Week 8 HW

The oligonucleotide primers used in the polymerase chain reaction are typically 20-30 nucleotides in length or longer; however, for purposes of this problem let's assume that six nucleotides is long enough. You wish to amplify the fragment shown below (the raised dots indicate several kilobases of DNA sequence not shown) and decide to design primers corresponding to the regions that are shown in bold. What primer sequences would you use? A. 5'-ACTTGC-3' and 5'-GTGGCA-3' B. 5'-ACTTGC-3' and 5'-TGCCAC-3' C. 5'-GCAAGT-3' and 5'-TGCCAC-3' D. 5'-GCAAGT-3' and 5'-GTGGCA-3'

B. 5'-ACTTGC-3' and 5'-TGCCAC-3'

A shotgun sequencing project yields the following sequence for a strand of DNA. 5′-GGTTTGGAGTAT-3′ In assembling the genome sequence from the short fragments, you look for other fragments that overlap the sequence above. Which of the following sequences overlaps with the sequence above? A. All of the sequences overlap with sequence above. B. 5′-TTTGGAGTATGG-3′ C. None of the sequences overlaps with the sequence above. D. 5′-AATTTGGAGTAT-3′ E. 5′-GGTTTGGAGTGG-3′

B. 5′-TTTGGAGTATGG-3′

Consider the restriction enzymes below. What type of DNA ends would they produce (5' overhangs, 3′ overhangs, or no overhangs)? A. Alu1: 5′ overhang; BAM HI: 5′ overhang; KpnI : 5′ overhang B. Alu1: no overhang; BAM HI: 5′ overhang; KpnI: 3′ overhang C. Alu1: 3′ overhang; BAM HI: no overhang; KpnI : no overhang D. Alu1: no overhang; BAM HI: 3′ overhang; KpnI : 5′ overhang

B. Alu1: no overhang; BAM HI: 5′ overhang; KpnI: 3′ overhang

You collect a sample of your patient's tuberculosis (Strain P) and conduct VNTR analysis at a single locus. The results are shown below. What should you do now? A. Prescribe Isoniazid B. Collect more data C. Prescribe Ethambutol D. Prescribe Rifampin

B. Collect more data

The bacterium M. tuburculosis causes tuberculosis and infects approximately one third of the world population. VNTR analysis (i.e., DNA fingerprinting) is a useful technique for identifying specific strains of tuberculosis. In the following questions, you will pretend to be a doctor treating a patient with tuberculosis. You are not sure which antibiotic medication to prescribe because some strains of tuberculosis common in your geographic area (Strains X, Y, and Z) are resistant to certain antibiotics. This information is summarized in the diagram below. You collect a sample of your patient's tuberculosis (Strain P) and conduct VNTR analysis at two different loci. The results are shown below. Does this data prove that your patient is infected with strain Y? A. Yes it's definitely Strain Y B. No, it could still be a different strain other than X, Y, or Z. C. The more loci you test, the more probable it is that the strain is a match. When examining 5-10 loci, the chance that two random strains share the same DNA fingerprint is about one in a billion.

B. No, it could still be a different strain other than X, Y, or Z.

You collect a sample of your patient's tuberculosis (Strain P) and conduct VNTR analysis at two different loci. The results are shown below. What should you do now? A. Collect more data B. Prescribe Rifamipin C. Prescribe Ethambutol D. Prescribe Isoniazid

B. Prescribe Rifamipin

A weapon (W) left behind at a crime scene is typed for a variable number tandem repeat (VNTR). The DNA from the weapon includes bands from the victim (V) as well as those from the perpetrator. Which of the suspects A-E has VNTR bands that are consistent with those of the perpetrator? A. suspect D B. suspect B C. suspect A D. suspect E E. suspect C

B. suspect B

In the diagram below, the horizontal lines represent DNA strands in a double-stranded molecule, the vertical lines mark the positions of cleavage sites for a particular restriction enzyme, the arrows show the positions of primers used in the polymerase chain reaction to amplify the region, and the numbers are the number of nucleotides between successive restriction sites. Suppose that the population contains a restriction fragment length polymorphism (RFLP) for this region of DNA. Some DNA molecules contain the site Y, whereas other DNA molecules lack this site. If we use the symbol Y+ to denote the allele containing the Y site and Y- to denote the allele lacking it, then what bands would be observed in the heterozygous genotype Y+/ Y- after amplification and cleavage with the restriction enzyme? A. 5 kb B. 3 kb and 2 kb C. 5 kb, 3 kb, and 2 kb D. None of the answer options is correct. E. 5 kb and 3 kb

C. 5 kb, 3 kb, and 2 kb

Can it be determined from the data in Table 13.1 which eukaryotic species has the largest genome? Can it be determined which species has the greatest number of chromosomes? A. no, yes B. yes, yes C. no, no D. yes, no

C. no, no

The accompanying gel diagram shows the bands obtained for a single variable number tandem repeat (VNTR) in evidence obtained at a crime scene (W) and genomic DNA from three suspects A-C. Which suspect CANNOT be ruled out as the source of the DNA in the sample? A. suspect B B. suspect C C. suspect A D. All suspects can be ruled out. E. No suspects can be ruled out.

