Lecture 14: DNA Replication and Repair

Practice vocabulary flashcards for Lecture 14 covering DNA replication enzymes, mechanisms of synthesis, replication forks, proofreading, and DNA repair pathways.

Semiconservative Replication

The model of DNA replication in which the two parental strands separate and each acts as a template for building a new complementary strand, resulting in daughter molecules consisting of one original strand and one newly synthesized strand.

S Phase

The specific synthesis phase during interphase of the cell cycle during which DNA replication occurs.

Origin of Replication

Special sites on the chromosome where DNA replication begins and where the two parental DNA strands are initially separated to form a replication bubble.

Replication Bubble

The open region formed by the unwinding and separation of the two DNA strands at an origin of replication, from which replication proceeds bidirectionally.

Replication Fork

A Y-shaped region located at each end of a replication bubble where parental DNA strands are unwound and new strands elongate.

Helicase

An enzyme that untwists and unzips the parental double helix at the replication forks, separating the two strands to make them available as templates.

Single-Strand Binding Protein

A protein that binds to and stabilizes single-stranded DNA until it can be used as a template, while also removing other proteins from the DNA.

Topoisomerase

An enzyme that relieves overwinding strain ahead of replication forks by breaking, swiveling, and rejoining DNA strands; it is a clinical target for chemotherapy drugs and ciprofloxacin (cipro).

Primase

An enzyme that starts an RNA chain from scratch by synthesizing a complementary RNA primer one nucleotide at a time using the parental DNA strand as a template.

RNA Primer

A short initial strand of RNA, approximately $5\text{–}10\text{ nucleotides}$ long, whose free $3'$ end provides the required starting point for DNA polymerase to begin synthesizing DNA.

DNA Polymerase III

The primary bacterial replication enzyme that synthesizes a new DNA strand by continuously adding complementary nucleotides to an RNA primer or pre-existing chain using the parental DNA as a template.

DNA Polymerase I

The bacterial enzyme that removes RNA primer nucleotides from the $5'$ end and replaces them with DNA nucleotides by adding onto the $3'$ end of the adjacent fragment, though it cannot covalently seal the backbone.

DNA Ligase

An enzyme that catalyzes phosphodiester bonds to join Okazaki fragments on the lagging strand, as well as joining the $3'$ end of replacement DNA to the rest of the leading strand.

Leading Strand

The new complementary DNA strand synthesized continuously by DNA polymerase along the template strand, moving directly toward the replication fork.

Lagging Strand

The discontinuously synthesized DNA strand that elongates in a direction away from the replication fork, produced as a series of short segments.

Okazaki Fragments

The series of short segments synthesized on the lagging strand during replication, each initiated with an RNA primer and subsequently joined by DNA ligase.

$5' \rightarrow 3'$ Direction

The mandatory direction in which all new DNA strands must elongate, because incoming nucleotides can only attach spatially to an available free $3'$ hydroxyl group.

Nucleoside Triphosphates

The free-floating precursor molecules (dATP, dCTP, dGTP, dTTP) in the nucleus that supply both nucleotide monomers and the energy needed to form phosphodiester bonds during replication.

Pyrophosphate

A two-phosphate molecule released when a nucleoside triphosphate joins a growing DNA chain; its subsequent hydrolysis into $2\,\text{P}_i$ supplies the energy for phosphodiester bond formation.

Bacterial DNA Elongation Rate

The rate at which DNA polymerases synthesize new DNA in bacteria, approximately $500\text{ nucleotides per second}$.

Human DNA Elongation Rate

The rate of new strand synthesis catalyzed by DNA polymerases in human cells, approximately $50\text{ nucleotides per second}$.

Mismatch Repair

A DNA repair pathway where specialized repair enzymes detect, excise, and correct errors in base pairing that escaped initial polymerase proofreading.

Nucleotide Excision Repair

A DNA repair mechanism in which a nuclease excises damaged or deformed stretches of DNA (such as those from chemical agents or UV radiation), DNA polymerase replaces the missing nucleotides, and DNA ligase seals the nick.

Nuclease

An enzyme that cuts out and removes damaged or altered segments of DNA strands during nucleotide excision repair.

Xeroderma Pigmentosum

An inherited genetic disorder caused by a defect in nucleotide excision repair enzymes, which prevents the repair of UV-induced DNA damage and results in extreme sun sensitivity and skin lesions.

Telomeres

Repetitive, non-coding sequences of DNA located at the ends of eukaryotic chromosomes that protect genomic integrity.

Template Strand

The pre-existing parental DNA strand that serves as the physical mold and provides the complementary sequence for synthesizing a new daughter strand.

Base Pairing Rule

The biochemical rule dictating that across a DNA double helix, a purine always hydrogen-bonds specifically with a pyrimidine (adenine pairs with thymine, and guanine pairs with cytosine).

Proofreading

The enzymatic self-correction process by which DNA polymerases check newly synthesized DNA as it is made and immediately replace incorrectly paired nucleotides.

Sliding Clamp

A ring-shaped protein that tethers DNA polymerase III to the template strand, facilitating continuous and processive elongation along the DNA molecule.