DNA Replication

Cells spend most of their time in a stage of the cell cycle called interphase, collectively the G1, S, and G2 phases, in which a cell grows, replicates its DNA, and grows again. By replicating its genetic material, the cell creates a duplicate so that one copy of the DNA can be allocated to each of the new daughter cells in a process called segregation. This means that each copy of the cell's DNA is distributed to the new cells. DNA replication is semi-conservative, the idea that each strand of DNA serves as a template for a new strand so that after replication, each molecule has one old and one new strand. There are two main steps in DNA replication, both of which are driven by enzymes. In the first step, the DNA molecule is unwound and the strands are separated or unzipped. This exposes the nitrogenous bases. The enzyme DNA helicase separates the two strands of the double helix by breaking the hydrogen bonds that hold them together. In the second step, free-floating nucleotides in the nucleus (or, for prokaryotes, in the cytoplasm) are attached to the correct exposed bases. The enzyme DNA polymerase that assembles the new strands of DNA from the template strands. These two steps occur simultaneously at different points along the DNA strand.

DNA polymerase starts at the 3' end of the strand. This is where there is an exposed hydroxyl (OH–) group on the sugar backbone. Although DNA polymerase is the main catalyst for the process, it cannot start unless there is a primer present. A primer is a short strand of RNA (ribonucleic acid) that is complementary to the DNA template and marks the origin of replication. DNA polymerase then adds further nucleotides. In prokaryotic cells, DNA is unzipped and replication happens in both directions. This forms two replication forks at this replication bubble (the location on a replicating DNA molecule where the new strands will be produced). Prokaryotic DNA is circular in shape and tends to be shorter than eukaryotic DNA, so it can be duplicated much faster. For example, the entire genome, or the genetic material of an organism, of some strains of the bacterium Escherichia coli can replicate every 20 minutes. Eukaryotic DNA is linear and much longer. It replicates at multiple replication forks at the same time. This allows the process to move much faster than if the DNA only replicated from a single point.

When DNA replicates, each of the two new strands grows differently at the replication fork. The new strands are always built in the 5'-to 3'-direction. The strand of DNA that is formed continuously during DNA replication, called the leading strand, forms at the 3' end of the original strand, meaning the first base added is the beginning of the 5' end of the new strand. It grows in the 3' direction as the DNA unzips. The strand of DNA that is synthesized in short segments during DNA replication is called the lagging strand and is oriented in the opposite direction. Just like at the leading strand, the nucleotides are added in the 5'-to-3' direction, but in this case they are added in short, discontinuous sections. Each chunk of nucleotides that is added is synthesized in the opposite direction from which the replication fork is moving. Each of these discontinuous sections of new DNA is called an Okazaki fragment. Eventually, the current fragment meets the previous fragment, and an enzyme called DNA ligase joins them together. In summary, both strands are synthesized in the 5'-to-3' direction; however, the leading strand is synthesized continuously, one base at a time, while the lagging strand is synthesized in the discontinuous Okazaki fragments. dNTP serves as the substrate for this to happen.