Dr. Reichler’s Bio 325 TTh 9:30-11am
Exam #1 September 26, 2006
Read each question carefully and don’t hesitate to
ask if a question seems unclear. If possible, answer each
question in the space provided, but if needed, continue on the
back. If you use a drawing as part of your answer, be sure to
also include a written explanation. These questions have specific
answers, although for some, more than one answer is possible. To
receive full credit you must clearly and fully answer the question
being asked. This exam is worth 103 points with the points for
each question noted in parentheses.
1. Apply rules 1 and 2 of Strong Inference (the parts prior to actually
doing any experiments) to answer the following question: What is
the function of non-coding DNA? (8pts)
Must use Strong Inference and make
multiple hypotheses and experiments to eliminate hypotheses.
Ex: hypo’s- It is an energy source. It has no
function. It contains important regulatory information.
Expt- eliminate the non-coding DNA and see if the cell has less
energy, or regulation of gene expression is disrupted, etc.
2. Explain how using controls and doing statistical analysis relates to
Strong Inference. (6pts)
Rule three of Strong Inference states
that we need reliable results if we are to eliminate the correct
hypotheses. Using statistics and doing controls is part of
getting reliable results.
3. Transposons are examples of genes acting as replicating units.
Relate transposons to two other gene definitions. (6pts)
Any two of:
Genes code for proteins- some
transposons make transposase, a protein, that is involved in moving the
Genes are units of heredity-
transposons are inherited from the parents.
Genes cause diseases- when a
transposon disrupts another gene, that can cause a disease by
disrupting the normal function of the gene product.
Genes are switches- transposons can
disrupt genes thereby disrupting normal development.
4. Describe two problems that would prevent a human gene from being
properly expressed in bacteria. (6pts)
Eukaryotic promoters do not work in
bacteria, eukaryotic promoters need transcription factors.
Eukaryotic genes typically have introns, and bacteria cannot splice out
5. If a transposon was inserted into an intron, would the gene product
still be properly produced? Why or why not? (6pts)
Either: Yes, the intron will be
spliced out along with the transposon thereby having no effect on the
final mRNA. No, the transposon will disrupt proper splicing of
the intron thereby causing the mRNA to have additional and improper
6. What is the connection between birth weight and finger length in
human sexuality? (6pts)
Both show differences with older
biological brothers that correlate with increased probability of
homosexuality. And both indicate environmental factors in the
womb that may be affecting fetal development.
7. Is the 5’-cap or the poly-A tail more critical for initiation of
translation? How do we know this? (6pts)
5’-cap. In the luciferase
expression in tobacco plants, it was seen that eliminating the cap or
tail had a significant effect on mRNA half-life, but when the cap was
eliminated barely any protein was produced relative to how much was
produced when the tail was eliminated.
8. Give two examples of RNA changing the sequence of a protein.
For each example, briefly describe the mechanism for how RNA changes
the protein sequence. (6pts)
RNA editing- mRNA sequence is changed
based on guide RNA sequence. Hothead mutation- hypothesized that
RNA is coding for a template that is correcting a mutation in the DNA.
(Almost no one had two correct
answers for this question. So one correct answer was counted as
full credit. If you gave two correct answers, you received bonus
9. How could an organism with 5,000 genes produce more unique proteins
than an organism with 8,000 genes? (6pts)
By alternate splicing the organisms
with 5,000 genes could produce many more than 8,000 gene products.
10. How could a processed mRNA be longer than the DNA coding region
that it was transcribed from? (6pts)
If it had few or no introns, when the
poly-A tail is added, it could be longer than the DNA coding region.
11. How could improper localization of a protein cause a cell to fail
to properly respond to an environmental stimulus? (6pts)
Any of: Many receptors are
localized to the plasma membrane. If the receptor was not
properly localized, the cell would not perceive the signal.
Calcium channels must be properly
localized to the various membranes to allow increases in calcium during
Some calcium signaling specificity is
accomplished by the pairing of calcium channels and the next
effector. Lack of this pairing would disrupt the signaling.
12. Describe two changes (not insertions or deletions) to a single
nucleotide in the coding region of a gene that would change many amino
acids in the protein. (6pts)
Any two of: Change the start
codon. Change the stop codon to a non-stop codon. Change
the intron/exon border so that the intron is not spliced.
13. You know the sequence of a protein’s amino acids and the DNA that
codes for it. How could you use this information to determine if
this was a membrane bound or secreted protein? (6pts)
Compare the amino acid sequence and
the DNA to see whether a signal peptide is removed.
14. In the response of plant roots to different concentrations of Nod
factors, it was observed that 1nM Nod factor caused calcium to increase
from the tip towards the nucleus while 10nM Nod factor caused calcium
to increase from the nucleus toward the tip. How could these two
patterns of calcium increases give different responses in the
cell? Describe an experiment to test your hypothesis. (6pts)
Specificity in calcium signaling can
be accomplished through spatial pairing of incoming calcium and the
next effector. I could add calcium to specific parts of the cell,
and see whether the proper response was obtained based on the part of
the cell where calcium was added.
15. In the work on calcium signaling in guard cells, what experiment
disproved the switch hypothesis? Briefly describe the experiment
and the result that disproved the switch hypothesis. (8pts)
Either experiment showing that even
when more calcium was added, short delay between spikes or longer
spikes, that the stomata did not close.
16. Heart muscles respond to the hormone epinephrine by contracting,
while muscles controlling blood flow relax in response to
epinephrine. Based on this information, would you expect the
cells in these two muscles to be expressing the same or different
genes? Explain. (6pts)
Different genes. The same
signal can give different responses by being transduced via different
effectors or perceived by different receptors.
Bonus: Why were measurements of calcium changes in guard cells a
critical first step for the success of the experiments in which
researchers induced calcium changes in guard cells? (3pts)
How could they have known what timing
the spikes of calcium had. Without having an idea of the
wild-type calcium spikes, they would have needed many, many experiments
trying hundreds of different combinations of delays between spikes and
durations of spikes. By knowing the wild-type pattern, they could
quickly zone in on the critical timing of the spikes.