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Bio 3324

Molecular Biology

Exam I

October 1, 2013

This exam is worth a total of 100 points

1. a. Nucleic acids can be reversibly denatured and renatured. What bonds are
being broken and reformed? Give two methods used to denature nucleic acids.
(3 pts.)
b. Chromosomes are composed of double stranded DNA. When there are many
genes located on a single chromosome, are all the transcripts copied from the
same DNA strand? What regulatory element tells the RNA polymerase which
strand to copy? (3 pts.)
c. When the human genome was first sequenced, there was much disagreement
about how many functional genes it encoded. Computer programs were used to
search for open reading frames (ORFs). What is an open reading frame? (3 pts.)
d. In any given double stranded DNA sequence how many potential reading
frames are there? (3 pts.)
2. a. RFLPs and SNPs can be used to create genetic linkage maps. How do
RFLPs differ from SNPs? Can RFLP or SNP maps be combined with genetic
maps created using the inheritance of phenotypic traits? Why or why not? (4
pts.)
b. Would you expect to find an RFLP located in intergenic regions of the
genome? Why or why not? (3 pts.)
c. A mutant polymorphic form of the gene encoding BRCA 1 predisposes women
to both ovarian and breast cancer. It is inherited with the RFLP BC985 95.9% of
the time and inherited with RFLP BC782 93.6% of the time. Both of these RFLPs
are used diagnostically to predict who is at risk of getting breast cancer. Are
either of these polymorphisms a cause of breast cancer in women (explain your
answer). (3 pts.)
d. What is the distance in bp between RFLP BC985 and BC782, assuming they
are on the same side of the BRCA 1 gene. Ignore the length of the gene itself. In
humans 1% recombination is equal to 1 x 106 bp. (4 pts.)
3. a. What fraction of the human genome by percentage is represented by
exons? What fraction makes up the largest fraction of the genome? What is the
role of this fraction? (3 pts.)

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b. What is the distinction between a constitutively expressed gene and one that is
regulated? Which class would you expect to be shared by multiple cell types and
why? (3 pts.)
c. Why is there a large variation in genome size among organisms in the same
genus? (3 pts.)
d. About 10% of the genome are "pseudogenes".
one mechanism of how it might arise. (3 pts.)

What is a pseudogene?

Give

4. a. The article "Evo-Devo and an Expanding Evolutionary Synthesis: A genetic

theory of Morphological Evolution" by Sean Carroll explores the mechanisms of
the evolution of morphological diversity. According to this hypothesis the driving
force of morphological diversity are mutations in the cis-regulatory elements
(CREs). What are CREs? (3 pts.)
b. In Carroll's review he states that most modern "toolkit proteins" were already
present in ancient animals prior to the Cambrian period, 500 million years ago.
Give the functions of two categories of toolkit proteins. (4 pts.)
c. The molecular basis of morphological divergence (organisms looking different)
in the different phyla is due to heterotopy and heterchrony of conserved toolkit
genes. What do these terms refer to and how do they explain changing
morphology? (4 pts.)
5. a. Given the following results of restriction digest, draw the circular restriction
map of the plasmid. Fragment lengths are given in kb (10 pts.)

BL
8.2
4.1

RI/Hindlll
8.2
3.6
0.5

Hindlll

BamHI

11.8
0.5

9.9
2.4

RI/BamHI
4.2
4.1
2.4
1.6

Hindlll/BamHI
5.2
4.2
2.4
0.5

6. a. In cloning a foreign fragment of DNA into a plasmid, it is best to digest the

plasmid and fragment with two different restriction enzymes. Why is this better
than cutting each with only one enzyme? (3 pts.)
b. In the hybridization method Northern blotting, an RNA sample is run on an
agarose gel containing a substance to prevent RNA secondary structure from
forming. After transfer to a filter, the filter is hybridized with a radioactive probe
for the gene wnt, and two bands are detected on the x-ray film. Give one
interpretation of this result. (3 pts.)

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c. A powerful new technology makes use of "chips" that have short

oligonucleotide DNA spots deposited in an array of columns and rows. What
does each spot represent? These chips are hybridized with fluorescently tagged
DNAs from two different samples. How are these "probes" generated. (4 pts.)
d. One sample is isolated from normal breast tissue and another from malignant
breast tissue. The result shows that 55 genes show increased signal intensity in
the malignant sample, compared to the control. How would you interpret this
result? (3 pts.)
7. a. What is the definition of a replicon? Why is it necessary to have 10,000
replicons in the human genome? (3 pts.)
b. Draw a bi-directional replication fork indicating the 5' and 3' ends of the
parental and daughter strands. (4 pts.)
c. Why do only half the daughter strands need to be synthesized as short
Okazaki fragments? (3 pts.)
d. Show two different mechanisms that various organisms use to prime DNA
replication. (4 pts.)
8. a. When describing the properties of DNA polymerases, one usually describes
fidelity and processivity. Define these terms. (4 pts.)
b. RNA polymerases can start "de novo" whereas DNA polymerases cannot.
What does that mean? (3 pts.)
c. What are the roles of the following replication proteins: (4 pts)
i)
ii)
iii)
iv)

helicase
primase
single strand binding protein
clamp

d. If a DNA polymerase had a mutation in the 3'-5' exonuclease subunit, what

would be the consequence for the cell? (3 pts.)
Honors Problem (10 pts.)
Bacteria reproduce by binary fission and seem to be immortal. We, and other
eukaryotes, according to Leonard Hayflick, have cells that undergo a finite
number of divisions (about 60) and then die. What property of bacterial

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chromosomes differ from ours that may be responsible for the difference in
lifespan of the cells?

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