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Page # Possible Actual

points
points

3 15

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5 6

6 12

7 8

8 9

9 6

10 14

11 8

12 8

13 5+2 bonus

Total:

BIOLOGY 221
EXAM 3 FOR 2017C

KEY!!!
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Penn ID #:______________________________

Directions:

• There are 15 pages to this exam. 13 pages of questions and 2 extra blank sheets. Make sure your exam is
complete.

• You will have 75 minutes to complete this exam.

• Do not write on the back of the exams. Answers written on the back of pages will not be graded!

• All answers must be provided in the space allotted following each question.
You may use the genetic code page and the blank pages as scrap paper, however these pages
will not be reviewed during grading.

•Please be short and concise with your answers.

Full credit will be awarded for correct answers that are not otherwise diluted with
extraneous or erroneous information.

• Write your answers in PEN. Exams completed in pencil will not be considered for regrade.

By signing my name to the top of this exam, I pledge my honor that I have upheld the Code of
Academic Integrity of the University of Pennsylvania in completing this examination.
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Multiple Choice (3 pts each) please circle all correct answers:

1. Mutant bacteria are used for the Ames Test. What molecules are they not able to make on their own?

A. Lysine
B. Histidine
C. DNA
D. Methionine
E. Phospholipids

2. If a plate has very few colonies on it after the Ames test, what does this mean?

A. The chemical did not cause mutations in Salmonella

B. The chemical was a mutagen
C. The chemical was a carcinogen
D. The liver enzymes didn’t work
E. The plates on which the bacteria were spread were not made properly

3. Which of the following is/are considered genetically engineered organisms?

A. A potato plant produced by somatic hybridization

B. An apple tree whose genome has been edited using CRISPR/Cas technology to remove a gene that
causes cut fruit to turn brown.
C. A rice plant expressing from a T-DNA insertion a gene isolated from a related variety of wild rice
that make rice more nutritious.
D. Sheep produced by embryo transfer to a surrogate mother
E. Enviro-Pigs; transformed pigs that release less phosphate in their manure due to high levels of
expression of the pytase gene from E. coli.

4. Which technique/s can be used to propagate “seedless” fruits?

A. Artificial insemination
B. Embryo rescue
C. Somatic hybridization
D. Induced Tetraploidy
E. Induced Mutagenesis

5. Which technique/s is/are used to combine desirable traits without the exchange of genetic material?

A. Artificial insemination
B. Induced Mutagenesis
C. Somatic hybridization
D. Grafting
E. None of the above
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6. A group of bodies are found buried in a forest. The police suspect they may include the missing Jones
family (two parents and two children). They extract DNA from bones and using PCR examine two genes
A and B, which are known to contain tandem repeats of variable length. They also analyze the DNA from
two other men. The results are below, where the numbers indicate the number of copies of the tandem
repeat in each allele of the gene.

(9 pts)

Gene A Gene B
Male 1 8/9 5/7
Male 2 6/8 5/5
Male 3 7/10 7/7
Woman 8/8 3/5
Child 1 7/8 5/7
Child 2 8/8 3/7

6a. Which children could be a child of the woman?

A. Child 1 only
B. Child 2 only
C. Both Child 1 and Child 2
D. Neither Child 1 nor Child 2

6b. Which children could be a child of Male 1?

A. Child 1 only
B. Child 2 only
C. Both Child 1 and Child 2
D. Neither Child 1 nor Child 2

6c. Which child could be a child of both the woman and male 3?

A. Child 1 only
B. Child 2 only
C. Both Child 1 and Child 2
D. Neither Child 1 nor Child 2
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7. A mystery gene is being studied, we’ll call it gene M for short.

Bone marrow cells were treated as indicated in the figure with “+” indicating the presence of the
compound listed and “ – ” indicating the absence of the compound listed.
GAPDH is a housekeeping gene, which means that its transcription is unaffected by any of the treatments.
GM-CSF is a growth factor normally secreted in the bone marrow.
Below is a northern blot probed for gene M (top panel) and GAPDH (bottom panel).

7a. A northern blot measures (2 pt) (Circle the right answer/s).

A. The level of DNA

B. The level of mRNA
C. The level of protein
D. The level of phospholipids

7b. Estimate the relative amount of gene M in this Northern blot for lanes 1 to 4.
Use one the following numbers for each lane and not words: 0.1, 1, 0.05, 0.5
(a number cannot be used twice). (4 pts).

