lec7-DNA Replication Fundamentals

Comprehensive vocabulary regarding the mechanisms, enzymes, and error-correction processes involved in prokaryotic and eukaryotic DNA replication.

Semi-conservative replication

A replication strategy where each parent strand acts as a template for a newly synthesized strand, resulting in identical copies of the parent DNA.

Helicase

Enzymes that unwind the strands of DNA by utilizing energy from the hydrolysis of $ATP$.

Bidirectional replication forks

The two points formed at the origin of replication that move in opposite directions as they unwind double-stranded DNA.

$5'$ to $3'$ direction

The direction in which new DNA strands are synthesized, as DNA polymerase adds nucleotides to the free $3'OH$ of the growing strand.

Phosphodiester bonds

The chemical bonds that join nucleotides together in a polynucleotide chain.

Deoxynucleoside triphosphates (dNTPs)

Molecules with three phosphate groups attached to the $5'$ carbon of deoxyribose; they provide the nucleotides and energy for DNA synthesis.

Inorganic pyrophosphate ($PP_i$)

The molecule cleaved from an incoming dNTP during synthesis, whose hydrolysis provides the energy for nucleotide addition.

DNA polymerase III

A holoenzyme dimer that synthesizes the bulk of DNA in E. coli at a rate of approximately $1,000$ nucleotides per second.

Primase

The enzyme that synthesizes a short RNA primer to provide the free $3'OH$ needed for DNA polymerase III to begin synthesis.

Leading strand

The DNA strand that is synthesized continuously in the $5'$ to $3'$ direction toward the replication fork.

Lagging strand

The DNA strand synthesized discontinuously in short fragments in the direction opposite to the movement of the replication fork.

Okazaki fragments

Short fragments of DNA synthesized on the lagging strand that are later joined together by DNA ligase.

DNA polymerase I

An enzyme that removes RNA primers and synthesizes DNA in their place during the replication of the lagging strand.

DNA ligase

The enzyme responsible for joining Okazaki fragments into a continuous DNA strand.

Topoisomerases

Enzymes that relieve supercoiling ahead of the replication fork; Type II (gyrase in E. coli) cuts both DNA strands and requires $ATP$ to pass the coil through the gap.

Single-stranded binding protein ($SSBP$)

Proteins that prevent separated DNA strands from re-annealing during the replication process.

Sliding clamp

A protein complex that keeps DNA polymerase III firmly attached to the DNA, providing it with high processivity.

$$6.4 \times 10^9$$

The number of base pairs in the diploid human genome that must be accurately recreated during DNA replication.

Proofreading

The process where DNA polymerases use $3'-5'$ exonuclease activity to remove and replace incorrectly inserted bases.

Mismatch repair

A repair machinery in E. coli that identifies incorrect base pairs in the new, unmethylated strand and replaces the DNA to correct errors missed by proofreading.

$1$ in $10^{10}$ bases

The reduced error rate of DNA synthesis achieved through the combination of proofreading and mismatch repair.

DNA polymerase $\alpha$

A eukaryotic polymerase that assembles primers and initiates synthesis of the leading strand and Okazaki fragments, but lacks proofreading activity.

DNA polymerase $\gamma$

The eukaryotic polymerase specifically responsible for synthesizing mitochondrial DNA.

Replicon

A unit of DNA replication; eukaryotes form numerous replicons, whereas prokaryotes have only one.