What is a Protein Made of?

We all know protein can be found in meat, eggs, dairy products, beans, and protein powder. “Protein,” as a food item, can come from a large variety of sources, but what exactly is a protein? Any Bio 101 student can tell you protein is one of the four macromolecules of life. It’s an important building block to any organism and, while it is found in steak, steak is not a “protein” in the scientific sense. Specific proteins are found in large quantities in muscular tissues, but many proteins are found in every other cell in every organism. They act as micromachines that perform functions ranging from producing energy to transporting molecules to defining cellular structure.

Kinesin, a motor protein, walks along a microtubule filament to transport cellular cargo

Let’s get to the root of this question and take a look at the origin of a protein. To do this, we will need to start with everyone’s favorite macromolecule: DNA. Our DNA is a long strand of molecules called nucleotides arranged into sections called genes that are actually blueprints for different proteins. Each gene includes information that is transcribed to RNA, reorganized, and translated into an amino acid sequence by a ribosome. This process, known as protein synthesis, is where the ribosome looks at three-nucleotide-long “words”, called codons, to know which amino acid to attach next. Amino acids are the building blocks of protein. They are simple molecules containing an amine group, a carboxyl group, and varying side chains all connected by two carbon atoms. Their simple structure allows them to make chains linked by peptide bonds between the carboxyl carbon and amine nitrogen.

The backbone of every amino acid has the same formula

This initial assembly of the amino acids is what biochemists refer to as the “primary structure” of a protein — but at this stage the protein is far from complete! Once the sequence is assembled, some interesting things start happening. Remember those side chains? They interact with their neighbors to form the protein’s “secondary structure” — typically a series of zig-zagging β-sheets and spiraling α-helices. These sheets and helices in turn interact with their neighbors, and their neighbors’ amino acids. Typically, the hydrophobic (water-fearing) amino acid side chains “flee” to the interior of the protein, and the hydrophilic (water-loving) amino acids move to the surface. This protein folding reorganizes and folds the secondary structure components into a complete protein! This is the “tertiary structure” of proteins. Many proteins stop here, but some combine with other proteins to create large assemblies that work in concert to achieve a single purpose. These assemblies are the “quaternary structure”.

An alpha helix showing hydrophilic residues in cyan and hydrophobic residues in orange. The green lines represent interactions that stabilize the helix. Notice how the hydrophobic and hydrophilic side chains are positioned. This will determine how and where the helix folds in the tertiary structure.

Each protein is built at a specific time with a specific task to complete and they’re very specialized. Proteins start working for you at the moment of conception, when they get busy transporting chromosomes during cell division. They give you energy by facilitating the transfer of hydrogens. They even keep you safe by binding and removing pathogens from your body. This last job is completed by proteins called antibodies and leads us to the question of our next blog: What is an Antibody? Come check it out in two weeks!

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