Chem 40 Nucleic Acids Problem Set Due Tuesday, March 22, 2016

1. In samples of DNA from two unidentified strains of bacteria, X and Y, adenine comprises 17%
(strain X) and 32% (strain Y) of the total bases.
A. What relative proportions of A, G, T and C would you expect to find in these two strains of
bacteria?
B. One of these strains of bacteria was isolated from a hot spring at 69°. Which strain would you
expect to have come from the hot spring? Explain your reasoning.
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2. In the Meselson-Stahl experiment, what would be the % dsDNA molecules containing N after 10
generations?

3. The template strand of a DNA fragment that codes for a peptide from an anaerobic bacteria was
sequenced using the Sanger method. The results are as follows:

G C A T

A. Determine the base sequence of the double-stranded DNA coding for the peptide. Indicate
the 5’ and 3’ ends of the DNA and label the template and coding strands.
B. Determine the sequence of the mRNA encoded by the DNA fragment.
C. What is the peptide sequence coded for by the mRNA?

4. The anaerobe that produces the peptide in the previous number was found in a nuclear waste
dump. Another anaerobe found in the same area produces a toxic peptide with the sequence
Met-Ala-Ala-Ser-Ser-Thr. The biochemists working on the project speculated that the toxin may
be the effect of a mutation event.
A. What is the likely sequence of the mRNA that produced this peptide?
B. What are the exact, specific mutations in the DNA strand that specified the mRNA of the
novel bacteria that led to the production of the more toxic peptide?

5. Given the partial DNA sequence of gene X

5’-GACGCTCGAATGAGTCCCGCATGTGTT-3’ (template)
3’-CTGCGAAGCTACTCAGGGCGTACACAA-5’ (coding)
A. What is the polypeptide product if translation started from the first base?
B-D. Give the effect of the following mutations on the protein product.
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B. base substitution of the last base of the 5 codon in the coding strand to A
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C. insertion of T in between the 8 and 9 codons in the template strand
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D. deletion of the 1 base in the template strand
6. For each of the ff. conditions, specify: (a) The specific process affected, and (b) the effect on the
process. (5 pts.)

Condition Affected process Effect on process

A. non – addition of 5’ cap in

eukaryotic mRNA
B. a mutated 16s rRNA

C. exposure to cycloheximide

D. Mutation of TATAAA to
TATTAA in a prokaryotic
promoter
E. Presence of bromouracil

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7. Plasmid Plasmid X contains 2 antibiotic resistance genes, one for ampicillin (Amp ) and one for
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tetracycline (Tet ). An EcoRI restriction site is present in the Amp gene. A DNA fragment Y is
to be cloned into plasmid X. Both plasmid X and fragment Y were treated with EcoRI, the two
molecules were ligated, and then introduced into bacterial host cells.
A. In what cell media (specify antibiotic/s present) will the bacteria grow if the recombinant
plasmid is present?
B. In what cell media will the bacteria grow if it was not able to get any plasmid?
C. In what cell media will the bacteria grow if plasmid X that failed to ligate to insert Y is
present?
D. In what media will the bacteria grow if plasmid X did not ligate with insert Y, but also did not
religate with itself?

8. A 1000 bp EcoRI restriction fragment contains a gene you are interested in. The fragment was
divided into 4 fractions; one fraction was untreated, one was digested with HindIII, another was
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digested with SmaI, and the 4 fraction digested with both HindIII and SmaI. Below is shown an
agarose gel of the appropriate digests.

Draw a restriction map (a linear representation of the DNA fragment) showing the position of the
restriction sites and the distances, in bp’s, between the HindIII, SmaI, and EcoRI sites.