In this problem, 6 amino acids have been randomly selected from the 129 amino acids in lysozyme; they are shown as solid spheres. The remainder of the protein is shown as a cloud of tiny dots.
Your task is to find out which of the 6 amino acids are on the surface of the protein and which are on the interior of the protein.
For each of these amino acids, fill in the table as appropriate:
Leucine (Leu) 56 Arginine (Arg) 21 Asparagine (Asn) 39 Arginine (Arg) 5 Arginine (Arg) 128 Tyrosine (Tyr) 20
Inside
Outside
Hydrophobic
Hydrophilic
Inside
Outside
Hydrophobic
Hydrophilic
Inside
Outside
Hydrophobic
Hydrophilic
Inside
Outside
Hydrophobic
Hydrophilic
Inside
Outside
Hydrophobic
Hydrophilic
Inside
Outside
Hydrophobic
Hydrophilic
Hint: The dots are your most useful clue, if you can see all or part of an amino acid without any dots on it, then that amino acid is (at least partly) on the surface of the protein. If you can not see the amino acid without dots on it in any orientation, then that amino acid is on the inside. Remember that you can identify an amino acid by leaving the cursor over any of the atoms in that amino acid. This is shown below:
An "Inside" example An "Outside" example
Notice that all of the atoms in the highlighted amino acid are covered with dots representing other atoms in the protein. Notice that, although some highlighted atoms are covered with dots representing other atoms in the protein, many of the highlighted atoms are visible without dots on them.
Polar (may participate in hydrogen bonds):
• Glutamine - Gln
• Asparagine - Asn
• Histidine - His
• Serine - Ser
• Threonine - Thr
• Tyrosine - Tyr
• Cysteine - Cys
• Methionine - Met
• Tryptophan - Trp
Hydrophobic (normally buried inside the protein core):
• Alanine - Ala
• Isoleucine - Ile
• Leucine - Leu
• Phenylalanine - Phe
• Valine - Val
• Proline - Pro
• Glycine - Gly
Charged: ******Are usually found close to the surface
• Arginine - Arg
• Lysine - Lys
• Aspartic acid - Asp
• Glutamic acid - Glu
To determine which of the 6 amino acids are on the surface and which are on the interior of the protein, you can follow these steps:
1. Examine the amino acid structure: Look at each amino acid and identify which atoms are visible without any dots on them. These atoms represent the exposed part of the amino acid and are likely located on the protein's surface.
2. Leucine (Leu) 56: Hover your cursor over any of the atom in Leucine 56. If you can see all or part of Leucine 56 without any dots on it, then it is on the surface of the protein. Otherwise, it is on the interior.
3. Arginine (Arg) 21: Follow the same process for Arginine 21. If you can see it without any dots on it, it is on the surface. Otherwise, it is on the interior.
4. Asparagine (Asn) 39: Repeat the process for Asparagine 39.
5. Arginine (Arg) 5: Apply the same approach to Arginine 5.
6. Arginine (Arg) 128: Do the same analysis for Arginine 128.
7. Tyrosine (Tyr) 20: Lastly, examine Tyrosine 20.
Using the provided hint, carefully observe each amino acid and identify whether they are on the surface (outside) or the interior (inside) of the protein. Additionally, determine if each amino acid is hydrophobic or hydrophilic based on its chemical properties. Fill in the table with your findings.
For example, for Leucine 56:
Inside:
Outside:
Hydrophobic:
Hydrophilic:
Follow this format for all 6 amino acids to complete the entire table.