Name:_________________________________

   

BIOLOGY 221

FINAL FOR 2012

Page # Possible Actual
points points
3 6
4 6
5 9
6 7
7 6
8 12
9 5
10 9
11 8
12 12
13 10
14 10

Total:

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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 120 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.

Signature:

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Multiple choice – may be more than one correct answer.

1. The Figure below shows the expression pattern (shading) of a hypothetical gene, Anterior
Domain Patterning-1 (ADP-1) in a 4 cell staged C. elegans embryo (3 pt).

Based upon the figure above, circle the statements below that are consistent with a model for the
regulation of ADP-1

a) A transcription factor expressed specifically in the ABa and ABp cells promotes the
transcription of ADP-1 only in these cells.

b) An RNA binding complex similar to that formed by Nanos and Pumilo binds to the
ADP-1 transcript specifically in the EMS and P2 cells and inhibits translation.

c) A microRNA expressed specifically in the EMS and P2 cells inhibits translation of

ADP-1.

d) A transcription factor expressed specifically in the EMS and P2 cells inhibits

transcription of ADP-1.

e) None of the above.

2. Consider the pedigree below for a rare human muscle disease and circle all possible
explanations that are consistent with the pattern of inheritance shown in this pedigree (3 pt)?

a) Y-linked dominant inheritance

b) X-linked recessive inheritance
c) X-linked dominant inheritance
d) Mitochandrial Inheritance
e) None of the above

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3. The father of Mr. Spock, first officer of the starship Enterprise, came from planet Vulcan;
Spock's mother came from Earth. A Vulcan has pointed ears (determined by allele P), adrenals
absent (determined by A), and a right-sided heart (determined by R). All these alleles are
dominant to normal Earth alleles. The three loci are autosomal, and they are linked as shown in
this linkage map:

If Mr. Spock marries an Earth woman and there is no (genetic) interference, what percentage of
their children will have Earth phenotypes for all three characters (3 pt)?

a) 3%
b) 15%
c) 20%
d) 34%
e) 68%

4. The Following diagram below of Anaphase 1 (3 pt):

a) Best explains Mendels observation of Independent assortment.

b) Best explains Mendels law of segregation.
c) Shows the separation of pairs of homologous chromosomes.
d) Demonstrates the separation of sister chromatids
e) None of the above

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5. Circle all of the true statements below (3 pt):

a) Autosomal trisomies are well tolerated in humans due to the ability of cells to
inactivate the extra autosome.

b) X-inactivation in female Drosophila often leads to a mosaic phenotype.

c) The abnormal phenotypes seen in females with Turner syndrome are absent in
wildtype males due to the presence of genes in the pseudoautosomal region of the Y-
chromosome.

d) Staining for Barr bodies can be used to unequivocally determine sex.

e) In both wildtype humans and Drosophila melanogaster the males are the heterogametic
sex.

6. If a mutation that inactivated telomerase occurred in a cell (telomerase activity in the cell =
zero), what do you expect the outcome to be (3 pt)?

a) The position of the centromere would shift at each replication cycle, eventually leading
to mutations in the genetic information and cell death.

b) The number of tandem repeats would increase with each replication cycle, eventually
leading to a large unstable chromosome and cell death.

c) The telomeres would shorten at each replication cycle, eventually leading to growth
arrest, or loss of essential genetic information and cell death.

d) DNA primase would be unable to bind to the 5´ end of the template strand,
eventually causing a reduction in chromosome size and cell death.

7. You are studying an E. coli gene that specifies a protein. A part of its sequence is –Ala–Pro–
Trp–Ser–Glu–Lys–Cys–His–. You recover a mutant for this gene that shows no enzymatic
activity. By isolating the mutant enzyme product, you find the following sequence: –Ala–Pro–.

