MCB 3201 Take-Home Final Exam (4/2014)
Name:_____________________________; PeopleSoft #__________________
Hand in the answer before 5:00 p.m. on April 29th 2014
Upon completing your exam, please check to make sure that your name and PeopleSoft
number are on your exam paper.
Part I: Define the following terms with simple sentences. (30%)
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DNA binding domain
Endocrine signaling
Nuclear receptor:
Activator
Homeo Domain
Cys2His2 Zinc Finger
Repressor
TBP
Epigenetic changes
miRNA:
Dicer:
Spliceosome:
hnRNP:
Stimulatory G protein:
Adenylyl cyclase:
Part II: Essay questions.
1.
In eukaryotic systems, there are many different types of transcription factors (activators
and repressors) that contain different DNA binding motifs. Please list 4 of the most
commonly found DNA binding motifs with a simple description of their characteristics. (5%)
2.
What types of genes are transcribed RNA polymerase I, II and III? How can you identify
whether a gene is transcribed by RNA polymerase II? (5%)
3.
DNase I foot-printing assay has been used to identify protein factors in a nuclear extract
that may bind to cis-acting elements in the regulatory region of a gene. (i). Please
describe the principle of this assay. (ii). In an attempt to identify the presence of protein
factors that may bind to the cis-acting element of a gene, nuclear extract was fractioned by
column chromatography and the resulting protein fractions were subjected to DNase I foot
printing assay. The results of the assay are shown below. From these results, could you
draw any conclusion? (10%)
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M, molecular marker; NE, no nuclear extract added; O, A cognate protein present in the
nuclear extract; FT, flow through protein from the column; 1-22, fractions eluted from the
column.
4. Gal4 activator contains a DNA binding domain and a functional domain, and these
domains can be identified by deletion mapping studies. In an attempt to identify the
DNA binding domain and the functional domain of Gal4 activator, a series of deletion
mapping assays were conducted and the data are presented below. Based on the data
presented below, please identify the locations of DNA binding domain and the
functional domain. Please explain how do you arrive to this conclusion. (10%)
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5.
Please design an experiment to demonstrate the function of “NLS” (nuclear localization
sequence) in transporting macromolecules into the nucleus. (10%)
6.
It is known that the mammary gland epithelial cells lining the immature ductules of the
mammary gland is induced to differentiate into acinar cells and to produce milk proteins
secreted into the mammary gland ducts during pregnancy. This induction process is
initiated by the binding of prolactin to a receptor residing on the membrane of the
mammary gland epithelial cells. (i) Please design an experiment to demonstrate the
presence of such receptors residing on the membrane of the mammary gland epithelial
cells? (ii). Please design a strategy for the purification of these receptor molecules. (iii).
How will you confirm that the receptor molecules you have purified is the real prolactin
receptor? (20%)
7.
Receptor tyrosine kinases and cytokine receptors share many signaling features.
Although following binding of the respective ligands to their receptors lead to activation of
kinases, settle differences are found with both receptors. What are the differences? (5%)
8.
There are at least 600 genes in human genome encoding protein kinases involved in
signal transduction pathways. These protein kinases are catalogued into four groups, and
each is activated by a different factor. What are these four groups of protein kinases and
their corresponding activating factor? (5%)
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