Name:

_______________________________________________________

Number ______________
Page # Possible Actual
points
points

3 8

4 8

5 8

6 10

7 10
BIOLOGY 221
8 4
EXAM 3 FOR 2015C
9 6
December 8, 2015
10 11

11 12

12 6

13 10

14 7

Total:

1
Name: _______________________________________________________

Penn ID #:______________________________

Directions:

• There are 17 pages to this exam. This includes the genetic code on page 15 of the exam 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 below, I pledge my honor that I have upheld the Code of Academic Integrity of the
University of Pennsylvania in completing this examination.

2
Name: _______________________________________________________

Multiple choice (2 pts each). There may be multiple answers. Choose all that apply.

1. In the diagram below, each of the five lines indicates the extent of a Drosophila deletion. A through G
represent adjacent chromosomal regions (for example, in line 3 regions D and E are deleted).
Regions A B C D E F G
1________
2_______________
3____________
4___________
5___________

When a radioactive DNA fragment corresponding to a Drosophila gene of interest was incubated with
chromosomes carrying each of the five deletions, it bound only to chromosomes carrying deletion 1 or
deletion 5. Based on this information, the gene of interest is located in region:
A) A or B.
B) C.
C) C or D.
D) D.
E) E, F, or G.

2. One concern of transgenic plants is the spread of round-up (glyphosate) resistance to native plants through
inter-species crosses (mating). One way to avoid or reduce this problem is to:
A) Use promoters to express the protein that confers glyphosate resistance only in pollen.
B) Use techniques that render transgenic plants sterile; e.g. terminator technology.
C) Use promoters to express the protein that confers glyphosate resistance everywhere in the plant
with the exception of the pollen.
D) Insert an intron into the gene conferring glyphosate resistance.
E) None of the above

3. Sanger DNA sequencing determines the nucleotide sequence because:

A) dideoxy nucleotides are incorporated into a growing DNA strand. (no penalty for A)
B) dideoxy nucleotides terminate the growing DNA strand.
C) fluorescently labeled dNTP nucleotides are incorporated into the growing DNA strand.
D) fluorescently labeled dNTP nucleotides are released from the growing DNA strand.
E) None of the answer options are correct.

4. Expression of a dsRNA molecule that targets actin in a cell will be associated with which of the following
effects:
A) upregulation of the actin mRNA
B) dicing of the actin mRNA by the enzyme Dicer
C) dicing of the dsRNA by the enzyme Dicer
D) decreased translation of the actin mRNA
E) piRNA production
F) miRNA production.

3
Name: _______________________________________________________

5. Plasmodium and Toxoplasma, two closely related protozoan eukaryotes, share genes of the same sequence
and structure. These genes are called:
A) Paralogs
B) Orthologs
C) Homologs
D) All of the above
E) None of the able

6. Many proteins used in medicine (human and veterinary) are produced using recombinant DNA technology.
For example Erythropoietin (EPO) is a glycoprotein hormone that promotes differentiation of erythroid
progenitor cells in bone marrow. It is administered to patients for treatment of anemia associated with chronic
renal failure. Functional EPO contains 40% carbohydrate (added in the ER), which plays an important role in
its activity. Based upon this information, in what system/s could functional EPO be produced?
A) Bacteria
B) Viruses
C) Yeast
D) Mammalian Cells
E) None of the above

7. The CAPRICE (CPC) transcription factor functions in both root hair and trichome development in
Arabidopsis thaliana. Below choose all statements that are correct regarding the role of CPC in these two
processes.
A) In root hair formation, CPC acts as an inhibitor of the active GL3 complex; whereas in trichome
formation it acts as an activator.
B) In trichome formation, CPC acts as an inhibitor of the active GL3 complex; whereas in root hair
formation it acts as an activator.
C) In both trichome and root hair formation CPC acts as an activator of the GL3 complex.
D) In both trichome and root hair formation CPC acts as a repressor of the GL3 complex.
E) None of the above are correct.

8. A recessive form of the Sleepiness gene (s) is caused by a single nucleotide polymorphism of the dominant
(S) gene. Two EcoR1 restriction sites flank the Sleepiness gene. The Sleepiness gene is 6 kb. Recessive
homozygotes fall asleep in class while heterozygotes and dominant homozygotes do not. The single
nucleotide change in the s allele also causes an additional EcoR1 restriction enzyme site at the SNP therefore
altering the restriction enzyme pattern. Which lane shows the heterozygote in EcoR1 digested DNA? Circle
the letter.

