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BIOL 221
Final Exam
12/20/13
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BIOL 221 Final Exam

1. During your semester in Costa Rica you discovered 3 new eye-color forms in Drosophila
melanogaster. After returning to Penn you established pure breeding stocks for each and
have provisionally designated these eye-color mutations as: evergreen (evr), grinch (grn),
and holly (hol). All eye-color phenotypes map to the X-chromosome.

a. What crosses would you perform to determine whether any of these mutations represent
allelic forms of the same gene? Specify the sex of each fly in each cross and the sex of the
progeny flies that would be examined for their phenotype. (3 points)

• Perform all pair-wise crosses between stocks

• Sex of parental generation is not important
• Examine female progeny - these are heterozygous for X-chromosomes

b. What results would you expect if all of the phenotypes were due to alterations in different
genes? (3 points)

All F1 female progeny would show wild-type eye color.

c. What results from the above crosses would you expect if evergreen (evr) and grinch (grn)
mutations were allelic? (3 points)

F1 females from the evr x grn cross would NOT exhibit a wild-type phenotype.

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BIOL 221 Final Exam

2. In marsupials like the tammar wallaby (a small kangaroo), X-chromosome inactivation

selectively inactivates the paternal X chromosome. As in humans, female kangaroos are XX
and males are XY.

a. Predict the coat color phenotypes of the progeny (separate by sex please) of a cross
between a female homozygous for a recessive mutant allele of an X-linked coat color
gene and a male hemizygous for the wild-type allele of this gene. (3 points)

female progeny: all mutant coat color

male progeny: all mutant coat color

b. Predict the coat color phenotypes of the progeny (separate by sex please) of a cross
between a female homozygous for a wild-type allele of an X-linked coat color gene and a
male hemizygous for a recessive mutant allele of this gene. (3 points)

female progeny: all wild-type coat color

male progeny: all wild-type coat color

c. How is this mechanism different from X activation in cats? What phenotypic

consequences do these different X inactivation mechanisms have for the coat color
phenotype? (3 points)

You would NOT expect coat color patching. In female cats, X-chromosome inactivation
is random during early development and this inactivation is propagated to the cell’s
descendants. In kangaroos, the male X-chromosome is always inactivated during
spermatogenesis. In this way, female wallabies contain cells with a single active and
maternally derived X-chromosome.

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BIOL 221 Final Exam

3. A 5-generation pedigree is shown in the Figure below. Dark symbols represent individuals
affected with a very rare disease. Light symbols represent unaffected individuals. Please
note that this is a "simplified" pedigree in which unrelated and unaffected mating partners
(male or female) are not shown. For example, the male partners for individuals II-1 & II-3
and the female partner for individual II-2 are absent from the diagram. Also note that the
phenotypes of fifth generation individuals are not displayed - see (c) below.

V
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

a. What type of inheritance underlies the pedigree? (3 points)

X-linked dominant

b. Support your hypothesis, in part, a by briefly describing the features of this pedigree that
are unique to this mode of inheritance. (3 points)

Affected fathers pass the trait on to all of their daughters and none of their sons.

(Affected mothers pass the trait on to 50% of their children, regardless of sex, but this is
true for autosomal dominant inheritance also.)

c. Calculate the probability that the following individual (not shown on the pedigree) will
inherit the disease: the daughter of V-2 and V-15 (3 points)

Answer: 5/8

Explanation (see next page):

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BIOL 221 Final Exam

P(A) = P(V-2 has the allele and V-15 does not) = ½ * ½ = ¼

P(B) = P(affected daughter | V-2 has the allele and V-15 does not) = ½

P(C) = P(V-15 has the allele and V-2 does not) = ½ * ½ = ¼

P(D) = P(affected daughter | V-15 has the allele and V-2 does not) = 1

P(E) = P(both V-15 and V-2 have the allele) = ¼

P(F) = P(affected daughter | both V-15 and V-2 have the allele) = 1

P(G) = P(neither V-15 nor V-2 has the allele) = ¼

P(H) = P(affected daughter | neither V-15 nor V-2 has the allele) = 0

P(daughter of V-2 and V-15 has the disease) =

P(A)*P(B) + P(C)*P(D) + P(E)*P(F) + P(G)*P(H) =
(¼ * ½) + (¼ * 1) + (¼ * 1) + (¼ * 0) =
1/8 + ¼ + ¼ = 5/8

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BIOL 221 Final Exam

4. Imagine that in mice the dominant allele T confers long tail length, while the recessive allele t
confers short tail length. In addition, the dominant allele E confers big ears, while the
recessive allele e confers small ears.

