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Modeling Protein Structures Using Pipe Cleaners

This document outlines an educational activity where students model protein structures using pipe cleaners and beads to represent amino acids. The objectives include understanding the relationship between amino acid sequences and protein properties, as well as the impact of protein folding on functionality. The activity emphasizes the role of various amino acids and bonding types in determining protein structure and behavior in different environments.

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yangyin2342
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Download as PDF, TXT or read online on Scribd
6 views

Modeling Protein Structures Using Pipe Cleaners

This document outlines an educational activity where students model protein structures using pipe cleaners and beads to represent amino acids. The objectives include understanding the relationship between amino acid sequences and protein properties, as well as the impact of protein folding on functionality. The activity emphasizes the role of various amino acids and bonding types in determining protein structure and behavior in different environments.

Uploaded by

yangyin2342
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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Modeling Protein Structure Using Pipe Cleaners

Objectives: After completing this activity, you will be able to:


 Explain the connection between the sequence and the subcomponents
of a biological polymer and its properties.
 Refine representations and models to explain how the subcomponents
of a biological polymer and their sequence determine the properties of
that polymer.
 Use models to predict and justify that changes in the subcomponents of
a biological polymer affect the functionality of the molecule.

In this activity, you will model the tertiary level of protein structure using pipe cleaners. Pipe cleaners are an ideal
building material since they are flexible and repositionable. We will also use beads to represent various amino acid
types. You will need to review the various levels of protein structure before performing this activity.

The type of amino acids that a protein is constructed from dictates what shapes the protein will
bend and fold into, as many proteins are not functional until they have been folded into a proper
configuration. Recall from first-year biology that proteins are synthesized from nucleotide
instructions found in DNA molecules that have been copied to mRNA molecules that code for each
amino acid. These amino acids, carried by tRNA are then assembled at the ribosome per the
copied sequence encoded for by mRNA. The protein then achieves its functionality when it is
bent and folded into a biochemically functional, thermodynamically stable form. However, some
proteins are functional only when they are not bent. Furthermore, failure of a protein to fold
PrP, a misfolded protein correctly can lead to malfunctioning, even toxic, protein molecules.
that causes bovine
spongiform Proteins are aided in the folding process by other proteins known as chaperonins. These proteins
encephalopathy (BSE),
or “mad cow” disease help newly synthesized proteins fold into the correct configuration.

For this activity, you will use the following pieces of equipment:
 Pipe cleaners (about 20 inches long)
 Craft beads:
o Yellow: hydrophobic amino acids
o Blue: positively (+) charged amino acids
o Red: negatively (–) charged amino acids
o White: hydrophilic (polar) amino acids
o Green: amino acid Cysteine
 Rubber bands
 Colored lab tape

Instructions:
1. The pipe cleaners will be the backbone of your protein; however, it is not the primary structure of your protein.
Your teacher will model a protein with primary structure for you so that you can see the difference between the
two structure types.

2. Choose a mixture of at least 10 craft beads to place on your pipe cleaner. These will represent the different
amino acids of your protein. You will choose what order these will go in along your protein chain…be creative!
Be sure to space them apart evenly. You will need to twist two pipe cleaners together to form a long chain for
the protein backbone.

Modeling Protein Structures Using Pipe Cleaners 2012


3. Here’s where the science comes in:

Basic Laws of Chemistry that Drive Protein Folding

Stably folded proteins simultaneously satisfy several basic laws of chemistry including:

 Hydrophobic sidechains (yellow tacks) will be buried on the inside of the globular protein, where they
are hidden from polar water molecules.
 Charged sidechains (blue and red tacks) will be on the surface of proteins where they often neutralize
each other and form salt bridges.
 Polar sidechains (white tacks) will be on the surface of the protein where they can hydrogen bond with
water.
 Cysteine sidechains (green tacks) often interact with each other to form covalent disulfide bonds that
stabilize protein structure.

4. Recall that tertiary structure of proteins also involves ionic bonding interactions as well as hydrogen bonding
interactions. To show bonding, attach the amino acids which are bonding with a rubber band or paper clip and
use a piece of tape to label the type of bond represented.

5. In the space on the next page, sketch your pipe cleaner protein and label it appropriately.

Questions: Answer these in your BILL.


1. Describe how proteins are formed.
2. How is the protein’s structure affected by:
a. The presence of hydrophilic amino acids?
b. The presence of hydrophobic amino acids?
c. Various bonding types (be specific and identify the various bonds)?
3. Explain how your protein would behave in an aqueous environment and why.
4. Describe factors that will affect the protein’s shape.
5. How do changes in the protein’s shape affect its function?
6. What biological process can cause protein shape (and function) to change?

Modeling Protein Structures Using Pipe Cleaners 2012

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