Understanding DNA Replication - GRE Subject Test: Biology

RNA polymerase is an enzyme that transcribes RNA from DNA; it is not essential for DNA replication. This enzyme is easy to confuse with primase, whose primary function is to synthesize the RNA primers necessary for replication. DNA polymerase add nucleotides during replication, synthesizing the daughter strand from the parental template. Helicase is responsible for separating double-stranded DNA. Single-strand binding proteins are needed to keep DNA from reannealing after it has been denatured by helicase.

DNA replicates in a semiconservative process. Parental strands are used as templates to synthesize daughter strands, which remain adhered to the parental template creating hybrid molecules of old and new DNA.

The original DNA molecules is "unzipped" by helicase to create the replication fork. DNA polymerase then begins to recruit nucleotides to bind to the exposed template, building the new DNA strand along the parental strand.

Before replication, the DNA helix must be unwound so that the strands can be replicated by DNA polymerase. This unwinding is accomplished by DNA helicase, which interferes with the hydrogen bonds between nucleotide pairs. This intervention creates a small separation between the two strands, known as the replication fork. DNA polymerase binds to the replication fork and recruits nucleotides to build the new DNA strand.

Topoisomerase is responsible for cleaving phosphodiester bonds in order to release torsional tension in the DNA backbone. DNA ligase synthesizes phosphodiester bonds, both on the daughter strand of DNA and in the regions cleaved by topoisomerase. Primase is responsible for synthesizing RNA primers that serve to help recruit and bind DNA polymerase in the replication fork.

In order for DNA polymerase to begin synthesizing base pairs, an RNA primer is needed to assist the binding of DNA polymerase to the DNA template strand. This primer is synthesized by the enzyme primase. Because DNA polymerase always needs an RNA primer before it can bind, primase must synthesize RNA primers on both the leading and lagging strands.

RNA polymerase transcribes molecules of RNA from DNA sequences during transcription, and is not involved in DNA replication.

DNA replication occurs during the S phase of the cell cycle, significantly before prophase of mitosis. During prophase chromosomes are condensed into easily segregated forms, but replication has already occurred. The S phase is the intermediate period of interphase in the cell cycle. The G2 phase follows the S phase, and is subsequently followed by the M phase (mitosis).

The short fragments synthesized on the lagging strand are known as Okazaki fragments. DNA replication does occur in the 5' to 3' direction; this is also the reason that the lagging strand must be synthesized away from the replication fork. DNA is denatured (separated) at the replication fork by an enzyme known as helicase, which breaks the hydrogen bonds between base pairs to allow DNA polymerase and other replication proteins to bind to single-strand DNA.

DNA polymerase I replaces the RNA primer gap with DNA nucleotides. This polymerase is unique in that it has 5' 3' exonuclease activity. This RNA primer is created by primase, it is removed and replaced with DNA by DNA polymerase I, and the remaining nick is sealed by DNA ligase. Bacterial DNA polymerase III, in contrast, is the main polymerase for bacterial elongation. The function of DNA polymerase II is not completely understood. The remaining answer choices are not involved in prokaryotic DNA replication.