DNA replication

Deoxyribonucleic acid, that is, DNA ( DNA is its acronym in English), constitutes the identity of each cell, as it is its genetic material. When a cell divides to form two cells, either through mitosis or meiosis, the biomolecules and organelles must duplicate to make each new cell. In eukaryotic cells, the DNA is found within the cell’s nucleus, and must be replicated exactly to ensure that the two new cells are identical to the one that originated them, and also that they have the correct number of chromosomes. The process of duplicating DNA is called  replication .; it is an essential process in cell growth and reproduction, as well as in cell repair processes. The DNA replication process has several steps and involves various proteins called replication enzymes , as well as RNA , ribonucleic acid.  In eukaryotic cells , the cells that make up animals and plants, DNA replication occurs in the S phase of the cell cycle .

These are the key aspects of DNA replication:

• Deoxyribonucleic acid, commonly known as DNA, is a nucleic acid that has three main components: a sugar, deoxyribose; a phosphate group; and a nitrogenous base.
• Since DNA contains the genetic material of an organism, it is important that it is copied exactly when a cell divides. The complex biochemical process that leads to copying of DNA is called replication.
• Replication involves the production of identical strands of DNA from a double helix DNA molecule.
• Enzymes are vital to DNA replication, as they catalyze very important steps in the process.
• The general process of DNA replication is extremely important for both cell growth and reproduction of organisms. It is also vital in the cell repair process.

the structure of dna

DNA or deoxyribonucleic acid is a type of molecule known as a nucleic acid. It is composed of deoxyribose, a sugar that has five carbon atoms (C ₅ H ₁₀ O ₄ ), a phosphate, and a nitrogenous base. DNA is made up of two spiral-shaped strands of nucleic acid that are linked together to form a double helix. The intertwined helix shape allows DNA to be a molecule called chromatin and is the component of chromosomes. Prior to DNA replication, chromatin unfolds allowing the cellular replication processes of the DNA strands to take over.

Preparing for replication

Step 1: formation of the replication fork

Before the DNA replication process begins, the two intertwined strands that make it up must be separated. DNA is made up of four bases called adenine (A), thymine (T), cytosine (C) and guanine (G), organized in pairs that join the two chains together, forming bridges. Adenine only bonds with thymine, and cytosine only bonds with guanine. To separate the two DNA strands these bridges formed by the bases must be broken. This process is carried out by an enzyme known as DNA helicase. DNA helicase sequentially disrupts the hydrogen bond between the bases that form each bridge between the two strands, pulling them apart and, in the process, transforming the double helix into a Y-shaped branching assembly known as a replication fork, as is shown in the figure.

As a consequence of the separation of the chains and taking into account that the bases that form the bridges are different in each chain, each one will have a different composition after the division. The end of the bridge that remains on each strand after separation is expressed as 5′ or 3′. The 5′ end has a phosphate (P) group while the 3′ end has a hydroxyl (OH) group. This directionality is important in the replication process, as it occurs only in the 5′ to 3′ direction. However, as stated, forking the division generates different ends on each chain. One string will be oriented in the 3′ to 5′ direction, the leading string, while the other will be oriented 5′ to 3′, the lagging string. Therefore,

Replication begins

Step 2: initiation binding

The main chain is the easiest to replicate. Once the DNA strands have been separated, a short piece of RNA, a starter molecule, attaches to the 3′ end of the strand, providing the starting point for replication. These initiation molecules are generated by the enzyme DNA primase.

DNA replication: elongation

Step 3: Elongation

Enzymes known as DNA polymerases are responsible for creating the new strand through a process called elongation. There are five different types of DNA polymerases in both bacteria and human cells. In bacteria such as E. coli, polymerase III is the main replication enzyme, while polymerase I, II, IV and V are responsible for checking and repairing any errors that occur in the chain. DNA polymerase III binds to the strand at the initiation site and begins adding new complementary base pairs to the replicating strand. In eukaryotic cells, alpha, delta, and epsilon polymerases are the major polymerases involved in DNA replication. Because replication proceeds in the 5′ to 3′ direction on the main strand, the new strand is continuously formed.

The lagging chain starts replication from multiple initiators. Each primer is separated by several bases. DNA polymerase adds pieces of DNA, called Okazaki fragments, to the stretches of strand located between the primers. Thus, the replication process is discontinuous, since it alternates in the lengths of the chain between the initiators.

Step 4: Termination

Once the continuous and discontinuous strands are formed, an enzyme called exonuclease removes all RNA primers from the original strands. These primers are then replaced with the corresponding bases. Another exonuclease proofreads the newly formed DNA to verify it, removing and replacing any errors that may have occurred in the process. Another enzyme called DNA ligase joins the Okazaki fragments into a single strand. Linear DNA ends present a problem, as DNA polymerase can only add nucleotides in the 5′ to 3′ direction. The ends of the parent strands consist of repeating DNA sequences called telomeres. Telomeres act as protective caps at the end of chromosomes to prevent nearby chromosomes from fusing. A special type of DNA polymerase enzyme called telomerase catalyzes the synthesis of telomere sequences at the ends of DNA. Once complete, the parent strand and its complementary DNA strand are linked together in the well-known double helix fashion. At the end of the replication process, two DNA molecules are produced, each containing a strand from the original molecule and a new strand produced in the replication process.

replication enzymes

DNA replication would not occur without the participation of enzymes that catalyze various steps in the process. The main enzymes involved in the eukaryotic DNA replication process are:

• DNA helicase: Unfolds and separates the double strand of DNA as it moves along the length of the molecule. It thus forms the replication fork by breaking the hydrogen bonds that form the bridges between pairs of DNA nucleotides.
• DNA primase: A type of RNA polymerase that generates primers for the process. Primers are short RNA molecules that act as templates at the starting point of DNA replication.
• DNA polymerases: synthesize new DNA molecules by adding nucleotides to the leading and lagging DNA strands.
• Topoisomerase or DNA gyrase: Unfolds and intertwines DNA strands to prevent DNA from tangling.
• Exonucleases: A group of enzymes that remove nucleotide bases from the end of a DNA strand.
• DNA ligase: joins DNA fragments forming phosphodiester bonds between nucleotides.

Summary

DNA replication is a process that generates identical DNA strands from a single double helix DNA molecule. Each new DNA molecule consists of one strand from the original molecule and one strand formed in the process of replication. Before replication, the DNA unfolds and the strands of the double helix separate. A Y-shaped replication fork is formed which serves as a template for replication. Primer molecules attach to separated DNA strands, and DNA polymerases add new nucleotide sequences in the 5′ to 3′ direction.

This nucleotide incorporation is continuous on the leading strand and fragmented on the lagging strand. Once the elongation of the DNA strands is complete, the new strands are checked for errors, repairs are made as necessary, and telomere sequences are added to the ends of the DNA.

Fountain

• Reece, Jane B., and Neil A. Campbell. Campbell Biology . Benjamin Cummings, 2011.
• Lehninger. Principles of Biochemistry – Omega, 6th Edition 2014