DNA Replication and Repair Practice Flashcards

A comprehensive set of 80 vocabulary flashcards covering DNA replication models, enzymes, repair mechanisms, and associated diseases as detailed in the lecture transcript.

Semiconservative model

DNA replication model where each daughter DNA double helix contains one parental strand and one newly synthesized strand.

Conservative model

A model of DNA replication that was ruled out by the Meselson–Stahl experiment.

Dispersive model

DNA replication model ruled out after the second round of replication in the Meselson-Stahl experiment.

Meselson–Stahl experiment

Study that labeled bacteria with heavy and light nitrogen isotopes to determine the mode of DNA replication.

$$^{15}N$$

The heavy isotope of nitrogen used to label DNA in the Meselson–Stahl experiment.

$$^{14}N$$

The light isotope of nitrogen used to label DNA in the Meselson–Stahl experiment.

Replication origins

Specific sites on eukaryotic chromosomes where DNA synthesis begins; eukaryotic chromosomes have multiple of these.

Replication forks

Y-shaped junctions that form at each replication origin and move away from each other as replication proceeds.

DNA polymerase

Enzyme that catalyzes the addition of nucleotides to the $3'$ end of a growing DNA strand using a parental template.

DNA polymerase $\beta$

Eukaryotic polymerase primarily involved in the repair of DNA damage.

DNA polymerase $\text{γ}$

Polymerase responsible for the replication of mitochondrial DNA.

DNA polymerase $\text{α}$

One of the polymerases involved in chromosomal DNA replication and copying the ends of linear chromosomes.

DNA polymerase $\text{δ}$

Polymerase involved in chromosomal DNA replication and filling gaps in the lagging strand during repair.

DNA polymerase $\text{ε}$

One of the major polymerases involved in eukaryotic chromosomal DNA replication.

Arthur Kornberg and Sylvy Ruth Levy

Researchers mentioned in the transcript associated with DNA polymerase.

$5' \text{-to-} 3'$ direction

The fundamental direction in which all known DNA polymerases synthesize DNA.

Deoxyribonucleoside triphosphates

The chemical form in which nucleotides enter the DNA synthesis reaction.

Pyrophosphate ($PP_i$)

A chemical group released when a nucleoside triphosphate is covalently linked to a growing DNA strand.

Asymmetrical replication fork

A structure where one new DNA strand is made continuously and the other is made in short pieces.

Leading strand

The new DNA strand that is synthesized continuously in the $5' \text{-to-} 3'$ direction.

Lagging strand

The DNA strand synthesized as a series of short fragments (Okazaki fragments) in the $5' \text{-to-} 3'$ direction.

Okazaki fragments

Short DNA pieces synthesized on the lagging strand that are later joined together.

DNA helicase

Enzyme that uses the energy of ATP hydrolysis to unwind the DNA double helix ahead of the replication fork.

Single-strand DNA-binding protein

Protein that binds to exposed DNA to prevent base pairs from re-forming before replication.

Sliding clamp

Protein that keeps DNA polymerase attached to the template during synthesis.

Clamp loader

Protein that uses ATP hydrolysis to lock the sliding clamp onto the DNA.

Primase

Enzyme that synthesizes short lengths of RNA to act as primers for DNA synthesis.

RNA primers

Short lengths of RNA, about $200$ nucleotides apart in eukaryotes, that initiate DNA synthesis.

Nuclease

Enzymes that remove RNA primers during the synthesis of the lagging DNA strand.

DNA ligase

Enzyme that joins Okazaki fragments by using ATP to activate the $5'$ phosphate of one fragment.

Taq DNA polymerase

First heat-resistant enzyme sourced from Thermus aquaticus used for PCR.

Thermus aquaticus

Species of bacteria that can tolerate high temperatures and provides the enzyme for PCR.

PCR (Polymerase Chain Reaction)

Process that can produce over a million-fold copy of target DNA within a few hours.

Torsional stress

Tension developed during replication and transcription, relieved by supercoiling or topoisomerases.

DNA topoisomerases

Enzymes that relieve torsional stress by generating temporary nicks in the DNA backbone.

Topoisomerase I

Enzyme in all cells that cleaves one strand of DNA to allow unwinding, producing a relaxed-circle conformation.