What is the most likely molecular basis for this mutation (3 pt)?

a) A nucleotide substitution converting UGG to UGA

b) A nucleotide substitution converting UGG to UAA
c) A nucleotide substitution converting UGG to UGC
d) A nucleotide substitution converting UGG to AUG

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8. The cDNA clone for the human gene encoding tyrosinase was radioactively labeled and used
in a Southern analysis of EcoR1-digested genomic DNA of wild-type mice. Three mouse
fragments were found to be radioactive (were bound by the probe). When albino mice were used
in this Southern analysis, no genomic fragments bound to the probe. Explain these results in
relation to the nature of the wild-type and mutant mouse alleles (3 pt).

a) The albino mice are missing the tyrosinase gene.

b) The albino mice are missing EcoR1 sites so the genomic DNA was not digested.

c) If the human tyrosinase gene was inserted into albino mice, the albino mice would
produce (human) tyrosinase.

d) Wild-type mice contain two EcoR1 sites within its tyrosinase gene, but albino mice are
lacking these two EcoR1 sites. This explains the three fragments seen on the Southern
blot of wild-type mice.

e) None of the above

9. Can you induce nonsense mutations (UAG, UAA, and UGA) by treating wild-type strains with
mutagens that cause only A·T → G·C transitions in DNA (2 pt)?

a) Yes
b) No

10. You are studying proteins having roles in translation in the mouse. By analyzing all the
predicted proteins of the mouse genome, you identify a set of mouse genes that encode proteins
with sequences similar to those of known eukaryotic translation-initiation factors. You are
interested in determining the phenotypes associated with loss-of-function mutations of these
genes. Should you use forward- or reverse-genetics approaches to identify these mutations (2 pt)?

a) Forward
b) Reverse

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11. You have indentified a viral vector that is able to randomly insert single copies of DNA into
the genome of tumorigenic cells. A graduate student in your lab has engineered this virus to
contain single wildtype copies of either a tumor suppressor gene or a proto-oncogene that is
mutated in some tumors studied by the lab. The graduate student plans on expressing the
appropriate viral vector (i.e. one with a wild-type copy of the gene mutated in the tumor cell line)
into the tumor cell clones.

a) What effect would expression of this viral vector containing a wild-type copy of
Retinoblastoma (Rb) have on the tumorigenic phenotype of cells that are homozygous for a
mutation in Rb (3 pt).

b) What effect would expression a wild-type copy of Ras have on the tumorigenic phenotype of
cells expressing oncogenic Ras (3 pt)?

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12. A cross is made between a completely wild-type (met+ thi+ and pur+) Hfr E. coli strain and
an F- strain that is auxotrophic for methionine, thiamine and purine (met-, thi-, pur- ), and has a
plasmid the confers resistant to kanamycin (KanR), an antibiotic that kills wild-type E.coli. From
interrupted mating experiments, you know that the met+ marker is the furthest from the F
insertion site.

a) If you wanted to use this cross to calculate the distances between the met pur and thi
genes on what selective media would you first plate all of the recombinants and why (4
pt)?

From a series of replicate plates you get the following recombinants.

280 met+ thi+ pur+

0 met+ thi+ pur-
6 met+ thi- pur+
52 met+ thi- pur-

b) Draw the order of the genes relative to the F plasmid insertion (4 pt).

c) Indicate on your map above the distances between each of these genes (4 pt)

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13. As a breeder of petunias, you are always interested in finding new colors of flowers. In a
recent buying spree you obtained pure-breeding varieties with white (w), fuchsia (f), coral (c),
plum (p), amethyst (m) eggplant (e), acai (a; dark puple nearly black) or violet (v) flowers. In
order to determine how flower color is controlled in petunia you start by crossing each of the
individual pure-breeding lines (P1) to the acai line, since it has the darkest flowers.

As shown in the Table 1 below, all of the F1 plants have acai colored flowers. In the F2 you find
a 3:1 ratio of acai colored flowers to the other parental (P1) phenotype.

Table white fuchsia coral plum amethyst eggplant violet P1

1 (w) (f) (c) (p) (m) (e) (v)
acai acai acai acai acai acai acai acai F1
selfed 3a:1w 3a:1f 3a:1c 3a:1p 3a:1m 3a:1e 3a:1v F2

a) What can you conclude from these data (3 pt)?

You then set up pair-wise crosses between all of the other individuals and get the following F1
results.

Table 2 white fuchsia coral plum amethyst eggplant violet

white white acai coral acai acai acai acai
fuchsia acai fuchsia acai acai amethyst acai acai
coral coral acai coral acai acai acai acai
plum acai acai acai plum acai plum plum
amethyst acai amethyst acai acai amethyst acai acai
eggplant acai acai acai plum acai eggplant eggplant
violet acai acai acai plum acai eggplant violet

b) Based upon these results how many different genes are represented by these 7 lines (2
pt)?

