What is a Protein? Learn about the 3D shape and function of macromolecules

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 the structures of all
living things. Despite this wide range of functions, all
proteins are made out of the same twenty building blocks, called amino acids.
The way these twenty 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 a side chain attached to a central carbon atom. The side chain is the only part
that varies from amino acid to amino acid and determines its properties.
Hydrophobic amino acids such as leucine and isoleucine have carbon rich side chains, which
don’t interact well with water. Hydrophilic amino acids such as serine, or threonine interact
well with water. Charged amino acids like glutamic acid or arginine interact with oppositely
charged amino acids or with water. The primary structure of the protein is the
linear sequence of amino acids as encoded by DNA.
The amino acids are joined by peptide bonds, which link an amino group and a 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 folds into two types of secondary structures stabilized by
hydrogen bonds. A protein chain can fold into a rigid alpha
helix, forming regular patterns of hydrogen bonds between the backbone atoms of nearby
amino acids. Backbone atoms of the chain can interact side-by-side
to form beta sheets. Many proteins fold into a compact globular
shape, with 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 to hold 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 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 cell membranes
allowing the synchronized contraction of muscle cells.
The hormone insulin is a small, stable protein that can easily maintain its shape while traveling
through the blood to regulate blood sugar levels.
Alpha amylase is an enzyme with a catalytic site that begins the breakdown of carbohydrates
in our saliva. Ferritin forms a hollow shell that stores
iron from our food. Learn more about the functions and 3D structures
of nucleic acids, proteins, and molecular machines at the RCSB Protein Data Bank.