The structure of genes

For any molecule to be recognized as the material responsible for transmitting genetic information, it must fulfil certain requirements dictated by our knowledge of the continuity of species and the process of evolutionary change. (1) It must contain biologically useful information in a stable form. This information is contained in the form of a linear array of genes, i.e. specific stretches of DNA, most of which code for a single protein. An average gene is perhaps 1000−2000 base pairs in length. (2) The genetic material must be capable of being accurately replicated, and transmitted faithfully from generation to generation. (3) The genetic material must be able to express itself in such a way as to direct the synthesis of all the different proteins characteristic of the organism, cell type or developmental stage. The amino acid sequence of each individual protein is determined by the nucleotide sequence of its corresponding gene(s). However, it will be seen later that proteins are not synthesized on the genes directly. Instead, an RNA intermediary, called messenger RNA (mRNA), is first synthesized (transcribed) using the DNA as a template. This mRNA then directs the synthesis of a specific polypeptide, the amino acid sequence being determined by the order of nucleotides in the mRNA which in turn reflects the DNA sequence from which it was transcribed. Gene expression therefore represents the flow of information from DNA to RNA to protein (page 202). (4) Finally, although in general the genetic information should be stable, it must nevertheless be capable of some variation or mutation, even if only very infrequently, to explain the observed characteristics of evolutionary change.

The bacterial chromosome

The whole of the genetic information contained within a single bacterial cell or eukaryotic nucleus is called the genome. In eukaryotes this is distributed between a number of different chromosomes, the number being characteristic of the species. Each eukaryotic chromosome is a highly condensed structure composed of both DNA and nuclear proteins, organized in a very specific manner (page 311), while the bacterial genome is present as a single chromosome (i.e. a single DNA duplex), with very little associated protein. The E. coli chromosome contains about 4 million base pairs in its DNA and is circular, although in vivo this circle must be folded very compactly since the contour length of the DNA is about 1000 times the diameter of the bacterial cell. A property of circular DNA molecules which contributes to this tight packing is supercoiling: the twisting of the double-helical axis itself to form a higher order of twisting, known as a superhelix or supercoil.

Not all simple DNA molecules are circular. Some viral DNAs are linear, whereas others may interconvert between a linear form in the virus particle and a circular form in the bacterial host cell.

The mechanism of DNA synthesis

The first DNA-synthesizing enzyme to be discovered was isolated from E. coli in 1956 by Kornberg and became known as DNA polymerase I or the Kornberg enzyme. For DNA synthesis in vitro, DNA polymerase requires (a) all four deoxynucleoside triphosphates (dATP, dGTP, dCTP and TTP)−these are the immediate precursors of DNA − (b) Mg²⁺, (c) a small amount of DNA or RNA primer − this is necessary because DNA polymerase I can only add deoxyribonucleotides to the 3’-OH terminus of a pre-existing DNA or RNA molecule, it cannot initiate DNA synthesis de novo − and (d) a DNA template. During DNA synthesis, DNA polymerase I synthesizes a complementary copy of the template, from which it follows that the primer must be able to base pair with the template.

DNA synthesis proceeds by a nucleophilic attack by the 3’-OH group of the primer on the α-phosphorus atom of the incoming deoxynucleoside triphosphate, to form a phosphodiester bond (Figure 20.4). Pyrophosphate is released and is hydrolysed by pyrophosphatase, thereby driving the polymerization reaction in the forward direction. Synthesis therefore occurs in a 5′ to 3′ direction; the enzyme remains attached to the DNA throughout and is not released after each nucleotide addition.

As stated above, DNA polymerase I requires a template. The probability of making a covalent phosphodiester bond is very low unless the incoming deoxynucleotide is the correct one to base pair with the corresponding one on the template. Nevertheless, since the possibility exists, DNA polymerase must possess a ‘proof-reading’ mechanism to correct the occasional mistakes which might otherwise lead to a mutated gene and be detrimental to the organism. Proof-reading is achieved by a 3′ → 5′ exonuclease activity associated with the DNA polymerase, which is able to recognize an incorrectly incorporated nucleotide and hydrolyse the corresponding bond, thereby ensuring extremely accurate DNA replication.