D. All suspects can be ruled out.

The bacterium M. tuburculosis causes tuberculosis and infects approximately one third of the world population. VNTR analysis (i.e., DNA fingerprinting) is a useful technique for identifying specific strains of tuberculosis. In the following questions, you will pretend to be a doctor treating a patient with tuberculosis. You are not sure which antibiotic medication to prescribe because some strains of tuberculosis common in your geographic area (Strains X, Y, and Z) are resistant to certain antibiotics. This information is summarized in the diagram below. You collect a sample of your patient's tuberculosis (Strain P) and conduct VNTR analysis at a single locus. The results are shown below. In human VNTR analysis there are usually two bands on the gel for each locus tested. Why does only one band appear for each tuberculosis strain on the gel above? A. You only added one primer to the PCR reaction so only one region was copied. B. Each strain has identical VNTR regions on both copies of its chromosome. C. You added half as much DNA polymerase to your PCR as you should have, so only one region was copied. D. These prokaryotic cells only have one chromosome and therefore only one copy of this VNTR locus.

D. These prokaryotic cells only have one chromosome and therefore only one copy of this VNTR locus.

(Refer to picture) Suppose you know the sequence of a region of DNA in an organism, but you want to know the unknown sequences that flank the known sequence. Cleverly, you cleave the DNA with a restriction enzyme that cleaves at restriction sites outside the known sequence, and then use DNA ligase to form a circle as shown below. The dark blue portion of the circles represents double-stranded DNA whose sequence is known, and the light blue portion the flanking regions whose sequences are unknown. The numbered arrows are places where you consider designing PCR primers, with the 3' end of each primer indicated by the arrowhead. Which primers would you use to amplify the light blue region of the circle? A. 1 and 4 B. 2 and 3 C. 2 and 4 D. 3 and 4 E. 1 and 3 F. 1 and 2

E. 1 and 3

A certain restriction enzyme cleaves double-stranded DNA at the sequence shown below, where the slash indicates where each strand is cleaved. Note that the cleavage results in a two-base pair single-stranded region at the 5' end that allows the cleaved ends to undergo base pairing. 5'-AA/ATTT-3' 3'-TTTA/AA-5' Which of the restriction enzymes, that cleave double-stranded DNA as shown below, would produce overhanging ends able to pair with those produced by the enzyme described above? A. 5'-GGAT/CC-3' 3'-CCTA/GG-5' B. 5'-AAA/TTT-3' 3'-TTT/AAA-5' C. 5'-AATA/TT-3' 3'-TT/ATAA-5' D. 5'-GGA/TCC-3' 3'-CCT/AGG-5' E. 5'-GG/ATCC-3' 3'-CCTA/GG-5'

E. 5'-GG/ATCC-3' 3'-CCTA/GG-5'

You collect a sample of your patient's tuberculosis (Strain P) and conduct VNTR analysis at a single locus. The results are shown below. Can you rule out any of the strains based on this analysis? A. Strain X can be ruled out B. Strain Y can be ruled out C. Strains X, Y, and Z can be ruled out D. Strain X and Y can be ruled out E. Strain Z can be ruled out

E. Strain Z can be ruled out

In the diagrams below, the horizontal lines represent double-stranded DNA and the numbers are regions within the DNA. The sites labeled W, X, Y, and Z denote the locations of cleavage sites for the restriction enzymes W, X, Y, and Z, respectively. The DNA at the left is located in a bacterial plasmid vector and that on the right is located in chromosomal DNA. Each restriction enzyme produces ends that can pair with the ends of other DNA fragments produced by the same restriction enzyme but not with the ends produced by any of the other enzymes shown. A researcher plans to produce a clone with the genomic DNA inserted into the vector in the orientation 1-4-3-2. Which two enzymes should be used to cleave the vector and the chromosomal DNA to produce complementary ends that will lead to this result? A. Wand X B. W and Z C. X and Z D. W and Y E. X and Y F. Y and Z

E. X and Y