Updated: May 12, 2019
Kathleen Hamrick Will Brooks, Ph.D.
[Editor’s Note: The following article was written by A.P. auxiliary staff scientist Will Brooks and one of his students. Dr. Brooks holds a Ph.D. in Cell Biology from the University of Alabama at Birmingham and serves as Assistant Professor of Biology at Freed-Hardeman University.]
One of the goals within the discipline of biology is to define life. This goal, however, is no simple task. While we can have an intuitive understanding of what it means to be alive, forming this understanding into a precise definition of life poses a dilemma for scientists. Life comes in many shapes, sizes, colors, and forms, so placing all these variations of life into one nice definition is seemingly impossible. To circumvent this problem, scientists have defined life by stating characteristics shared by all life forms. To be considered “alive,” a system of molecules must possess each of these characteristics. Examples include (1) the ability to sense and respond to stimuli, (2) the ability to acquire and utilize materials for energy, (3) the ability to store genetic information in the form of DNA, and (4) the ability to self-replicate. All living organisms share these basic characteristics, and those systems of molecules which lack even one of these basic characteristics is not considered to be a living organism.
Deoxyribonucleic acid (DNA) is the genetic material used by all living organisms to code for life. DNA can be thought of as the genetic fingerprint of each organism because it is unique to each species of organism. During the process of self-replication, this genetic code is duplicated and identical copies (discounting rare instances of mutation) are given to each progeny of an organism, maintaining the fingerprint and thus the identity of that organism. The function of DNA as the genetic material of an organism is to provide a code for the production of another group of molecules known as proteins. Proteins serve a host of functions for an organism. They are known, appropriately, as the workhorses of a cell, because they carry out the vast majority of organismal tasks, including catalysis.
A catalyst is any substance capable of increasing the speed of a chemical reaction. Within each living organism on Earth, millions of chemical reactions take place every minute. The majority of these reactions are prompted by a very large group of protein catalysts known as enzymes. These enzyme-mediated chemical reactions range from those used to synthesize various metabolites to those used to break down ingested foods. By serving as enzyme catalysts, proteins play a crucial role in all living organisms. For without enzymes, organisms would be both unable to break down the food that they ingest and unable to make the necessary metabolites needed to sustain life.
While the vast majority of functional enzymes within living organisms are proteins, scientists have discovered that another group of molecules, known as ribonucleic acids (RNAs), are also capable of catalyzing some chemical reactions (Kruger, et al., 1982). RNAs are very similar in structure to DNA, differing only in the type of sugar used to form the molecules—DNA utilizes deoxyribose and RNA utilizes ribose. While DNA is the vital genetic code that is passed down between parents and offspring, RNA also plays an important role. Ribonucleic acids are a messenger system that carries the DNA code from the cell’s nucleus, the home of DNA, to the cellular cytoplasm where proteins are synthesized. These are known as messenger RNAs (mRNA). Furthermore, another group of RNAs, known as ribosomal RNAs (rRNAs), is used along with proteins to build the cellular structure known as the ribosome, which is the cellular location at which proteins are made. So, RNA plays several related roles in the process of protein production: (1) it carries the genetic code from DNA to the ribosome, (2) it helps form the structure of the ribosome, and (3) it functions in catalysis.
While there are a few other examples (reviewed in Fedor and Williamson, 2005), the catalytic properties of RNA are best seen in the ribosome. When proteins are synthesized by an organism’s cells, small units known as amino acids are chemically linked together to form a long, linear chain. This chain of amino acids is known as a polypeptide or protein. The chemical bond that links together each amino acid in the chain is called the peptide bond. Because each of the 20 amino acids are very similar in structure, the same peptide bond is formed between every unit of the polypeptide chain. The chemical reaction that forms this peptide bond requires catalysis. The protein-rRNA complex that we know as the ribosome has long been known to serve as the site as well as the catalyst in forming the peptide bond. But, scientists were surprised to discover that the protein component only serves as a structural element of the ribosome. It is the RNA component of the ribosome that serves as the catalyst (Nissen, et al., 2000). This catalytic RNA has thus been termed a ribozyme.
Later it was discovered that yet another group of RNAs, the small nuclear RNAs (snRNA), were also capable of catalyzing a chemical reaction (Valadkhan and Manley, 2001). When produced by the cell, mRNA must undergo a series of maturation steps before it is fully functional as a genetic message (Alberts, et al., 2002, pp. 317-327). One of these steps toward maturity is the process of splicing. Newly synthesized mRNA contains large regions, spread