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Many of the proteins in a cell are recycled on a regular basis and serve as a source of amino acids for new protein synthesis. Ubiquitin is a very small protein that is so named because it is ubiquitous in eukaryotic cells and has a highly similar structure between greatly different organisms. It functions as a tag that attaches to proteins to target them, generally for degradation. The process of adding this tag to the targeted proteins is known as the ubiquitination pathway. Subsequently, these proteins are broken down into small pieces in a structure known as a proteasome.
Proteins are molecules composed of units of amino acids strung together by peptide bonds. They can undergo a great deal of modifications, one of which is having compounds attached to the beginning or end of the protein molecule. Many proteins are enzymes, which speed up reactions. One type of enzyme is a protease, which degrades other proteins under specific and highly regulated circumstances. The ubiquitination pathway involves the activity of proteases.
Ubiquitin is an ever-present molecule in higher organisms. It is not found in bacteria. This small protein is found within cells. It has an unusually high number of molecules of the amino acid lysine, and there are seven of these compounds present.
Original work on ubiquitin suggested that target proteins, especially those that were defective, bound to a particular lysine molecule on this protein tag. Now it is known that proteins to be degraded can bind to various lysine groups or even to the end group of this ever-present protein. The process of the binding of the protein to ubiquitin to start the process of ubiquitination is energy-intensive. Normally, the cleavage of a peptide bond releases energy. In this case, it utilizes a molecule of the cell’s energy currency adenosine triphosphate (ATP).
The ubiquitination pathway is complex. Even the binding of ubiquitin to the targeted protein involves three different enzymes. One activates the ubiquitin and is known as E1. There are dozens of different types of enzymes involved in step two, known as E2, in which the activated ubiquitin is attached to a conjugating enzyme. Step 3 utilizes one of hundreds of different types of enzymes that recognize different proteins to be degraded and attaches the target protein to a lysine group on the ubiquitin molecule.
Ubiquitination takes place within a complex called a proteasome. This is a large structure in which proteases degrade the ubiquitinylated protein. It is broken down into smaller fragments of amino acids known as peptides. These pieces can be easily degraded into their component amino acids by peptidases and used as an amino acid source to synthesize new proteins. In some cases, the process produces active peptides involved in cellular metabolism.
The discovery that the ubiquitination pathway led to the proteins being degraded within the proteasome was ground breaking work. It earned the Nobel Prize in Chemistry for the three scientists involved. As more research has been conducted on this process, it has turned out to be much more complicated than originally thought. Proteins can have ubiquitin added in an array of fashions, such as in a chain. This process has implications across the spectrum of physiology, infectious diseases, and genetic disorders.