DNA Polymerase transcript DS

DNA Replication

The process where a cell makes an identical copy of its entire genome. Both strands of the double-stranded DNA act as templates for the synthesis of new, complementary strands, resulting in two double-stranded DNA molecules.

Semi-Conservative Replication

The model of DNA replication where each of the two resulting DNA molecules contains one original ("parental") strand and one newly synthesized ("daughter") strand.

Anti-parallel Strands

The structural arrangement of DNA where the two strands run in opposite directions; one runs 5' to 3', and the other runs 3' to 5'. This is a fundamental feature that dictates the mechanism of replication.

Local Unwinding

The initial step in replication where specific regions of the double-stranded DNA helix are separated into two single strands to serve as templates.

Single-Strand Binding Protein (SSB)

Proteins that bind to and stabilize the single-stranded DNA templates after unwinding, preventing them from re-annealing or forming secondary structures.

Primase

A specialized RNA polymerase that synthesizes short RNA sequences called primers. These primers provide the essential 3' hydroxyl group that DNA polymerase requires to begin DNA synthesis.

RNA Primer

A short segment of RNA (typically about 20-22 nucleotides long) synthesized by primase and base-paired to the DNA template. It provides the starting point, or "kick-starter," for DNA polymerase.

Origin of Replication

Specific, defined DNA sequences where replication is initiated. The DNA helix is locally opened at these sites, forming a replication bubble.

Replication Bubble

A region where the two strands of the DNA double helix have been separated and unwound to allow for the synthesis of new strands. It expands as replication proceeds.

Replication Fork

The Y-shaped region at either end of a replication bubble where the double-stranded DNA is being actively separated and the new strands are being synthesized.

Leading Strand

The new DNA strand that is synthesized continuously in the 5' to 3' direction toward the replication fork. Its synthesis proceeds in the same direction as the movement of the replication fork.

Lagging Strand

The new DNA strand that is synthesized discontinuously in the 5' to 3' direction away from the replication fork. It is produced as a series of short fragments called Okazaki fragments.

Okazaki Fragments

Short, newly synthesized DNA fragments on the lagging strand. They are later joined together to form a continuous strand.

DNA Ligase

The enzyme that seals the nicks in the DNA backbone. It catalyzes the formation of a phosphodiester bond between the 3' end of one Okazaki fragment and the 5' end of the next, creating a continuous strand.

Replisome

The large, multi-protein molecular machine that carries out DNA replication at the fork. It includes helicase, primase, DNA polymerases, and other accessory proteins working in a coordinated complex.

DNA Helicase

The enzyme that unwinds the double-stranded DNA at the replication fork. It uses ATP to break the hydrogen bonds between base pairs, separating the two template strands. Often depicted as a six-subunit ring.

Sliding Clamp

A protein complex that forms a ring around the DNA, tethering DNA polymerase to the template strand. This dramatically increases the processivity of DNA polymerase, allowing it to add thousands of nucleotides without falling off.

Trombone Model

A model describing the replication of the lagging strand. The lagging strand template forms a loop, allowing the DNA polymerase to synthesize Okazaki fragments in the 5' to 3' direction while the entire replisome moves in one direction. The loop expands and contracts like a trombone slide.

Telomere Replication Problem

A caveat to replication: the ends of linear chromosomes (telomeres) cannot be fully replicated by the standard replication machinery, leading to gradual shortening. This is dealt with by a separate specialized mechanism.

Replication Fidelity

The high accuracy of DNA replication. While DNA polymerase has proofreading (3'-5' exonuclease) activity, it is not perfect, and rare mistakes lead to mutations, meaning the copies are "designed to be identical" but are not always perfect.