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Table 2 white fuchsia coral plum amethyst eggplant violet

white white acai coral acai acai acai acai
fuchsia acai fuchsia acai acai amethyst acai acai
coral coral acai acai acai acai acai acai
plum acai acai acai plum acai plum plum
amethyst acai amethyst acai acai amethyst acai acai
eggplant acai acai acai plum acai eggplant eggplant
violet acai acai acai plum acai eggplant violet

Assuming that flower color is controlled by a linear, biosynthetic pathway (as shown below):

c) Indicate on this pathway where each of the genes and their corresponding alleles are
acting in this pathway (3 pt).

d) Based on the above pathway, what would be the phenotype of an amethyst;coral

double mutant (2 pt)?

e) Based upon the pathway above and the phenotype of the F1 individuals shown in
Table 2, rank all of the alleles of the VIOLET gene in order of most to least functional (4
pt).

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14. In a mutant strain iso381 of E coli, a leucine tRNA that recognizes codon 5’-CUG-3’ in
normal cells has been altered so that it now recognizes the codon 5’-GUG-3’. A missence
mutation, which affects amino acid 10 of a particular protein is suppressed in mutant iso381 cells.

a) what is anti-codon of the affected leu tRNA, and what specific base pair mutational
event (transition or transversion, and of what specific base pair) has occurred in mutant
iso381 cells? In 1-2 sentences explain your answer. (2pts)

b) What amino acid would normally be present at position 10 of the protein (without the
missence mutation) and why? (2 pt)

c) What amino acid would be put in at position 10 if the missence mutation is not
suppressed (so in normal cells)? Explain your answer in 1-2 sentences. (2 pt)

d) What amino acid is inserted into position 10 if the missence mutation is suppressed (that
is, in mutant iso381 cells) and why? (2pts)

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15. Based upon the gel below:

a.) Identify the synthesized strand and label the 5’ and 3’ ends (2 pt)

b.) Identify the template strand and label the 5’ and 3’ ends (2 pt)

c.) The double stranded helix (2 pt)

d.) Using the double-stranded helix above, define all 6 reading frames, and note which
encode complete Open Reading Frames (6 pts).

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16. A vector contains a β-Galactosidase promoter followed by a Poly-linker containing multiple

Restriction Enzyme sites.
The poly-linker contains these Restriction Sites: B= BglI E= EcoRI H=HindIII N=NotI

You also have a cDNA clone encoding the red protein in a different vector, and you want to
subclone the red cDNA into pUC18 for expression.

A) To subclone the red cDNA into pUC18 for expression, which restriction enzyme or enzymes
would you use and why? (4 pts)

B) Draw the map of the red cDNA subcloned into pUC18 vector, noting all restriction sites that
are present in the new clone that were present in either former clone. Include all features like the
B-gal promoter, its direction, the red cDNA and its direction. (6 pts)

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17. You are studying the regulation of a eukaryotic gene involved in memory called Absent
Minded. Animals with mutants in this gene have severe short-term memory loss.
You want to understand what controls the levels of Absent Minded gene expression to see if
you can increase its expression in normal animals, and therefore increase short-term memory.
Using mutational mapping of the promoter, you identify two 10 bp regions of the promoter
that when mutated strongly reduce expression of the Absent Minded promoter in vivo. You
purify the proteins that bind these promoter elements and call the proteins ABR1 and ABR2.

To be sure that these proteins are involved in activation of the Absent Minded promoter,
you fuse the Absent Minded promoter to the LacZ gene and test the levels of expression in
strains that lack the ABR1 and ABR2 genes (ΔABR1 and ΔABR2). You get the following
results:

Condition Strain in vivo Transcription units

Condition1: Wild Type 2000 Units
Condition2: ΔABR1 50 Units
Condition3: ΔABR2 200 Units
Condition4: ΔABR1+ΔABR2 50 Units

A) Is only ABR1, only ABR2, or are both required to activate transcription of the Absent
Minded promoter to wild type levels in vivo, and why? (2 pts)

B) What do you conclude about the activity of ABR1 from the data that shows that condition 2
gives same level of transcription as condition 4, and why? (4 pts)

C) What can you conclude about the activity of ABR1 from the data that shows that condition 3
gives more activity than condition 2 and why? (4 pts)

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