Protein Folding with 15 Tacks and a 4-Foot Mini Toober
Proteins are more than an important part of your diet. Proteins are complex molecular machines that are involved in nearly all of your cellular functions. Each protein has a specific shape (structure) that enables it to carry out its specific job (function).
A core idea in life sciences is that there is a fundamental relationship between biological structure and the function it must perform. At the macro-level, Darwin recognized that the structure of a finch’s beak was related to the food the finch ate. This fundamental structure-function relationship is also true at all levels below the macro level, including proteins and other structures at the molecular level.
In this activity you will explore the structure of proteins and the chemical interactions that drive each protein to fold into its specific structure.
Each protein is made of a specific sequence of amino acids. There are 20 amino acids involved in protein structure. Each amino acid consists of a unique combination of atoms and has a specific shape. The combination of atoms in each amino acid determines its properties which in turn cause the protein to fold into its correct structure. Amino acids are often called the “building blocks” of proteins and they can combine into hundreds of thousands of different sequences.
Based on the atoms in each amino acid, the amino acid could be hydrophobic, hydrophilic, positively charged, or negatively charged.
Hydrophobic and Hydrophilic Properties
What do you think hydrophobic means? Separate the word ‘hydrophobic’ into its two parts — hydro and phobic. Hydro means water and phobia means fear or dislike, so hydrophobic side chains (yellow tacks) don’t like water. Hydrophobic side chains are also referred to as non-polar side chains.
Now can you guess what hydrophilic means? Philic means likes or attracted to, so hydrophilic side chains (white tacks) like water. Hydrophilic side chains are also referred to as polar side chains.
Acidic and Basic
Can you think of acids you have around your house? Lemon and fruit juices, vinegar and hydrogen peroxide, phosphoric acid (in dark sodas) are common household acids. Acids taste sour and are typically liquids.
Can you think of bases you have around your house? Tums, baking soda, drain cleaner and soap are common bases. Bases taste bitter and can be a liquid or solid.
What happens when you mix lemon juice or vinegar with baking soda? They neutralize each other.
A cysteine can interact with another cysteine to form a disulfide bond that helps stabilizes the folded protein.
With 15 tacks and a mini toober you can explore the principles of chemistry that drive protein folding. The color-coded tacks represent the properties of the amino acids.
1. Select 15 colored tacks according to the list below. The chart below indicates the properties of the colored side chains.
2 blue tacks
2 red tacks
6 yellow tacks
3 white tacks
2 green tacks
2. Mix your colored tacks together and place them on the mini toober about 3 inches apart.
Note: As you push the tacks into the mini toober, they may hit the wire in the middle and not go in all of the way. Reposition your tack so that it goes slightly above or below the wire.
Be careful not to push the tack through to the other side of the mini toober where it can poke your finger. If you compress the foam near a tack it could also poke your finger. Also be careful not to tear the foam with the tack.
3. Now fold your protein, following the principles of chemistry that drive protein folding.
A stable protein simultaneously satisfies all of the principles of chemistry that drive protein folding, as described in A through D below.
A. Hydrophobic (non polar) amino acids (yellow tacks) will be buried on the inside of the globular protein, where they are hidden from polar water molecules.
B. Charged amino acids (blue and red tacks) will be on the surface of the protein where they often neutralize each other to form an electric bond (salt bridges).
C. Hydrophilic (polar) amino acids (white tacks) will be on the surface of the protein where they can interact with water by forming hydrogen bonds.
D. Cysteine amino acids (green tacks) often interact with each other to form covalent disulfide bonds that stabilize protein structure.
A chart of the side chains and their properties is below.
Proteins perform critical functions in all of our cells. Without proteins life wouldn’t exist. With your group or class, can you think of some of some specific proteins and describe what function they perform?
Proteins are involved in your metabolism, cell structure, immune system, DNA expression, protein folding, transport, movement, communication, and storing energy.