Activities
Build a Simple Protein
Materials
- Styrofoam balls (about an inch or less in diameter) to represent
the atoms and sticks to represent the bonds.
- Hot-glue gun
- Different color paints for each atom type (C- gray, O-red, H-white,
N-blue etc.)
Procedures:
- Color Carbon atoms gray, Oxygen atoms red, Nitrogen atoms blue, and
hydrogen atoms white.
| Amino Acid |
3-Letter Code |
1-Letter Code |
Properties |
Structure (un-ionized
form) |
|
Phenylalanine
|
Phe
|
F
|
aromatic
hydrophobic
neutral
|
|
- Here is a 3D computer visualization of Phenylalanine.
- Assemble Phenylalanine.
- Color Carbon atoms gray, Oxygen atoms red, Nitrogen atoms blue, and
hydrogen atoms white.
| Amino Acid |
3-Letter Code |
1-Letter Code |
Properties |
Structure (un-ionized
form |
|
Aspartate
|
Asp |
D
|
polar
hydrophilic
charged (-)
|
|
- Here is a 3D computer visualization of Aspartate.
- Assemble Aspartate.
- Color Carbon atoms gray, Oxygen atoms red, Nitrogen atoms blue, and
hydrogen atoms white.
| Amino Acid |
3-Letter Code |
1-Letter Code |
Properties |
Structure (un-ionized
form |
|
Isoleucine
|
Ile
|
I
|
aliphatic
hydrophobic
neutral
|
|
- Here is a 3D computer visualization of Isoleucine.
- Assemble Isoleucine.
- Now you are ready to assemble a simple protein.
- See peptide
bonds
- View the protein assemble:
- Connect all 3 amino acids together following these rules and referring
to 3D computer visualization.
- The chain direction is defined as pointing from the amino end (N-terminus)
to the carboxyl end (C-Terminus).
DISCUSSION:
Now examine your model especially the side chains. In the protein you
assembled there are three types of side chains. Phenylalanine is an aromatic
residue as distinguished by the hexagonal structure. Its side chain (hexagonal
part) is nonpolar, which means it will try to avoid water when it is part
of a large folding protein structure. (The protein you assembled is too
small to fold) Phenylalalanine will try to stay close to the core of the
protein away from water. It will try to form bonds with other aromatic
amino acids.
Aspartate or Aspardic Acid ha a polar side chains of hydrogen bonds.
Which means if Aspartate is a part of a large protein, it will stay in
the outside parts of the folded protein structure in contact with water.
Isoleucine has nonpolar side chains which are are branched and stiff.
Since it is nonpolar it will tend to fold away from water.
AUTHOR: TUG SEZEN
|
