1. DNA Tools and Biotechnology

2. The photograph shows Rainbow and CC (CC is Rainbow’s clone)
The photograph shows Rainbow and CC (CC is Rainbow’s clone). Why is CC’s coat pattern different from Rainbow’s given that CC and Rainbow are genetically identical?
random X chromosome inactivation
heterozygous at coat color gene locus
environmental effects on gene expression
all of the above
Answer: D

3. The photograph shows Rainbow and CC (CC is Rainbow’s clone)
The photograph shows Rainbow and CC (CC is Rainbow’s clone). Why is CC’s coat pattern different from Rainbow’s given that CC and Rainbow are genetically identical?
random X chromosome inactivation
heterozygous at coat color gene locus
environmental effects on gene expression
all of the above 3

4. Which is an incorrect statement about STRs (Short Tandem repeats)?
They are tandemly repeated units of 5- to 10 nucleotide sequences
The number of repeats is polymorphic from person to person
Two alleles of an STR may differ in an individual
They occur in specific regions of the genome
PCR is used to amplify particular STRs.
Answer: A 4

5. Which is an incorrect statement about STRs (Short Tandem repeats)?
They are tandemly repeated units of 5- to 10 nucleotide sequences
The number of repeats is polymorphic from person to person
Two alleles of an STR may differ in an individual
They occur in specific regions of the genome
PCR is used to amplify particular STRs. 5

6. Which of the following beneficial traits have not resulted from DNA technology and genetic engineering of crop plants?
Delayed ripening
Resistance to drought
Resistance to herbicides
Resistance to salinity
Superweeds
Answer: E

7. Which of the following beneficial traits have not resulted from DNA technology and genetic engineering of crop plants?
Delayed ripening
Resistance to drought
Resistance to herbicides
Resistance to salinity
Superweeds

8. Which of the following is not a correct statement about third generation sequencing?
A single DNA molecule is sequenced on its own
Different bases interrupt an electric current for a particular length of time a compound and an isotope; a molecule
DNA moves through a small nanopore a molecule and a compound; a molecule
DNA must be cut into fragments or amplified
Answer: D 8

9. Which of the following is not a correct statement about third generation sequencing?
A single DNA molecule is sequenced on its own
Different bases interrupt an electric current for a particular length of time a compound and an isotope; a molecule
DNA moves through a small nanopore a molecule and a compound; a molecule
DNA must be cut into fragments or amplified 9

10. Place the steps in a cycle of PCR (Polymerase Chain Reaction) in the correct order:
Annealing—Cool to allow primers to form hydrogen bonds with ends of target sequence
Extension—DNA polymerase adds nucleotides to the 3 end of each primer
Denaturation—Heat briefly to separate DNA strands
3-1-2
3-2-1
1-2-3
2-3-1
1-3-2
2-1-3
Answer: A
Figure 20.8 10

11. Place the steps in a cycle of PCR (Polymerase Chain Reaction) in the correct order:
Annealing—Cool to allow primers to form hydrogen bonds with ends of target sequence
Extension—DNA polymerase adds nucleotides to the 3 end of each primer
Denaturation—Heat briefly to separate DNA strands
3-1-2
3-2-1
1-2-3
2-3-1
1-3-2
2-1-3 11

12. Which of the following is an example of “recombinant DNA”?
combining alternate alleles of a gene in a single cell
manipulating a meiotic crossing-over event
cloning genes from homologous pairs of chromosomes
introducing a human gene into a bacterial plasmid
alternate alleles assorting independently
Answer: D
Concept Recombinant DNA is a DNA molecule formed when segments of DNA from two different sources—often different species—are combined in vitro (in a test tube). 12

13. Which of the following is an example of “recombinant DNA”?
combining alternate alleles of a gene in a single cell
manipulating a meiotic crossing-over event
cloning genes from homologous pairs of chromosomes
introducing a human gene into a bacterial plasmid
alternate alleles assorting independently 13

14. This segment of DNA is cut at restriction sites 1 and 2, which creates restriction fragments A, B, and C. Which of the following electrophoretic gels represents the separation of these fragments? a) b) c) d)
Answer: A
See Figure Negative DNA moves toward the positive pole; smaller DNA fragments move faster. 14

15. This segment of DNA is cut at restriction sites 1 and 2, which creates restriction fragments A, B, and C. Which of the following electrophoretic gels represents the separation of these fragments? a) b) c) d) 15

16. There is a lot of information in the figure on the next slide.
Scientific Skills Exercise
There is a lot of information in the figure on the next slide.
1) The top diagram depicts the very large regulatory region upstream of the Hoxd13 gene. The area between the slashes represents the DNA located between the promoter and the regulatory region.
2) The diagrams to the left of the bar graph show, first, the intact DNA and, next, the three altered DNA sequences. A red X indicates the segment (A, B, and/or C) that was deleted in each line of transgenic mice.
3) The horizontal bar graph shows the amount of Hoxd13 mRNA that was present in the digit-formation zone of each transgenic 12.5-day-old embryo paw relative to the amount that was in the digit-formation zone of a wild-type mouse that had the intact regulatory region (top bar = 100%). The paw images have blue stain visible where the Hoxd13 mRNA is located.
Answer: B 16

17. 17

18. Which of the four treatments was the control for the experiment?
the wild-type mouse C
the transgenic mouse with all three segments deleted N
the transgenic mouse with segments B and C deleted
the transgenic mouse with only segment C deleted
Answer: A 18

19. Which of the four treatments was the control for the experiment?
the wild-type mouse C
the transgenic mouse with all three segments deleted N
the transgenic mouse with segments B and C deleted
the transgenic mouse with only segment C deleted 19

