DNA Replication

Before one cell can divide into two cells, the cell must make a copy of the cellular DNA so that after cell division, each cell will contain a complete complement of the genetic material. Replication is the cellular process by which DNA or the cellular genome is duplicated with almost perfect (and sometimes perfect) fidelity. The replicative process in prokaryotic cells, such as Escherichia coli (E. coli ) cells, is best understood and will be described in detail, and the aspects that differ in replicating eukaryotic cells will be noted.

Replication starts by the separation of the strands of DNA and the formation of a local "bubble" at a specific DNA site called the origin of replication (ori). A helicase enzyme uses energy from ATP hydrolysis to effect this action. Single-strand DNA binding proteins stabilize the strands during the subsequent steps. The original DNA strands will function as the templates that will direct synthesis of the complementary strands. A nucleotide on the template strand will determine which deoxyribonucleotide (dNTP) will be incorporated in the newly synthesized strand. This replication

model is called semiconservative replication. The opening of the DNA produces two replication forks (see Figure 1), both of which will be the sites for replication. The forks will move in opposite directions relative to the replication machinery, with DNA replication occurring bidirectionally.

To initiate the synthesis of the two strands, a primer strand is needed, which is made by the enzyme primase. This small primer is an RNA molecule, which has a 5′ - and a 3′ -end . Replication requires the 3′ -hydroxyl group of the deoxyribose. This group is "attacked" by the phosphate of the incoming dNTP, because all DNA polymerases can extend DNA only from the 3′ -end (synthesis occurs in the 5′→3′ direction on the primer strand). Because the strands of DNA have opposite orientations, the replication process for each strand is considerably different. Extension of each strand requires very different operations that involve synthesis of a leading strand and a lagging strand. Leading strand synthesis, which progresses toward the fork in a continuous manner, begins with primase synthesizing a short RNA primer at the ori, followed by the action of DNA polymerase III, which incorporates deoxyribonucleotides into the strand, until strand synthesis is complete. If an incorrect nucleotide in incorporated, a proofreading activity in the mechanism removes it and the synthesis continues. Lagging strand synthesis progresses in the direction opposite to fork movement, with the new DNA strand synthesized in 1,000 to 2,000 nucleotide fragments called Okazaki fragments. Each fragment must also be initiated with a primer, followed by synthesis utilizing DNA polymerase III. When the Okazaki fragments are completed, DNA polymerase I both removes the RNA primers and simultaneously replaces the RNA with DNA. This occurs similarly for the single primer on the leading strand. The DNA fragments are then sealed together to produce a continuous strand by the enzyme DNA ligase.

The size of the genomic DNA in eukaryotic cells (such as the cells of yeast, plants, or mammals) is much larger (up to 10⁺¹¹ base pairs) than in E. coli (ca. 10⁺⁶ base pairs). The rate of the eukaryotic replication fork movement is about fifty nucleotides per second, which is about ten times slower than in E. coli. To complete replication in the relatively short time periods observed, multiple origins of replication are used. In yeast cells, these multiple origins of replication are called autonomous replication sequences (ARSs). As with prokaryotic cells, eukaryotic cells have multiple DNA polymerases. DNA polymerase δ, complexed with a protein called proliferating cell nuclear antigen (PCNA), is thought to synthesize the leading strand, whereas DNA polymerase α is the replicase for the lagging strand. Eukaryotic genomes have linear DNA strands and require a special enzyme, called telomerase, to replicate the ends of the chromosomes.

see also Base Pairing; Deoxyribonucleic Acid (DNA).

William M. Scovell

Bibliography

Garrett, R., and Grisham, Charles M. (1995). Biochemistry. Fort Worth: Saunders College.

Nelson, David L., and Cox, Michael M. (2000). Lehninger Principles of Biochemistry, 3rd edition. New York: Worth.

DNA Replication

DNA, short for deoxyribonucleic acid, is a double-stranded, helical molecule that forms the molecular basis for heredity. For DNA replication to occur, this molecule must first unwind, or "unzip," itself to allow the information-encoding bases to become accessible. The base pairing within DNA is of a complementary nature and, consequently, when the molecule unzips, due to the action of enzymes, two strands are temporarily produced, each of which acts as a template. A replication fork is first made—the DNA molecule separates at a small region and then the enzyme DNA polymerase adds complementary nucleotides to each side of the freshly separated strands. The DNA polymerase adds nucleotides only to one end of the DNA. As a result, one strand (the leading strand) is replicated continuously, while the other strand (the lagging strand) is replicated discontinuously, in short bursts. Each of these small sections is finally joined to its neighbor by the action of another enzyme, DNA ligase, to give a complete strand. This whole process gives rise to two completely new and identical daughter strands of DNA.

