MCB 3201 Take-Home Final Exam-2015
Please make sure to provide your name and PeopleSoft number on the answer paper.
Hand in your answer paper to my office in TLS Room 413A before 4:00 p.m. on April 30th,
2015.
Part I: Define the following terms with simple sentences. (20%)
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
DNA binding domain
Endocrine signaling
Nuclear receptor
Homeo Domain
Cys2His2 Zinc Finger
miRNA
Dicer
Spliceosome:
Stimulatory G protein:
Adenylyl cyclase:
Part II: Essay questions.
1.
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%)
2.
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 you arrive to this conclusion. (5%)
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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? (5%)
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.
Please design an experiment to demonstrate the function of “NLS” (nuclear localization
sequence) in transporting macromolecules into the nucleus. (5%)
5.
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? (15%)
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6.
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%)
7.
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%)
8.
What are the differences among hnRNAs, snRNAs miRNAs siRNs and snoRNs? (10%)
9.
There are a number of conserved sequences found in an mRNA which dictate where
splicing occurs. Where are those sequences found relative to the exon/intron junctions?
What is the significance of these sequences in the splicing processes? What is role of the
branch point “A” found in the intron in the splicing process? (5%)
10.
The yeast two-hybrid system is a powerful molecular genetic method to identify a
protein(s) that interacts with a known protein or protein domain. You have isolated the
glucocorticoid receptor (GR) and have evidence that is a modular protein containing an
activation domain, a DNA binding domain and a second ligand binding-activation domain.
Further analysis reveals that in the pituitary cells the GR is anchored in the cytoplasm in
the absence of its hormone ligand. This result lead you to speculate that GR binds to an
inhibitory protein in the cytoplasm of the pituitary cells. (i) Describe how a yeast-two
hybrid analysis system could help you to identify the protein with which GR interacts. (ii)
How would you specifically identify the domain in the GR that binds the inhibitor? (20%)
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