Dr. Reichler’s Bio 311C   MWF 1-2pm    Print Name:______________KEY_______
Exam #3   December 4, 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 100 points with the points for each question noted in parentheses.

1. Using rules 1 and 2 of Strong Inference, the parts prior to doing experiments, answer the following question:  What is the function of IP3 in a cell? (8 pts)
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 is involved in calcium signals.  Expt-  Eliminate IP3 and see if cell can make energy or transduce a calcium signal.

2. The conversion of glutamic acid and ammonia to glutamine has a DG of +3.4kcal/mol while the conversion of ATP to ADP and Pi has a DG of –7.3kcal/mol.  Why can one molecule of ATP not be used to produce two molecules of glutamine? (6 pts)
Even though there is more than double the energy released by ATP than is needed for the production of glutamine, 3.4 x 2= 6.8kcal/mol.  Energy transfer is never 100% efficient.  So the loss of energy to entropy will mean that one ATP is needed for each production of glutamine.

3. The final product of photosynthesis is quickly consumed for the plant’s metabolism, and some of the intermediate products are also quickly consumed.  If, under various conditions, you wanted to measure the efficiency of photosynthesis, what would you measure, and how would this measurement reflect photosynthetic efficiency? (6 pts)
Measure oxygen production.  Water is split to provide electrons to replace those liberated from pigments after light is absorbed by the pigments.

4. What is the difference between what happens to the electrons after the electron transport chain in photosynthesis and cellular respiration? (8 pts)
In photosynthesis the electron is accepted by NADPH.  In cellular respiration the electron is accepted by oxygen.

5. For each G3P produced by the Calvin cycle, how many total carbon atoms moved through the cycle?  Explain. (6 pts)
18.  3CO2’s added to 3 RuBP (5C) = 18 carbons for each G3P.

6. Overall glycolysis is exergonic, but some of glycolysis is endergonic.  Explain. (6 pts)
Initially 2 ATPs are expended to break down glucose, and then 4 ATPs are formed by substrate phosphorylation.

7. What stimulus would a human cell need to respond to that would involve a change in cellular respiration?  Would this response involve changes in DNA packaging?  Why or why not? (6 pts)
Oxygen availability.  Low oxygen would meant that the cells would need to switch to lactic acid fermentation.  This will not involve changes in DNA packaging.  The cells need to make the switch rapidly.
What organic molecules are available.  Sugar, amino acids, fats, etc?

8. With regards to the final step in ATP production, what is one similarity and one difference between the production of ATP in cellular respiration and photosynthesis?  (besides where they occur) (6 pts)
Any one of:
Similar- Both involve chemiosmosis of protons through ATP synthase to produce ATP.
Different- Photosynthesis- makes all of its ATP via ATP synthase; electron excited again in PSI;
Cellular respiration- also makes some ATP via substrate phosphorylation; electron donated to oxygen;

9. Some responses to signal transduction involve changes in gene expression.  How can calcium be involved in the movement of the signal from the exterior of the cell to the nucleus? (6 pts)
The release of IP3 by PhosphoLipase C can diffuse into the cell activating calcium channels that then release calcium thereby activating calcium sensitive proteins that can eventually activate a transcription factor that will bind to a promoter and activate gene expression.

10. Would two different cells responding differently to the same signal express different genes?  Why or why not? (6 pts)
Yes, they must have either different receptors and/or different effectors leading to different signal transduction and different responses.

11. The genes coding for two proteins “stopthepain” and “handcramp” are both expressed in people during test taking.  Would you expect their promoters to be similar or different?  Why? (8 pts)
Similar.  Similar expression likely involves the binding of similar transcription factors to similar promoter sequences.

12. Bacteria do not have enhancers like in eukaryotic cells, but there are still cases in bacteria in which a sequence thousands of nucleotides away from the transcription start site can affect transcription.  Describe how, in bacteria, a sequence far away from the start of transcription can affect transcription. (8 pts)
Any one of:  Repressors are coded for by genes away from the promoter where they can block the binding of RNA polymerase.  CAP is coded for by a gene away from the promoter where it binds to increase the binding of RNA polymerase as in the lac operon.

13. What are one similarity and two differences between DNA replication on the leading and lagging strands? (6 pts)
Similarity (any one of)- Need RNA primer.  Start with Primase.  Use ligase.  Add nucleotides at 3’ end.  Reads template in 5’ direction.

Differences (any two of)
Leading strand:  Continuous replication.  Need single primase, primer, ligase, DNA polymerase.  Follows helicase.  No gap at end.
Lagging strand:  Discontinuous replication (Okazaki fragments). Need multiple primase, primer, ligase, DNA polymerase.  Moves away from helicase.  Leaves gap at end.

14. Would you expect the histones adjacent to the gene that codes for histones to be acetylated during DNA replication?  Why or why not? (8 pts)
Yes.  As more DNA is made, more histones are needed.  Acetylation of histones unpackages nearby genes thereby increasing transcription.

15. If a gene on one sister chromatid has a mutation, would you expect the gene on the other sister chromatid to have that same mutation?  Why or why not? (6 pts)
Any of:  Yes, the DNA in sister chromatids is replicated DNA so the sequences should be the same.
No, if the mutation occurred during DNA replication.