GTS351 Semester test 2 : DEPARTMENT OF BIOCHEMISTRY, GENETICS AND MICROBIOLOGY DIVISION OF GENETICS

Fig. 2. Schematic representation of a transcription factor protein binding to DNA, with three of the same
kind of motif represented in purple, yellow and red.
1.1. Name the motif in Fig. 2 and briefly discuss the defining characteristics of such a motif.

1.2. Explain how the inclusion of tandem repeats of this type of motif can increase the specificity of binding of
this transcription factor (that is, allow it to target only a small number of promoters in the genome).

1.3. Before the crystal structure of the protein indicated in the figure was resolved, scientists only had
information on the DNA element bound by the transcription factor (indicated in blue in Fig. 2). Name a
technique the scientists could have used to identify the transcription factor that binds to this DNA element.
Assume the scientists do not have any idea which TF might bind to the element.

Question 2 [7]
Coupling is an important principle underlying eukaryotic gene expression. Formulate a definition of coupling
and briefly discuss how histone modifications and the process of transcriptional elongation are coupled to premRNA
splicing and polyadenylation. Your answer must relate to coupling itself – you will not get marks for
discussing the processes of splicing or polyadenylation in general.

Question 4 [7]
You have been offered a position at the South African Cancer Research Institute and became part of the
group that studies the carcinoembryonic antigen (CEA). Overexpression of CEA is commonly associated with
colon, lung, and liver cancers and as such it is a therapeutic target.
In Fig. 4 below a partial sequence for CEA is show, as well as a newly designed shRNA molecule that you wish
to test as a therapeutic. You will deliver this shRNA into the nucleus of cells using a virus-mediated delivery
system. Carefully study the sequences below and then answer the following questions.