Lecture 12: Eukaryotic transcriptional control
A few questions covering earlier lectures have been included here to review the background needed for this lecture.
1. Dinstinguish among the three types of eukaryotic RNA polymerases in terms of the function of each.
2. What are the major differences in organization between prokaryotic and eukaryotic genes.
3. Summarize the modifications that must be made in a transcript produced by RNA polymerase II before it can be translated.
4. Explain why more complex controls over gene expression are needed in multicellular eukaryotic organisms than in prokaryotic organisms.
5. What are the features that distinguish enhancer sequences from functional parts of the basic promoter, such as the CAAT box and the TATA box?
6. How is a distant enhancer site believed to activate transcription? (What mechanism allows it to exert its effect over a considerable distance?)
7. Identify the three different domains that a protein must possess as a minimum to function as a ligand-responsive transcription factor (for example, a steroid hormone receptor). What role is played by each of these domains?
8. Describe the regulatory mechanisms that allow the budding yeast, Saccharomyces cerevisiae to turn on genes for galactose utilization when galactose is available.
9. The GAL4 binding site in yeast is commonly referred to as an upstream activating sequence (UAS). Does it satisfy all of the criteria of an enhancer site? Explain your answer.
10. Describe the sequence of events that results in expression of the genes that are needed for galactose utilization in yeast. Be sure to identify the regulatory protein that galactose interacts with and the way in which it triggers the gene expression process.
11. What are three major types of transcription factors (classified in terms of their DNA-binding domains)?
12. What two types of domains must a protein possess to be a transcription factor? Discuss the relative specificity of each.
13. What role does the GAL80 protein play in the control of galactose utilization genes in budding yeast?
14. What effect would you expect from a mutation in the GAL4 protein that rendered it incapable of binding to the GAL80 protein?
15. What effect would you expect from a mutation in the GAL80 protein that rendered it incapable of binding galactose?
16. Dnguish between each of the following pairs in a manner that makes it clear you know what each is and how they differ.
a. Activator and coactivator
b. Enhancer and upstream activating sequence
c. Hormone response element and steroid hormone receptor
d. General transcription factor and activator
e. Cytosine and 5-methyl cytosine
17. The frequency of CG sequences in eukaryotic genomes is lower than expected based on the CG content of the DNA of each species and an assumption of random occurrence of all possible dinucleotide sequences.
a. Describe a modification of CG base pairs that occurs more frequently in inactive parts of the genome than in actively transcribed genes.
b. Describe a mutational process that could preferentially convert CG sequences to other sequences in the genetically inactive portion of the genome.(You may need to go back to lecture 6 for the answer).
c. How would you explain the failure of DNA repair mechanisms to reverse the preferential loss of CG sequences?
d. How is the DNA modification from part a retained when DNA replicates?
e. What is the evidence that the modification in part a acts indirectly to inhibit transcription of inactive genes (see boxed example 8.4 if you are having trouble with this one).
18. Activation factors and basal transcription factors such as the TATA binding protein are able to recognize specific nucleotide sequences within double stranded DNA. (You may want to look at figure 2.11 while answering this set of questions -- note that the top of each base pair as drawn corresponds to the major groove).
a. Explain how protein molecules, which tend to be bulky molecules, are able to detect differences in nucleotide sequence in various regions of a double-stranded DNA molecule.
b. What features of an AT base pair are seen in the major groove?
c. What features of a GC base pair are seen in the major groove?
d. An AA sequence or an AT sequence would result in the same two base pairs being next to each other in the double helical DNA. How do you think a DNA binding domain is able to distinguish between the two? (This will require a bit of speculation).
e. What mechanism is commonly employed by transcription factors and activator proteins to read palindromic sequences, such as typical hormone response elements?
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