Lane 1: 1

Lane 2: 0.5

Lane 3: 0.1

Lane 4: 0.05
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7c. What is the reason to probe the northern for GAPDH in this experiment, when what we are really
interested in are the levels of gene M (3 pts)?

A. To see if GAPDH also changes by the treatment.

B. GAPDH serves as a loading control, so we know that we are loading equal amounts on each lane
and can then interpret the effects of the growth factor and cycloheximide
C. To determine if gene M affects the levels of GAPDH
D. To determine the size of the GAPDH transcription unit
E. Nothing; Probing for GAPDH is a waste of time and money

7d. Based on the data shown in the Northern, what conclusion can you draw about the transcriptional
response of gene M to GM-CSF? (3 pts)

A. GM-CSF has no effect on transcription

B. GM-CSF increases transcription of gene M by 50%
C. GM-CSF decreases transcription of gene M by 50%
D. GM-CSF decreases transcription of gene M dramatically, to less than 10% of its normal level.
E. Not possible to make a conclusion regarding gene M transcription from the blot.

7e. To make the right conclusion for 7D, which two lanes are you comparing? (3 pts)

Lanes 1 and 2

7f. Based on the data shown in the Northern, what conclusion can you draw about the effect of
cycloheximide on the level of transcription of gene M? (3 pts)

A. It has no effect on transcription

B. It increases transcription of gene M by 90%
C. It decreases transcription of gene M by 90%
D. It shuts transcription off.
E. Not possible to make a conclusion regarding gene M transcription from the blot.
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8. A segment of DNA is digested with restriction enzymes EcoRI and Hind III, alone or in combination,
yielding the fragments shown here in kb (8 pts).

EcoRI: 4.0, 3.0, 1.0

EcoRI + HindIII: 3.5, 3.0, 1.0, 0.5

Hind III: 4.5, 3.5

Draw a restriction map of this linear DNA segment, indicating where the EcoRI and HindIII sites are
relative to each other, and indicating the kb sizes in between each restriction site.

Answer can be either:

END - 3.0 kb - [EcoRI] – 0.5kb – [HindIII] – 3.5 kb - [EcoRI] – 1.0 kb – END

EcoRI: 3, 4, 1 kb

HIND III: 3.5 kb, 4.5 kb

HindIII + EcoRI: 3, 0.5, 3.5, 1

END - 1.0 kb - [EcoRI] – 3.0 kb – [EcoRI] – 0.5 kb – [Hind III] – 3.5 kb – END

EcoRI: 1, 3, 4

HindIII: 3.5, 4.5

EcoRI + Hind III: 1, 3, 0.5, 3.5

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9. You are screening three new artificial sweeteners for potential mutagenicity using the Ames test. Two
bacterial strains with either a frameshift or a transition mutation were used for this test. The test produced
the following number of revertant colonies on the specified media (9 pts).

Strain 1:

Artificial Sweetener Transition mutant Transition mutant + Transition mutant +

control (no chemical) chemical chemical + liver
enzymes

Sweetener #1 18 230 17

Sweetener #2 23 18 23

Sweetener #3 19 305 300

Strain 2:

Artificial Sweetener Frameshift mutant Frameshift mutant + Frameshift mutant +

control (no chemical) chemical chemical + liver
enzymes

Sweetener #1 3 5 6

Sweetener #2 8 7 95

Sweetener #3 7 9 6

9a. What type of mutations, if any, does each sweetener produce:

Sweetener #1: transitions

Sweetener #2: frameshift

Sweetener #3: transitions

9b. Which sweeteners, if any, are mutagenic to bacteria? #1 and #3

9c. Which sweeteners if any, are mutagenic to bacteria only when treated with liver enzymes? #2
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#2

10. The restriction enzymes XhoI and Sal I cut the specific sequences as shown below:

XhoI 5’-C TCGAG – 3’

3’-GAGCT C – 5’

Sal I 5’-G TCGAC– 3’

3’-CAGCT G – 5’

10a. Does XhoI leave a 5’ overhang, a 3’ overhang, or is it a blunt end cutter (circle the correct
answer). (2 pts)

A. 5’overhang

B. 3’overhang

C. Blunt end

10b. Can the sticky ends created by XhoI and SalI be ligated together? (2 pt)

YES or NO

Answer one of the two below, depending upon whether you answered yes or no to the above.

