DNA replication is a process of multiplying DNA as the genetic material of living things. This process is very important in the stage of cell breeding or division (phase S of the cell cycle). The duplicated DNA material will then be divided into each new cell.
Why study DNA replication?
- Genetic material: need to be known, to see heredity.
- Replication of genetic material: it is necessary to know how the material is reproduced and passed from one cell to another
Cells and from one generation to a new generation of living things - How is genetic material reproduced precisely and quickly?
DNA replication model
3 replication models proposed in the 1950s
Conservative model
- Both original strands act as templates / molds
- Produced 2 DNA molecules:
- 1 parent molecule
- 1 new molecule.
Semiconservative model
- Each strand acts as a mold
- Produced 2 new DNA molecules, each consisting of 1 strand of origin and 1 new strand.
Dispersive model
- DNA molecules are cut into pieces during replication
- The pieces replicate
- New pieces are formed
- Pieces of original and new DNA form 2 DNA molecules consisting of random pieces of new and old DNA pieces.
Steps in the DNA replication process
Initiation
The DNA in eukaryotic cells has ARCs (autonomously replicating sequences) that act as the origin of replication and they contradict each other from bacterial origin (ORI). ARCs consist of 11 base pairs plus two or three additional short nucleotide sequences with 100 to 200 base pairs along the DNA area.
The main group of six proteins, collectively known as ORC (Origin Recognition Complex), binds to the origin of replication, marking DNA replication precisely at the appropriate time through the cell cycle. Early site recognition of replication, by a protein component of DnaA polymerase produced by the dnaA gene.
The formation of replication forks.
A replication fork is a structure that forms when DNA replicates. This replication fork is formed by a helicase enzyme that breaks the hydrogen bonds that unite the two strands of DNA, making the double strand open into two branches each consisting of a single strand of DNA.
Each of these branches becomes a “mold” for the formation of two new strands of DNA based on the sequence of complementary nucleotides. Polymerase DNA forms new strands of DNA by extending oligonucleotides (RNA) formed by primase enzymes and called primers.
Lengthening DNA strands.
DNA Polymerase forms a new strand of DNA by adding nucleotides in this case, deoxyribonucleotide to the tip of the growing hydroxyl free nucleotide. In other words, the new DNA chain (“child” DNA) is synthesized from the direction of 5’→3′, while DNA polymerase moves on the “parent” DNA in the direction of 3’→5′.
Nevertheless, one of the parent DNA strands on the replication fork is oriented 3’→5′, while the other strand is oriented 5’→3′, and the helicase moves open the double strand of DNA in the direction of 5’→3′. Therefore, replication must take place in both opposite directions.
Leading strand formation.
In DNA replication, leading strands are DNA strands synthesized in the direction of 5’→3′ continuously. In this strand, DNA polymerase is able to form DNA using a 3′-OH tip free of an RNA primer and DNA synthesis takes place continuously, in the direction of replication fork movement.
Formation of Lagging strand.
Lagging strand is a strand of DNA located on the opposite side of the leading strand at the replication fork. These strands are synthesized in segments called Okazaki fragments. The length of Okazaki fragments reaches about 2,000 long nucleotides in bacterial cells and about 200 long nucleotides in eukaryotic cells.
In this strand, primates form a primary RNA. DNA Polymerase can thus use OH 3′ free clusters in the primary RNA to synthesize DNA in a direction of 5’→3′. The primary fragments of the RNA were then removed (e.g. With RNase H and DNA Polymerase I) and a new deoxyribonucleotides was added to fill the gaps previously occupied by RNA. DNA Ligase, then connects the fragments of Okazaki, so that the lagging strand synthesis becomes complete.
DNA polymerases are unable to ‘fill’ the missing covalent bonds. The remaining gaps are sealed by DNA ligase. This enzyme catalysts the formation of phosphodiester bonds between 3′ – OH from one strand of 5′-P from another strand. DNA ligase is activated by AMP (adenosine monophosphate) as a ‘cofactor’.
In E. Coli, AMP is brought from NAD+ nucleotide. In eukaryotic cells, AMP is marked from the ATP. Ligase are not involved in chain lengthening; rather, they act as installers of enzymes to glue ‘cracks’ through DNA molecules.
Post replication modification of DNA,
Once DNA is replicated, the two most recent synthesized strands are paired to enzymatic modifications. These changes usually involve the addition of certain molecules to specialize in dots along the double helix. In this way, cell tags, or labels, DNA, so that it can distinguish its own genetic material from various foreign DNA that might be able to get into the cell.
Post-replication modification of DNA may also affect the way molecules are bound. DNA is a major factor of modification with the addition of methyl groups to some adenine and cytosine residues. Methyl groups are added by DNA methylase after nucleotides have been combined with DNA polymerases.
The addition of methyl to cytosine forms 5-methylcytosine and methylation of adenine forms 6–
Methylase appears only in a few special nucleotide sequences. In eukaryotic cells, for example, methylation generally appears when cytosine coexists to guanine on the 3′-OH side (5′ P-CG-3’OH). The methylation pattern is specific to the given species, acting like a signature for the DNA of the species.
This is noteworthy because the methyl group protects DNA against resistance to certain enzymes called ‘restriction endonucleases’. Therefore, foreign DNA through a cell is digested with ‘restriction endonucleases’. In certain cells, ‘restriction endonucleases’ can cut DNA at certain specific points where methylase DNA is added to a methyl group.
Methylation patterns, protect DNA from digestion by cells that have endonucleases but do not resist the restriction of enzymes produced by other species cells. These restrictions simplify the exchange of DNA between cells from species produced by cells of different species. DNA methylation at certain points may end up at the closest conversion of B-DNA to Z-DNA forms.
In the form of B-DNA, hydrophilic methyl groups of the main groove, produce the right settings. By converting it into a Z-shape, methyl groups form hydrophilic areas that help stabilize DNA. This local conversion (from B-DNA to Z-DNA) may affect the function of some genes.
Similarities of DNA Replication Process in Eukaryotes and Bacteria
Information about this replication process comes from research on DNA replication in bacteria and bacteriophage. There are basically many similarities between the process of replication of bacteria and eukaryotes. It’s just that the protein components in the eukaryotes replication mechanism are more numerous. For example, the SSB protein in eukaryotes consists of three subunits whereas in bacteria only one unit.
Similarly, eukaryotic DNA primase consists of multisubunit enzymes in eukaryotes. This protein complex consists of DNA polymerase called DNA polymerase α-primase. This protein complex initiates each Okazagi fragment on a lagging strand with the NRA and then passes on the primary RNA with a short segment of DNA.
At this point, two major eukaryotic replication polymerase enzymes, δ and ε came and complemented each segment of Okazaki and simultaneously also extended the leading strand.
Another complexity in DNA replication is the presence of nucleosome structures. Eukaryotes chromosomes are arranged structurally repetitive in the form of nucleosomes. Basically, this structure can slow down replication work on eukaryotes 10 times slower.
In addition, nucleosomes are arranged throughout intervals of 100-200 nucleotides so that the length of Okazaki fragments in eukaryotes is shorter, which is 100-200 nucleotides compared to 1000-2000 nucleotides in bacteria.
