Replication, of DNA

DNA replication is an enzyme-catalyzed process that begins with a partial unwinding of the double helix at various points along the chain, brought about by enzymes called helicases. Hydrogen bonds are broken, the two strands 

FIGURE 24.4 A representation of semiconservative DNA repiication. The originai doubie-stranded DNApar-tiaiiy unwinds, bases are exposed, nucieotides iine up on each strand in a compie-mentary manner, and two new strands begin to grow. Both strands are synthesized in the same 5 — 3 direction, one continuously and one in fragments. 

Addition of nucleotides to a growing chain takes place in the 5 3 direction and is catalyzed by DNA polymerase. The key step is the addition of a nucleoside 5 -triphosphate to the free 3 -hydroxyl group of the growing chain, with loss of a diphosphate leaving group. 

CHAPTER 24 biomolecules NUCLEIC ACIDS AND THEIR METABOLISM 

Each new double helix is comprised of one strand that was part of the original molecule and one strand that is newly synthesized. Not surprisingly, this is a very simplistic description of a quite complex process, catalysed by enzymes known as DNA polymerases. The precursors for synthesis of the new chain are the nucleoside triphosphates, dATP, dGTP, dTTP, and dCTP. We have already met ATP when we considered anhydrides of phosphoric acid (see Box 7.25) these compounds are analogues of ATP, though the sugar is deoxyribose rather than ribose. 

DNA stores the genetic information for a cell, but it is RNA that participates in the processes by which this information is used. RNA molecules are classihed according to their function or cellular location. Three major forms are found in prokaryotic cells  

The codon combinations are shown in Table 14.2. A codon can be the DNA sequence in the coding strand or, alternatively, the related sequence found in mRNA. The table shows the mRNA sequences, since we shall be using these during consideration of protein synthesis. The DNA sequences merely have thymine (T) in place of uracil (U), as appropriate. The sequence is always listed from the 5 -end to the 3 -end. 

It is the sequence of bases along one of the strands of the DNA molecule, the coding strand, that provides the information for the synthesis of proteins, especially enzymes, in an organism. A complementary sequence exists along the second strand, and this is termed the template strand. A gene is that segment of DNA that contains the information necessary for the synthesis of one protein. 

Each amino acid in a protein is specihed by a sequence of three nucleotides, termed a codon. A 

Naturally occurring DNA exists in many forms. Single- and double-stranded DNAs are known, and both can exist in linear and circular forms. As a result, it is difficult to generalize about all possible cases of DNA replication. Since many DNAs are double-stranded, we can present some general features of the replication of double-stranded DNA, features that apply both to hnear and to circular DNA. Most of the details of the process that we shall discuss here were first investigated in prokaryotes, particularly in the bacterium Escherichia coli. We shall use information obtained by experiments on this organism for most of our discussion of the topic. Section 10.6 will discuss differences between prokaryotic and eukaryotic replication. 

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FIGURE 11.21 Replication of DNA gives identical progeny molecules because base pairing is the mechanism determining the nucleotide sequence synthesized within each of the new strands during replication. 

DNA is very susceptible to radical-induced damage. The structural changes in DNA can cause cytotoxicity affecting the replication of DNA in vivo. 

DNA is the carrier of the genetic information of all cells and many viruses. Two important points follow from this simple statement. First, DNA must be replicated in order for cell division to take place, hi cell division, one cell becomes two and each must have its own store of genetic information. The genetic information is stored in chromosomes and each chromosome contains a single molecule of DNA. Secondly, the replication of DNA must be a very precisely controlled process. The goal is for each daughter cell to have exactly the same genetic information as the parent cell, which requires that each chromosomal DNA molecule replicated in the course of... 

DNA poiymerases a family of enzymes that are involved in the replication of DNA. 

In regenerating rat liver only pre-existing H4 was phosphorylated at the peak of DNA synthesis [116,117]. The modification has a half-life of two hours and may be involved in replication of DNA [109,116,117]. The histidine kinases in yeast and Physarum polycephalum nuclear extracts are unable to phosphorylate H4 in... 

Figure 11-2. The prokaryotic DNA replication fork. A schematic representation of semi-conservative replication of DNA by different mechanisms on the leading and lagging strands by DNA polymerase III (DNA pol III) is shown. Other enzymes and accessory proteins that participate in initiation, elongation, and ligation phases of the process are indicated, with DNA pol I depicted as having just dissociated from a completed Okasaki fragment. SSBs, single-stranded DNA binding proteins.

Although these drugs effectively Inhibit the replication of DNA In all cells, they are highly toxic to rapidly proliferating cells, such as cancer cells and cells Infected by virus. 

Compared with the process in bacteria, replication of DNA of a human cell requires multiple origins of replication, each of which leads to copying of replicons, regions 30 to 300 kilobase pairs in size. 

Craddock VM, Flenderson AR. 1978. De novo and repair replication of DNA in liver of carcinogen-treated animals. Cancer Res 38 2135-2143. 

A higher degree of complexity is offered by the elegant work by Nicolaou and coworkers (Li and Nicolau, 1994) (see Figure 7.9). In this case, the self-replication of DNA is based on a triple helix. 

It prevents the replication of DNA viruses and its clinical use is limited to herpes simplex keratitis. 

Replication of DNA in S phase is subject to strict control in the cell cycle (review Stillman, 1996), resulting in the following observations ... 

Replication of DNA does not occur with complete precision, but rather has an intrinsic inaccuracy. The error rate for incorporation of nucleotides in DNA replication is of the order of one error per 10 - 10 correctly incorporated nucleotides. 

Kornberg, A., Some aspects of the enzymatic replication of DNA the repair of partially single-stranded templates. Proc Natl Cancer Conf, 1964.5 735 1. 

Replication of DNA is an enzymatic process that starts with the partial unwinding of the double helix. Just before the cell division, the double strand begins to unwind. As the strands separate and bases are exposed, new nucleotides line up on each strand in a complementary fashion, A to T, and C to G. Two new strands now begin to grow, which are complementary to their old template strands. Two new identical DNA double helices are produced in this way, and these two new molecules can then be passed on, one to each daughter cell. As each of the new DNA molecules contains one strand of old DNA, and one new, the process is called semiconservative replication. 

Figure 6.38 Basic processes involved with replication of DNA and the transcription and translation of its encoded information into RNA and thence protein. Source Modified from Ref. 11.

Work with the carcinogen acetylaminofluorene found that residues of the compound in ribosomal RNA may correlate more closely with liver tumor formation than residues in DNA. Direct interactions with the mechanisms of protein synthesis, or with DNA and RNA polymerase enzymes, can also be seen as possible mechanisms. For instance, a modification of the polymerase enzymes by a carcinogen, either directly or indirectly, could lead to the erroneous replication of DNA or RNA and hence the permanent incorporation of a mutation. 

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