Genetics: Analysis and Principles 5th Edition by Robert Brooker

Exercise 37

As described in Chapter 20 and in experimental question E5, a gel retardation assay can be used to determine if a protein binds to DNA. This method can also determine if a protein binds to RNA. In the combinations described here, would you expect the migration of the RNA to be retarded due to the binding of a protein
a. mRNA from a gene that is terminated in a -independent manner plus protein
B. mRNA from a gene that is terminated in a -dependent manner plus protein
C. Pre-mRNA from a protein-encoding gene that contains two introns plus the snRNP called U1
D. Mature mRNA from a protein-encoding gene that contains two introns plus the snRNP called U1
Question E5
A gel retardation assay can be used to study the binding of proteins to a segment of DNA. This method is described in Chapter 20. When a protein binds to a segment of DNA, it retards the movement of the DNA through a gel, so the DNA appears at a higher point in the gel (see the following).
a.
Lane 1: 900-bp fragment alone
Lane 2: 900-bp fragment plus a protein that binds to the 900-bp fragment
In this example, the segment of DNA is 900 bp in length, and the binding of a protein causes the DNA to appear at a higher point in the gel. If this 900-bp fragment of DNA contains a eukaryotic promoter for a protein-encoding gene, draw a gel that shows the relative locations of the 900-bp fragment under the following conditions:
Lane 1: 900 bp plus TFIID
Lane 2: 900 bp plus TFIIB
Lane 3: 900 bp plus TFIID and TFIIB
Lane 4: 900 bp plus TFIIB and RNA polymerase II
Lane 5: 900 bp plus TFIID, TFIIB, and RNA polymerase II/TFIIF