DNA Replication and Repair (1B) - MCAT Biological and Biochemical Foundations of Living Systems

The primer strand $3'$-OH group. The 3'-OH attacks the alpha phosphate of the incoming dNTP, forming a phosphodiester bond during chain elongation.

The template is read in the $3' \to 5'$ direction. Antiparallel strand orientation requires the template to be read 3' to 5' for new strand synthesis in the 5' to 3' direction.

DNA is synthesized in the $5' \to 3'$ direction. DNA polymerases add nucleotides to the growing chain's 3' end, ensuring synthesis proceeds from 5' to 3'.

Cleavage of dNTP to dNMP with release of pyrophosphate ($PP_i$). Hydrolysis of the high-energy bonds in dNTP releases pyrophosphate, providing the energy to make the reaction exergonic.

The strand synthesized continuously in the same direction as fork movement. It allows continuous elongation toward the replication fork without interruption as the helix unwinds.

The strand synthesized discontinuously as Okazaki fragments. Synthesis occurs in short segments away from the fork due to the antiparallel nature of DNA strands.

Unwinds the parental double helix at the replication fork. Helicase uses ATP hydrolysis to separate DNA strands, creating single-stranded templates for polymerase access.

Stabilize ssDNA and prevent reannealing or secondary structure formation. SSBs coat exposed single strands to maintain their accessibility and prevent unwanted structures during replication.

Relieve supercoiling/torsional strain ahead of the replication fork. They introduce temporary strand breaks to relax positive supercoils generated by unwinding at the fork.

Topo I cuts $1$ strand; topo II cuts $2$ strands (ATP-dependent). Type I relaxes supercoils via single-strand nicks without ATP, while type II passes strands through double-strand breaks using ATP.

Synthesizes short RNA primers to provide a free $3'$-OH. Primase, an RNA polymerase, creates RNA segments that DNA polymerase extends, as it cannot start chains de novo.

Seals nicks by forming phosphodiester bonds between adjacent DNA ends. It catalyzes the ATP-dependent formation of phosphodiester bonds to join Okazaki fragments or repair breaks.

Increases processivity by tethering DNA polymerase to DNA. The clamp encircles DNA and binds polymerase, enhancing its ability to synthesize long stretches without dissociating.

$3' \to 5'$ exonuclease activity. This activity removes incorrectly paired nucleotides from the 3' end, allowing replacement before synthesis continues.

They cannot initiate synthesis de novo; they require a preexisting $3'$-OH. DNA polymerases can only extend existing chains, requiring an RNA primer to supply the initial 3'-OH group.

DNA polymerase III. Pol III is the highly processive replicative enzyme responsible for most nucleotide addition during bacterial replication.

DNA polymerase I. Pol I uses its 5' to 3' exonuclease to excise RNA primers and polymerase activity to replace them with DNA.

After primer removal, the terminal lagging-strand segment cannot be fully replicated. Lagging strand synthesis leaves a gap at the 5' end after RNA primer removal, as no upstream 3'-OH is available for filling.

Each daughter duplex contains one parental strand and one newly synthesized strand. This mechanism, proven by Meselson-Stahl, preserves genetic information by using each parental strand as a template.

A pairs with T; G pairs with C (Watson–Crick base pairing). Specific hydrogen bonds between purines and pyrimidines ensure fidelity in template-directed synthesis and repair.

Base-base mismatches and small insertion/deletion loops that escape proofreading. MMR detects and excises errors like mismatches or loops post-replication, using strand discrimination to guide repair.

Small, non-bulky base lesions (e.g., deamination, oxidation) via DNA glycosylase. BER initiates with glycosylase removing altered bases, followed by strand incision and gap-filling for subtle damage.

Bulky, helix-distorting lesions (e.g., thymine dimers) by excising an oligonucleotide. NER excises a short single-stranded segment containing the lesion, then synthesizes a replacement using the intact strand.

Bulky, helix-distorting lesions typically repaired by NER. UV light causes covalent bonds between adjacent thymines, distorting the helix and triggering NER for removal.