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Biology 2581b
MIDTERM EXAM
March 1st, 2014 - 9am -12 noon
Version 111
40% of Final Mark
INSTRUCTIONS
This test paper is composed of 40 equally weighted questions covering 14 sides (excl. cover).
The last page contains a table of critical chi-square values. Please ensure that the exam is
complete.

Although there are no deliberate “tricks” on this paper there is ample opportunity to make
careless oversights; READ THE QUESTIONS CAREFULLY.

Answers will be subject to computerized matching analysis to detect cheating.

Since it is impossible to provide equal access to instructors during the Test, proctors will
NOT answer questions of interpretation.
All answers must be recorded on the Scantron sheets within the 3 hour time limit.

1. Fill in your NAME at the top of the scantron sheet and the exam paper
2. STUDENT NUMBER - Print the digits of your student number in the squares provided.
Mark the corresponding bubble in the column below each printed digit.
3. SECTION AND ANSWER SHEET - Leave these areas blank.
4. In the EXAM CODE section enter 111
5. Mark one choice from the alternatives provided for each question.
6. Submit your test paper and the Scantron sheet SEPARATELY.
1. The sequence of a region of a mature mRNA is 5’ – GUACUUCGAC – 3’. The sequence of
the corresponding template strand of the gene is

A. 5’ – GUCGAAGUTC – 3’
B. 5’ – GTCGAAGTAC – 3’
C. 5’ – CATGAAGCTG – 3’
D. None of the above.

2. Imagine that a disease affecting goats is found to be due to a new virus. This virus could be
grown in goat kidney cells cultured in the lab. The virus appears to contain four chemically
defined components, which we will call X, Y, Z, and W. Investigators wish to determine
which of these components carry the genetic information of the virus. An experiment was
thus conducted in which each of these components was radioactively labelled by growing
different batches of this virus in radioactive kidney cells. Radioactive virus from each of
these batches was allowed to attach to nonradioactive kidney cells. The cells were then
exposed to a Waring blender. The supernatant (containing the viral “ghosts”) and the
pelleted infected cells were then examined for radioactivity, with the following results:

% Radioactivity
Supernatant Pelleted cells
X 100 0
Y 80 20
Z 50 50
W 0 100

Based on these results, which of these components could NOT be carrying genetic information?

A. X
B. Y
C. Z
D. W

3. Which of the following statements is true?

A. Histones are rich in acidic amino acids.

B. A eukaryotic chromosome consists of thousands of individual,
non-contiguous DNA molecules.
C. Z-DNA is a left handed helix.
D. None of the options described in A, B, or C are true.

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4. The diagram below represents a eukaryotic gene including a regulatory region, 5’ and 3’
UTRs, exons, and introns. Based on the diagram, the translation initiation (start) codon
would be found in region X and the final mRNA transcript will have Y number of
introns.

X Y
A. 2 2
B. 3 2
C. 3 0
D. 7 0

5. Imagine that while studying bacteria living deep in the Atlantic Ocean you discover a
strange organism whose DNA contains a total of eight previously uncharacterized bases
distinct from the purines and pyrimidines found in our DNA. We will refer to these new
bases as A, B, C, D, E, F, G, and H. Types A and B are subsequently classified as
“marzines”, C and D as “orsines”, E and F as “pirines”, and G and H as “karvines”. The
total amount of information that could be encoded in a 586 nucleotide long piece of single
stranded DNA from this organism would be

A. 1172 bits.
B. 1758 bits.
C. 2344 bits.
D. None of the above.

6. Nucleosomal chromatin with a diameter of 10 nm can supercoil into a 30 nm super helix.

Which histone(s) is/are primarily responsible for this compaction?

A. Histones H4 and H3.

B. Histone H1 only.
C. Histones H2A and H2B.
D. Histones H2B only.

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7. Consider a long, linear molecule of dsDNA, one end of which is rotated four times with
respect to the other end introducing negative (-) writhe. The two ends are then joined
together to create a covalently closed circle. Which of the following statements is true?

A. The molecule is overwound.

B. The molecule is in an unfavourable state with respect to the initiation of
transcription.
C. The molecule is storing positive superhelical energy.
D. None of the options described in A, B, or C are true.

8. In pea plants, wild-type flowers display a purple colour phenotype. A researcher wishes to
discover genes involved in purple pigment deposition. To this end the researcher
independently isolates a total of four mutants (each homozygous recessive at a single locus
controlling flower colour) that have white flowers. To determine how many genes are
involved in pigment deposition the researcher performs a pair-wise series of
complementation crosses. In the table below a (-) sign indicates a cross between mutants
where only white-flowered progeny are observed. A (+) sign indicates a cross between
mutants where only purple flowered progeny are observed.

