Nucleotides, the building blocks of RNA and DNA, are themselves composed of a pentose sugar attached to a nitrogenous base on one side and a phosphate group on another. The sugar is either the 5-carbon sugar ribose or its close cousin, deoxyribose (the “deoxy” refers to a “missing” hydroxyl group on the 2-carbon, which has an H instead). The attached nitrogenous base can be a purine, which is a 6-member ring fused to a 5-member ring, or a pyrimidine, which is a single 6-membered ring. These bases are usually adenine (purine), guanine (purine), thymine (pyrimidine), and cytosine (pyrimidine) for DNA, with a substitution of uracil for thymine in RNA bases. However, there are also some unconventional and modified bases that show up in special situations, such as in tRNAs. In addition to being the monomer components of DNA and RNA, nucleotides have other important functions as well. The best known, adenosine triphosphate, or ATP, is the primary “instant” energy source for the cell by the energy released through hydrolysis of its terminal phosphate group.
DNA or RNA are built from nucleotides through linkages of the sugars, and the polymerization occurs by condensation reactions, but these bonds are not glycosidic bonds like with polysaccharides. Instead, bonds form between the 5’ phosphate group of one nucleotide and the 3’ hydroxyl group of another. These are phosphodiester bonds, and a quick glance at the structure (fig. 8) explains the naming: an ester bond is a carbonoxygen linkage, and the phosphodiester bond is a C-O-P-O-C, so there are two esters with a phosphorus linking them. With the purine or pyrimidine base on the 1-carbon, this arrangement places the bases on the opposite side of the sugar from the polymerizing phosphodiester bonds. This forms a sugar-phosphate backbone to the DNA/RNA, which then has the bases projecting out from it.
Figure 8. (A) DNA and (B) RNA differ by the presence of —OH on the 2-carbon of ribose but not deoxyribose and the use of uracil in RNA instead of thymine. Both are constructed from nucleotides like adenosine triphosphate (C).
The bases will then likely interact with the bases of other nucleotides, whether part of another nucleic acid strand or free-floating. Not only do they interact, but they interact with great specificity and consistency: adenines base-pair with thymines (or uracils) through two hydrogen bonds, while guanines interact with cytosine through three H-bonds. Note that while one extra hydrogen bond does not appear to be particularly significant, the attraction between G-C is 50% stronger than between A-T, and over long stretches of DNA, areas high in G-C content are significantly more difficult to unzip (separate strands) than areas high in A-T pairs. This specific base-pairing, known as Chargaff’s rules, is the basis for life: base-pairing is needed to make DNA double stranded, which gives an organism a built-in backup of genetic information and it is also the basis for transforming that information into proteins that form the bulk of a cell.
Nucleic acids, the long polymers of nucleotides, exist in either single or double stranded forms in vitro. However, in the cell, most RNA is single-stranded, and most DNA is double-stranded. This difference is important to their function: RNA is a temporary information transfer molecule for a particular gene, DNA is the permanent repository of all genetic information needed to make an organism. Therefore, RNA needs to be easily read, meaning that the bases need to be accessible, and not locked to a complementary strand. Its long-term stability is not particularly important because when it is made, usually many copies are made at the time, and it is only needed while the cell needs to make the protein it encodes. Conversely, the same strand of DNA is read over and over to make the RNA, and since there are only two copies of each chromosome (a chromosome is a single double-stranded DNA molecule) in a cell, the ability to maintain the integrity of the DNA is crucial. Because of base pairing, each strand of DNA contains all the information necessary to make a complete exact copy of its complementary strand.
Of course, the point of the genetic information in DNA is to encode the production of proteins that can then carry out the functions that define cellular life. Some of those functions, such as DNA replication, gene regulation, transcription, and translation, require the proteins to interact with a nucleic acid. Usually, part of the recognition process involves apposition of a positively charged region of the protein to the DNA (or RNA), which is a very negatively charged molecule, as expected from all the phosphates in the sugar-phosphate backbone. RNA, but not DNA (with some exceptions), can also interact with itself by complementary base-pairing. If a stretch of RNA sequence comes into contact with a stretch of RNA with a complementary sequence on the same molecule, then base-pairing can occur. Depending on the number of nucleotides between the complementary areas, secondary structures such as stem-and-loops and hairpins can form.