DNA in all organisms is a double-strand helix made of nucleotides with two pairs of complementary bases. The double helix is zipped open and new nucleotides with bases complementary to the opened strands are added in a 5' to 3' direction, with different ways of formation of the two new daughter strands called leading and lagging strands. Though the process is similar in prokaryotes and eukaryotes, the enzymes used are different.
DNA is the genetic material that is found in the nucleus of all living organisms. It is found directly in the cytoplasm of unicellular prokaryotes. In eukaryotes, it is bound within the membranes of the nucleus, or in organelles like mitochondria and chloroplast, making it one of the main difference between these two kinds of organisms. The DNA in prokaryotes is a single loop, while it is long and unlooped in eukaryotes. The long DNA in eukaryotes is tightly coiled around proteins to give chromosomes.
DNA contains hereditary information that is used to synthesis proteins, determine the structure and functioning of a cell, as well as the growth and development of the organism.
Structure and Chemistry of DNA
The DNA is a double-stranded helix made of basic units called nucleotides. Each nucleotide is made of deoxyribose sugar, phosphate, and base. The deoxyribose sugar of one nucleotide is bonded with the phosphate of the next by strong bonds to make up the backbone of the strand, and the complementary bases make up the rungs of the double helix, bonded by hydrogen bonds which connect the two strands and create a strong DNA molecule. One strand ends in a 5 prime (5') at the phosphate end, and the other strand ends at the 3 prime (3') end at the deoxyribose end.
There are four bases in all DNA of every organism. The complementary pairs are adenine and thymine, and guanine and cytosine. The complementary nature of the bases ensures the complementary sequence of the two strands and is what makes replication of DNA possible. The order or sequence in which the bases occur is the important message that DNA transfer, and is called the genome. Before a cell divides, it needs to duplicate its DNA, so that each daughter cell has an exact DNA copy.
When DNA replicates, the two strands are separated and both are used as templates, so that the two new DNA have one old strand and one newly added strand. This is called semi-conservative replication, and is responsible for the stable transfer of genetic information. There are two main stages of replication.
- Replication Fork Formation
The DNA that is tightly coiled is unwound to reveal the long double helix DNA strand. Segments of the two strands are then separated or unzipped, with the help of the enzyme Helicase, which breaks the hydrogen bonds between the two complementary bases to form the y-shaped replication fork. The point at which the fork occurs is called the origin of replication(ORI). The ORI exposes the 3' and 5' ends of the two strands.
- Addition of New Nucleotides
Nucleotides can be only added starting with a phosphate molecule or from the 5' end, complementary to the template that ends in 3'. This means that the process in which the two strands are formed differ. The old DNA strand ending in 3' forms the template for the leading strand, and the other strand ending in 5' is the template for the formation of the lagging strand.
A DNA polymerase enzyme attaches itself to the 3' or deoxyribose ended strand and adds nucleotides with bases complementary to bases on the old strand to form the leading strand from 5' to 3' in the direction moving towards the replication fork. This gives the first new double helix daughter DNA.
The lagging strand formation is more complicated, and happens in sections called Okazaki fragments. Many such segments maybe formed simultaneously. Initially, an RNA primer is attached by a Primase to a point on the 5' end strand, so that the first free nucleotide in the Okazaki fragment is again a 3' end. Then a second kind of DNA polymerase attaches itself and starts to add new complementary nucleotides in the opposite direction away from the replication fork. When a Okazaki fragment is complete, the RNA primer is removed and replaced by appropriate complementary nucleotides. Another DNA enzyme, Ligase, is used to bond the various fragments together to give a continuous strand that forms part of the second double helix daughter DNA.
Differences between DNA Replication in Prokaryotes and Eukaryotes
There are many differences between prokaryotes and eukaryotes. In prokaryotes, the DNA replication happens in the cytoplasm. Since the DNA is short, there is only one ORI, with one replication fork and one replication bubble. The enzymes used are simple proteins, and both strands are synthesised by DNA polymerase III. The replication is rapid, with 2000 base pairs being formed each second, with the aid of large Okazaki fragments of 1000-2000 nucleotides. The DNA replication is terminated by Topoisomerase II, which also separates the two interlocked loops of daughter DNAs.
In eukaryotes, the DNA replication happens in the nucleus. Since DNA size is considerably larger, there are many ORIs, replication forks and replication bubbles. The enzymes used are multi-complex proteins, where the leading strand is formed by DNA polymerase epsilon (ε), and the lagging strand by DNA polymerase delta (δ). The speed of replication is slow, with 200 base pairs being formed per second, with small Okazaki fragments of 100-200 nucleotides. Telemerase is the enzyme used to terminate the replication.