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PROTEIN MODELING
Name _________________________ Pr ____
Besides water, the most important molecules to living systems are the organic molecules.
These include carbohydrates, proteins, lipids, and nucleic acids. In this activity you will use ball-andstick models to make 3-dimensinal models of proteins. Use long sticks to join C to C or C to O and
short sticks to join H to other atoms.
Remember:
black = carbon
white = hydrogen
red = oxygen
blue = nitrogen
a stick = two electrons being shared, one from each atom
= a pair of shared electrons
= a single bond
If you need to share two electrons (a double bond) you will need to use two
springs.
Proteins are made of chains of amino acids. There are 20 different amino acids.
Using your molecular modeling kit, each team of two will build an amino acid. Two amino acids need
to be built at each lab desk. So if there are only three of you, one will need to work by him/herself.
Amino acids all have five major parts:
1. A Central carbon to which the other four parts are attached
a. An amine group (-NH2)
b. An acid group (-COOH)
c. A single hydrogen
d. An R group
Team #1:
Build the amino acid (threonine – polar uncharged)
diagramed to the right.
Baxter’s initials______
Team #2:
Build the amino acid (aspartic acid – negatively charged
molecule) diagramed to the right.
Baxter’s initials______
Save your models for the next step!!!
Comparing Amino Acids – Questions
1. Circle the groups coming off the CENTRAL CARBONS on the diagrams above that are NOT
the same in both threonine and aspartic acid..Note, the groups coming off the central
carbon can be in any orientation: to the right, to the left, at the top, or at the bottom.
a. These groups are called the “R” groups (which really means “radical,” or “residual,” but
we’re just going to call it the “Rest of the molecule”).
2. What are the OTHER three “groups” (one is actually just a single atom) that come off of the
central carbon?
a. __________________
b.__________________
c.__________________
3. Carbohydrates are made only of Carbon, Hydrogen, and Oxygen. What atom is new to amino
acids that you don’t find in carbohydrates? _____
a. This atom is part of the “amine” group. What is the formula for the amine group? _____
4. The other group (which is NOT the single hydrogen) is called the “acid” group (it is really an
organic acid). What is the formula for this organic acid? __________
5. Why did scientists name amino acids “amino acids”?
Proteins are made by hooking together 50 to 300 amino acids. Start building a protein by hooking
together the amino acids from the two teams. Hook together the AMINE GROUP of one amino acid to
the ACID GROUP of the other amino acid by taking off one H of the amine group and the -OH plus its
stick of the acid group. Then join those two parts together.
6. What is removed to allow the two amino acids to join? ___________
7. What does the term “dehydration” mean? _______________________________________
8. What does the term “synthesis” mean? _________________________________________
9. Why do you think what you just did is termed “dehydration synthesis”?
_________________________________________________________________________
Have me initial your product _____
Now “digest” your product by adding the water back in to where it came from.
1. What does the prefix “hydro” mean? ______________________
2. What does the suffix “lysis” mean? _______________________
3. Why do you think what you just did is termed “hydrolysis”?
__________________________________________________________________________
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Protein Folding
The R groups are critical to the role proteins play in the body. Although some proteins are used for
structure (e.g., in cell membranes, in muscles), most proteins are enzymes. Enzymes are catalysts for
chemical reactions. They make chemical reactions happen faster than they normally would. Enzymes
are globular proteins. Like their name sounds, they form globs, unlike linear proteins that form sheets
for muscles. The shape of the glob and the charges (+, -, or 0) all over the glob determine the function
of the enzyme.
In this activity you will model a protein folding.
Directions:
1. Working in groups of two, fold a toober into a 3dimensinal shape that has a pocket in it (Dr. Baxter will
demonstrate). Please be careful with the toobers. If you
mess one up, you will need to replace it (about $20).
Draw your folded toober here:
2. Using the list below, place tacks (amino acids) where appropriate. The tacks, as placed,
should make the molecule fold as you folded it.
Blue = + R group – will be attracted to the – R groups
Red = - R group – will be attracted to the + R groups
Yellow = non-polar hydrophobic R groups – these will be buried on the inside of the protein,
where they are hidden from polar water molecules.
White = polar hydrophilic R groups – will be on the outer surface where they can form
hydrogen bonds with water.
3. Carefully unfold your protein and list the amino acids in order, left to right, using these
simplified notations: +, -, NP (for non-polar), P (for polar). Write that list below
4. Using the chart of amino acids provided at each desk, match each +, -, NP and P to the name
of an amino acid that it could be. Using the abbreviations for each amino acid, write that list
below:
5. Now we’re going to reverse this procedure. Take all the tacks off your toober and straighten it
out. Take 15 tacks and place them at random along the toober. Make sure they are about
equally spaced. Now, using the +, -, polar, and non-polar guideline above, bend your toober
into the shape that these tacks demand.
6. Sketch your shape here:
7. Was this toober easy to fold? __________
a. Do you think everyone’s toober would be easy to fold?_____
b. What do you think happens to proteins that don’t fold? ______________________
c. Do you think your body would waste energy to make proteins that don’t work? ______