Dr. Reichler’s Bio 325   TTh 9:30-11am    Print Name:_____________KEY__________
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 DNA.
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 introns.

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 sequence.

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 points.)

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 signal transduction.
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.