Column: Proteins are mysterious yet essential biochemicals

Proteins are the most important of all biochemicals. They are involved in nearly all bodily processes in one way or another. Understanding their shapes and how the sequence of amino acids determines the shapes is an ongoing and central problem, the most pressing and most intriguing one in biochemistry.

Proteins perform an important variety of functions throughout our biochemical systems. These include structure, regulation, enzymes, signaling, transportation and defense.

Although there are techniques for determining the shape of existing proteins, it is a long and expensive process, and not 100% accurate. There is no sure way to predict the shape of a particular protein from the genome, even if the sequence of amino acids is known precisely. Predicting the shape of the proteins that are formed is a mystery, for now.

Only 20 distinct amino acids make all proteins. Genetic instructions join the amino acids into long chains. Each amino acid has one nitrogen atom and two hydrogen atoms on one end and a carbon atom, two oxygen atoms and one hydrogen atom on the other. This common chemistry allows them to be assembled in any order to make proteins.

The number of amino acid chains in various proteins ranges from a few to tens of thousands. The nucleotide sequence of their genes determines the sequences in the chain, which distinguish one protein from another.

For most proteins, the shape of the molecule is of equal importance to its composition. After a gene segment of DNA assembles the amino acids, the protein molecule folds into a unique structure that fits like a key into a lock to initiate or catalyze a reaction.

Proteins perform the primary actions within the cell, following the instructions specified by their genetic information. With few exceptions, other biological molecules are relatively inert elements upon which proteins act.

Merely knowing the amino acid sequence of a protein does not specify what the protein does, how it is shaped or other proteins with which it engages.

No one knows for sure how a cell “knows” which protein to make and when. For example, diseased cells may produce proteins that healthy cells do not, and vice versa. Even worse, many variables, such as whether someone has just had a glass of wine, can affect the type of proteins that the body produces.

One of the lessons learned from the Human Genome Project is that the old dogma of one gene coding for one protein is just not true. As it turns out, one gene can somehow give rise to many different proteins.

Proteins serve many functions. There are structural proteins, such as keratin (hair, nails, silk) and collagen (cartilage, ligaments and tendons, and the main protein component of bones and teeth). Muscle tissue, organs and red blood cells are also proteins.

Some proteins perform regulatory functions, such as transcription factors that bind to DNA while genes transcribe instructions to make other proteins. Other proteins selectively activate or deactivate the transcription factors.

Other proteins have signaling functions. Hormones, such as adrenaline, are proteins that act as signal molecules on their receptors. Insulin is a protein that helps energy-rich glucose molecules penetrate cell walls.

Defensive proteins can include everything from antibodies of the immune system, to toxins from bacterial metabolism or the venom of stinging and biting critters.

Transport proteins include the lipoproteins, of which high-density lipoprotein and low-density lipoprotein, are most common. They transfer all lipid molecules, predominantly cholesterol, phospholipids and triglycerides around the body, making them available to the cells.

A human body may contain as many as 90,000 different kinds of proteins, some of which may also bond with other molecules. One example is glycated hemoglobin, wherein oxygen-carrying hemoglobin protein molecules bond with glucose in the bloodstream.