DNA Replication and Repair Flashcards

A set of flashcards covering DNA replication models, enzymes, repair mechanisms, and associated diseases as described in the lecture notes.

Semiconservative model

The DNA replication model where each strand of a double helix serves as a template to specify the nucleotide sequence in its complementary strand, resulting in two helices each with one original and one new strand.

Conservative model

A hypothetical model of DNA replication, ruled out by the Meselson–Stahl experiment, where the original parental double helix remains intact.

Dispersive model

A hypothetical model of DNA replication where the parental double helix is broken into fragments and the resulting daughter helices contain a mix of old and new DNA.

Meselson–Stahl experiment

The experiment that ruled out the conservative and dispersive models of DNA replication by growing bacteria in mediums containing different isotopes of nitrogen.

$${}^{15}\text{N}$$

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

$${}^{14}\text{N}$$

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

Replication origins

Specific sites on a chromosome where DNA synthesis begins.

Replication forks

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

DNA polymerase

An enzyme that synthesizes new DNA using a parental strand as a template by adding nucleotides to the $3'$ end of a growing strand.

DNA polymerase $\alpha$

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

DNA polymerase $\beta$

A eukaryotic DNA polymerase involved primarily in the repair of DNA damage.

DNA polymerase $\gamma$

The eukaryotic DNA polymerase responsible for the replication of mitochondrial DNA.

DNA polymerase $\delta$

A eukaryotic DNA polymerase involved in chromosomal DNA replication and the filling of gaps after RNA primer removal on the lagging strand.

DNA polymerase $\epsilon$

A eukaryotic DNA polymerase involved in chromosomal DNA replication.

Arthur Kornberg and Sylvy Ruth Levy

Scientists credited with work regarding DNA polymerase.

Deoxyribonucleoside triphosphates

The form in which nucleotides enter the DNA synthesis reaction.

Pyrophosphate

The molecule released during the hydrolysis of the high-energy phosphate bond that drives the DNA synthesis reaction.

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

The direction in which DNA chain growth occurs and in which DNA polymerase synthesizes DNA.

Asymmetrical replication fork

The structural reality of DNA replication where both new strands are synthesized $5'\text{-to-}3'$, requiring one strand to be made discontinuously.

Lagging strand

The DNA strand that is synthesized discontinuously as a series of short fragments.

Leading strand

The DNA strand that is synthesized continuously.

Okazaki fragments

Short pieces of DNA synthesized in the $5'\text{-to-}3'$ direction that are joined together to form the lagging strand.

RNA primers

Short lengths of RNA that provide a starting point for DNA polymerase to begin synthesis.

Primase

An enzyme that synthesizes RNA primers along the lagging-strand template.

Nucleases

Enzymes that remove RNA primers from the DNA strand during the replication process.

DNA ligase

An enzyme that joins the $5'$ phosphate of one DNA fragment to the $3'$ hydroxyl group of the next, using the energy of ATP hydrolysis.

ATP hydrolysis

The energy-releasing reaction used by enzymes like DNA ligase, DNA helicase, and the clamp loader.

Polymerase Chain Reaction (PCR)

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

Thermus aquaticus

The heat-tolerant bacteria from which the heat-resistant Taq DNA polymerase was originally isolated.

Taq DNA polymerase

The first heat-resistant enzyme identified for use in PCR reactions.

Torsional stress

Tension developed in the DNA double helix during replication and transcription that is relieved by coiling or nicks.

Supercoils

Additional coiling of the DNA double helix formed to relieve torsional stress.

DNA topoisomerases

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

Type II topoisomerases

Homodimeric enzymes (Type IIA and IIB) that relieve tension by creating a double-strand break to allow another DNA segment to pass through.

Two-gate mechanism

The process by which type II topoisomerase uses an N-gate and a C-gate to transport a T-segment of DNA through a G-segment.

G-segment

The "gate" DNA segment that is bound, bent, and cleaved by a type II topoisomerase.

T-segment

The "transported" DNA segment that is captured and pushed through the DNA-gate in Type II topoisomerases.

N-gate

The gate in topoisomerase II where ATP binding traps the T-segment.

C-gate

The C-terminal gate that opens to release the T-segment following DNA transport.

Gyrase

A bacterial (E. coli) Type IIA topoisomerase.

Decatenase

A bacterial Type IV topoisomerase responsible for unlinking daughter chromosomes.

