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Practice_Exam3_fromF07_ans Loyola Chicago BIOL 382
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  • Title: Practice_Exam3_fromF07_ans
  • Type: Notes
  • School: Loyola Chicago
  • Course: BIOL 382
  • Term: Spring

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Genetics Molecular 382 Practice Exam 3 ANSWER KEY Answer to added question for Ch. 12: Briefly describe how bZIP proteins interact with their DNA binding site (you may draw a rough sketch too, if you wish). What is the role of the "b" domain? What is the role of the "ZIP" domain? - Refer to Fig. 12.11a&b for a picture. The "b" (basic") domain is responsible for contacting the DNA, while the "ZIP" domain is a dimerization domain that holds the two copies of the protein together. 1) Briefly compare and contrast the Group I and Group II self-splicing mechanisms (describe one major similarity and one major difference). i) Similarity (2 pts): - Attack by an OH group on the 5' splice site - No need for additional proteins (i.e. spliceosome-independent) ii) Difference (2 pts): Group II: 2'-OH from A makes intramolecular attack and forms a lariat-shaped intermediate/intron Group I: 3'-OH from GTP makes intermolecular attack - no lariat-shaped intron 2) Each of the items in list A recognizes one of the items in list B. Match each item in list A with the appropriate item in list B. (6 pts) List A: 1) U1 snRNP 2) U2 snRNP 3) U4/U6-U5 snRNP List B: a) 3' splice site b) 5' splice site c) branch site match from list B (just give letter): 1) _b (5' splice site) _ 2) _c (branch site) __ 3) _a (3' splice site) _ Page 1 of 4 3) The following are the results of an in vivo splicing assay with different mutants of a certain yeast gene. The black and white boxes are exons, the lines are intronic sequences, and the cross-hatched box is a conserved sequence found in all yeast introns. What are the two major conclusions that can be drawn from this experiment and its results? (6 pts) Wild Type Spliced Mutant # 1 Conserved intronic sequence deleted. Not spliced. Mutant # 2 AG Non-intron sequence inserted downstream of conserved sequence. Aberrantly spliced. Mutant # 3 AG Conserved sequence moved into downstream exon. Aberrantly spliced. Conclusion 1: The conserved intronic sequence is absolutely required for splicing to occur (from mutant #1) Conclusion 2: The conserved intronic sequence designates the immediate downstream AG as the 3' splice site (from mutants 2 and 3) Page 2 of 4 4) The mechanism by which the 5' cap is added to pre-mRNA is a 3-step process. Outline the details of each step of this mechanism. For each step, include what the starting molecule looks like, what the end product looks like, is what added, and which enzyme is involved. (Note: this is not a chemistry class, so I will not grade you on chemical structures, but you should include the basics (i.e. nucleotides, phosphate groups, methyl groups, etc.) (5 pts) Also refer to Fig. 15.4. 5'-ppp-A..........3' RNA triphosphatase (removes gamma-phosphate from the first nucleotide of the mRNA) 5'-pp-A............3' Guanylyl transferase (adds GMP from GTP, giving off PPi ) Gp-pp-A...........3' Methyl transferase (adds CH3 to G from SAM/AdoMet) m7 Gp-ppA.............3' 5) The gel below shows the results of a cellular localization assay. Two constructs of the Xenopus U1 snRNA gene (one with a polymerase II promoter, the other with a polymerase III promoter) were injected into nuclei of Xenopus oocytes so that they could be transcribed by the respective polymerase. After 12 hours the RNA was extracted from the entire oocyte (T), the nucleus (N) or the cytoplasm (C), and analyzed via electrophoresis. The 5S gene functions as an internal control. What conclusion can you draw about U1 that has been transcribed by Pol II vs. U1 transcribed by Pol III? (4 pts) U1 RNA made by Pol II (normal situation) is found in the nucleus as well as the cytoplasm. This RNA is capped normally and is able to be exported into the cytoplasm where it will associate with proteins. U1 RNA made by Pol III (engineered) is only found in the nucleus. Presumably this RNA does not have a cap and therefore does not get exported out of the nucleus. Apparently the transcription by different polymerases will affect the behavior of the U1 transcript (possibly by affecting whether or not it gets capped). Page 3 of 4 6) The following graph shows the results of a translation assay for viral mRNAs with various modifications. What conclusion about 5' caps and 3' Poly(A) tails can you draw from this experiment ? (4 pts) Cap+, poly(A)+ Cap-, poly(A)+ Cap+, poly(A)Cap-, poly(A)- This one is open to a little bit of interpretation, especially when it comes to comparing +cap/-tail with cap/+tail, but what is clear is that capped and tailed mRNAs are translated most efficiently. In other words, capped mRNAs are translated more efficiently when tailed, and tailed mRNAs are translated more efficiently when capped. An mRNA that has neither is translated least efficiently. Having one or the other leads to an intermediate level of translational efficiency. Page 4 of 4

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