Proteins fold into complex 3
dimensional patterns. The amino acid sequence of a protein determines this pattern. The
amino acids that do not like water tend to cluster in the protein’s core where
water is excluded. Amino acids that like water are typically found on the surface of the
protein where they can interact with water. A random amino acid sequence will rarely fold
properly into a compact 3-D shape. So the amino acid sequence is very important to ensure
that a protein folds properly.
Some segments of a protein may form helixes. Others form sheets.
Because of the complexity, the structure of proteins is best illustrated with cartoons.
Rather than drawing the amino acids that form the helix, the cartoon model just draws the
helix. The sheets are drawn as straight lines with arrows on the end. The protein
bacterial rhodopsin is shown in figure 3.13. Notice the helixes. Also note that black and
gray are used to represent amino acids that contain information.
Figure 3.13: Bacterial Rhodopsin
The protein that composes the eye lens in mammals is called crystallin.
It tends to form sheets instead of helixes. Its cartoon representation is shown in figure
3.14. Again, black and gray represent amino acids that carry information. Figure 3.14 also
shows crystallin using the space filling model for the atoms (right side). That is all of
the atoms in the protein are represented by spheres. It is very hard to visualize the
structure of a protein using this model. This is why the cartoons are so useful. When
viewing these structures, keep in mind that they are formed by hundreds and sometimes
thousands of amino acids.
Figure 3.14: Carton and Space Fill Model for Crystallin
 
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