20. The hypothesis was that all three segments of the regulatory region are required for highest expression of the Hoxd13 gene. Is this hypothesis supported by the results?
Yes; when any of the segments were deleted, the expression level dropped to less than 100% of the control.
No; they did not delete the promoter, so the gene could still be expressed even without the segments.
Yes; when all three segments were present, the expression level was at 100%.
No; even when segments were deleted, the Hoxd13 gene was still being expressed.
Answer: A 20

21. The hypothesis was that all three segments of the regulatory region are required for highest expression of the Hoxd13 gene. Is this hypothesis supported by the results?
Yes; when any of the segments were deleted, the expression level dropped to less than 100% of the control.
No; they did not delete the promoter, so the gene could still be expressed even without the segments.
Yes; when all three segments were present, the expression level was at 100%.
No; even when segments were deleted, the Hoxd13 gene was still being expressed. 21

22. What was the effect on the amount of Hoxd13 mRNA when segments B and C were both deleted?
Only about 60% of the control amount of Hoxd13 mRNA was produced.
The deletion of segments B and C had no effect on the amount of Hoxd13 mRNA produced.
Only about 35% of the control amount of Hoxd13 mRNA was produced.
Only about 5% of the control amount of Hoxd13 mRNA was produced.
Answer: C 22

23. What was the effect on the amount of Hoxd13 mRNA when segments B and C were both deleted?
Only about 60% of the control amount of Hoxd13 mRNA was produced.
The deletion of segments B and C had no effect on the amount of Hoxd13 mRNA produced.
Only about 35% of the control amount of Hoxd13 mRNA was produced.
Only about 5% of the control amount of Hoxd13 mRNA was produced. 23

24. Look at the blue stain in the in situ hybridization for the transgenic mouse lacking segments B and C. How would you describe the spatial pattern of gene expression in the embryo paw as compared to the control?
There is very light blue stain in the center of each digit zone as compared to the control.
The blue stain is generally lighter than in the control, but all four digit zones are still visible.
There is almost no blue stain anywhere in the paw as compared to the control.
There is no blue stain at the base of the paw as compared to the control.
Answer: B 24

26. Look at the blue stain in the in situ hybridization for the transgenic mouse lacking segments B and C. How would you describe the spatial pattern of gene expression in the embryo paw as compared to the control?
There is very light blue stain in the center of each digit zone as compared to the control.
The blue stain is generally lighter than in the control, but all four digit zones are still visible.
There is almost no blue stain anywhere in the paw as compared to the control.
There is no blue stain at the base of the paw as compared to the control. 26

27. What was the effect on the amount of Hoxd13 mRNA when just segment C was deleted?
The deletion of segment C had no effect on the amount of Hoxd13 mRNA produced.
Only about 60% of the control amount of Hoxd13 mRNA was produced.
Only about 35% of the control amount of Hoxd13 mRNA was produced.
Only about 5% of the control amount of Hoxd13 mRNA was produced.
Answer: B 27

28. What was the effect on the amount of Hoxd13 mRNA when just segment C was deleted?
The deletion of segment C had no effect on the amount of Hoxd13 mRNA produced.
Only about 60% of the control amount of Hoxd13 mRNA was produced.
Only about 35% of the control amount of Hoxd13 mRNA was produced.
Only about 5% of the control amount of Hoxd13 mRNA was produced. 28

29. How would you describe the spatial pattern of gene expression in the embryo paw lacking segment C as compared to the control and to the paw lacking segments B and C?
The digit zones are not visibly stained as they are in the control and the paw lacking B and C.
The top of the paw is stained darker than both the control and the paw lacking B and C.
The base of the paw is stained darker than both the control and the paw lacking B and C.
The digit zones are defined with darker stain than both the control and the paw lacking B and C.
Answer: A 29

30. How would you describe the spatial pattern of gene expression in the embryo paw lacking segment C as compared to the control and to the paw lacking segments B and C?
The digit zones are not visibly stained as they are in the control and the paw lacking B and C.
The top of the paw is stained darker than both the control and the paw lacking B and C.
The base of the paw is stained darker than both the control and the paw lacking B and C.
The digit zones are defined with darker stain than both the control and the paw lacking B and C. 30

31. Suppose the researchers had only measured the amount of Hoxd13 mRNA and not done the in situ hybridizations. What important information about the role of the regulatory segments would have been missed?
The interaction of the regulatory region with the promoter would have been missed.
The interaction among the different segments of the regulatory region would have been missed.
The mRNA would not have been blue; therefore it could not have been measured for the results shown in the bar graph.
The spatial patterns of Hoxd13 gene expression in the paws would have been missed.
Answer: D 31

32. Suppose the researchers had only measured the amount of Hoxd13 mRNA and not done the in situ hybridizations. What important information about the role of the regulatory segments would have been missed?
The interaction of the regulatory region with the promoter would have been missed.
The interaction among the different segments of the regulatory region would have been missed.
The mRNA would not have been blue; therefore it could not have been measured for the results shown in the bar graph.
The spatial patterns of Hoxd13 gene expression in the paws would have been missed. 32

33. Suppose the researchers had only done the in situ hybridizations and not measured the amount of Hoxd13 mRNA. What important information would have been missed?
The information about which regulatory segments were deleted would have been missed.
The spatial patterns of Hoxd13 gene expression in the paws would have been missed.
Qualitative data about Hoxd13 mRNA levels would have been missed.
Quantitative data about Hoxd13 mRNA levels would have been missed.
Answer: D 33

34. Suppose the researchers had only done the in situ hybridizations and not measured the amount of Hoxd13 mRNA. What important information would have been missed?
The information about which regulatory segments were deleted would have been missed.
The spatial patterns of Hoxd13 gene expression in the paws would have been missed.
Qualitative data about Hoxd13 mRNA levels would have been missed.
Quantitative data about Hoxd13 mRNA levels would have been missed. 34