DNA Replication Process
The process of how the DNA replicates itself is not as complicated as it may seem. In fact, it’s a very interesting, not to mention, simplistic process. The only confusing or complicated part is that there are a number of chemicals and enzymes that need to be remembered.
The five carbon atoms in a pentose are numbered in a certain order.
This order is very important as it orients the direction of strands in the DNA. The process of DNA replication consists of the addition of nucleotides, but nucleotides can only be added to the end consisting of the 3rd or carbon atom also known as the 3 prime atom (3'). Image 2 shows the position of the five carbon atoms in a pentose.
UNWINDING AND SEPARATING:
A DNA molecule has a helical or spiral like structure. So, as the first step in the replication process, an enzyme called topoisomerase unwinds the molecule from its supercoiled state. After being unwound, the DNA is now in a simplified state i.e. it now looks something similar to a ladder, the pentose-phosphate molecules acting as the side rail, with the complementary nitrogenous bases, bonded through hydrogen bonds, acting as the rungs.
Next, in order to replicate, the two strands must be separated. A protein called helicase does this action. This protein breaks the hydrogen bonds joining the nitrogenous bases, essentially breaking the rungs of the ladder.
The separation process of the two single strands of DNA simultaneously creates a ‘Y’ shaped fork called replication fork. These two strands act as templates for the DNA polymerase to make new strands of DNA.
Out of the two strands in the fork, one strand, called the Leading strand, is oriented towards the fork i.e. the 5' carbon atoms in its nucleotides are positioned towards the bottom of the fork (called the 3’ to 5’ direction). The other strand, known as the Lagging strand, is oriented away from the fork i.e. the 5' carbon atoms in its nucleotides are positioned to the bottom of the fork (from the 5’ to 3’ direction).
NUCLEOTIDE FORMATION AND BONDING:
An enzyme called DNA polymerase is responsible for the formation of nucleotides. It reads the split DNA strands to formulate and form new bases and nucleotides complementary with the existing ones. It adds nucleotides from the end of the strand towards the fork, following the direction if the helicase as it “unzips” the DNA.
Nucleotides can only be added from the 3’ end of another nucleotide. So, it is relatively easier for the DNA polymerase to add nucleotides to the leading strand as its 5’ end is away from the fork. But since the lagging strand has its 3’ end away from the fork, the addition of nucleotides becomes more complicated.
ADDITION OF NUCLEOTIDES TO THE LEADING STRAND:
Adding nucleotides to the leading strand is relatively simple. The DNA polymerase reads the leading strand as a template and forms/adds new nucleotides that are complementary with the existing one. It works towards the fork, walking along the DNA strand, adding nucleotides from the 3’ end of the strand, simultaneous to the helicase breaking the nitrogenous bonds. But it cannot start producing on its own. That’s why a short piece of RNA called a primer comes along and binds to the end of the strand. It acts as the starting point for the polymerase.
ADDITION OF NUCLEOTIDES TO THE LAGGING STRAND:
The addition of nucleotides to the lagging strand is comparatively more complicated. Since the DNA polymerase only works towards the fork and adds nucleotides from the 3’ end, and since the 3’ end is away from the fork, there are more steps needed to add nucleotides to the lagging strand.
First, numerous RNA primers made by an enzyme called primase is added to various points along the lagging strand. These primers bunch together to form short sequences of DNA nucleotides called okazaki fragments. The okazaki fragments are discontinuous and are dispersed. From the okazaki fragments, the DNA polymerase acts and creates nucleotides towards the 5’ end, filling up the gaps between the dispersed fragments. Once all the bases are matched up and nucleotides are fitted, the primers in-between are stripped away by an enzyme called exonuclease and the gaps are filled in by new nucleotides made by the DNA polymerase. The two finished strands are proof read and properly sealed by another enzyme called the DNA ligase.
The final result is two DNA molecules — each consisting of an old and a new strand.This arrangement is known as a semiconservative arrangement. Following the replication, the new DNA strands automatically wind into its original helix formation and undergoes supercoiling around histones to form chromosomes.