Mutant # 1 2 3 4
1 - - + +
2 - + +
3 - +
4 -

Based on the researcher’s results, how many genes are involved in purple pigment
deposition?

A. 1
B. 2
C. 3
D. 4

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9. Which of the following statements accurately describes the results of Avery's experiments
that defined "the active principle" (derived from heat killed S strains) that was capable of
transforming living R cells into virulent S cells?

A. The “active principle” was present in a purified sample that contained almost
nothing but protein.
B. DNA digesting enzymes destroyed the ability of the “active principle” to transform
living “R” cells to virulent “S” cells.
C. The extraction of lipids by ultracentrifugation abolished the ability of the “active
principle” to transform living “R” cells to virulent “S” cells.
D. None of the statements described in A, B, or C is accurate.

10. The structural backbone of chromosomes (i.e. the central scaffold) is

A. made up predominantly of histone proteins.

B. made up predominantly of non-histone proteins.
C. made up of kinetochore motor proteins.
D. None of the above.

11. Which of the following statements regarding the human genome is true?

A. The human genome possesses significantly more genes than species such as
Arabidopsis or mice.
B. Only a small proportion of the human genome is repeated elements.
C. Only a small proprotion of the human genome codes for protein.
D. None of the options described in A, B, or C are true.

12. In the Athabaskan tree spider, a series of alleles occurs at the r locus. All alleles affect the
colour of the spider: r d = dark-red, r m=medium-red, r l = light-red, and r p = very pale pink. The
order of dominance is r m > r l > r p > r d. If a medium-red female, heterozygous for dark-red, is
crossed to a light-red male, heterozygous for pale-pink, the ratio of phenotypes expected among
the progeny spiders would be

A. 2 medium-red: 1 light-red: 1 very pale-pink.

B. 1 dark-red: 1 medium-red.
C. 1 dark-red: 1 medium-red: 1 light-red: 1 very pale-pink.
D. None of the above.

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13. In Drosophila, curved bristles and purple eyes are both caused by recessive alleles (cr and p
respectively) . The dominant wild-type alleles (cr+ and p+) are responsible for straight bristles
and red eyes, respectively. A fly displaying curved bristles and purple eyes is mated to a
homozygous cr+ p+ fly and the F1 progeny are test-crossed. The F2 are distributed as follows:
60 flies with curved bristles and purple eyes; 40 flies with curved bristles and red eyes; 40 flies
with straight bristles and purple eyes; 60 flies with straight bristles and red eyes. What are the
values of i) X2 and ii) p, for a test of the hypothesis that the cr and p genes are unlinked?
(NOTE: A chi-square table is attached to the last page of this exam).

A. X2 = 2; 0.5 < p < 0.9

B. X2 = 4; 0.01 < p < 0.05
C. X2 = 8; 0.01 < p < 0.05
D. None of the above.

14. In a certain breed of cat, the alleles G and g determine black and grey fur respectively.
However, the allele w of a gene on a separate chromosome is epistatic to the G and g colour
alleles resulting in white fur (W has no effect on colour). If animals of genotype G/G; W/w
are crossed to one another, what phenotypic ratio is expected in the progeny?

A. 9 grey, 3 white, 4 black

B. 12 black, 3 grey, 1 white
C. 9 black, 6 grey, 1 white
D. None of the above.

15. Out of 1350 progeny of a three-point testcross there were 8 double crossover recombinants,
whereas 25 had been expected on the basis of no interference. The interference value is

A. 0.32
B. 0.68
C. 3.125
D. None of the above.

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16. Which of the following statements regarding the double strand break repair model of
recombination are true.

i) recombination is initiated by a single stranded break in one chromatid

ii) resolution of Holliday junctions in the same plane result in crossing over
iii) branch migration can result in the creation of heteroduplex regions no greater
than 5 kbp in length

A. Only i) is correct.
B. Only i) and ii) are correct.
C. All are correct.
D. None are correct.

17. A cross was made between an eeddGG female and an EEDDgg male. The resulting F1
females were test-crossed and 1000 offspring were produced. The F2 phenotypes and
numbers are shown below. Which genes are linked?

