Protein Folding Activity

Protein Folding Instructions
Background: Proteins are the molecules that carry out most of the cell’s day-to-day
functions. While the DNA in the nucleus is "the boss" and controls the activities of the
cell, it is the proteins that "do the work." In this activity you will examine the structure of
proteins and how their structure is related to their function.
Proteins are made from a chain of amino acids and are folded into a variety of shapes. A
chain of amino acids is called a polypeptide chain. A protein may consist of one or more
polypeptide chains. The shape of the protein will determine its function.
The R groups on the amino acids determine the properties of that amino acid. The
properties of the amino acids also determine the final confirmation of the proteins.
1. If there are only 20 amino acids, how are there thousands of different proteins?
because it has more than one combination in the amino acids
2. How does a protein's shape determine its function?
it is reflected in its unique folded structure
Procedure: To help you understand how a protein is constructed and how its structure is
related to its function, you and your lab partner(s) will build a model of a protein. A
protein’s shape, and ultimately its function, is determined by four levels of structure.
1. Take a pipe cleaner and the following beads: `
Number of Beads Color Amino acids
6 Blue Asn, Gln, Ser(2),

Thr, Tyr
8 Yellow Gly, Leu, Met, Phe,

Pro, Trp, Val(2)
2 Green Cys(2)
2 Pink Asp, Glu
2 Purple His, Lys
2. Place the beads in the following order on the pipe cleaner:
Met, Lys, His, Val, Ser, Leu, Asp, Glu, Cys, Asn, Tyr, Val, Phe, Trp, Pro, Ser,
Thr, Gln, Cys, Gly.
3. Leave a little of the pipe cleaner at each end free so that you can fold it back to prevent
the beads from falling off.) The beads represent the amino acid sequence in a
polypeptide that was specified by the DNA. Find the chart of amino acids in your
text. Look at the R group on each of the following amino acids, and Label each as
nonpolar, polar, negatively charged, or positively charged on your data sheet.
(You can find a chart to help you at the end of this document.)
4. The secondary structure of a protein results when parts of the polypeptide coil (alpha
helix) or fold (beta pleated sheet). Take your string of beads and either fold the
strand back and forth accordion style, or coil it around your pencil to form a
spiral, or do a little of both. You have now made the secondary structure.
5. The third level of organization is called the tertiary structure and this is created when
the folded, twisted chain of amino acids folds back on itself to form the overall
shape of the polypeptide. Take your polypeptide chain and fold it so that the free
ends meet.
6. Many proteins are made of more than one polypeptide chain. Take your polypeptide
chain and join it with the polypeptide chain of the students at your table. You now
th
have a protein model that is demonstrating quaternary (4 level) structure.
How does the final shape of your molecule determine its function?
Protein Folding Data Sheet
Step 1:
Find the chart of amino acids in your text. Look at the R group on each of the following
amino acids, and identify each as nonpolar, polar, negatively charged, or positively
charged.
Draw the structure of an amino acid and label the functional groups:
What kinds of bonds hold this structure together? Covalent
Step 2:
The polypeptide is now in the secondary conformation; the pleats and helices are due to
Hydrogen bonds.
Step 3:
The tertiary conformation is where the peptide looks like a globular protein. Here are the
rules to follow when forming the tertiary structure
a. In a watery environment, polar amino acids want to have contact with water
b. In a watery environment, nonpolar amino acids want to be near each other and
_____________ from water
c. Positively charged amino acids are ________________ to negatively charged amino

acids
d. When you think you have folded the protein correctly, raise your hand to show your
teacher.
Using a spare sheet of paper given to you by Mrs. Craft, draw a picture of your folding
protein, color in the amino acids in their correct colors.
What determines how a protein folds?
Step 4:
For some proteins, the tertiary conformation is its functional form. However, for some
proteins to function, they need to associate with other tertiary structures (called subunits)
creating what is called the ________________ conformation.
Why are some of the structures formed in the class different? How does this relate to
chaperonins? Google chaperonin and provide the definition below.
Analysis:
1. Why are proteins such important molecules in living cells?
because proteins contains stuff that we need and it has a lot of it more than cells
2. If we use an analogy that compares a cell to a factory, why could DNA be called "the
boss" and proteins be called "the factory workers"?
3. Egg white is normally a thick clear liquid containing protein. When heated, it turns into
a white semi-solid. Explain why and how you think this happens.
4. Why are proteins among the most diverse macromolecules?
there are 20 different chemically distinct amino acids that form long chains, and
the amino acids can be in any order.
5.How does the structure of a protein determine its function?
it is determined by its unique folded structure

Protein Folding Activity

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Protein Folding Instructions

because it has more than one combination in the amino acids

2. How does a protein's shape determine its function?

it is reflected in its unique folded structure

1. Take a pipe cleaner and the following beads: `

Number of Beads Color Amino acids

6 Blue Asn, Gln, Ser(2),

8 Yellow Gly, Leu, Met, Phe,

2 Pink Asp, Glu

2 Purple His, Lys

2. Place the beads in the following order on the pipe cleaner:

Protein Folding Data Sheet

What kinds of bonds hold this structure together? Covalent

c. Positively charged amino acids are ________________ to negatively charged amino

What determines how a protein folds?

1. Why are proteins such important molecules in living cells?

4. Why are proteins among the most diverse macromolecules?

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