10c. If yes, can the ligated sequences be cut by XhoI or by Sal I (2 pts)

A) XhoI
B) Sal I
C) Both Xho I and Sal I
D) Neither XhoI nor Sal I

If no, if you re-ligate an XhoI overhang to itself, can that site now be cut by SalI? (2 pts)

YES or NO

NO POINTS if this because 10b is wrong!!!

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11. Aqua-Advantage Salmon have been genetically engineered to grow faster and larger than wild-
salmon. In order to prevent outcrossing of the Aqua-Advantage Salmon with wild-salmon, all Aqua-
Advantage Salmon are female and triploid. (8 pts)

11a. How does this prevent genetic mixing of the wild and Aqua-Advantage Salmon?

Triploid individuals (like the seedless watermelons) are generally sterile.

11b. What other effects (discussed in lecture) might triploidy have on the phenotype of the fish
beyond genetic isolation from the wild salmon?

As we discussed in lecture, increases in ploidy generally correlate with increases in size. Hence these fish
would likely be larger than their diploid counterparts.

12. Species can be combined by performing interspecies crosses or by creating somatic hybrids. What are
the major genetic differences between the lines created using these two techniques (I don’t want to know
the differences between the techniques; I only want to know the major differences between the resulting
plants – i.e. the genetic differences between the F1s and the regenerated somatic hybrids). (6 pt)

F1 hybrids of interspecies crosses are the product of fusion of two haploid gametes. In contrast, the
somatic hybrids are the product of fusion of two diploid somatic cells. Therefore, the lines created by
somatic hybridization would have higher ploidy than the traditional F1 hybrids. In addition, somatic
hybrids have two complete sets of chromosomes from both of the two donor species. This means that the
original lines generated by somatic hybridization are more likely to be fertile than those F1s generated by
traditional interspecies crosses where homolog pairing during meiosis I is disrupted.
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13. Floral patterning in Arabidopsis thaliana is controlled by sets of overlapping genes that cooperatively
specify organ identity. You’ll recall from your reading that the activity of AP2 is controlled by
miRNA172.

What floral phenotype would you expect if miRNA172 were expressed in all whorls of the flower? To
answer this question, please fill in the table below (you may use the blank space bellow the table in
formulating your answer but only what is written in the table will be graded).

(8pts)

Proteins Present Whorl Identity

Whorl 1 SEPs AG carpel

Whorl 2 SEPs AG AP3 PI stamen

Whorl 3 SEPs AG AP3 PI stamen

Whorl 4 SEPs AG carpel

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14. Monoecious plants like Arabidopsis thaliana make perfect flowers that contain both male and female
organs in the same flower. In contrast, dioecious plants have male and female plants. In a hypothetical
dioecious plant, you find that the flowers contain sepals, petals and then two whorls of stamens.

Assuming that floral patterning in this plant is controlled by the same genes as Arabidopsis thaliana fill in
the gene expression profile for A, B and C class proteins in this dioecious male plant (you may use the
blank space bellow the table in formulating your answer but only what is written in the table will be
graded).

(8 pts)

Proteins Present

Whorl 1 AP1 AP2 (A Class)

Whorl 2 AP1 AP2 (A Class) and AP3 PI (B Class)

Whorl 3 AP3 PI (B Class) AG (C Class)

Whorl 4 AP3 PI (B Class) AG (C Class)

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15. P-elements are type 2 DNA transposons commonly found in flies. A normal P-element is shown
below. The central region of the P-element contains 3 introns (500 bp in total) and 4 exons, which allow
for the expression of transposase.

2.9 Kb

Exon 1 Exon 2 Exon 3 Exon 4

Intron 1 Intron 2 Intron 3

30 bp
30 bp inverted
Inverted repeat
repeat

a) What is the predicted size (in base pairs) of the mRNA made by this P-element?

2.9 – 500 – 60 = 2,340 bp

b) If you added a 1 kb insertion into intron 1, what would be the size of the P-element after transposition?

2,340 bp + 1000 = 3,340

16. For 2 extra credit points: Where is the 2017 final exam for BIOL221 being held?

; ) Chem 102!
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