Download Activity: Protein Exploration!

Activity: Protein Exploration!
IHS Biology / Adapted from 3-D Molecular Designs
Introduction
Proteins are more than an important nutrient in your diet they are complex molecular machines that are involved in
nearly all of your cells’ functions! Each protein has a specific
shape (structure) that enables it to carry out its specific job
Insulin, a small protein
(function). This structure-function relationship is a core
(51 amino acids)
theme in biology. At the macroscopic level, for example, you
know that the structure of a bird’s beak determines the food it can eat. Structure-function
relationships are also true at all levels below the macroscopic level, including proteins and other
structures at the molecular level.
Here are some important facts about proteins:
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Each protein is made of a specific sequence of amino acids. Twenty different amino acids are
found in proteins.
Each amino acid consists of two parts – a backbone and a sidechain. The backbone is the
same in all 20 amino acids and the sidechain is different in each one.
Each sidechain consists of a unique combination of atoms that determines its 3D shape and
its chemical properties.
Based on the atoms in each amino acid sidechain, it could be hydrophobic, hydrophilic, acidic
(negatively charged), or basic (positively charged) – see sections below!
When different amino acids are linked together in a particular sequence to make a protein, the
unique properties of the amino acids’ side chains determine how the protein folds into its final 3D
shape. The structure of the protein allows it to perform a specific function in our cells.
Hydrophobic and hydrophilic sidechains
What do you think hydrophobic means? Separate the word hydrophobic into its two parts – hydro
and phobic. Hydro refers to water and phobia means dislike or fear, so hydrophobic sidechains
“don’t like” (don’t mix with) water. Hydrophobic sidechains are also called non-polar sidechains.
Now can you guess what hydrophilic means? Philic means likes or attracted to, so hydrophilic
sidechains “like” (mix easily with) water. Hydrophilic sidechains are also referred to as polar
sidechains. Hydrophobic and hydrophilic sidechains affect the shape of a protein because cells
(where proteins are found) contain so much water.
Acidic (negatively charged) and basic (positively charged) sidechains
Lemon and other fruit juices, vinegar, and phosphoric acid (in Coca-cola™) are common household
acids. Acids generally taste sour and are typically liquids. Can you think of bases you have around
your house? Tums®, baking soda, and soap are common bases. Bases taste bitter and can be
liquids or solids.
Acidic and basic side chains ionize – that is, they have a negative (acidic) or positive (basic) charge.
When they are part of a protein, these charged amino acids behave in the usual ways: like charges
repel; opposite charges attract.
In our next activity, you will explore the structure of proteins and the chemical
interactions that drive each protein to fold into its specific shape!