4
Name: _______________________________________________________

9. Muller discovered that X-rays can mutagenize chromosomes in crosses whereby he mutagenized specific
Drosophila, and then scored the effects in the F2 progeny. Which statements below describe his
experiments?
A) He mutagenized male flies and then scored their fertility after crossing to female flies.
B) He mutagenized male flies and then scored their viability after crossing to attached-X female flies.
C) He mutagenized females flies, and then scored the viability of male progeny.
D) He mutagenized males, crossed them to females with a Bar-eyed chromosome, then scored
females with Bar-eyes in the next generation.
E) He mutagenized males and scored those progeny with Bar eyes.
F) None of the above describes his experiments.

10. Which of the following is/are true of reverse transcriptase?

A) it is required for the movement of DNA transposons.
B) it catalyzes the synthesis of DNA from RNA.
C) it is required for the genomic movement of retrotransposons.
D) It is expressed in germ cells, but not somatic cells of the body.
E) The Drosophila P-element encodes reverse transcriptase.

11. Which of the following would be considered a genetically engineered organism?

A) A mint plant produced by the process of somatic hybridization.
B) A wheat plant expressing genomically integrated recombinant DNA in from rice.
C) Grapefruit plants selected for increased furocoumarin production following induced
mutagenesis.
D) Hybrid poinsettia expressing an extra-chromosomal piece of viral DNA that induces white
striping of the leaves.
E) Cows produced by surrogate mothers via embryo transfer.

12. Which of the following is/are not a verified mechanisms of asymmetric cell division?
A) Asymmetric inheritance of cytoplasmic components between daughter cells.
B) Asymmetric positioning of the daughter cells in the stem cell niche.
C) Asymmetric inheritance of histones (old versus new) during cell division.
D) Asymmetric inheritance of old versus new DNA.
E) Asymmetric inheritance of plasma membrane localized fate determinants.

5
Name: _______________________________________________________

13. Shown below is a list of statements (A–K) and types of mutations (1–6). On the blank line following each
mutation, write the letter(s) of all statements that apply to that type of mutation. Note that each statement may
be used more than once and each type of mutation may have more than one correct statement.
(6pts total (1 pt each A-F; 0 points if an answer is missing letter or has a wrong letter))

A) a mutation that changes UUA to UUG

B) a mutation that gives methionine instead of leucine
C) created by the addition of a nucleotide to a coding region
D) a stop codon is read as an amino acid
E) a chemically similar amino acid is replaced by the mutation
F) a mutation that changes CCU to ACU
G) a nucleotide in a coding region gives this type of mutation
H) mutation does not alter the peptide
I) a mutation changing UAU to UAG
J) premature termination codon is responsible for this mutation
K) a chemically different amino acid is replaced by the mutation
1) missense mutation (g) b,e,f,k

2) silent mutation (g) a,h

3) frameshift mutation c,g

4) nonsense mutation (g) I,j,

5) synonymous mutation (g) a,h

6) nonsense suppressor mutation d

14. Consider the following mutations, and for each explain whether you expect it to be: potentially promoting
cancer (yes or no) and indicate whether you expect each mutation to be dominant or recessive.(4 pts)

a) a mutation that destroys the active site of an enzyme necessary to promote cell cycle

Potentially cancer promoting (yes or no)?

Dominant or recessive?

b) a point mutation that renders constitutively active one of the signaling proteins in the Ras pathway

Potentially cancer promoting (yes or no)?

Dominant or recessive?

c) a null mutation in a gene encoding an apoptotic (apoptosis-promoting) protein

Potentially cancer promoting (yes or no)?

Dominant or recessive?

d) Of the above a, b and c, which describe an oncogene and which a tumor suppressor gene?
Oncogene: b
Tumor suppressor gene: c

6
Name: _______________________________________________________

15. You wish to amplify by PCR a portion of the human myc gene. The 10 bp of sequence of the ends of the
DNA are the following:

5’-GCTCAATCGC-(150bp)-CGTTAGCTAG-3’

Which primer pairs would work for amplifying this gene? (2 pts)

A) 5’-GCTCAATCGC and 5’-CGTTAGCTAG

B) 5’-GCTCAATCGC and 5’-CTAGCTAACG
C) 5’-GCTCAATCGC and 5’-CGCTAACTCG
D) 5’-GCAATCGATC and 5’-CGCATTGAGC

b) When you amplify this piece of DNA with the primers you selected, what size in DNA bp of PCR product
or products do you expect to get? Indicate the bp length(s), and why you expect that or those size products in
1-2 sentences. Do you expect this/these products to be single-stranded or double-stranded products? (4 pts)

I expect to get a PCR product that is the entire length of the DNA sequence above, plus the size of the primers
– so 150 bp plus 10 for each primer so 170 bp.

