Essential Cell Biology: Chapter 6 - DNA Replication and Repair

Vocabulary flashcards covering the molecular mechanisms of DNA replication, replication fork enzymology, eukaryotic polymerases, telomere maintenance, chemical DNA damage, and DNA repair pathways from Chapter 6 of Essential Cell Biology.

Semiconservative Replication

The mechanism of DNA replication in which each daughter DNA double helix is composed of one conserved (old) strand from the parent DNA and one newly synthesized strand.

Meselson–Stahl Experiment

An experiment that proved DNA replication is semiconservative by growing E. coli in heavy ($^{15}\text{N}$) and light ($^{14}\text{N}$) nitrogen isotopes and analyzing DNA band density using cesium chloride gradient centrifugation.

Replication Origin

Specific DNA sequences recognized by initiator proteins that locally open and pull apart the two strands of the DNA double helix to expose single-stranded templates.

Replication Fork

A Y-shaped junction formed at a replication origin where DNA replication machinery actively synthesizes new DNA strands bidirectionally away from the origin.

Direction of DNA Synthesis

The universal direction in which all new DNA strands are polymerized, occurring strictly from the $5'$ end to the $3'$ end as nucleotides are added to the free $3'\text{-hydroxyl}$ group.

Deoxyribonucleoside Triphosphate (dNTP)

The incoming building block substrate for DNA synthesis that enters as a nucleoside triphosphate; hydrolysis of its high-energy phosphate bond and release of pyrophosphate drives the polymerization reaction.

Leading Strand

The newly synthesized DNA strand at a replication fork that is made continuously in the $5'\text{-to-}3'$ direction toward the unwinding fork.

Lagging Strand

The newly synthesized DNA strand whose direction of elongation is opposite to fork movement, requiring it to be synthesized discontinuously in short pieces via a backstitching mechanism.

Okazaki Fragments

Short pieces of DNA synthesized discontinuously in the $5'\text{-to-}3'$ direction on the lagging strand template (approximately $1200$ nucleotides long in bacteria).

Proofreading

The self-correcting mechanism of DNA polymerase that removes incorrectly paired nucleotides from the $3'$ end of the growing strand before adding the next nucleotide, reducing errors to $1$ in $10^7$ copied.

Polymerizing (P) and Editing (E) Sites

The two distinct catalytic domains within DNA polymerase; synthesis occurs at the P site, whereas a mispaired $3'$ end transiently unpairs from the template and shifts to the E site for exonucleolytic cleavage.

Primase

An RNA polymerase that synthesizes short RNA primers (about $10$ nucleotides in length) in the $5'\text{-to-}3'$ direction along the template strand without requiring a base-paired $3'$ starting end.

DNA Helicase

An enzyme that uses the energy of ATP hydrolysis to pry apart and unwind the parent DNA double helix ahead of the replication fork.

Single-Strand DNA-Binding Protein (SSB)

A protein that binds exposed single-stranded template DNA behind the helicase to prevent base pairs from re-forming before replication occurs.

Sliding Clamp

A circular ring-shaped protein that keeps DNA polymerase firmly attached to the template strand while sliding along during strand synthesis.

Clamp Loader

A protein complex that harnesses the energy of ATP hydrolysis to lock the sliding clamp onto DNA around the primer-template junction.

DNA Topoisomerase

An enzyme that relieves overwinding and torsional strain ahead of the replication fork by creating transient single-strand breaks in the double helix and resealing them once relaxed.

DNA Ligase

An enzyme that uses the energy of ATP hydrolysis to activate the $5'$ phosphate of one DNA fragment and join it to the adjacent $3'\text{-hydroxyl}$ end, sealing nicks in the sugar-phosphate backbone.

DNA Polymerase I

A bacterial repair DNA polymerase that fills in the gaps left after RNA primers are degraded by nucleases and proofreads as it fills in the sequence.

DNA Polymerase III

The primary replicative DNA polymerase in bacteria that carries out continuous leading strand synthesis and Okazaki fragment elongation on the lagging strand.

DNA Polymerase $\alpha$ (alpha)

A eukaryotic DNA polymerase that works alongside primase to initiate replication by synthesizing a short stretch of DNA onto the RNA primer.

DNA Polymerase $\epsilon$ (epsilon)

A eukaryotic DNA polymerase responsible for continuously synthesizing the majority of the leading strand.

DNA Polymerase $\delta$ (delta)

A eukaryotic DNA polymerase that synthesizes most of the lagging strand as Okazaki fragments and aids in gap filling during DNA repair.

DNA Polymerase $\gamma$ (gamma)

The specialized eukaryotic DNA polymerase that replicates mitochondrial DNA.

DNA Polymerase $\beta$ (beta)

A eukaryotic DNA polymerase that primarily functions in DNA repair, particularly in base-excision repair.

Telomeres

Repetitive noncoding DNA sequences located at the ends of eukaryotic chromosomes that protect linear chromosome ends from genetic loss during rounds of replication.

Telomerase

An enzyme containing an integral RNA template that elongates the $3'$ end of eukaryotic chromosome template strands, resolving the end-replication problem of the lagging strand.

Depurination

A spontaneous chemical reaction driven by water collisions that hydrolyzes purine bases (guanine or adenine) from deoxyribose, leaving the sugar-phosphate backbone intact but lacking a base.

Deamination

A spontaneous chemical alteration where an amino group on a nucleotide base is lost and replaced with a keto group (for example, converting cytosine to uracil).

Thymine Dimer

A lesion caused by ultraviolet (UV) radiation in sunlight that causes two adjacent thymine bases on a DNA strand to covalently bond together, stalling replication machines.

Base Excision Repair

A cellular repair pathway consisting of three steps: damage excision by specific nucleases, gap resynthesis by repair DNA polymerase, and backbone sealing by DNA ligase.

Mismatch Repair

A post-replication surveillance system that detects and replaces mispaired nucleotides exclusively on the newly synthesized DNA strand using the parent strand as a template, raising replication fidelity to $1$ mistake per $10^9$ nucleotides.

Nonhomologous End Joining (NHEJ)

A double-strand break repair mechanism in which broken ends are trimmed by specialized nucleases and joined by DNA ligase, frequently resulting in nucleotide loss at the repair site.

Homologous Recombination

A high-fidelity double-strand break repair pathway that uses an undamaged homologous DNA template, $5'$ end resection, and strand invasion to repair DNA breaks flawlessly without loss of nucleotides.

Taq Polymerase

A thermostable DNA polymerase isolated from the bacterium Thermophilus aquaticus that remains functional at $95^\circ\text{C}$ during PCR amplification cycles.

Primer Melting Temperature ($T_m$)

The estimated denaturation temperature for short oligonucleotide primers up to $30\text{ base pairs}$, calculated using the formula: $T_m(^\circ\text{C}) = 2(A + T) + 4(G + C)$.

Dideoxyribonucleoside Triphosphate (ddNTP)

A nucleotide analog lacking both the $2'$ and $3'\text{-hydroxyl}$ groups (such as ddCTP) that prevents further strand elongation and acts as a chain terminator when incorporated into DNA.

Germline Mutation

A mutation occurring in reproductive germ cells that is heritable and passed on to all cells of future generations (e.g., the $A\text{-to-}T$ point mutation in the $\beta\text{-globin}$ gene causing sickle-cell anemia).

Somatic Mutation

A non-heritable genetic mutation occurring in ordinary body tissues that accumulates over a lifetime and can lead to uncontrolled cell proliferation and cancer.