Name: _________________________________

Analytic Problem Set 5: Control of Gene Expression (Module 5)

This analytical problem set will be graded (worth 15 points).

To get full credit,
a. Answer all the questions below:
For the multiple choice, you can bold or highlight the correct answer
For the other questions: write in complete sentences and give thorough answers
(one sentence will not be sufficient)
b. Hand in ON LINE on Canvas before class on Friday
We will be reviewing the answers in class, so no late homework will be accepted.

Questions:
1. (3 point) In Module 5, you learned several ways in which eukaryotic transcription
differs from the process of bacterial transcription. List three of those ways below.

2. You have a culture of human endothelial cells. You break open the cells, and separate
all the DNA and RNA away from the other parts of the cell.
You then mix the nucleic acids with special beads that have the following short
DNA sequence bound to them, consisting of all T nucleotides (that is:
TTTTTTTTTTTTTT).
You separate the beads from the rest of the mixture, and then look to see which
type of nucleic acid is bound to them.

a. (1 point) Which of the following types of nucleic acid would be most likely to be
stuck to the beads?
(a) DNA
(b) tRNA
(c) rRNA
(d) mRNA

b. (1 point) Explain why you chose your answer to part a.

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3. (1.5 point) In the nucleus of a cell, the RNA is modified before it can exit the cell.
What are the three types of ways that the RNA is covalently modified to become mature
mRNA?

4. For many years students have been taught the one gene-one protein theory of
eukaryotic cells: that genes in eukaryotes only one protein (unlike those in bacteria that
often code for more than one).
Based on what you learned in this module, explain in a few sentences the way in which
why is the expression one geneone protein not always true for eukaryotic genes? (1
point)

5. In this module, we talked about how some genes are expressed in all cells, while others
are specific to certain cell types.
Below is an RNAseq data, like the one showed in Lecture 18. It shows the levels of
expression of mRNAs expressed from two genes: Gene X and Gene Y.

a. (1 point) State which gene is more likely to be a housekeeping gene, and explain
your answer.

b. (1 point). Which region of Gene Y corresponds to an intron: the one marked 1 or the
one marked 2? Explain your answer.

1 2
Number of

Liver
reads

Brain

Gene X Gene Y
Position on chromosome

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6. (1 point) You have identified a set of human genes that are expressed at much higher
levels when the cells are exposed to the hormone cortisol. Based on what you learned in
this class, you hypothesize that the same cortisol-responsive transcriptional activator
regulates all of these genes.
Which of the following statements below should be true if your hypothesis is
correct?

a.) The cortisol-responsive genes must all be in an operon.

b.) All of the cortisol-responsive genes share a DNA sequence in their regulatory
regions that binds the cortisol-responsive transcriptional activator.
c.) All of the cortisol-responsive genes must have exactly the same set of activators
binding to their regulator regions (enhancers and promoters).

Read the following paragraph, and then answer questions X-Y

This question is about a protein that is found in liver and kidney cells in mice called
Livkid. You are trying to understand the gene regulation of Livkid, so you first look for a
cell that doesn't have that protein. You are able to find one: skin cells do not express
Livkid.
To understand how gene regulators interact with the promoter of Livkid, you clone a
fragment just upstream of the Livkid gene, which contains the promoter. You then clone
that piece of DNA upstream of the gene for green fluorescent protein (GFP), and insert
this entire piece of recombinant DNA into mice.

You find GFP is expressed the same way that Livkid is: you see GFP glowing in the
in liver and kidney cells but not in skin cells.
After more experiments, you demonstrate that there are three regions in the promoter that
contribute to this expression pattern labeled A, B, and C in the figure belo.
Assume that a single and unique transcription factor binds each site such that:
o protein X binds site A
o protein Y binds site B
o protein Z binds site C.
You want to determine which region is responsible for tissue-specific expression,
and create mutations in the promoter to determine the function of each of these
regions. In the figure below, if a site is missing, it means that it is mutated such
that it can not bind its corresponding transcription factor.

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 Promoter for Livkid Is Livkid expressed in:
Liver? Kidney? Skin?

7. Which of the following proteins is most likely to function as a repressor? (1 point)

(a) factor X
(b) factor Y
(c) factor Z
(d) none of the above

8. Which of the following protein(s) are likely to act as gene activators? (1 point)
(a) factors X and Y
(b) factors X and Z
(c) factors Y and Z
(d) factor X only

9. In what tissue is factor Z normally present and bound to the DNA? (1 point)
(a) kidney
(b) liver
(c) skin
(d) none of the above

10. (1.5 points) Name one thing you learned in Module 5 that you didnt know before,
and that you found interesting.

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