Download Chp. 14 worksheet

A. Krakowski • Bio 76, Chp. 14
Chp. 14 worksheet
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1. Regarding the NOVA video clip:
a) What is the “recipe,” and what is the “cook?”
The “recipe” is the messenger RNA (mRNA) that leaves the nucleus and goes to the cytoplasm to be
translated (“cooked”) into protein by the “cook.”
b) What triggers the “cop” to start chopping up the recipe? Explain using the correct
biological terms. Refer to the figure from your notes if you need a hint.
Double-stranded RNA molecules are what look suspicious to the “cop.” Since mRNA is a single-stranded
transcript of the DNA sequence found in the nucleus, there shouldn’t be a double-stranded version of this
transcript out in the cytoplasm. In fact, the complement to the mRNA (the other strand of the double-stranded
RNA that is identical to the DNA sequence that was transcribed) shouldn’t exist. The presence of doublestranded RNA molecules such as these out in the cytoplasm suggests to the cell that there may be a viral
infection, and that these double-stranded RNA molecules may in fact be viral products. So, the cell triggers the
“cop” to chop up the double-stranded RNA, triggering RNAi, which will destroy any similar RNA sequences.
2. So, how does RNAi relate to Biomanufacturing?
a) How do you think RNAi could work as a drug?
Since many diseases are caused by the production of mutant proteins (or sometimes by the
overproduction of proteins), RNAi offers a way to “turn down” or “silence” the expression of these
mutant or overproduced proteins. This type of disease therapeutic doesn’t just treat symptoms of a
disease, it attacks a disease by treating its root cause.
b) If a biomanufacturing company wanted to make an RNAi-based drug, what types of
molecules would they be manufacturing, and how would they get their drug to the
right place in the patient?
They’d be manufacturing a double-stranded RNA molecule that has the same sequence as the mRNA that
encodes a mutant protein, or possibly an overexpressed non-mutant protein. Since RNA is less stable than
DNA, this effect would be transient . . . so, a trick to get around this involves using DNA plasmid vectors
that encode a piece of single-stranded RNA that has two complementary regions, causing the regions to
base-pair immediately upon transcription and form what’s called a “hairpin.” So, the company really just
has to generate plasmid DNA and then (here’s the hard part) figure out how to deliver the plasmid DNA to
the cells that need it. So far, viral vectors have proven to be most successful at this.
3. Why are we talking about protein structure in Biomanufacturing anyway?
a) Why might a company that manufactures a pharmaceutical product care about protein
structure?
Because drugs and other biomanufacturing products are often regulators of a protein’s activity. In order to
regulate a protein’s activity, a drug will generally need to bind to that protein in a specific location and
orientation. Therefore, in order to design the drug or to understand how the drug regulates the protein, the R
& D department of the biomanufacturing company will probably want to know the protein’s structure and see
where the drug binds within this structure.
b) Can you think of an example of a biomanufacturing product (a hypothetical one or
one we’ve discussed) for which the company manufacturing the product would want
to know about a protein’s 3-D structure?
One that we’ve talked about already would be Gleevec, the small molecule inhibitor of the ABL kinase
enzyme that is overactive in chronic myelogenous leukemia. By solving the structure of the ABL kinase
with and without Gleevec bound to it, it was clear that Gleevec was binding inside the active site of the
ABL enzyme, preventing the substrate from binding and effectively shutting off the enzyme’s activity.