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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: 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!