Student Name: All questions are worth 5 pts. each. GENETICS EXAM 3 FALL 2004 1. a) is a technique that allows you to separate nucleic acids (DNA or RNA) by size. b) Name one of the materials (of the two that we discussed) that forms the gelatinous matrix in the procedure described in part (a). 2. If you were trying to clone a restriction fragment using the puc18 vector, following ligation of the DNAs and transformation of E. coli, you should spread the bacteria onto nutrient agar containing to select for bacteria that contain a plasmid and to select for those bacteria that contain a plasmid with an insert. 3. When doing automated sequencing, what two functions are performed by ddntps? a) b) 4. The FISH technique allows you to a) find interesting sequence homologies. b) determine the approximate genomic location of a cloned gene. c) search for clone of a specific gene in a library. d) determine whether two DNA clones contain similar sequences. 5. If you were to cut a DNA clone with various restriction enzymes (single enzyme digests) and all pairwise combinations of double enzyme digests, and then determine the sizes of the resulting DNA fragments, this would allow you to a) determine the DNA's sequence. b) determine the tissues in which a cloned gene is transcribed. c) construct a restriction map. d) All of the above are true. e) None of the above are true. 6. Which of the following does not represent a clone? a) one bacteria colony. b) plasmid DNA isolated from a single bacteria colony. c) a single molecule of genomic DNA ligated to a vector DNA molecule. d) lambda bacteriophage contained within a single plaque. e) All of the above are clones. f) None of the above are clones.
7. If you were trying to predict whether an individual would eventually develop a particular genetic disease, and the DNA sequences of both the normal and mutant alleles are known, which of the following would provide the most accurate prediction? a) RFLP (Restriction Fragment Length Polymorphism) analysis b) SSLP (Simple Sequence Length Polymorphism) analysis c) VNTR (Variable Number Tandem Repeat) analysis d) ASO (Allele Specific Oligonucleotide) analysis 8. Why do restriction enzymes cut the DNA of invading bacteriophage, but not the bacteria cell's own chromosomal DNA? a) The bacteria's chromosomal DNA does not have any recognition sequences for the restriction enzymes it produces. b) For each restriction enzyme, the bacteria produce a corresponding modification enzyme that methylates the recognition sites in the bacteria cell's DNA. c) For each restriction enzyme, the bacteria produce a corresponding modification enzyme that methylates the recognition sites in the bacteriophage's DNA. d) The bacteria only produce the restriction enzyme when bacteriophage DNA enters the cell. 9. Which of the following is involved in determining an individual s DNA fingerprint? a) cdna b) minisatellites c) restriction mapping d) library screening 10. In making a library using a λ vector, insert DNA fragments are ligated directly to the vector's a) stuffer fragment. b) cos sites. c) BamHI sticky ends. d) antibiotic resistance gene. 11. Which of the following vectors would allow you to make a complete genomic library with the fewest possible clones from an organism that has a genome size of 10 8 bp? a) cosmid b) plasmid (e.g., puc18) c) M13 d) lambda 12. The cdna for a eukaryotic gene is 1.5 kb long. This cdna clone is used to isolate a genomic clone that contains the same gene. If you digested the genomic clone with the restriction enzyme BamHI, and hybridized a Southern blot of this DNA with the cdna probe and found that only the 3kb and 7kb bands hybridized to the probe, what is the most likely explanation for this result? A map of the genomic clone is below. 3 kb 5 kb 7 kb a) the gene is present as a tandem duplication. b) the 5 kb BamHI fragment is included in an intron. c) the genomic clone is not really gene B, just a related gene. d) the gene is constitutively expressed.
13. Which of the following may be a useful feature of some cloning vectors, but is not a necessary feature of all cloning vectors? a) Means of selection (i.e., identifying bacteria that contain recombinant DNA molecules) b) Origin of replication c) lac z gene d) Cloning sites 14. Assume you have identified an RFLP that is closely linked to a gene in which you are interested. Which of the following approaches would this allow you to use to clone the gene? a) Conserved sequence probe. b) Reverse translation to produce an oligonucleotide probe. c) Transposon tagging. d) Chromosome walking. 15. Which of the following is the most effective way to identify clones in a library that contain a specific gene? a) Screen the library with a radioactive probe. b) Isolate the DNA from randomly selected library clones and hybridize Southern blots containing their DNAs with a radioactive probe. c) Sequence the DNA of randomly selected library clones. d) Any of the above would work equally well. e) None of the above 16. If you used a cloned mouse gene as a probe to hybridize to a northern blot containing RNA from the sources indicated below, what two things would this tell you about the gene? (a) (b) 17. a) If you were to cut eukaryotic DNA with restriction endonucleases that have the following recognition sequences, which would produce fragments that could be ligated into a vector that had been cut with the restriction enzyme SfoI? Arrows indicate where the enzymes cut DNA. Circle each correct answer. SfoI cuts the following sequence: GGCGCC CCGCGG #1 GGCGCC #2 AGCGCT #3 GGCGCC #4 GCGC #5 CCGG CCGCGG TCGCGA CCGCGG CGCG GGCC b) Of those that were able to ligate to the vector, which, if any, would you definitely be able to separate away from the vector by cutting with SfoI?
18. Southern blots are used to a) determine a gene's nucleotide sequence. b) study the transcription of a cloned gene. c) determine if two DNA molecules contain similar sequences. d) isolate genomic clones. 19. You have identified a family that shows an inherited pattern of a dominant autosomal genetic disease, which is caused by a mutant allele of gene "D". A pedigree of the family is shown below. Affected individuals are shaded in. You perform SSLP analysis and obtain the data shown below the pedigree. a) Diagram the structure of the homologous chromosomes of the parents, including the location and alleles of the disease-causing gene and the location of the SSLP and the forms of the SSLP on each chromosome. b) Diagram the homologous chromosomes of child #7 and explain how this pattern was produced. 20. a) If you have a clone of a gene and want to isolate a clone of a similar gene from another species, what approach would you take? Assume that this is being done prior to completion of the genome project for this other species. b) Now assume that this species' genome project has been completed. Would this change your approach to cloning this related gene? Briefly explain your answer. 21. The diagram below represents an autoradiograph produced by a DNA sequencing gel (the old fashioned kind). Write out the double stranded sequence, noting the 5' and 3' ends of each strand and noting which strand is the template and which strand was synthesized during the sequencing reaction.
22. The diagram below represents a region of genomic DNA and the arrows indicate the locations of PCR primers. a) On the above diagram, indicate the 5' and 3' ends of each PCR primer. b) On the above diagram, indicate the region of genomic DNA that would be amplified by PCR. c) Name the 3 steps in each PCR cycle: 23. a) Of the two approaches that may be taken to perform a genome project, which one first requires the assemble of a physical map of the genome? b) Which genome project approach most heavily relies on computers to assemble contigs from the sequences of many small clones? 24. a) What is the preferred vector for making a genomic library if you are trying to assemble a physical map of the genome, as in 23a? c) What are STS s and how are they used to assemble physical maps? 25. Once the entire sequence of a genome is determined, what two approaches are used to map the locations and structures of genes?