Molecular Biology, Spring 2006

Problem Set #7 (Lectures 14 & 15)

Lodish et al. Molecular Cell Biology “Review the Concepts” chapter end problems:
12-1 – In the case of a protein-coding gene, gene control beyond regulation of
transcriptional initiation can be regulated by controlling the stability of the corresponding
mRNA in the cytoplasm, by controlling the rate of translation, and by controlling the
cellular location so that newly synthesized protein is concentrated where it is needed.

12-7 – The term hnRNA describes heterogeneous nuclear RNA's that consist of several
different types of RNA molecules that are found in the nucleus. Small nuclear RNA's
bind to splice sites and participate in splicing reactions. Small nucleolar RNAs play a
similar role in tRNA processing and can help to position methyltransferases near
methylation sites. Micro RNAs and short interfering RNAs are involved in gene
silencing. Both are derived from longer precursor molecules and become part of the RISC
complex.

12-14 – A plant deficient in Dicer activity shows increased susceptibility to RNA viruses
because Dicer is not present to degrade a portion of the viral double-stranded
intermediates that viruses synthesize during replication. Without Dicer, all of these viral
mRNAs are available for further viral infection.

A) A new drug targets the mRNA exporter complex. What is the potential for this
new drug as an antibiotic? Would your answer change if HIV was the target? What
about Burkitt’s lymphoma? Carefully consider specificity and potential toxicity in
your analysis.

It would not work for AB because there is no exporter complex in prokaryotes, therefore
no target for drug. For HIV it is not specific enough to block just HIV export out of the
nucleus and would block all export therefore there wouldn’t be translation of anything
toxicity. Burkitts lymphoma???

B) The Ras protein is a GTPase that functions in many growth-factor signaling

pathways. In its active form, with GTP bound, it transmits a downstream signal
that leads to cell proliferation; in its inactive form, with GDP bound, the signal is
not transmitted. Mutations in the gene for Ras are found in many cancers. Of the
choices below, which alteration of Ras activity is most likely to contribute to the
uncontrolled growth of cancer cells? Can you reach a definitive conclusion?
1) A mutation that prevents Ras from being made
2) A mutation that increases the affinity of Ras for GDP
3) A mutation that decreases the affinity of Ras for GTP
4) A mutation that decreases the affinity of Ras for its downstream targets.
5) A mutation that decreases the rate of hydrolysis of GTP by Ras.
Now consider the same question (Which alteration of Ras activity is most likely to
contribute to the uncontrolled growth of cancer cells?) but with the choices
“flipped”. Can you reach a definitive conclusion?
1B) A mutation in which Ras is constitutively made.
2B) A mutation that decreases the affinity of Ras for GDP
3B) A mutation that increases the affinity of Ras for GTP
4B) A mutation that increases the affinity of Ras for its downstream targets.
5B) A mutation that increases the rate of hydrolysis of GTP by Ras.

Cannot answer because 1-4 are all equally likely to occur

C) True/False. Sequences of cellular RNAs (obtained from cDNA libraries) provide

the most reliable way to identify genes in human chromosomal DNA. Explain your
answer. What if the question were re-phrased to read “Sequences of cellular RNAs
(obtained from cDNA libraries) provide the most reliable way to identify regulatory
elements in human chromosomal DNA. Would your answer change? Explain.
What approach would you use to answer the second question?

True for eukaryotes because the cDNA copy would match the mRNA copy through
complementary interactions. Not sure for regulatory elements.

D) (From Molecular Biology of the Cell, 4th Edition, Wilson & Hunt)
RsaI A encodes green vision and RsaI B encodes red vision

E) In principle, a eukaryotic cell can regulate gene expression at any step in the
pathway from DNA to active protein (see diagram below).

1) Place the types of control listed below at appropriate places on the diagram
above.
a) mRNA degradation control – as mRNA  nucleotide or protein
b) protein activity control—from protein to modified protein or aa or just at
level of modified protein due to what function it has
c) protein stability control—from protein to modified protein or aa
d) RNA processing control—from DNA RNA
e) nuclear export and localization control—mRNA from nucleus to cytosol
f) transcriptional control- DNARNA
g) translational control- RNAprotein
Is there more than one type of process that can contribute to each of the above
control mechanisms????

2) Which of the types of control listed above are unlikely to be used in bacteria?
Nuclear export bc no nucleus in prokaryotes

3) What are some of the drugs we discussed in class and where do they exert their
influence with regards to the controls listed on the diagram above?

Neomycin, kanamycin, gentamycin inhibit translation by interacting with 16s rRNA

Diptheratoxin- bind EF and inhibit elongation during translation