1 Chemical biology concepts
a) Brie y explain the dierence between the Pzer/Moderna and Johnson & Johnson vaccines.
How is each one delivered? Does it go into the nucleus or stay in the cytoplasm? What is
the actual antigen that generates the immune response? (8 points)
1
2 Mechanisms and molecular structure
a) The modied nucleotide is used in the Pzer coronavirus vaccine. Draw the structure of
. Explain which base is replaced with and why this modication is necessary. (8 points)
b) Draw a schematic illustrating how to use in vitro selection to make an RNA aptamer that
binds pyrrollsine, one of the natural amino acids used by archaea, but not eukaryotes or bac-
teria. (8 points)
c) Does lysine or arginine make stronger salt bridges with aspartic acid? Draw a picture to
explain your answer. (6 points)
2
3 Literature questions
These questions are about the Haurwitz et al 2010 paper about the Csy4 CRISPR endonuclease,
which is available on the class website.
a) In your own words, brie y explain what a CRISPR-Cas system is, and why is it important
in bacteria and archaea. (6 points)
b) In your own words, what is the biological function of Csy4? Why is there more than one
endonuclease in the CRISPR-Cas9 system? (What does Cas9 do and how is it dierent?) (6
points)
c) In your own words, please explain the experiment shown in Figure 3. What did the researchers
do? Describe the results and the quality control metric(s) used. It may be useful to refer to
the structures shown in Figure 2 in your explanation. (8 points)
3
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