a. You cross pure-breeding males with long tails and big ears with pure-breeding females
with short tails and small ears. Then you intercross the F1 siblings. 16% of the F2 have
short tails and small ears. Are these two genes linked? Explain your reasoning in one
sentence. (3 points)

Yes, they are linked. If they were unlinked, only 1/16 (6.25%) would have short tails and
small ears.

b. If you testcross F1 males by crossing them to females with short tails and small ears, what
phenotypic and genotypic ratios do you expect? (3 points)

Parents: T,E / T,E x t,e / t,e

F1: T,E / t,e x T,E / t,e
F2: 16% t,e / t,e

Therefore, from each F1 animal, there were the following classes of gametes with the
following frequencies:
T,E: 0.4
t,e: 0.4
T,e: 0.1
t,E: 0.1

When you cross T,E / t,e x t,e / t,e you expect:

40% T,E / t,e (long tails, big ears)
40% t,e / t,e (short tails, small ears)
10% T,e / t,e (long tails, small ears)
10% t,E / t,e (short tails, big ears)

c. If you stated that the genes were linked in part (a), calculate the distance between the two
genes. (3 points)

10 + 10 / 100 = 0.2 = 20 map units

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BIOL 221 Final Exam

5. Two unrelated infants were born with trisomy 21. The infants and their chromosomally
normal parents were genotyped by PCR with respect to four TRPs on chromosome 21. The
genotyping results for each TRP are separated by horizontal lines in the Figure below. The
bands below each individual on the pedigrees represent the products of the PCR for the
indicated TRP for that individual.

For each family, in which parent’s gametes and in which meiotic division did the nondisjunction
occur? Briefly explain your reasoning (1-2 sentences). (8 points)

Family 1: Mother, meiosis II. The daughter always inherits two copies of the same TRP allele
from the mother.

[Note: to receive ANY credit, your explanation had to make sense.]

Family 2: Father, meiosis I. Based on TRP4, the NDJ must have occurred in meiosis I because
the daughter has three different TRP alleles. With that information, it’s clear that the NDJ must
have occurred during spermatogenesis because the daughter always receives both of her father’s
TRP alleles. (Note that based just on TRPs 1-3, NDJ in meiosis II during oogenesis seems
possible.)

[Note: to receive ANY credit, your explanation had to make sense. Partial credit to students who
correctly deduced that the NDJ had to happen in meiosis I, but didn’t explain how they figured
out in which parent’s gametes.]

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BIOL 221 Final Exam

6. Imagine the replication bubble drawn below occurs in a temperature-sensitive mutant E. coli
strain that lacks both the 5’-3’ exonuclease activity of DNA polymerase I AND DNA ligase
activity when cells are exposed to high temperature (400 C). (These cells retain both
enzymatic activities at normal temperature of 370 C.)

Draw and label the new daughter strands that would be synthesized at both replication forks
at the restrictive (high) temperature. Your drawing should: (4 points)

• Clearly label 5’ ends and 3’ ends (one end has already been labeled for you).
• Distinguish different types of nucleic acids (if relevant).
• Indicate separation between fragments that are not joined by phosphodiester bonds.
(Please briefly describe how this separation is indicated on your drawing).
• Differentiate leading and lagging strands.

