BIO 344-QUIZ#7
1.Suppose that you are writing a paper about a certain gene. So far you have sequenced the
entire DNA and know the location of the TATA box and the approximate location of the
transcriptional start site. Explain in detail how you would map this start site down to the specific
first nucleotide by using the two techniques that we used in class
Two methods are S1 nuclease mapping and primer extension. These techniques are clearly
shown in the notes and book. I couldn’t clarify any better with text explanation
2. One way to identify important upstream elements of a promoter is by doing deletions. Linker
scanning mutagenesis is another. Explain how this procedure works.
Exchange regions of upstream DNA with regions of “null” DNA. Next assay for transcription.
If transcript is lost, then you must have replaced an important region
3. There are three general categories of transcription factors in eukaryotes. Basal factors are
required for initiation at almost all promoters. Their function is to determine the site of initiation
by interacting with the TATA box. A second type of factors are upstream factors. These interact
with upstream elements such as GC boxes. Finally inducible, or regulated factors are similar to
upstream factors only they are regulatory and interact with enhancers and silencers.
4. Class II promoters are sites where mRNA transcription initiates. This process is complex and
involves many different proteins. Answer the following questions about this process.
a)what is the first protein factor to bind to the promoter?
TFIID
b)what is the subunit of this protein factor that actually interacts with DNA called?
TBP (TATA-binding protein)
c)where does it interact?
At the TATA box through the minor groove
d)there are 8-10 other components that make up this factor. What are their functions?
Interact with Initiator, Downstream elements for TATA-less promoters. Also interact with
upstream activators (SP1, Gal4)
e)next, two other transcription factors bind. What are they and what is their function?
TFIIA-interact with TBP, DNA
TFIIB-interact with PolII-TFIIF complex
f)finally RNAPII can come in, but not without the help of which factor?
TFIIF
e)now we have formed the pre-initiation complex, but we can’t clear the promoter and go into
the elongation phase without the binding of two other factors. What are they?
TFIIE- stimulate transcription,
TFIIH- helicase, ATPase, kinase