Chapter 1: New Beginnings

The Basics of DNA:

DNA (deoxyribonucleic acid) is a biological molecule found in all forms of life, excepting some types of viruses. DNA is known as a polymer molecule, which means that it is made up of many subunits. In DNA, these subunits are known as nucleotides/bases, of which there are four types; adenine (A), thymine (T), guanine (G), and cytosine (C). Each nucleotide in DNA has three main sections; a phosphate group, a deoxyribose sugar, and the nucleotide (either A, T, C or G). These nucleotides are joined together via phosphodiester bonds between the phosphate group of one nucleotide's phosphate group and another nucleotide's deoxyribose sugar to form a phosphate backbone, which makes up the backbone of DNA. The DNA molecule also has direction (i.e. it has a beginning and an end). The beginning is known as the 5' (five prime) end, and the end is known as the 3' (three prime). New DNA bases (nucleotides) join on to the 3' end of the existing DNA molecule. (figure 1).

As well as nucleotides being able to join to adjacent nucleotides via phosphodiester bonds, each type of nucleotide is able to bond to another specific nucleotide perpendicular (at right angles to) the phosphate backbone via H-bonds in a process known as base pairing. In DNA, adenine (A) is able to base pair to thymine (T), and guanine (G) to cytosine (C). Nucleotides which base pair are called complementary, therefore A & T are complementary, as are G & C. In nature, DNA is rarely found as a single strand, instead it is found as a complex of two DNA strands, one wrapped around the other to give the familiar double stranded helix structure associated with DNA. Each DNA strand is anti-parallel and complementary to the other (i.e. their directions are opposite and where one strand has, for example, an A, the other will have a T). The DNA strand which is in the 5' to 3' orientation is called the sense strand, and the strand which runs from 3' to 5' is known as the antisense strand (figure 2).

DNA's primary role in cells is to store genetic information. The information stored on DNA molecules refers to the characteristics and functions of a cell, and therefore the entire organism. In multicellular organisms (e.g. animals), each cell contains identical genetic information, however the information which is used depends on the type of cell. For example, cells which make up the eyes will use information corresponding to sight and eye colour, while muscle cells will use information which corresponds to contraction and relaxation of the cells during use.
The genetic information on DNA is stored in discrete units called genes. Each gene contains information which corresponds to at least one characteristic/function of the cell (And therefore the organism), and is encoded in the language of nucleotides. The sequence of nucleotides within a gene (e.g. ATTCTGCTA) is used to produce a specific molecule (normally a protein). This process is described in more detail in the next section; 'Translation and Transcription'. (Figure 3).

The Basics of RNA:

RNA (ribonucleic acid) is another polymer molecule which shares some similarity with DNA. The subunits which make up RNA (called ribonucleotides/bases) are similar to those which make up DNA, however they have a few crucial differences. The first is that while both DNA and RNA bases contain a phosphate group and the nucleotide, instead of a deoxyribose sugar, ribonucleotides have a ribose sugar. In addition, in RNA there is no thymine (T) bases, instead there is another type of base called uracil (U). A and U are complementary in RNA. Excepting these differences, the basic structure of RNA is very similar to that of DNA; they both have directions (5' to 3'), and both have their subunits joined by phosphodiester bonds to form a phosphate backbone (figure 4).

Another difference between DNA and RNA is that RNA is often found as a single strand, as opposed to the double stranded helix of DNA. Although this may make it seem like RNA will be found as a linear molecule, it is important to realise that this is not the case; RNA can actually have more complex structures than DNA. As the RNA strand is not bound to another RNA strand, it has all of its ribonucleotides free to base pair, which they do. The ribonucleotides can bind with complementary bases on the same RNA strand, or indeed with those on other RNA strands to form an RNA-RNA complex (although it is rare that this complex will have the double helix structure of DNA). This allows RNA to have a great many structures (figure 5).

As many diferent structures of RNA can be formed within a cell, it is perhaps not surprising that there are many types of RNA, each with different functions within the cell. Three types of RNA are used in the process of utilising the genetic information stored on DNA, and is described in the next section; 'Transcription and Translation'. Other functions of RNA are described in the section 'The Functions of RNA'.

The Basics of Proteins:

Proteins are another type of biological molecule, which is a polymer like DNA and RNA, however the subunits which make up proteins are known as amino acids. There are 21 types of (natural) amino acid, and all of them share a similar structure; a hydrogen group (H), a carboxylic acid group (COOH), an amino group (NH2), and a functional group (R). The functional group is different for each type of amino acid. Unlike with DNA and RNA, amino acids are no joined by phosphodiester bonds, but by amide bonds between the carboxylic acid group of one amino acid, and the amino group of another.

The interactions of the functional groups, both with other functional groups of the same/different proteins, and with other molecules/etc. in its environment, gives the protein its overall function (figure 6). These functions can range from catalytic speed up the rate of a reaction) to structural (shape/strength of a cell), to virulence (causing disease). As has been eluded to before, these proteins are encoded for by DNA and the production of them involves RNA. In the next section we will see how exactly this mechanism works.