paper and beads don t fall off. Then, place the beads in the following order on the pipe cleaner:

Transcription

1 Beady Pipe Cleaner Proteins Background: Proteins are the molecules that carry out most of the cell s dayto-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. Answer the first three questions on your DATA SHEET. Whenever you see this STAR ( ) symbol, you should be marking on your DATA SHEET. 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. Retrieve the following materials: a. One (1) colored pipe cleaners b. Six (6) green beads c. Eight (8) white beads d. Two (2) yellow beads e. Two (2) red beads f. Two (2) blue beads g. Paper N terminus h. Paper C terminus 2. On your pipe cleaner, put an N-terminus label at one end and pinch the end of the pipe cleaner so the paper and beads don t fall off. Then, place the beads in the following order on the pipe cleaner: N-terminus - Met, Lys, His, Val, Ser, Leu, Asp, Glu, Cys, Asn, Tyr, Val, Phe, Trp, Pro, Ser, Thr, Gln, Cys, Gly. Color Amino acids in your polypeptide Green Asn, Gln, Ser(2), Thr, Tyr White Gly, Leu, Met, Phe, Pro, Trp, Val(2) Yellow Cys(2) Red Asp, Glu Blue His, Lys 3. Be sure you evenly space the beads along your pipe cleaner. When you have all beads arranged on the pipe cleaner, put the C-terminus paper at the far end (opposite the C-terminus).

2 4. The beads represent the amino acid sequence in a polypeptide that was specified by the DNA. The amino acids are held together by peptide bonds. This structure that you have in front of you represents your PRIMARY STRUCTURE OF YOUR POLYPEPTIDE. a. Draw/color-in your PRIMARY STRUCTURE for your polypeptide on your Student Data Sheet and answer the related questions. Be sure to add the N-terminus and C-terminus on your diagram 5. The secondary structure of a protein results when parts of the polypeptide coil or fold. Take your string of beads and either fold the strand back and forth accordion style (to represent a beta-pleated sheet ), or coil it around your pencil to form a spiral (to represent a alpha helix ), or do a little of both. These bonds are caused by hydrogen bonding between hydrogens on the amine groups and oxygens on the carboxyl group of each amino acid. You have now made the SECONDARY STRUCTURE FOR YOUR POLYPEPTIDE. a. Draw the SECONDARY STRUCTURE for your polypeptide on your Student Data Sheet. 6. 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. a. Refer to the chart of amino acids below. Color Class Amino acids in your polypeptide Green Asn, Gln, Ser(2), Thr, Tyr White Gly, Leu, Met, Phe, Pro, Trp, Val(2) Yellow Cys(2) Red Asp, Glu Blue His, Lys b. Look at the R group on each of the amino acids on your polypeptide. Look back at the PRIMARY structure you colored, on your Student Data Sheet (, label each amino acid using the following designations: i. nonpolar (NP) ii. polar (P) iii. negatively charged (NC) iv. positively charged (PC)

3 v. place a STAR on ANY amino acids that contain a sulfhydryl group c. Now, create your Tertiary Structure using the information you have for each amino acid: i. Start by folding your protein so that all of the hydrophobic, nonpolar sidechains are buried on the inside of your protein, where they will be hidden from polar water molecules. ii. Next, fold your proteins so the acidic and basic (charged) sidechains are on the outside surface of the protein and pair one negative sidechain with one positive sidechain so that they come within one inch, thereby neutralizing each other. iii. Continue to fold your protein making sure that your hydrophilic, polar sidechains are also on the outside surface of your protein where they can hydrogen bond with water. iv. Last, fold your protein so that the two Cysteine sidechains are positioned opposite each other on the inside of the protein where they can form a disulfide bond that helps stabilize your protein. Disulfide bonds are covalent bonds that form between the sulfur groups of cysteines, thus stabilizing the tertiary shape. d. Draw the TERTIARY STRUCTURE for your polypeptide on your Student Data Sheet and answer the related questions. 7. Many proteins are made of more than one polypeptide chain. Take your polypeptide chain and join it with the polypeptide chain of a fellow classmate. You now have a protein model that is demonstrating quaternary structure. a. Draw the QUATERNARY STRUCTURE for your polypeptide on your Student Data Sheet and answer the related questions.

4 Name: Date: Block: Protein Folding Data Sheet 1. Draw the structure of an amino acid and label the functional groups: 2. If there are only 20 amino acids, how are there thousands of different proteins? 3. How DO YOUT THINK a proteins shape determine its function? 4. DRAW the PRIMARY structure of your POLYPEPTIDE below: WHAT KIND of bonds hold this PRIMARY structure together? 5. DRAW the SECONDARY structure of your POLYPEPTIDE below: WHAT KIND of bonds hold this PRIMARY structure together? 6. DRAW the TERTIARY structure of your POLYPEPTIDE below: In a watery environment, polar amino acids want to have contact with In a watery environment, nonpolar amino acids want to be near each other and from water Positively charged amino acids are to negatively charged amino acids Cysteine side chains want to be near each other because they can form stabilizing bridges *Hint: The strongest interaction between the side chains is a covalent bond formed between cysteine molecules.

5 7. DRAW the QUATERNARY structure of your POLYPEPTIDE below: Analysis: 1. Why are proteins such important molecules in living 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 "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 this happens. 4. Why are proteins among the most diverse macromolecules? 5. How does the structure of a protein determine its function? 6. What is the role of chaperonins in protein folding? 7. Egg white is normally a thick, clear liquid that contains protein. When you cook an egg the white becomes a white semi-solid. However, if you start to heat it up and then cool it down then the white returns to clear. Explain what is happening. 8. Visit the link below a. Describe the structure of collagen. b. Why is collagen one of the most abundant proteins in the human body?