Type II topoisomerase

Eukaryotic homodimers that use a two-gate mechanism to manage DNA transport and relieve tension.

N-gate

The component of type II topoisomerase that traps a second DNA segment upon ATP binding.

T-segment

The second DNA segment that is captured and pushed through the DNA-gate in type II topoisomerase.

DNA-gate

The gate in topoisomerase II that opens to allow the T-segment to pass through the G-segment.

C-gate

The C-terminal gate that opens to release the T-segment from the type II topoisomerase.

Gyrase

The bacterial ($E. coli$) Type IIA topoisomerase.

Decatenase

The bacterial ($E. coli$) Type IV topoisomerase used for unlinking daughter chromosomes.

Nuclear localization sequences (NLS)

Sequences contained in the C-terminal domain of Human Type II$α$ topoisomerase.

Telomerase

Enzyme that replicates the ends of eukaryotic chromosomes by extending the template strand.

$1$ incorrect base per $10^9 \text{ to } 10^{10}$ nucleotides

The approximate error rate of DNA replication after correction.

Proofreading

The self-correcting property of DNA polymerase that removes incorrectly paired nucleotides.

P mode

The polymerizing mode of DNA polymerase.

E mode

The editing or proofreading mode of DNA polymerase that cleaves incorrect nucleotides.

Depurination

Chemical reaction that removes guanine or adenine from DNA, occurring $5000$ times per cell per day.

Deamination

Reaction that converts cytosine to uracil, occurring to about $100$ bases per cell per day.

Thymine dimers

Damage where two adjacent thymine bases become covalently attached due to ultraviolet radiation.

Base excision repair (BER)

Mechanism that involves the removal of a mismatched T and replacement with a C.

Apurinic endonuclease I (APE1)

Enzyme that cuts the DNA backbone at the abasic site during base excision repair.

Nucleotide excision repair (NER)

System that recognizes double-helix distortions and repairs thymine dimers.

XP (xeroderma pigmentosum) protein complex

A protein group that repairs UV-induced DNA damage; mutations cause skin cancer predisposition.

Mismatch excision repair

Repair system using the MSH2-MSH6 complex to remove errors that escape proofreading.

Lynch Syndrome

Hereditray predisposition to nonpolyposis colorectal cancer caused by MSH2 or MLH1 mutations.

Methyl mismatch repair (MMR)

Bacterial system using MutS, MutL, and MutH to fix mismatches based on DNA methylation.

MutS

Bacterial protein that recognizes the DNA mismatch in the MMR system.

Nonhomologous end joining

Double-strand break repair strategy where ends are cleaned and joined, often losing nucleotides.

Homologous recombination

Flawless repair strategy for double-strand breaks using an undamaged double helix as a template.

H2AX

Histone protein whose phosphorylation on serine 139 helps direct DNA damage repair pathways.

Sickle-cell anemia

Disease caused by a single nucleotide change changing glutamic acid to valine in $\text{β}$-globin.

Colon cancer

A disease caused by the accumulation of multiple mutations, with incidence increasing with age.

arCpG

Age-related CpG sites that show increased or decreased methylation status with age.

Age-related methylation

Epigenetic changes that can cause the silencing of tumor suppressor genes.

$$1000 \text{ nucleotides per second}$$

The rate of DNA replication in bacteria.

$$100 \text{ nucleotides per second}$$

The rate of DNA replication in eukaryotes.

DNA pol I

Bacterial enzyme responsible for the removal of RNA primers.

RNase H

Eukaryotic enzyme responsible for the removal of RNA primers.

DNA pol III

Bacterial enzyme responsible for strand elongation.

Replication bubble

Structure formed by two replication forks moving in opposite directions away from an origin.

G-segment

The DNA segment bound and bent by type II topoisomerase that is eventually cleaved.

Melanoma

A type of skin cancer that hereditary xeroderma pigmentosum predisposes individuals toward.

MutH

Bacterial enzyme in the MMR system that cleaves the unmethylated GATC sequence.

ATPase

Function of Human Type II$α$ topoisomerase that hydrolyzes ATP.

Tyrosyl residue

Active site component of topoisomerases that binds with DNA.

Type IIB

Classification of type II topoisomerases found in Archaea.

Flush ends

Level ends produced when nucleases "chew back" broken double-strand DNA during nonhomologous end joining.