5’

Red bits - RNA primers

Orange bits - new DNA strands
Long fragments - leading strands
Short fragments - Okazaki fragments of lagging strands

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BIOL 221 Final Exam

7. For each of the following statements, explain in 2-3 sentences why each is false and provide
any relevant cis-acting elements and trans-acting factors required to make the statement true.

a. Neither prokaryotic nor eukaryotic RNA polymerases are “promoter blind.” Both bind
directly to the conserved TATA and promoter proximal sequences immediately upstream
of the transcriptional start site. (3 points)

Prokaryotic RNA polymerase sigma subunit does bind directly to the -10 (TATA) and -
35 sequences, whereas eukaryotic RNA polymerase does not. Instead, eukaryotic TFIID
(and TBP in particular) bind these sequences, and helps recruit and position RNA
polymerase for transcription initiation.

b. In E. coli, deletion or mutation of the lacI repressor protein in glucose-rich media confers
maximal transcription of the lac operon. (3 points)

Maximal activation of RNA polymerase at the lac operon requires activation of the CAP
protein, which occurs when cellular cAMP levels rise as glucose is exhausted from the
growth medium.

c. In the mammalian β-interferon enhanceosome, the enhancer-binding proteins (NF-kB,

IRFs, c-Jun, ATF2) bind directly to RNA polymerase to promote its catalytic activity.
(3 points)

The enhancer-binding proteins create a platform for assembly of epigenetic modifiers

GCN5, CBP, and SWI/SNF complexes, which modify chromatin structure and help
recruit RNA polymerase.

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BIOL 221 Final Exam

8. We spent some time discussing the pre-mRNA processing in eukaryotes.

a. What are two major functions associated with the 7meG cap structure? (3 points)

The 7meG cap (1) protects the mRNA from 5’-3 exonucleases, (2) promotes transport
from the nucleus to the cytoplasm, and (3) promotes mRNA translation (extra points if
they mention eIF4E and eIF4G).

b. What processing events occur at the 3’ end of a pre-mRNA of a transcript? Specify

whether these events occur before or after termination. (3 points)

The transcript is first cleaved downstream of a conserved AAUAAA sequence, and then a
polymer of ~200 A residues is synthesized (extra points for enzyme names).

c. How are the processing enzymes recruited to the pre-mRNA as it is being transcribed?
(3 points)

Pre-mRNA processing complexes interact directly with the amino acid repeats in the
RNA polymerase II carboxy-terminal tail. Which complexes are recruited depends on
differential phosphorylation of repeated Ser2 and Ser5 residues.

9. This semester, we discussed the lin-4 microRNA, which regulates lin-14 and considered
several experiments performed with loss-of-function mutations in these genes. Is there an
epistasis relationship between these two genes? If so, which gene is epistatic? Explain your
reasoning in one sentence. (3 points)

lin-14 is epistatic to lin-4 because the double loss-of-function mutant will have a lin-14
loss-of-function phenotype.

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BIOL 221 Final Exam

10. You are studying a rare recessive disease and you have mapped the disease locus to a small
chromosomal region. To identify the disease locus more precisely, you decide to look for
linkage disequilibrium with respect to two distinct dimorphic SNPs (SNP1 and SNP2) that
are in the chromosomal region you have identified. A diagram of the chromosome with the
positions of the SNPs indicated is below:

In the population you are studying, the frequencies of the A variant of SNP1 and the G
variant of SNP1 are 0.9 and 0.1, respectively. The frequencies of the C variant of SNP2 and
the A variant of SNP2 are both 0.5. The frequencies of haplotypes of individuals in the
population with the disease are shown in the table below:

Haplotype: Individuals with the disease:

SNP1 A SNP2 C 10
SNP1 A SNP2 A 90
SNP1 G SNP2 C 1
SNP1 G SNP2 A 10

a. Is SNP1 in linkage equilibrium with the disease-causing allele in this population? Briefly
explain your reasoning. (3 points)

The ratio of SNP1 A : SNP1 G in the overall population is 9:1. The ratio of SNP1 A :
SNP1 G in the affected population is roughly equivalent (100:11). Therefore, SNP1 is in
linkage equilibrium with the disease-causing allele.

b. Is SNP2 in linkage equilibrium with the disease-causing allele in this population? Briefly
explain your reasoning. (3 points)

The ratio of SNP2 C : SNP2 A in the overall population is 1:1. In comparison, the ratio of
SNP2 C: SNP2 A in the affected population is highly skewed to favor SNP A (11:100).
Therefore, SNP2 is in linkage disequilibrium with the disease-causing allele.

c. Which of the two SNPs is likely closer to the disease locus? Briefly explain. (3 points)

