In this problem, you will explore the protein lysozyme.
Lysozyme is present in hen egg whites and helps to protect the developing chick from bacterial infection by destroying the cell wall of certain bacteria. Lysozyme does this because it is an enzyme, a protein that catalyzes a chemical reaction. In this case, lysozyme catalyzes the breakdown, hydrolysis, of part of the bacterial cell wall. Without a cell wall, the bacteria rapidly burst and die.
Viewing Molecules + open
(A) INSIDE AND OUTSIDE
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.
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For each of these amino acids, fill in the table as appropriate:
Leucine (Leu) 25 Serine (Ser) 81 Serine (Ser) 24
- unanswered InsideOutside
- unanswered Hydrophoydrophilic
- unanswered InsideOutside
- unanswered Hydrophoydrophilic
- unanswered InsideOutside
- unanswered Hydrophoydrophilic
Valine (Val) 92 Alanine (Ala) 10 Lysine (Lys) 1
- unanswered InsideOutside
- unanswered Hydrophoydrophilic
- unanswered InsideOutside
- unanswered Hydrophoydrophilic
- unanswered InsideOutside
- unanswered Hydrophoydrophilic
Hint: The dots are your most useful clue, if you can see most of an amino acid without any dots on it, then that amino acid is considered to be on the surface of the protein. If you cannot 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 the majority 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.
To determine whether each of the 6 amino acids is on the surface or interior of the protein, we need to examine their positions in relation to the protein structure.
1. Start by observing the dots surrounding each amino acid. If an amino acid has most or all of its atoms covered with dots, it suggests that it is located on the inside of the protein. Conversely, if you can see the amino acid without any dots on it, it indicates that the amino acid is on the surface of the protein.
2. Based on the provided information, let's fill in the table:
Leucine (Leu) 25 - Outside - Hydrophobic
Serine (Ser) 81 - Inside - Hydrophilic
Serine (Ser) 24 - Outside - Hydrophilic
Valine (Val) 92 - Inside - Hydrophobic
Alanine (Ala) 10 - Inside - Hydrophobic
Lysine (Lys) 1 - Outside - Hydrophilic
Remember that hydrophobic amino acids tend to be found in the interior of proteins, while hydrophilic amino acids tend to be found on the surface. So, based on the information provided, Leucine (Leu) 25, Serine (Ser) 24, and Lysine (Lys) 1 are located on the outside of the protein. Serine (Ser) 81, Valine (Val) 92, and Alanine (Ala) 10 are located on the inside.
I hope this helps you determine the location of the amino acids within the protein!