Molecular Biology: DNA Replication and Gene Transcription

Posted on Sep 28, 2025 in Biology

DNA Replication: The Process of Duplication

DNA replication is the process by which a DNA macromolecule produces two identical copies of the original.

Key Steps and Enzymes in DNA Replication

Arthur Kornberg studied the DNA replication process in 1956. In bacteria, there is typically a single origin of replication.

Initiation and Strand Separation

The process starts with an enzyme called Helicase. This enzyme breaks the hydrogen bonds (H-bonds) between the chains, allowing their separation. As the two strands separate, supercoiling occurs in the rest of the molecule, thus involving other enzymes, Topoisomerases, which eliminate these torsional tensions (supercoils).

Subsequently, Single-Strand Binding (SSB) proteins are involved, whose function is to keep the two complementary strands separate. With all these components in place, the replication fork is formed.

The replication process is bidirectional, meaning a helicase works in one direction and another works in the opposite direction. The two replication forks form a replication bubble. DNA replication occurs simultaneously on both strands.

DNA Polymerase Functions

The main enzyme involved in this process is DNA Polymerase (known as Pol I, II, and III):

  • Pol I and Pol III: Responsible for replication and error correction.
  • Pol II: Responsible for repairing DNA damaged by various physical agents.

DNA Polymerase III is primarily involved in synthesis.

Synthesis Requirements and Directionality

DNA Polymerase requires three components:

  1. A DNA template (pattern).
  2. A primer strand.
  3. The nucleotides it will join.

DNA Polymerase always copies the strand in the 5′ to 3′ direction. Before DNA Polymerase can begin synthesis, RNA Polymerase must intervene because it does not require a pre-existing primer (though it still needs a template). This specific RNA Polymerase is called Primase.

Primase synthesizes a small RNA fragment consisting of ribonucleotides, called the primer. This snippet acts as the starting point for DNA Polymerase.

Leading and Lagging Strands

  • The strand that is copied continuously is called the leading strand.
  • The strands that are copied in the opposite direction of the replication fork are synthesized through a series of fragments called Okazaki fragments.

The lagging strand grows in the 5′ to 3′ direction, but discontinuously. RNA Polymerase (Primase) synthesizes an RNA fragment (about 40 nucleotides). Subsequently, DNA Polymerase synthesizes a DNA fragment (about 1000 nucleotides) in the 5′ to 3′ direction. After leaving a space, RNA Polymerase performs its function again, and the process is repeated.

Expression of the Genetic Message

Genetic expression involves two main processes: Transcription and Translation (or protein biosynthesis).

Transcription: DNA to RNA Synthesis

Transcription is the process of switching the DNA sequence into an RNA sequence. This requires DNA, ribonucleotide triphosphates, and RNA polymerases.

Transcription in Prokaryotes

  1. Initiation: RNA polymerase recognizes a region of DNA called a promoter. RNA polymerase moves from a closed configuration to an open one and unwinds the DNA to start RNA formation. This RNA is formed from a single DNA strand, which serves as the template.
  2. Elongation: RNA polymerase transcribes the DNA in the 5′ to 3′ direction, thereby extending the RNA chain.
  3. Termination: This occurs when the polymerase reaches a sequence rich in cytosine and guanine. This causes the end of the RNA to become self-complementary. It forms a loop and separates from the DNA.
  4. Maturation: Maturation is generally not needed for mRNA in prokaryotes, but if tRNA or rRNA is formed, it involves a primary transcript that is cut and joined to form the corresponding mature RNA.

Transcription in Eukaryotes

  1. Initiation: RNA Polymerase II is set at a DNA region that is the promoter zone. There are nucleotide sequences that RNA Polymerase recognizes, called consensus sequences (e.g., CAAT, TATA boxes).
  2. Elongation: The process is the same as in prokaryotes, transcribing RNA in the 5′ to 3′ direction. When about 30 nucleotides have been synthesized, the cap is added.
  3. Termination: This relates to a specific DNA sequence (e.g., TTATTT). Poly-A Polymerase intervenes to add a succession of adenine nucleotides (the poly-A tail) at the 3′ end.

This process forms the Heterogeneous Nuclear RNA (hnRNA). This transcript contains two types of sequences:

  • Introns: Sequences that do not contain information for proteins.
  • Exons: Sequences that do contain information for proteins.

RNA Maturation (Splicing)

Maturation takes place in the nucleus. Introns form loops, are cut out, and the exons are spliced together. This results in the mature mRNA.

Both mRNA and tRNA also undergo maturation processes. tRNA maturation highlights the addition of the CCA triplet at the 3′ end. The mature rRNA is derived from nucleolar RNA.