Proteins

Proteins are the molecules of life. Some proteins are muscle. Other proteins send signals within and between cells, turn genes on and off, form the skeleton of cells, burn energy, catalyze and inhibit chemical reactions, control the immune system. Proteins do it all.

Although every school course in biology tells more about proteins than this single web page, this page's related links form an reasonable introduction.

Protein Structure

Proteins are long chains of amino acids. Only twenty amino acids in various combinations form proteins, so for simplicity, each amino acid is often represented by a letter of the alphabet. Therefore, a protein can be written as a sequence such as MALWMRLLPL. These amino acids are the beginning of the protein insulin. Insulin is a small protein: here is it's complete list of amino acids:

MALWMRLLPL LALLALWGPD PAAAFVNQHL 
CGSHLVEALY LVCGERGFFY TPKTRREAED 
LQVGQVELGG GPGAGSLQPL ALEGSLQKRG

Many proteins are ten, twenty, or a hundred times bigger than insulin. But all proteins are chains of the same 20 amino acids. There are hundreds of thousands of proteins, each different in the sequence of its amino acids.

If you know a protein's sequence of amino acids, you can identify it. This is the basis of protein identification by mass spectrometry.

Within cells, proteins fold these one-dimensional chains into an amazing variety of three-dimensional structures. These 3D structures allow proteins to perform their wide range of functions. You can get an idea of the wide variety of protein structures by following the "Protein pictures" related links on the left.

Much of protein science is devoted to learning these 3D structures and how to predict a protein's function from its structure. A major computational biology problem is predicting the 3D structure from the 1D structure. . You can also participate in the computational biology of protein folding with the "folding@home" project.

Protein Functions

Proteins work together in pathways — sequences of chemical reactions — to perform a wide variety of functions:

• Metabolism — proteins mediate chemical reactions that use oxygen to burn food for energy. These pathways are complex but well studied. The related links show maps of thousands of proteins in the metabolic pathways.
• Signaling — hormones are proteins that signal between cells usually in the blood. Proteins also send signal from one nerve cell to another. Signaling pathways, however, are usually interactions among proteins within a cell.
• Regulation — proteins called enzymes control chemical reactions in cells. Proteins also form gateways in cellular membranes to control what passes into or out of a cell.
• Cellular structure — proteins define cell shape and form.
• Transportation — proteins move oxygen, sugar, nutrients and wastes into and around cells. They also move other proteins from where they are made to where they are used.
• Movement - proteins contract muscles and move cells.
• DNA Transcription — proteins turn genes on and off.
• Immune System Functions - special proteins identify germs and other foreign substances and mark them for destruction.

Proteins as Molecular Machines

Many proteins are neither rigid nor static. They change shape, open and close, twist and turn. This ability to move lets proteins be tiny machines that can grab and release, push or pull. The animations in the related links can give you an idea of the variety of movements that proteins can make.

Unique structures and shape shifting enable proteins to be astounding effective catalysts.

Proteins as Catalysts

A catalyst speeds up a chemical reaction. Iron rusts somewhat faster when wet; in other words, water catalyzes rusting. But so what? Inorganic catalysts are dull.

In contrast, enzymes — proteins that act as catalysts — make life possible. Whereas water speeds up rusting only somewhat, enzymes speed up cellular reactions thousands or millions of times. A chemical reaction that takes a fraction of a second with enzymes would take years without it.