplished in two ways. Briefly describe one. [2 pts]

7. What is a nucleosome? Describe its involvement in the structure of chromosomes and regulation of gene expression. [4 pts]

8. Define the following terms in a few short sentences: [2 pts]

Swi/Snf (as a general class of enzymes):

CG Islands:

9. According to the journal article below

Rougeulle, C., and Avner, P. (December 2003). Controlling X-inactivation in mammals: what does the centre hold? Seminars in Cell and Developmental Biology, Volume 14, Issue 6: pages 331-340.

a). what aspects of the X-inactivation process are proposed to be controlled by the Xic? [2 pts]

b.) What name is given to the gene that is antisense to Xist at the X-inactivation center? [2 pts]

10. Considering the phenomenon of random X inactivation, what problems could arise if one X carries a deleterious gene? Provide and discuss an example. [3 pts]

11. In general terms, how does hypermethylation of certain genes contribute to cancer? [2 pts]

12. Why does deacetylation of histones increase the affinity of DNA for the nucleosome surface? [2 pts]

13. What is the result when selected C nucleotides are methylated at specific C-G sequences that are associated with inactive genes? What DNA repair mechanism can correct this, and is it an effective one? [3 pts]