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About Nucleotides
Nucleic acids are polymers. This means they are strings of individual small molecule units joined together to make the larger nucleic acid molecules. In the case of nucleic acids, the individual units are called nucleotides. These have a consistent structure containing a pentose sugar, a phosphate, and a nucleobase which provides the variability between different sequences of DNA.
The part of the nucleotide that provides the variability that allows for different DNA or RNA sequences to exist is the nucleobase, which provides the "nucleic" part of the name nucleic acid. This is a nitrogen containing molecule, either a pyrimidine or a purine, that can integrate into the DNA or RNA molecule (Figure 1). These nucleobases are basic (with an alkaline pH) and can form hydrogen bonds with other bases on the basis of charge complementarity. The nucleobases adenine, cytosine and guanine are found in both DNA and RNA, whereas thymine is found only in DNA and uracil is found only in RNA.
Figure 1: The five nucleobases found in nucleic acids, adenine (A), cytosine (C) and guanine (G), which are found in both DNA and RNA, thymine (T) which is only found in DNA, and uracil (U), which is found only in RNA. Adenine and guanine, which have two rings are purines, whereas cytosine, thymine and uracil which have one ring are pyrimidines. These form a bond with the pentose sugar via the nitrogen atom at the bottom right of each molecule.
The nucleobases bind to the nucleic acid backbone. The main part of this backbone is the pentose sugar, which is a saccharide molecule like glucose, only instead of having six carbon atoms it contains five (Figure 2). In RNA this pentose sugar is ribose, whereas in DNA the sugar is deoxyribose, which differs from ribose in that it has one fewer oxygen atoms, hence the name, deoxy-. The name of this pentose sugar lends the name ribo- or deoxyribo- in the full name of the nucleic acid.
Figure 2: Pentose sugars are sugars containing five carbon atoms, which like other sugars form a cyclic structure of carbon atoms, and a single oxygen atom, which in this case is a pentagonal ring. Ribose (left) is the sugar found in RNA, and has the formula C5H10O5, so has as many oxygen atoms as carbon atoms. Deoxyribose (right) by contrast has the formula C5H10O4 and is short of one oxygen atom compared to ribose, hence the deoxy- in the name. Carbon atoms in the pentose sugar are numbered 1 to 5, starting from the right hand side with the carbon that binds to only one carbon atom as well as the bridging oxygen molecule, and finishing at the carbon atom on the branch. The different number of oxygen atoms in the two molecules is reflected in the carbon 2, which in ribose has a -OH group, whereas in deoxyribose this group is a hydrogen atom. Phosphate groups in a single nucleotide bind to the 5 carbon, while the 3 carbon binds to the phosphate group of an adjacent nucleotide, and the 1 carbon binds to the nucleobase.
The smallest part of the nucleotide unit is the phosphate group (Figure 3). Phosphate is a compound containing phosphorus (phosp-) and oxygen (-ate) together. Phosphate is also found in potassium phosphate (saltpetre, used to make gunpowder) and in phosphoric acid, an ingredient in most cola. As an acidic molecule, it gives rise to the "acid" part of the name of the nucleic acid.
Figure 3: The phosphate group which is attached to the pentose sugar in nucleic acids. The phosphate sugar forms a bridge between adjacent nucleotides in the nucleic acid chain, binding to the 5 carbon of one pentose sugar and the 3 carbon of the pentose sugar in an adjacent nucleotide.
The pentose sugar is the backbone of the nucleic acid, and it is to this that the nucleobase binds to the 1 carbon of the sugar, while the phosphate binds to the 5 carbon (Figure 4). These units can polymerize, as the phosphate group in the nucleotide is able to bind to another atom on a nearby pentose sugar molecule, namely the carbon 3 atom. This allows the units of phosphate and pentose sugar groups to repeat, with variance at the nucleobases, to give different DNA and RNA sequences. Furthermore, as the phosphate group is attached to the 5 carbon of one nucleotide and the 3 carbon of another, this gives rise to the description of the directionality of nucleic acid sequences, which are described as being read in a 5' (5 prime) to 3' (3 prime) direction, which is that the sequence is read from the end of the sequence with the free phosphate group attached at the carbon 5 to the end of the sequence with a free carbon 3 without a phosphate attached to it.
Figure 4: Monomeric nucleotides (left) found in DNA and RNA. These are the nucleotide monomers that polymerize into the polymeric DNA and RNA molecules (right). The monomers contain adenosine as their nucleobase, and so when they are incorporated into DNA or RNA sequences, they have the code A in the reported sequence, but they differ in the pentose sugar, as the nucleotide incorporated into DNA (top) has one fewer oxygen atom than the nucleotide incorporated into the RNA. These nucleotides polymerize into DNA and RNA (right), DNA (top) and RNA (bottom) sequences are read in a direction from the 5' to '3 terminal, which means they are read from the end which has the phosphate group attached to the 5 carbon.
Nucleic acids exist in a variety of lengths, from short sequences of a few nucleotides that are used to initiate the polymerase chain reaction (PCR), to chromosomes, which are huge lengths of DNA which contain parts of an organism's genome.