Protein Folding Instructions

AP Biology

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?

2. How does a proteins shape determine its function?

Procedure: To help you understand how a protein is constructed and how its structure is related to it 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:

1. 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.

1. 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.
2. Thesecondarystructureofaproteinresultswhenpartsofthepolypeptidecoilorfold.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.
3. 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.
4. 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 have a protein model that is demonstrating quaternary (4thlevel) 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?______

Step 2:

The polypeptide is now in the secondary conformation; the pleats and helices are due to ______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

1. In a watery environment, polar amino acids want to have contact with ______
2. In a watery environment, nonpolar amino acids want to be near each other and ______from water
3. Positively charged amino acids are ______to negatively charged amino acids
4. Cysteine side chains want to be near each other because they can form stabilizing ______bridges
5. Whenyouthinkyouhavefoldedtheproteincorrectly,raise your hand to show your teacher.

*Hint:The strongest interaction between the side chains is a covalent bond formed between cysteine molecules.

Draw a picture of your folding protein, color in the amino acids in their correct colors.

What determine how a protein folds? What bonds are made first?

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?

1. Ifweuseananalogythatcomparesacelltoafactory,whycouldDNAbecalled"theboss" and proteins be called the "the factory workers"?

1. Egg white is normally a thick clear liquid containing protein. When heated, it turns into a white semi-solid. Explain why and how this happens.

1. Why are proteins among the most diverse macromolecules?

5.How does the structure of a protein determine its function?