Biology 105: Introduction to Genetics PRACTICE FINAL EXAM 2006 Part I: Definitions Homology: Comparison of two or more protein or DNA sequence to ascertain similarities in sequences. If two genes have an almost identical DNA sequence, they are homologous and will likely code for proteins with similar function. Reverse transcriptase Enzyme that uses RNA as a template to synthesize a complementary DNA Allostery: When enzymes have a specific structure, certain molecules or effectors bind to a certain site on the enzyme changing the shape of the protein and thereby change its function cdna library library generated from mrna after first converting the RNA into cdna using Reverse transcriptase Transformation Bacterial transformation is the process by which bacterial cells take up DNA molecules which then changes the bacteria. e.g. Antibiotic sensitive to antibiotic resistance
Part II Short Answer 1. Describe the reasons for the degeneracy of the genetic code Multiple codons for some amino acids Wobble in codon-anti-codon pairing 2. How will a genomic library made from human liver cells and a cdna library made from a human liver cells differ? cdna library will lack intergenic, promoter and introns sequences 3. A Drosophila geneticist in Seattle finds a recessive mutation on the tip of the X chromosome that produces bent wings. Independently, a researcher in Katmandu finds a mutation that maps to the tip of the X chromosome that produces a similar bent wing phenotype. Describe the crosses (and potential outcomes) that must be performed to determine whether these mutations are in the same or different gene. w/w female crossed to a w/y male wing shape in the female will determine whether mutations are in the same or different genes.
4. A new operon is discovered in which Z is the enzyme whose expression is being regulated by the genes b and j. They have the following properties: Activity (+) or inactivity (-) of the Z gene Genotype Inducer absent Inducer present b+ j+ Z+ - + b- j+ Z+ + + b+ j- Z+ + + b+ j- Z+/j+ - + b- j+ Z+/b+ + + Which of the genes (b or j) is equivalent to the repressor gene and which is equivalent to the operator gene of the lac operon? Explain your reasoning. J is repressor (works in trans) B is operator (does not work in trans) 5. Some human cancers are associated with translocations. What is the molecular basis of this phenomenon. Deletion of genes at site of translocation Fusion of genes and formation of novel hybrid proteins
6. What is the C-value paradox. What is the resolution to this paradox. Amount of total DNA content varies from species to species. The reason for the variation in DNA content were not clear and this was called the C-value paradox. Sequencing of the genomes of multiple species showed that the amount of intergenic (non-coding) DNA increased in organisms with higher C-values compared to organisms with lower C-values. Part III Multiple Choice 1. ( D ) Which of the following is not a general feature of plasmids used in recombinant DNA technology a. origin of replication b. unique restriction site c. antibiotic resistance gene d. gene encoding reverse transcriptase 2. ( C ) Trisomy 21 in humans is primarily caused by a. maternal nondisjunction at Meiosis II b. paternal nondisjunction at Meiosis II c. maternal nondisjunction at Meiosis I d. paternal nondisjunction at Meiosis I e. mitotic recombination in the female germ cells 3. ( D ) The is a cis-acting sequence that serves as the binding site for RNA polymerase a. exon b. poly-a tail c. 5 cap d. promoter e. none of the above 4. ( A ) A given RFLP is defined by a. a specific restriction enzyme and a specific probe b. a specific restriction enzyme and a specific polymerase c. a specific restriction enzyme and a specific promoter d. a specific restriction enzyme and a specific post-translational modification e. none of the above
5. ( B ) An E. coli strain possesses the following phenotype F(O c )/I + P + O + Z + Y + where O c is a mutation in the operator that prevents repressor binding. The structural genes a. will be transcribed in the presence and absence of lactose b. will be transcribed only if lactose is present c. will not be transcribed under any conditions Multiple Choice continued 6. ( C ) The intron is a. a segment of DNA that is spliced out in the nucleus b. a segment of DNA that is spliced out in the cytoplasm c. a segment of RNA that is spliced out in the nucleus d. a segment of RNA that is spliced out in the cytoplasm e. a gene with no known function 7. ( B ) An mrna with the sequence GGGGGGGGGGGGG derived from the following gene 5 GGGGGGGGGGGGG 3 was isolated 3 CCCCCCCCCCCCCC 5 These results indicate the strand is the template strand and the gene is transcribed from a. top, left to right b. bottom, left to right c. top, right to left d. bottom, right to left e. depends on whether or not introns are present in this gene 8. ( D ) All of the following occur in the nucleus except a. addition of a poly A tail b. addition of a 5 cap c. removal of intervening sequences d. linking amino acids through peptide bond formation e. both c and d 9. ( E ) A technique for identifying specific RNA fragments among large and complex mixture of RNA fragments is known as a. PCR b. Southern Blotting
c. DNA fingerprinting d. Cloning e. None of the above Part IV Extended Calculation I. In mouse HindIII restriction digests, Probe AA3 picks up a simple RFLP consisting of two alternative alleles of 1.7kb and 3.8kb. A mouse heterozygous for the dominant allele of bent tail and the just described RFLP is mated with a wild-type mouse that shows only the 3.8kb fragment. Forty percent of the bent-tail progeny are homozygous for the 3.8kb RFLP and 60 percent are heterozygous for the 3.8kb and the 1.7kb RFLPs. A. For a mouse heterozygous for the RFLPs, diagram the relative position of the probe with respect to the HindIII restriction sites for each allele (there is more than one answer). ------------ -------------------------- ----------------------- 1.7 ------------ --------------------------------------------- ----------------------- 3.8 ----------- probe ----------- probe B. Is the bent-tail locus linked to the RFLP locus? Draw the parental and progeny chromosomes to illustrate your answer. Yes it is linked because of the 60:40 ratio of the dominant bent tail phenotype B D -----------1.7 x b-------------3.8 b-------------3.8 b-------------3.8 Progeny: or B D -----------1.7 b-------------3.8 B D -----------3.8 b-------------3.8 30% (60% of bent tail) 20% (40% of bent tail)
C. What RFLP types do you expect among the wild-type offspring and in what proportions? Explain your reasoning. b-----------3.8 30% (parental class) b-----------3.8 or b------------3.8 b------------1.7 20% (recombinant class) D. Could this analysis have been performed using Northern rather than Southern blots? Explain your reasoning. No Extended Calculation II. A 9kb fragment of human DNA that has EcoRI sticky ends is cloned into the plasmid PBR007 at its single EcoRI restriction site. The resulting recombinant plasmid is digested with EcoRI and then, separately, with BamHI. In addition, a third digest is performed, in which EcoRI and BamHI are used together. The resulting fragments are run out on a gel. Below are the diagrams of the gel patterns from each digest: EcoRI BamHI EcoRI + BamHI 10kb 9kb 8kb 6kb 5kb 7kb 5kb 4kb 2kb 1kb A. How many kbs is the PBR007 plasmid without the insert?
10kb B. How many EcoRI and BamHI sites are present in the newly formed recombinant plasmid? 2 EcoRI and 3 BamHI C. Draw a restriction map of the recombinant plasmid. In your map, distinguish between the human DNA fragment and the plasmid. Indicate the restriction sites and the distances between the restriction sites. E-7kb-B-2kb-E-4kb-B-5kb-B-1kb D. If Southern blot analysis was performed on the double digest using the original 9kb insert as a probe, which bands would this probe hybridize to? 9 kb EcoRI 8kb and 6kb BamHI 7kb and 2kb double