Molecular Mechanisms of DNA Replication and Synthesis

Initiation Phase: Unwinding the Double Helix

The initiation phase involves the unwinding and opening of the double helix. This process initiates in a region of DNA called the origin of replication (oriC point). Helicases break the hydrogen bonds of the nitrogenous bases, and as the double helix unwinding occurs, it creates tensions that could lead to more coiling. Therefore, topoisomerases break and rejoin strands, while SSB proteins (Single-Strand Binding proteins) bind to the template strands to prevent any recurrence of winding. A replication bubble is formed, containing two Y-shaped areas called replication forks, where new DNA strands will be synthesized.

Elongation: Synthesizing New DNA Strands

During elongation, a new strand of DNA is synthesized on each strand of the original double helix using DNA polymerases. The specific functions include:

• DNA Polymerase: Joins the nucleotides that form DNA.
• Exonuclease: Deletes nucleotides whose bases are mismatched, as well as fragments of RNA.

To initiate synthesis, a fragment of approximately 10 nucleotides of RNA, called a primer (cebador), is required. This is synthesized by an RNA polymerase called primase, which reads the template strands in the 3'-5' direction. As the two chains are antiparallel, synthesis in the 3'-5' sense occurs without interruption; this is known as the leading strand (or leader). The strand oriented 5'-3', known as the lagging strand (delayed strand), undergoes discontinuous synthesis of small DNA fragments of about one thousand nucleotides, called Okazaki fragments. Each fragment requires an RNA primer synthesized by primase. DNA polymerase eliminates the primer and replaces it with DNA, and DNA ligase welds all the fragments obtained.

Corrigendum: DNA Proofreading and Evolution

DNA polymerase acts as an exonuclease and removes mismatched nucleotides. This corrigendum mechanism is very efficient, but occasionally a mutation occurs, which can be very important for evolution.

DNA Replication in Eukaryotes

The replication process in eukaryotes is similar to prokaryotes. However, eukaryotic chromosomes have very long molecules, so DNA replication is initiated simultaneously at several points in each chromosome called replicons. There are five types of DNA polymerases (α, β, γ, δ, and ε). Specifically, polymerase γ is involved in the DNA replication of mitochondrial DNA. In eukaryotes, DNA is found associated with histones, proteins that prokaryotes do not have, which duplicate during replication. The combination of histones and DNA forms a nucleosome. New histones join the lagging strand, while the old ones remain on the leading strand. Upon removing the last primer, DNA polymerase cannot fill the gap because it is unable to synthesize in the 3'-5' direction. Because of this, the end of the chromosome, the telomere, narrows each time the cell divides. This process is associated with aging and cell death.

Bidirectional Replication Growth

Bidirectional replication means that from the origin, replication grows in both directions because both strands are replicated simultaneously in both directions.