DNA replication
DNA replication is the process of doubling DNA before dividing the cell. Doubling occurs in the S-phase of interphase of the cell cycle.
Obviously, the self-copying of genetic material in living nature is a necessity. Only in this way new cells can contain as much DNA as it was in the original. Through replication, all genetically programmed features of structure and metabolism are transmitted in a series of generations.
In the process of cell division, each DNA molecule from a pair of identical go away in its daughter cell. Thus, accurate transmission of hereditary information is ensured.
When DNA is synthesized, energy is consumed.
Mechanism of DNA replication
The DNA molecule itself (without doubling) is a double helix. In the process of replication, the hydrogen bonds between its two complementary chains are broken. And on each separate chain (or the strand), which now serves as a template (or matrix), a new chain complementary to it is being constructed. Thus, two DNA molecules are formed. Each molecule receives one chain from the original DNA, the other is newly synthesized. Therefore, the mechanism of DNA replication is semiconservative (one chain is old, one is new).
This replication mechanism was proved in 1958.
In a DNA molecule, the chains are anti-parallel. This means that one strand goes in the direction from 5' end to 3', and complementary strand - on the contrary. Digits 5 and 3 denote the carbon atoms in deoxyribose, which is part of each nucleotide. Through these atoms, nucleotides are linked together by phosphodiester bonds. And where there is the 3' link in one chain, the other has the 5', since it is inverted, that is, it goes in the different direction.
The main enzyme, which performs the build-up of a new strand of DNA, is able to do it only in the one direction. Namely, attach each following new nucleotide only to the 3' end. Thus, the synthesis can proceed only in the direction from 5' to 3'.
Chains of the original DNA are antiparallel, so synthesis must go on them in different directions. If DNA chains were completely divergent at first, and then a new complementary one was built on them, then this would not be a problem. However in reality, the strands diverge at certain points (origins of replication), and in these places the synthesis begins almost immediately on the template DNA strands.
So-called replication forks are formed here. On one template, the synthesis goes in the direction of divergence of the fork, and that synthesis occurs continuously, without breaks. On the second matrix, the synthesis goes in the opposite direction from the direction of divergence of the chains of the original DNA. Therefore such reverse synthesis can only perform by making pieces, which are called Okazaki fragments. Later these fragments are "sewn" together.
A new chain that replicates continuously is called the leading chain. The one, that is synthesized through Okazaki fragments, is the lagging strand, since fragmentary replication is slower.
On the illustration, the strands of the parental DNA gradually diverge in the direction in which the leading chain is synthesized. The synthesis of the lagging chain goes to the opposite side of the divergence, therefore it is forced to be carried out by pieces.
Another feature of the main DNA synthesis enzyme (polymerase) is that it can not start the synthesis itself, just continue. It needs a primer. Therefore, a small complementary portion of RNA is first synthesized on the matrix strand, then the chain is grown with polymerase. Later primers are removed, holes are built up.
In the scheme, primers are shown only on the lagging chain. In fact, they are also on the leading. However, only one primer per a fork is needed here.
Since the chains of the maternal DNA do not always diverge from the ends, but at the points of initialization (origins of replication), then not exactly forks, but bubbles are formed.
In each bubble there can be two forks, i.e., the chains of matrix DNA will diverge in two directions. However, they can doing it only in one. If the discrepancy is bidirectional, then from the origin of replication on one DNA strand the synthesis will go in two directions - forward and backward. This means that continuous synthesis will be carried out in one direction, and in the other side with Okazaki fragments.
Prokaryotic DNA is not linear, but has a ring structure and only one origin of replication.
In the figure, red and blue circles are the two strands of the original DNA molecule. The new chains are shown in dotted lines.
In prokaryotes, self-copying of DNA is performed faster than in eukaryotes. If the rate of replication in eukaryotes is hundreds of nucleotides per second, then the prokaryotes reach a thousand or more.
Replication Enzymes
DNA replication is provided by a complex of enzymes called the replicome. The total enzymes and proteins of replication are more than 15. The following are the most significant.
The main enzyme of replication is the already mentioned DNA polymerase (in fact, there are several different), which directly carries out chain building. This is not the only function of the enzyme. Polymerase is able to "check" which nucleotide is trying to join the end. If unsuitable, the enzyme removes it. In other words, partial DNA repair, i.e., its correction of replication errors, occurs at the stage of synthesis.
In the nucleoplasm (or the cytoplasm in bacteria), nucleotides exist in the form of triphosphates, ie, they are not nucleotides, but deoxynucleoside triphosphates (dATP, dTTP, dGTP, dCTP). They are similar to ATP, which has three phosphate groups, two of which are bound by a macroergic linkage. When such linkage are broken, a lot of energy is allocated. Also in deoxynucleoside triphosphates, two bonds are macroergic. The polymerase separates the last two phosphates (together) from the nucleoside triphosphate and uses the released energy for the DNA polymerization reaction.
The helicase enzyme separates the strands of the original DNA, rupturing the hydrogen bonds between them.
Since the DNA molecule is a double helix, the breaking of the bonds provokes an even greater twist (supercoiling). Imagine a rope made of two twisted ropes relative to each other, and you pull the end of one rope to the right and the other rope to the left. The woven part will become even more twisted, it will be more tight.
To eliminate additional twisting, it is necessary that the double helix rapidly rotate around its axis, "dumping" the emerging supercoiling. However, this requires a lot of energy. Therefore, in the cells another mechanism is realized. The topoisomerase enzyme breaks one of the strands, passes the second chain through the gap, and again connects the first one. This eliminates the emerging supertwists.
The separated strands of matrix DNA are trying to reconnect with their hydrogen bonds. To prevent this, DNA-binding proteins act. These are not enzymes in the sense that they do not catalyze reactions. Such proteins attach to the DNA strand and do not allow the complementary chains of the original DNA close.
Primers are synthesized by RNA primase. And they are removed by exonuclease. After removing the primer, another type of polymerase fills the hole. However, chunks of DNA do not cross-link.
The parts of the synthesized chain are joined by the another enzyme of replication - the DNA ligase.