Tyrosyl residue

An amino acid in the active site of human Type II$\alpha$ topoisomerase that binds with DNA during cleavage.

Nuclear localization sequences (NLS)

Sequences located in the C-terminal domain of human Type II$\alpha$ topoisomerase.

Topoisomerase I

Enzyme present in all cells that cleaves one strand of DNA to allow unwinding and produce a relaxed-circle conformation.

Topoisomerase II

An enzyme required for more than just relieving tension; it manages double-strand passage and requires ATP binding.

Telomerase

The enzyme responsible for replicating the ends of eukaryotic chromosomes by extending the template strand.

Telomeres

The repetitive DNA sequences found at the ends of linear eukaryotic chromosomes.

$10^9$ to $10^{10}$

The frequency range showing that replication is not perfect, with roughly one incorrect base incorporated per this many nucleotides.

Proofreading

The self-correcting process of DNA polymerase where it checks and corrects errors as it synthesizes DNA.

Polymerizing mode (P)

The functional state of DNA polymerase where it adds nucleotides to the growing DNA strand.

Editing mode (E)

The functional state of DNA polymerase where it cleaves an incorrect nucleotide from the strand.

Depurination

A chemical reaction that can remove guanine or adenine (purine bases) from the DNA molecule.

Deamination

The chemical reaction that frequently converts cytosine to uracil within DNA.

$5000$

The approximate number of purine bases lost every day from the DNA of each human cell due to depurination.

Thymine dimers

Covalent attachments between two adjacent thymine bases, often caused by ultraviolet radiation.

Ultraviolet (UV) radiation

The component of sunlight that serves as a common cause of thymine dimer formation in skin cells.

DNA mismatch repair system

A cellular mechanism that removes replication errors that escape the proofreading of DNA polymerase.

Base excision repair

A repair mechanism used to remove specific mismatched bases, such as replacing a mismatched T with a C.

Apurinic endonuclease I (APE1)

An enzyme that cuts the DNA backbone at an abasic site during base excision repair.

Nucleotide excision repair

A repair mechanism that recognizes double-helix distortions and corrects damage like thymine dimers.

XP protein complex

A complex of proteins (XP-A through XP-G) involved in nucleotide excision repair.

Xeroderma pigmentosum

A hereditary disease caused by mutations in XP genes, resulting in a predisposition to UV-induced skin cancers.

Mismatch excision repair

The specific system involving the MSH2-MSH6 complex that removes mispaired DNA segments.

MSH2-MSH6 protein complex

The specific protein complex that binds to a mispaired segment of DNA to initiate mismatch repair.

Lynch Syndrome

A disease predisposition to nonpolyposis colorectal cancer caused by inheritable loss-of-function MSH2 or MLH1 mutations.

MutS

The bacterial protein responsible for recognizing DNA mismatches.

MutL

The bacterial protein that forms a complex with MutS and MutH during mismatch repair.

MutH

The bacterial protein that cleaves the unmethylated GATC sequence during mismatch repair.

Nonhomologous end joining

A DNA repair strategy for double-strand breaks where ends are cleaned by a nuclease and joined, often resulting in the loss of nucleotides.

Homologous recombination

A flawless repair strategy for double-strand breaks that uses an undamaged double helix as a template.

Histone H2AX

The specific histone protein that is phosphorylated during the DNA damage and repair pathway.

Serine $139$

The specific residue on the H2AX histone protein where phosphorylation occurs during the repair process.

Sickle-cell anemia

A disease caused by a single nucleotide change resulting in a glutamic acid to valine substitution at the $6^{\text{th}}$ amino acid position in β-globin.

β-globin

The gene where a specific mutation causes sickle-cell anemia when two mutant copies are present.

Carcinogenesis

The process by which cancer is caused, often driven by the accumulation of multiple mutations over time.

DNA methylation

A chemical modification of DNA that changes with age and can cause the silencing of tumor suppressor genes.

arCpG

Age-related CpG sites whose methylation levels increase or decrease as a function of age.

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 single-stranded DNA to prevent base pairs from reforming before replication is complete.

Sliding clamp

A protein that keeps DNA polymerase attached to the template strand as it synthesizes new DNA.

Clamp loader

A protein that uses ATP hydrolysis to lock the sliding clamp onto the DNA molecule.