EDg 197
eDG 201
edg 45
eDg 51
EdG 49
EDG 55
Edg 199
edG 203

A. E and D are linked.

B. E and G are linked.
C. D and G are linked.
D. all three genes are linked.

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18. An organism heterozygous for three genes AaBbCc was mated to a homozygous aabbcc
individual, resulting in the progeny distribution below.

ABC 327
aBC 44
AbC 30
ABc 3
abC 4
aBc 25
Abc 53
abc 319

The map distance between A and C is

A. 12.9 map units.

B. 18.9 map units.
C. 20.6 map units.
D. None of the above.

19. How many different transitions and transversions are listed below?

GC to CG
GC to AT
AT to GC
AT to CG
CG to TA
TA to AT
TA to GC
TA to CG

A. Two transition and three transversions.

B. Three transition and four transversions.
C. Four transition and four transversions.
D. None of the options described in A, B, or C are correct.

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20. New mutagens are discovered on a daily basis. For example, a strange compound (that
glows blue in the dark) was recently found within a deep Panamanian cave. After thorough
analysis it was determined that this compound interacts with DNA and causes T’s to
mispair with either T or C. What type of base pair changes will this result in?

A. TA to AT and TA to CG
B. AT to TA and AT to GC
C. AT to TA and AT to CG
D. None of the above

21. A section of DNA undergoing replication is shown below. A slippage event occurs while
adding A’s across from a run of T’s. If the template strand (bottom strand) slips by TWO
nucleotides relative to the strand which is being extended by the DNA polymerase (top
strand). What will be the length of the run in the replicated strand after the slippage event?

5’ GCTCAAA
3’ CGAGTTTTTTTTGAT

A. 8
B. 7
C. 6
D. None of the above.

22. Methyl directed mismatch repair has been extensively studied in bacteria. Which of the
following statements about this process is correct?

A. Methylation occurs randomly and therefore errors introduced during replication are
repaired randomly.
B. To distinguish between newly synthesized and old DNA strands, DNA polymerases
introduce methylated bases during replication.
C. When repairing a mismatch which occurred during replication the old strand is
used as a template by the DNA polymerase since the old strand is methylated.
D. None of the above.

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23. Which of the following definitions have been used to discriminate between wild-type and
mutant alleles?

A. A wild-type allele is more frequent than the corresponding mutant allele.

B. The wild-type allele is the one which was identified before the mutant allele.
C. A mutant allele has a negative impact on the organism while the wild-type allele
does not.
D. All of the above.

24. A mutation changes a GCU codon to a GCA codon. Both codons code for alanine. This
type of mutation is referred to as a

A. frame shift mutation.

B. non-sense mutation.
C. missense mutation.
D. silent mutation.

USE THE INFORMATION PROVIDED IN THE PARAGRAPH BELOW TO ANSWER

QUESTIONS 25-28.

Proteins often have more than one functional domain. The GREEN protein which was
identified in a rare tropical plant has an N-terminal domain which allows it to be transported
into the chloroplast. Its internal domain is an enzymatic domain which allows the protein to
catalyze a reaction when inside the chloroplast. The C-terminal domain of the GREEN
protein is a protein interaction domain. Only when the GREEN protein forms homodimers
can it perform its enzymatic reaction. Three different mutant alleles have been identified for
GREEN: allele 1 has a mutation which prevents the translocation into the chloroplast,
allele 2 has a mutation which allows the enzyme to recognize and catalyze a second
substrate as a homodimer, and allele 3 carries a mutation that translates into a protein which
cannot form any homodimers. Which of the following statements is correct?

25. Allele 1 is a

A. null allele.
B. hypomorphic allele.
C. dominant loss of function allele.
D. dominant negative loss of function allele.
E. neomorphic allele.

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26. Allele 2 is a

A. null allele.
B. hypomorphic allele.
C. dominant loss of function allele.
D. dominant negative loss of function allele.
E. neomorphic allele.

27. Allele 3 is a

A. null allele.
B. hypomorphic allele.
C. dominant loss of function allele.
D. dominant negative loss of function allele.
E. neomorphic allele.

28. If a plant is heterozygous for allele 2 and allele 3, the plant will

A. have no enzymatic capability.

B. be able to catalyze one substrate.
C. be able to catalyze two substrates.
D. None of the above.

29. Which of the following pieces of data would you not be able to determine by Southern
hybridization using genomic DNA as a template?

A. The copy number of a particular gene within a genome.

B. The expression level of a particular gene.
C. The copy number of related genes within a genome.
D. All of the pieces of data described in options A, B, or C could be determined
through Southern Hybridization.

