Download [001-072] pierce student man

[001-072] PIERCE STUDENT MAN
8/22/01
13
2:01 PM
Page 36
Transcription
*1. Write the consensus sequence for the following set of nucleotide sequences.
A G G A G T T
A G C T A T T
T G C A A T A
A C G A A A A
T C C T A A T
T G C A A T T
**2. List at least five properties that DNA polymerases and RNA polymerases have in common. List at
least three differences.
*3. An RNA molecule has the following percentages of bases: A = 23%, U = 42%, C = 21%, G = 14%.
a. Is this RNA single-stranded or double-stranded? How can you tell?
b. What would be the percentages of bases in the template strand of DNA that contains the gene for
this RNA?
**4. Shown below is a DNA molecule that is part of the RNA-coding sequence of a transcription unit.
The top strand is the template strand. Indicate the direction of transcription and give the sequence
found on the RNA molecule transcribed from this DNA. Label the 5' and 3' ends of the RNA.
5'–G C A A A T G G C A T G T A–3' ← template strand
3'–C G T T T A C C G T A C A T–5'
**5. Write out a hypothetical sequence of bases that might be found in the first 40 nucleotides of a promoter of a prokaryotic gene. Include both strands of DNA and label the 5' and 3' ends of both strands.
Be sure to include any consensus sequences found in the promoter and the start site for transcription.
36
Pierce, Genetics: A Conceptual Approach
[001-072] PIERCE STUDENT MAN
8/22/01
2:01 PM
Page 37
Pierce, Genetics: A Conceptual Approach
Chapter 13 Transcription
**6. The diagram below represents a transcription unit on a DNA molecule.
a. Assume that this DNA molecule is from a prokaryotic cell. Draw in the approximate location of the
promoter and terminator for this transcription unit.
b. Assume that this DNA molecule is from a eukaryotic cell. Draw in the approximate location of an RNA
polymerase II promoter.
c. Assume that this DNA molecule is from a eukaryotic cell. Draw in the approximate location of an
internal RNA polymerase III promoter.
Transcription start site
5'
3'
3'
5'
Template strand
**7. The following DNA nucleotides are found near the end of a prokaryotic transcription unit. Find
the terminator in this sequence.
a. Mark the point at which termination will occur.
b. Is this an intrinsic terminator or a rho-dependent terminator?
c. Draw a picture of the RNA that will be transcribed from this DNA, including its nucleotide sequence
and any secondary structures that form.
3'–AGCATACAGCAGACCGTTGGTCTGAAAAAAGCATACA–5'
*8. A strain of bacteria possesses a temperature-sensitive mutation in the gene that codes for the rho
subunit of RNA polymerase. At high temperatures, rho is not functional. When these bacteria are raised
at elevated temperatures, which of the following would you expect to see?
a. Transcription never occurs.
b. All RNA molecules are shorter than normal.
c. All RNA molecules are longer than normal.
d. Some RNA molecules are longer than normal.
e. RNA is copied from both DNA strands.
Explain your reasoning for accepting or rejecting each of these five options.
***9. Enhancers are sequences that affect initiation of transcription occurring at genes that are hundreds
or thousands of nucleotides away. Enhancer-binding proteins usually interact directly with transcription
factors at promoters thus causing the intervening DNA to loop out. An enhancer from the bacteriophage
T4, which does not function by looping of the DNA, has been described (Herendeen, D. R. et al. 1992.
Science 256:1298–1303). Propose some additional mechanisms (other than DNA looping) by which this
enhancer might affect transcription at a gene thousands of nucleotides away.
37
[001-072] PIERCE STUDENT MAN
8/22/01
2:01 PM
Page 38
Pierce, Genetics: A Conceptual Approach
Chapter 13 Transcription
***10. The location of the TATA box in two species of yeast, Saccharomyces pombe and Saccharomyces
cerevisiae, differs dramatically. The TATA box of S. pombe is about 30 nucleotides upstream of the start
site, similar to the location for most other eukaryotic cells. However, the TATA box of S. cerevisiae can
be up to 120 nucleotides upstream of the start site. To understand how the TATA box functions in these
two species, a series of experiments was conducted to determine which components of the transcription apparatus of these two species could be interchanged. In these experiments, different components
of the transcription apparatus were switched in S. pombe and S. cerevisiae, and the effect of the switch
on the level of RNA synthesis and the start point of transcription was observed.
TFIID from S. pombe could be used in S. cerevisiae cells and vice versa, without any effect on the
transcription start site in either cell type. Switching TFIIB, TFIIE, or RNA polymerase did alter the level
of transcription. However, the following pairs of components could be exchanged without affecting
transcription: TFIIE together with TFIIH; and TFIIB together with RNA polymerase. Exchange of
TFIIE-TFIIH did not alter the start point, but exchange of TFIIB-RNA polymerase did shift it. (Li, Y.,
P. M. Flanagan, H. Tschochner, and R. D. Kornberg. 1994. Science 263:805–807.)
On the basis of these results, what conclusions can you draw about how the different components
of the transcription apparatus interact and which components are responsible for setting the start site?
Propose a mechanism for the determination of the start site in eukaryotic RNA pol II promoters.
38