Video 1
Protein Folding
Proteins are building blocks that help give your body structure and do work on your body. They move molecules, they make new molecules, they recycle old molecules, and this is just to name a few of the things they do. But maybe the most interesting thing is these protein building blocks are themselves made up of smaller building blocks called “amino acids”.
Here you can see a string of the amino acids, the different shapes that you can see represent the atoms that make up each amino acid. And here we have highlighted the 12 individual amino acids. To make it simpler, each different amino acid can be represented by a single letter. Now each amino acid is shown as the color ball, looking like beads on the string. That makes the protein’s structure easier to imagine. The order of the amino acids is only a part of the story.
Because of the different shapes of the individual amino acids, they like to fold into even more interesting three-dimensional shapes. This molecule is twisting into several different spiral or helical shapes, and then those are folding on each other. Take a look at the three-dimensional shape as we give the protein a spin, kind of looks like a log stacked in the fire place.
Here is the one-letter amino acid code revealing the identity of each amino acid. Again now you see the amino acids drawn to show the position of the each atom. This is like looking of the atomic skeleton of each amino acid. Just like you take up more space than just your skeleton would, see how much space each atom really occupies, this is the real shape of the protein.
Now you’ve seen an example of the protein taking shape, and several of the ways scientists visualize this tiny building blocks used throughput our body.
Video 2
What is a Protein Learn about the 3D shape and function of macromolecules?
Proteins play countless roles throughout the biological world, from catalyzing chemical reactions, to building structures of all living things. Despite this wide range of functions, all proteins are made out of the same 20 building blocks called amino acids. The way these 20 amino acids are arranged dictates the folding of the protein into its unique final shape and its function.
Amino acids are made of carbon, oxygen, nitrogen, hydrogen and sulfur atoms. These atoms form an amino group, a carboxyl group, and side chains attached to a central α-carbon atom. The side chain is the only part that varies from amino acid to amino acid and determines its property. Hydrophobic amino acid such as leucine and isoleucine have carbon-rich side chain, which don’t interact well with water. Hydrophilic amino acids such as serine or threonine interact well with water. Charged amino acid, like glutamic acid or arginine interacts with oppositely charged amino acids or with water.
The primary structure of proteins is the linear sequence of amino acids as encoded by DNA. The amino acids are joined by peptide bonds, which link the amino group and carboxyl group. A water molecule is released each time a bond is formed. Specific amino acid sequences give proteins their distinct shapes and chemical characteristics.
These protein chains often fold into two types of secondary structures, stabilized by hydrogen bond. a protein chain can fold into a rigid alpha helix, forming regular patterns of hydrogen bones between the backbone atoms of nearby amino acids. Backbone atoms of the chain can interact side by side to form the beta sheet.
Many proteins fold into a compact globular shape, the hydrophobic side chains sheltered inside away from the surrounding water. The functions of many proteins rely on this folded structure. For instance, hemoglobin forms a pocket for heme, a small molecule with an iron atom in the center that binds oxygen. Two or more polypeptide chains can come together to form one functional molecule with several subunits. The four subunits of hemoglobin cooperate so that the complex can pick up more oxygen in the lungs and release it in the body.
Many proteins rely on the ability to recognize the shape of the specific molecules in order to function correctly. The flexible arms of antibodies protect the body from disease, by recognizing and binding to foreign molecules and thus preventing the viral RNA or DNA to enter the cell. Collagen forms a strong triple helix that is used throughout the body for structural support. The calcium pump moves ions across our membranes allowing the synchronized contraction of muscle cells. The hormone insulin is a small, stable protein that can easily maintain its shape or travel to the blood to regulate blood sugar level. Alpha-amylase is an enzyme with a catalytic site that begins the breakdown the carbohydrates in the saliva. Ferritin forms a hollow shell that stores ion from our food.
Learn more about the functions and 3D structures of nucleic acids, proteins and molecular machines of the RCSB protein data bank.