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30. Recognition sequences for several restriction enzymes are shown below. The “ ^ ” symbol
indicates where the enzymes cut within the recognition sequence. Which restriction
fragments generated by these enzymes can be ligated?

Enzyme one: 5’ GC^TTAACG 3’

3’ CGAATT^GC 5’

Enzyme two: 5’ TATA^TTAATATA 3’

3’ ATATAATT^ATAT 5’

Enzyme three: 5’ GC^AATTCG 3’

3’ CGTTAA^GC 5’

A. Fragments generated by enzyme one and enzyme two.

B. Fragments generated by enzyme two and enzyme three.
C. Fragments generated by enzyme one and enzyme three.
D. Restriction ends generated by all three enzymes can be ligated in any combination.

31. How many of the following statements regarding agarose gel electrophoresis are correct?

i) Small DNA fragments travel faster than large ones.

ii) Small DNA fragments travel slower then large ones.
iii) DNA fragments migrate to the positive pole while RNA fragments go to
the negative pole.
iv) Both DNA and RNA fragments migrate to the negative pole.

A. Only one of the statements is correct.

B. Two of the statements are correct.
C. Three of the statements are correct.
D. All four of the statements are correct.

32. The power of chromosome jumping lies in its ability to identify DNA sequences that are

A. close to a known DNA sequence.

B. on a second DNA fragment which has overlapping DNA sequences.
C. on an adjacent fragment even though it has no overlap in sequence.
D. on the far end of the same DNA fragment.

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 33. You would like to make a degenerate probe for the amino acid sequence Ala Ile Tyr Ser
Arg. How many of the following sequences (written in RNA code) will be part of your
degenerate probe.

sequence 1: GCU AUA UAA UCG CGU

sequence 2: GCG AUU UAC UCA AGA
sequence 3: GCA AUG UAU UCU CGA
sequence 4: GCC AUC UAG UCC CGC
sequence 5: GCU AUU UAU AGU CGG

A. None of the five sequences.

B. One of the five sequences.
C. Two of the five sequences.
D. Three of the five sequences.
E. Four of the five sequences.

34. Southern Blot hybridizations can be performed in order to identify

A. a sequence complimentary to the probe.

B. a family of related genes.
C. a transposon sequence.
D. All of the above.

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USE THE INFORMATION PROVIDED IN THE PARAGRAPH BELOW TO ANSWER
QUESTIONS 35 and 36

You have identified two recessive mutations in honey bees that cause the bees to form four
legs (rather than the six legs observed in wild-type bees). You call one mutation four and
the other quatro. You cross a line homozygous for the four gene to a line heterozygous for
the quatro gene.

35. What ratio of WT to mutant phenotypes do you expect in the F1 if the mutations are in the
same gene?

A. All WT.
B. 25% mutants and 75% WT.
C. 50% mutants and 50% WT.
D. 75% mutants and 25% WT.
E. All mutant.

36. What ratio of WT to mutant phenotypes do you expect in the F1 if the mutations are in two
different genes?

A. All WT.
B. 25% mutants and 75% WT.
C. 50% mutants and 50% WT.
D. 75% mutants and 25% WT.
E. All mutant.

37. Transposons are often used to generate mutants. Which of the following statements
regarding transposon mutagenesis are correct?

i) Transposon copy number can be determined by PCR.

ii) Transposon copy numbers can be determined by Southern Blotting.
iii) Transposons can be targeted to specific gene sequences.
iv) Transposons can be tracked by integrating a selectable marker.

A. Only statements i) and ii) are correct.

B. Only statements ii) and iii) are correct.
C. Only statements iii) and iv) are correct.
D. Only statements ii) and iv) are correct.

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38. Genome size can differ between different individuals of the same species. For humans it was
determined that average genome size can differ by as much as ____ between different
healthy individuals.

A. 0.1%
B. 1%
C. 2%
D. 5%

39. When using DNA fingerprinting to identify minisatellite loci in the genomic DNA of
different individuals, what defines the size of the fragments containing the repeat sequence?

A. The size of the probe.

B. The number of repeats.
C. The position of the restriction sites relative to the repeats.
D. The number of repeats and the position of the restriction sites relative to the
repeats.

40. When using an oligonucleotide probe to distinguish between two SNP alleles, one requires

A. one probe that binds upstream of the SNP.

B. one probe that binds downstream of the SNP.
C. one probe that overlaps the SNP.
D. two probes; one of which binds upstreamof the SNP and another that binds
downstream of the SNP.
E. two probes; one of which binds within the SNP, and another that binds outside of
the SNP.

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