I expect this to be a double-stranded DNA product because both DNA strands will be amplified in the PCR
reaction.

16. A plasmid vector has a gene for erythromycin resistance (EryR) and a gene for ampicillin resistance
(AmpR). You cut the Amp gene with the restriction enzyme EcoRI, and add your donor DNA treated with the
same enzyme, and ligate the pieces together, then transform E coli.

a) If you plate your transformed E coli on agar plates with ampicillin, will bacterial colonies bearing plasmid
DNA grow? And if so, what do you expect the DNA in these colonies to be and why? If you do not expect
bacterial colonies to grow, then why not (2 pts)?

Yes, colonies will grow- these will be colonies with the plasmid vector that has re-ligated to itself and does
not contain donor DNA.

b) If you plate your transformed E coli on agar plates with erythromycin, will bacterial colonies bearing
plasmid DNA grow? And if so, what do you expect the DNA in these colonies to be and why? If you do not
expect bacterial colonies to grow, then explain why not (2 pts)?

Yes, colonies will grow- these will be colonies with the plasmid vector containing the donor DNA, as well as
colonies with the plasmid vector that has re-ligated back to itself.

7
Name: _______________________________________________________

c) If bacterial colonies grow, and you select and grow up ten colonies from the agar plate with ampicillin from
plate a (part a), and ten colonies from the agar plate with erythromycin from part b, do you expect the ten
random different colonies from each plate to contain plasmid DNA vectors that have the same restriction
maps or different restriction maps and why? (if you think that colonies will not grow on a or b, then state that)
(4pts).

Plate A (from part a) – same or different restriction maps? Why (1-2 sentences)?

Same because the same plasmid vector lacking any insert is present in all colonies.

Plate B (from part b) – same or different restriction maps? Why (1-2 sentences)?

Different because these colonies can bear the plasmid vector with no insert or can bear the plasmid vector
with a donor DNA insert. We do not expect the same donor DNA piece to be present in the plasmid of two
different bacterial colonies.

8
Name: _______________________________________________________

17. The diagram below shows results of Southern, Northern, and Western blot analyses for a particular gene
and its protein product. For each blot, the left lane shows results for materials extracted from a wild-type
organism, and the right lane shows results for materials extracted from a mutant organism. The probe for the
Southern and Northern blots is from the first exon of the gene; the probe for the Western blot is based on an
antibody to the gene product. (Assume that the sample origin in all blots is at the top.)

wt mutant wt mutant wt mutant

Southern Northern Western

What is the most likely nature of the mutation?

Circle one of the following (2pts) and explain your answer in no more than three sentences.

A) nonsense mutation in an exon

B) missense mutation in an exon
C) splice junction mutation
D) promoter mutation

Explanation in no more than three sentences (4pts):

A splice junction mutation that eliminates a splice junction and results in a larger transcript – and in this
case a larger protein product, indicated by the blots. The gene itself appears unaffected (Southern), while the
transcript (Northern) and protein product (western) are larger than normal.

9
Name: _______________________________________________________

18. In class, the situation was mentioned of an individual bearing a Robertsonian translocation of T(21,14),
and the potential outcomes when that person had children with a normal individual. The individual bearing
the Robertsonian translocation is a carrier for familial Down’s syndrome.

a) If two individuals that are carriers for this Robertsonian translocation married and had children, fill in the
table below using the symbols noted for the possible outcomes of offspring produced by the indicated gametic
chromosomal complements (8 pts).

N, for normal child

X, for inviable child
D, for child with Down’s syndrome
C, for those phenotypically normal individuals who are carriers for familial Down’s syndrome.

Mother’s meiotic products

21,14 14 21, T(21,14)T(21,14)

21, 14 N X D C

14 X X C X

21, T(21,14)D C X D

T(21,14) C X D C

b) Based on the above table, what are the chances that the couple will have a child with Down’s syndrome?
Explain your answer (3 pts).

