Download Serine Proteases Teaching Exercises

Protein Exploration Using the
Spacefill Models
1. There are three spacefill models (Chymotrypsin, Trypsin, Elastase).
a. Pick up each model and look at it. In this first part of the exercise, take note of
general similarities and differences in each of the three.
i. Each sphere represents an atom. Larger spheres represent carbon,
oxygen, nitrogen and sulfur. Smaller spheres represent hydrogen.
ii. Estimate the number of atoms present in each of these enzymes.
A. Chymotrypsin: 3591
B. Elastase: 2020
C. Trypsin: 2241
2. The coloring of these models was designed by David Goodsell.
a. Oxygen
i. If neutral, colored pink
ii. If charged, colored bright red
b. Nitrogen
i. If neutral, colored light blue
ii. If charged, colored bright blue
c. Carbon: white
d. Sulfur: yellow
e. Note: Hydrogen atoms are colored the same as the atom to which they are
attached.
f. Identify one atom of each coloring group.
g. Make comparisons between the three enzymes in terms of atoms that are
charged and atoms that are not. What do you notice about the overall content
of the charged atoms for each enzyme? What do you think that this might
mean in terms of function or location of the proteins?
3. Amino Acid Examination
a. Find examples of arginine, lysine, glutamic acid and aspartic acid (not that
these two acidic amino acids are hard to distinguish from one another). Notice
the distribution of charged amino acids. What significance might this
distribution have in terms of function?
b. Find examples of asparagine/glutamine, serine/threonine and histidine. Notice
the distribution of polar amino acids on the surface. What significance does this
have?
c. Find phenylalanine, tyrosine, tryptophan and methionine.
4. When these enzymes are made, they are initially in an inactive precursor state,
called zymogens. In order for the enzymes to become active, they will be cleaved
to arrange the linear amino acid sequence in such a fashion as to orient three
particular residues to form an active site for substrates to be bound. In these
enzymes, of the stabilizing factors in terms of structure is the presence of disulfide
bonds.
Serine Proteases Teaching Exercises – Page 1 of 2
a. Disulfide bridges are bonds made between two neighboring cysteine residues.
The sulfurs on these side chains can link together to form a disulfide bond. In
each of these enzymes, locate examples of disulfide bonds.
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Serine Proteases Teaching Exercises – Page 2 of 2