DNA polymerase I also has another exonuclease activity, but in this case hydrolysis occurs in a 5′ → 3′ direction and appears to serve two functions in vivo; (i) it is involved in removing RNA primers during DNA replication (see later) and (ii) it plays a role in DNA repair processes. That this is an important function is illustrated by experiments in which E. coli was exposed to ultraviolet light, which in large doses can cause adjacent pyrimidine residues situated in the same polynucleotide strand to become covalently cross-linked (Figure 20.5). Whereas normal E. coli cells are able to excise these pyrimidine dimers and repair their DNA, a mutant form which lacked DNA polymerase I was unable to do so and was therefore more readily killed by ultraviolet light. In humans, as in E. coli, exposure to ultraviolet light causes the production of stable pyrimidine dimers but, as shown in studies on skin fibroblasts, these are rapidly excised from the DNA of normal subjects. Sufferers from the rare inherited condition of xeroderma pigmentosa, however, appear to lack the enzyme responsible for nicking the DNA backbone in the vicinity of the pyrimidine dimers and skin cancer is a frequent result.

DNA replication in bacterial cells

DNA replication in E. coli (Figure 20.6) has the following properties. (a) Replication starts at a unique site on the circular bacterial genome, called the origin of replication. (b) Replication proceeds simultaneously in both directions around the genome, that is, it is bidirectional. In other words, there are two replication forks, one travelling clockwise and one anticlockwise, at about the same rate. (c) Replication is terminated at a point diametrically opposite the origin of replication.

Such an overall mechanism poses a number of problems at the molecular level. First, at a replication fork, both strands of the double helix must be replicated, but since they are antiparallel this would suggest 5′ → 3′ synthesis on one strand and 3′ → 5′ on the other; yet DNA polymerase can only synthesize in the 5′ → 3′ direction. This dilemma was resolved by Okazaki who found that one DNA strand is synthesized continuously in the expected 5′ → 3′ direction, whereas the opposite strand is synthesized discontinuously as short pieces of DNA known as Okazaki fragments (Figure 20.7). Each of these fragments is synthesized in the expected 5′ → 3′ direction and adjacent pieces are rapidly joined together by another enzyme called DNA ligase giving the appearance that overall growth is in the 3′ → 5′ direction.

The second problem is that the initiation of DNA synthesis requires a primer, base paired to the template, and each Okazaki fragment requires its own primer. In fact there is a specific RNA polymerase, called primase, which can synthesize short RNA primers of about ten nucleotides. RNA synthesis, unlike DNA synthesis, does not require a primer for initiation (page 000). These short RNA molecules then act as primers for DNA polymerase (Figure 20.8). It is now known that DNA polymerase I is not the major replicating enzyme in E. coli. Instead another enzyme, DNA polymerase III, carries out most of the replication in vivo, whereas DNA polymerase I is responsible for degrading the RNA primers after DNA synthesis by means of its 5′ → 3′ exonuclease activity and replacing it with DNA using its polymerase and 3′ → 5′ proof-reading activities.

The final problem in DNA replication is the unwinding of the double helix that is necessary for replication to occur, and the subsequent rewinding of the daughter molecules. The whole molecule does not unwind. Instead a small region of the helix around the replication fork is unwound with the aid of a number of specific proteins (Figure 20.8) including a helicase, which carries out the actual unwinding, and single-stranded DNA binding protein, which stabilizes the single strands and prevents them from base pairing. Finally, when the DNA helix of a circular genome is unwound this puts a tortional strain on the rest of the molecule. This strain is relieved by DNA gyrase which acts as a ‘molecular swivel’ and allows the DNA to relax. Having successfully unwound a region of double-stranded DNA, primase can then bind and synthesize an RNA primer, DNA polymerase III can bring about DNA synthesis, DNA polymerase I can replace RNA primer with DNA, and finally DNA ligase can join adjacent Okazaki fragments.