Bio 362 – Write the likely mRNA sequence of this gene when it is expressed in bacteria

13 Jun Bio 362 – Write the likely mRNA sequence of this gene when it is expressed in bacteria

Question
Bio362-2013

Exam III

Name

Question 1. (30 pts)
Given the following DNA template strand of reporter gene (a gene used to report on mRNA and
protein expression):
5’-CTATACTCCTCCATGTCTTACGTGGTAGTGGTGGTAGTGTACATCAAAAAAAAA-3’

a) Write the likely mRNA sequence of this gene when it is expressed in bacteria. (2 points)

b) Write the anticodon sequence of all tRNAs that could decode this mRNA (without Inosine
modifications in the tRNAs). Please make sure to indicate the correct directionality of
the codons and anticodons. (4 points)

c) What is the minimum number of tRNAs required to decode this mRNA? Explain your
answer. (2 points)

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Bio362-2013

Exam III

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d) Write the likely amino acids sequence of the protein produced from this gene (2 points)

e) Which approach/technique will you use to detect this mRNA? Briefly explain how this
approach works and what material/reagents you will need. (2 points)

f) Which approach/technique will you use to detect this protein? Briefly explain how this
approach works and what material/reagents you will need. (3 points)

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Bio362-2013

Exam III

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g) You have discovered a new viral protein called Snoop that is a sequence specific mRNA
modification enzyme. When you express Snoop in bacteria or eukaryotes, along with your
reporter gene (shown above), you notice that you are unable to detect the reporter mRNA or
its protein product.
i.

Explain why there is no detectable reporter mRNA or protein when Snoop is
expressed in bacterial. (5 points)

ii.

Explain which genes you will delete to stabilize the reporter mRNA and protein to
the effects of Snoop expression in bacteria? (5 points)

iii.

Explain why there is no detectable reporter mRNA or protein when Snoop is
expressed in eukaryotes. (5 points)

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Bio362-2013

Exam III

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Question 2. Please provide brief definitions for the following terms (no more than one or two
sentences (10 pts)
a. Attenuation

b. RRF

c. tmRNA

d. SspB

e. Molecular mimicry (Name one example)

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Question 3. (4 points)
Briefly describe how the rate of transcription by Pol II might influence the inclusion or
exclusion of an exon in the mature mRNA.

Question 4. (6 points)
You were given a six residue synthetic DNA oligonucleotide and asked to test its effects on
in vitro (in a test tube) protein synthesis. You find that this oligonucleotide inhibits bacteria
protein synthesis but not eukaryotic protein synthesis.
a) Briefly describe why this oligonucleotide inhibits bacterial protein synthesis. (4
points)

b) What is the likely sequence of this oligonucleotide? (2 points)

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Bio362-2013

Exam III

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Question 5. (10 points)
a) Briefly describe why the first base of stop codons is always U (not A, G, or C) and
the third base always an A or a G?

b) Why can RF2 accommodate either an A or a G at position 2 (UAA and UGA)?

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Bio362-2013

Exam III

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Question 6. (10 points)
You are the lab supervisor and someone gave you two precious tubes of RNA. One tube
contained bacterial mRNA and the other charged-tRNAs. The next day you found out
that one of the student mixed the two samples together into one tube, a BIG NO, NO.
After a lot of screaming and shouting you calm down and decide to purify the bacterial
charged-tRNAs away from the mRNAs –since you need both RNAs for your experiments.
Describe one simple way of achieving this purification.

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Bio362-2013

Exam III

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Question 7. (10 Points)
a. How can some organisms get away with having fewer than 20 synthetases, yet still
charge tRNAs with all 20 amino acids (5 points)

b. You have discovered a new anti-viral drug that only affects viral protein synthesis
without affecting normal/general eukaryotic protein synthesis. In a major scientific
conference you described in a simple sentence, or two, how your new drug
inhibits viral protein synthesis: (5 points)

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Question 9. (15 points)
You were asked by the Center for Disease Control to evaluate three mutant viruses that
infect eukaryotic cells. You infect three different cell cultures to examine the effect of each
virus on translation of the host and the viral RNAs
a. You find that Virus 1 produces an altered protease that degrades eIF2B. What are the
consequences of this cleavage on translation of the host and viral RNAs?

b. You find that Virus 2 produces an altered protease that degrades eIF4E. What are the
consequences of this cleavage on translation of the host and viral RNAs?

c. You find that Virus 3 produces an altered methyl transferase that methylates the 2’-OH
group of mRNAs on selected A residues, without modifying the polyA tail or affecting its
addition. What are the consequences of this modification on the host and viral RNAs?

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