SNP2 because it is in linkage disequilibrium with the disease-causing allele

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BIOL 221 Final Exam

11. Consider a patient with sporadic retinoblastoma. For each cell type listed below, state how
many alleles of Rb are in that cell and their genotypes (wild-type or mutant). (3 points)

a) a cell from a retinal tumor mut/mut (2)

b) a germ cell WT (1)

c) a neuron WT/WT (2)

Now consider a patient with inherited retinoblastoma and state how many alleles of Rb are in
each cell type and their genotypes: (3 points)

d) a cell from a retinal tumor mut/mut (2)

e) a germ cell WT or mut (1)

f) a neuron WT/mut (2)

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BIOL 221 Final Exam

12. Let’s say you just performed an extensive bioinformatic analysis of exome sequences (that is,
DNA sequences from protein-coding exons across the genome) in 500 distinct cancer cell
lines representing multiple tissue types (pancreas, breast, colon, etc.), using data from the
TCGA. You observe mutations in two autosomal genes of unknown function in more than
30% of these cells. The patterns of these mutations are distinct in the two genes. The
genetic alterations in Gene A consist mostly of nonsense mutations and are distributed across
the entire body of the gene. In contrast, all the mutations in Gene B map to only two specific
amino acid residues, and constitute only missense mutations.

a. Based on this information, would you classify these genes as oncogenes or tumor
suppressors? Provide 1-2 sentences to explain your reasoning. (4 points)

Gene A: Gene A is most likely a tumor suppressor gene, since the introduction of
nonsense codons represents loss-of-function mutations, and could occur at multiple
sites (as shown in class for BRCA1).

Gene B: Gene B is most likely an oncogene, since gain-of-function mutations are

typically restricted to a small number of specific amino acids that regulate biological
activity.

b. While analyzing a novel cancer cell line, you discover mutations in one allele of Gene A
and in one allele of Gene B. Based on the information described above, would you
expect to also observe mutations or alterations in the other allele of Gene A and the other
allele of Gene B? Provide 1-2 sentences to explain your reasoning. (4 points)

Gene A: Yes. You would expect to observe loss-of-heterozygosity for tumor suppressor
genes in a cancer cell, which means the second allele would also have a loss-of-
function mutation (or be epigenetically silenced.)

Gene B: No. Since oncogenes are dominant gain-of-function mutations, they do not
typically require mutations in the second allele.

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BIOL 221 Final Exam

13. Imagine you have generated a breast cancer cell line from each of two unrelated patients
(Patient A and Patient B), both of whom come from families with a history of inherited,
early-onset breast cancer. When grown in tissue culture, both cell lines die when exposed to
low doses of the PARP inhibitor olaparib. Now, imagine that you can fuse any two of these
cells at will, and their nuclei also fuse to generate tetraploid cells. When you test the
response of these fused cells to olaparib, you observe the following pattern:

Response of fused
Cell 1 Cell 2 tetraploid cell to olaparib
Patient A Patient A death
Patient B Patient B death
Patient A Patient B survival

a. Based on these observations, what can you conclude about the identity of the mutant
genes in Patient A and Patient B that predispose them to early-onset breast cancer? In
1-2 sentences, explain your reasoning. Please be as specific as possible about which
genes you expect to be mutated in Patient A and Patient B. (4 points)

“A” cells have mutations in either BRCA1 or BRCA2, whereas “B” cells must have
mutations in the other gene (BRCA2 or BRCA1, respectively), which makes them
deficient in homologous recombination, and hence sensitive to PARP inhibition. When
the “A” and “B” cells are fused, the mutations complement, so homologous
recombination function is restored, making the fused cells resistant to PARP inhibition.

b. Imagine that, after culturing the original diploid cells from Patient A in the absence of
PARP inhibitor for several weeks, you now expose them to olaparib, and most cells die.
However, a rare clone of cells emerges that is resistant to the drug. Based on the data
discussed in class, what is the most likely molecular basis of this new resistance? Again,
please be as specific as possible. Use 1-2 sentences to explain your reasoning. (4 points)

The most likely scenario is that a second mutation has occurred that restores the open
reading frame in the mutant BRCA1 (or BRCA2) gene. For example, a missense
mutation that introduces a stop codon in the body of the gene could revert to the original
(or different) amino acid, thereby producing a functional, full-length BRCA protein.

Have a nice holiday break!

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