In the semi-conservative method, two strands of the parent molecule unwind and each becomes a template for the synthesis of the complementary strand of the daughter molecule. A competing hypothesis, which would eventually be disproved, was the conservative hypothesis that states no unzipping occurs and a new DNA molecule is formed alongside the original parent molecule. Consequently, of the two molecules of DNA produced after a round of replication, one of them is the intact parent molecule. By using radioactively labeled nitrogen to produce new DNA over several generations of cell replication by a bacillus species , all of the DNA in the daughter cells contained labeled nitrogen. The bacilli were then placed in media containing unlabeled nitrogen. After a further round of DNA replication the DNA was examined and it was found to contain equal amounts of labeled and unlabeled nitrogen. In the second generation two types of DNA were found—half was identical to the DNA from the first generation and the remaining half was found to consist of entirely unlabeled nitrogen. These results are consistent with the zip fastener model of the semi-conservative hypothesis, but not at all consistent with the conservative hypothesis. Thus, it was shown that DNA replication proceeds via the semi-conservative replication method.

This method of replication, known as the semi-conservative hypothesis, was proposed from the outset of the discovery, with the description of the structure of DNA by biochemists James D. Watson and Francis Harry Compton Crick in 1953. In 1957, biochemist Arthur Kornberg first produced new DNA from the constituent parts and a parent strand, forming synthetic but not biologically active molecules of DNA outside the cell. However, not until the work of Matthew Meselson and Franklin W. Stahl in the late 1950s was the semi-conservative hypothesis conclusively proven true.

DNA replication The process whereby DNA makes exact copies of itself, which is controlled by the enzyme DNA polymerase. Replication occurs at rates of between 50 nucleotides per second (in mammals) and 500 nucleotides per second (in bacteria). The hydrogen bonds between the complementary bases on the two strands of the parent DNA molecule break and the strands unwind, each strand acting as a template for the synthesis of a new one complementary to itself (see DNA-binding proteins; primosome). DNA polymerases move down the two single strands linking free nucleotides to their complementary bases (see base pairing) on the templates. The process continues until all the nucleotides on the templates have joined with appropriate free nucleotides and two identical molecules of DNA have been formed. This process is known as semiconservative replication as each new molecule contains half of the original parent DNA molecule (compare conservative replication; dispersive replication). Sometimes mutations occur that may cause the exact sequence of the parent DNA not to be replicated. However, DNA repair mechanisms reduce this possibility. In eukaryotes, replication is initiated at numerous points, called origins of replication, along each DNA molecule and proceeds simultaneously at each site. See also discontinuous replication.

DNA Replication

DNA, an abbreviation for deoxyribonucleic acid, is a double-stranded, helical molecule (visually, it resembles a ladder that is twisted into a spiral staircase shape) that forms the molecular basis for heredity. For the manufacture of a new double helix of DNA to occur in the process of DNA replication, this molecule must first unwind itself to allow the information-encoding building blocks of the DNA (the bases) to become accessible.

The base pairing within DNA is specific; the base called adenine pairs with the base called thymine, and the base cytosine pairs only with the base called gua-nine. Put another way, the pairing is complementary. When a stretch of the DNA double helix separates into the two strands of bases due to the action of enzymes, each of the exposed strands acts as a template for the formation of a new strand that contains the complimentary sequence of bases. The process, which involves the coordinated activity of several different enzymes, produces two completely new and identical daughter strands of DNA.

This method of replication is known as the semi-conservative model. A competing hypothesis, which was eventually disproved, was the conservative hypothesis; it predicted that separating of the strands of the double helix was unnecessary, and that two new strands could form along side the existing strands even when they were linked together. Experiments conducted by Matthew Meselson and Franklin W. Stahl in the late 1950s that traced the incorporation of radioactive compounds into the newly forming DNA established beyond all doubt that the conservative model was incorrect.