There are 10 possible viable gametes. Of these 4 could be Down’s syndrome, so there is a chance of 2/5 or
40% that the couple will have a child with Down’s syndrome

10
Name: _______________________________________________________

19. In 1-3 sentences (maximum) define and state the purpose of each of the following techniques:
(6 pts)

a) Induced mutagenesis: Exposure of seeds to a mutagen source (often ionizing radiation) to induce mutations
that result in phenotypes that can be selected in field populations for desirable traits. Essentially induced
mutagenesis increases genetic diversity in the population and the possibility of beneficial new alleles.

b) Somatic Hybridization: The fusion of protoplasts in culture. This allows non-interbreeding species to be
hybridized potentially uniting several beneficial traits into one organism.

c) Embryo Rescue: The culture of nonviable seeds to propagate “Seedless” varieties.

20. In class we discussed two models for the generation of pattern: the Turing Reaction Diffusion model
(which largely applies to trichome and root hair spacing in plants) and the Wolpert Positional Information
model (the “French Flag” model, which applies to early patterning in Drosophila – discussed in the assigned
readings). In 2-3 sentences indicate the essential aspects of each of these two models. (6 pts)

Turing: Stochastic fluctuations in gene expression (asymmetries) are reinforced by autoregulation. An active
transcriptional complex regulates both the expression of an activator module (positive reinforcement) that
acts within the cells in which it is expresses and an inhibitory module that moves out from the source and
inhibits the establishment of transcriptional maxima in neighboring cells.

Wolpert: A point source morphogen travels some distance. Distance from the source is inversely related to
concentration. Downstream components have concentration dependent responses to the morphogen. This can
result in many different concentration domains.

11
Name: _______________________________________________________

21. Suppose that you are studying bristle development in flies. You suspect that you have found a gene that
acts as a master regulator of bristle initiation, what 3 experiments would you do to test your hypothesis (i.e.
how would you show necessity and sufficiency)? Be sure to indicate what results you would expect if your
hypothesis (master regulator) is correct. Phrase you answer in the form of: I would … and I would expect to
find … (6 pts)

Expt1: I would knock out the gene and if the hypothesis is correct, I would expect to see a loss of bristle
production.

Expt 2: I would express the gene in cells in which it is not normally expressed. If the hypothesis is correct, I
would expect to see an ectopic formation of bristles.

Expt3: I would examine the domain of gene expression. If the hypothesis is correct I would expect to see
protein produced at the time and in the place that bristles are developing.

12
Name: _______________________________________________________

22. During flower development, overlapping expression of 4 classes (A, B, C and E) of genes results in the
production of sepals, petals, stamen and carpels. Diagram the essential aspects of this model below. (3 pts)

miRNA172

AP3, PI
AP1, AP2 AG
Sep Genes

23. Suppose you used the APETALA1 (AP1) promoter to drive the expression of the PISTILATA (PI) and
APETALA3 (AP3) (B-class) coding sequences in an otherwise wild-type plant.

a) What affect would you expect this to have on the expression of the other floral homeotic genes (1 pt) (1
sentence) None

b) What affect would this to have on the identity of each of the whorls (2 pts)?

whorl 1_____petal________ whorl 3____stamen__________

whorl 2____ petal ______________ whorl 4_____carpel________

24. If you used the APETALA2 (AP2) promoter to drive the expression of the PISTILATA (PI) and
APETALA3 (AP3) coding sequences in an otherwise wild-type plant what affect would you expect this to
have on the development of the flower (4 pts)?

whorl 1______ petal______________ whorl 3________ stamen __________

whorl 2______ petal_____________ whorl 4_______ stamen __________

13
Name: _______________________________________________________

25. Five human genomic DNA clones present in BAC vectors were tested by hybridization for the presence
of size sequence-tagged sites designated STS1 through STS6. The results are given in the following table. “+”
indicates the STS tag is present in the clone, and “-“ indicates that the STS tag is not present in the clone.

STS1 STS2 STS3 STS4 STS5 STS6

Clone A + - + + - -

Clone B + - - - + -

Clone C - - + + - +

Clone D - + - - + -

Clone E - - + - - +

a) What is the order of the STS sites on the chromosome? (2 pts)

2-5-1-4-3-6

b) Draw a contig map of the BAC clones. Use a line for each clone, indicate the clone letter that the line
represents and the position and number of the STS sites on the clone, showing how the clones overlap to
make a single contig (5 pts).

14
Name: _______________________________________________________

15
Name: _______________________________________________________

16
Name: _______________________________________________________

17