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7.7: Discovering RNA: structure and some functions

DNA is not the only nucleic acid found in cells. A second class of nucleic acid is known as ribonucleic acid (RNA.) RNA differs from DNA in that RNA contains

  1. the sugar ribose (with a hydroxyl group on the 2’ C) rather than deoxyribose;
  2. it contains the pyrimidine uracil instead of the pyrimidine thymine found in DNA; and
  3. RNA is typically single rather than double stranded.

Nevertheless, RNA molecules can associate with an ssDNA molecule with the complementary nucleotide sequence. Instead of the A-T pairing in DNA we find A pairing with U instead. This change does not make any significant difference when the RNA strand interacts with DNA, since the number of hydrogen bonding interactions are the same. When RNA is isolated from cells, one population was found to reassociate with unique sequences within the DNA. As we will see later, this class of RNA, includes molecules, known as messenger or mRNAs, that carry information from DNA to the molecular machinery that mediates the synthesis of proteins. In addition to mRNAs there are other types of RNAs in cells. These include structural, catalytic, and regulatory RNAs. As you might have already suspected, the same hydrophobic/hydrophilic/H-bond considerations that were relevant to DNA structure apply to RNA, but because RNA is generally single stranded, the structures found in RNA are somewhat different. A single-stranded RNA molecule can fold back on itself to create double stranded regions. Just as in DNA, these folded strands are anti-parallel to one another. This results in double-stranded "stems" that end in single-stranded "loops". Regions within a stem that do not base pair will bulge out. The end result is that RNA molecules can adopt complex three-dimensional structures in solution. Such RNAs often form complexes with other molecules, particularly proteins, to carry out specific functions. For example, the ribosome, the macromolecular machine that mediates the synthesis of polypeptides, is a complex of structural and catalytic RNAs (known as ribosomal or rRNAs) and proteins. Transfer RNAs (tRNAs) are a integral component of the protein synthesis system. RNAs, in combination with proteins, also play a number of regulatory functions including recognizing and regulating the synthesis and subsequent behaviors of mRNAs, subjects typically considered in greater detail in courses in molecular biology.

The ability of RNA to both encode information in its base sequence and to mediate catalysis through its three dimensional structure has led to the “RNA world” hypothesis. It proposes that early in the evolution of life various proto-organisms relied on RNAs, or more likely simpler RNA-like molecules, rather than DNA and proteins, to store genetic information and to catalyze at least a subset of reactions. Some modern day viruses use single or double stranded RNAs as their genetic material. According to the RNA world hypothesis, it was only later in the history of life that organisms developed the more specialized DNA-based systems for genetic information storage and proteins for catalysis and other structural functions. While this idea is compelling, there is no reason to believe that simple polypeptides and other molecules were not also present and playing a critical role in the early stages of life’s origins. At the same time, there are many unsolved issues associated with a simplistic RNA world view, the most important being the complexity of RNA itself, its abiogenic (that is, without life) synthesis, and the survival of nucleotide triphosphates in solution. Nevertheless, it is clear that catalytic and regulatory RNAs play a key role in modern cells and throughout their evolution. The catalytic activity of the ubiquitous ribosome, which is involved in protein synthesis in all known organisms, is based on a ribozyme, a RNA-based catalyst.


  • Michael W. Klymkowsky (University of Colorado Boulder) and Melanie M. Cooper (Michigan State University) with significant contributions by Emina Begovic & some editorial assistance of Rebecca Klymkowsky.