DNA Replication in Prokaryotic and Eukaryotic Systems

Replication Definition: The process by which DNA makes a copy of itself.
Template Strand: The strand of DNA that serves as a guide for the synthesis of a new, complementary strand, also known as the parental strand.
Daughter Strand: The newly synthesized strand of DNA that is complementary to the template strand.
Requirements for Replication: Components necessary for DNA replication include:
- Deoxyribonucleoside triphosphates (dNTPs): The building blocks that DNA polymerase uses to synthesize new DNA strands.
- Enzymes: Such as DNA polymerases, helicases, primases, and ligases.

Conservative Replication: The original DNA molecule remains entirely intact, and a new copy is made.
Dispersive Replication: The parental DNA and new DNA are interspersed in both strands after replication.
Semiconservative Replication: Each new DNA molecule consists of one original strand and one new strand, as was proven by the Meselson and Stahl experiment.

Purpose of Experiment: To determine which model of DNA replication applies to E. coli—conservative, dispersive, or semiconservative.
Experimental Setup:
- E. coli was grown in a medium containing heavy nitrogen ($^{15}N$).
- Transferred to a medium containing light nitrogen ($^{14}N$) and allowed to replicate.
Observations:
- After the first round of replication, DNA appeared as a single band of intermediate weight (hybrid).
- After the second round of replication, two bands appeared: one light and one intermediate.
Conclusion: DNA replication in E. coli is semiconservative.

Process: A centrifuge tube filled with a heavy salt solution and DNA is spun at high speeds.
- Heavy DNA ($^{15}N$) migrates towards the bottom while light DNA ($^{14}N$) stays at the top, creating a density gradient.

Prokaryotic DNA replication begins at a unique site called the origin of replication.
Replication Fork and Bubble: The DNA unwinds creating a replication bubble with replication forks at each end.
Theta Representation: Common model in circular DNA, where parental DNA forms a structure resembling the Greek letter theta (Θ).
Products: Results in two circular DNA molecules.

Involves a break in one of the nucleotide strands initiating replication.
DNA synthesis occurs at the 3' end of the broken strand, displacing the 5' end to form a linear and a circular DNA molecule.

Each chromosome consists of multiple origins of replication, allowing faster duplication of long DNA strands.
At each origin, DNA unwinds, producing replication bubbles.
Adjacent bubbles fuse producing two identical linear DNA molecules.

New DNA strands are synthesized from dNTPs. During replication, the 3'-OH group of the last nucleotide attacks the 5'-phosphate group of the incoming dNTP, forming a phosphodiester bond.

Leading Strand: Synthesized continuously in the 5'-3' direction relative to the unwinding.
Lagging Strand: Synthesized in short segments called Okazaki fragments as it runs opposite to the direction of unwinding, each needing a new primer.

In prokaryotes, replication forks meet at a terminus region opposite the origin, leading to complete replication of the circular DNA.
In eukaryotes, telomerase adds telomeric repeats to chromosome ends to prevent degradation.

Eukaryotic DNA Polymerases include alpha (), delta (0), epsilon (0), and gamma (0), each with specific functions related to DNA synthesis and repair.
- Example: Polymerases delta and epsilon are involved in leading and lagging strand synthesis, while polymerase gamma is responsible for mitochondrial DNA replication.

Telomerase builds up telomere regions, which consist of repetitive sequences that prevent loss of essential DNA during replication.