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Name: page1 of 7 pages MOLECULAR BIOLOGY BIO372S January 19, 2010 First mid-term examination (one hour) Read each question carefully and put your answers on the exam page only in the spaces indicated. Good luck! Name: Signature: Student Number: ANSWERS IN BOLD GREEN, TYPE Name: page2 of 7 pages 1. You are given two micrograms of plasmid DNA. There are four EcoRI recognition-cut sites in the plasmid yielding four linear fragments. Two of the fragments are of known sizes and two of the fragments are of unknown sizes. (10 points) What are the sizes of the two unknown fragments? Answer here: (10 points) How many plasmid molecules were there? Answer here: (Essential information: base pair of DNA is 660 Daltons and Avogadro’s number is 6.02 X 1023) on Name: page3 of 7 pages Numbers 2 - 16, 15 questions, 2 points each (total of 30 points) 2. A. B. C. D. E. The chromosomal theory of inheritance holds that chromosomes vary in size. the number of chromosomes vary in individuals. chromosomes contain histone proteins. genes are arranged in a linear order on chromosomes. chromosomes condense during mitosis. 3. Some genes located on the same chromosome do not show perfect linkage because A. they are too close together. B. they are interrupted by other genes. C. crossover events occur between homologous. D. some genes are deleted. E. too many alleles are present. 4. A. B. C. D. E. The relationship between genes and enzymes was shown by Watson and Crick. Beadle and Tatum. Avery and McLeod. Morgan and Mendel. Miescher and Stern. 5. The early notion of one-gene/one-enzyme was not true because of which of the following? A. An enzyme can be composed of more than one polypeptide. B. Many genes contain the information for making polypeptides that are not enzymes. C. The end products of some genes are not polypeptides. D. An enzyme can be composed of more than one polypeptide, many genes contain the information for making polypeptides that are not enzymes and the end products of some genes are not polypeptides are all correct. E. Only An enzyme can be composed of more than one polypeptide and many genes contain the information for making polypeptides that are not enzymes are correct. Name: 6. A. B. C. D. E. page4 of 7 pages Which of the following would not be considered a mutation? permanent replacement of guanine with thymine in a DNA strand deletion of a gene segment insertion of an intron in the middle of an exon permanent replacement of cytosine with adenine crossing over of two gene regions during meiosis 7. A new insulin gene was isolated and a study was planned to look at the function of the promoter region. Which of the following would be the best choice for this study? A. southern analysis B. immunoblotting C. reporter gene assay D. PCR E. immunoprecipitation 8. A DNA fragment was treated with EcoRI restriction enzyme. The restriction pattern is shown below. How many fragments should be visible on a Southern blot if radioactively labeled probe "1" was used? A. B. C. D. E. 9. A. B. C. D. E. 0 1 2 3 4 A major measure measure measure monitor monitor function of reporter gene assays is to mutation rates of a gene. transcriptional levels. replication. luciferase activity. CAT activity. 10. Which of the following is not true about run-on transcription assay? A. Isolated nuclei are used in the assay. B. Cytoplasmic RNA is included in the assay. C. The reaction is done in the presence of labeled nucleotide. D. The assay can reveal the transcription rates of genes E. Genes being transcribed can be identified. Name: page5 of 7 pages 11. Which of the following isotopes would be the most appropriate for the end-labeling of a DNA strand with a radioactive phosphate via polynucleotide kinase? A. α-32P B. 35S C. β -32P D. γ -32P E. 14C 12. The experimental system (organism) first used to look at the relationship between genes and enzymes was Neuropsora crassa 13. During translation, the genetic code in mRNA is "read" by Codons or ribosomes 14. The process of making RNA from DNA is called Transcription 15. Crossing over between two homologous chromosomes occurs during prophase of meiosis I 16. In genome sequencing a “scaffold”: -Represents a region of unbroken, overlapping nucleotide sequence reads. -Contains sequence gaps. -Represents a physically continuous segment of the chromosomal DNA. -Is made up of contigs. Circle the statements above that are true of scaffolds. Name: page6 of 7 pages 16 (10 points). You have separate solutions of DNAs of increasing sequence complexity: i) T4 bacteriophage, ii) E. coli DNA, and iii) yeast DNA. The DNA is sheared to a uniform size of 200 bp. The DNA is thermally denatured and then placed in standard conditions allowing renaturation. Draw a plausible renaturation reactions for the three separate samples of DNA. Answer: three separate curves, fastest reassociating, T4, then E. coli, then yeast 17 (10 points). You now combine the three samples above into one sample, which is well mixed. The mixed DNA is now sheared to a uniform size of 200 bp. The DNA is thermally denatured and then placed in standard conditions allowing renaturation. Draw a plausible renaturation reaction. Must show ONE curve with three dips and three plateaus, the first dip for T4, second for E. coli and the third for yeast. Name: page7 of 7 pages 18 (10 points). Below is a density trace of a sample of DNA. Show a plausible corresponding melt curve for the same DNA. Must show one melt curve with an early rise due to the majority, light component of DNA, followed by a plateau and a small rise due to the minority heavier component. Density trace Melt curve 19 (10 points). Approximately how large is the genome of Neurospora crassa? About 40 million base pairs 20 (10 points). Jonathon Arnold in his commentary on the paper by Galagan et al. (2003) states: "Unlike its yeast relatives, however, Neurospora abhors repeated genes and other duplicated elements in the genome." This effect is due to RIPing. Show the dinucleotide frequency ratio (NpN/NpN) that best indicates RIPing: TpA vs. ApT