(Lecture 4/5) DNA Replication, DNA Damage, and DNA Repair

Comprehensive vocabulary flashcards covering eukaryotic DNA replication, cell cycle dynamics, replication enzymes, telomeres, mutations, human genetic pathologies, and DNA repair pathways.

Genome

The complete set of genetic material in a cell or organism.

Diploid (2n)

Having two complete sets of chromosomes (22 pairs of autosomal chromosomes plus sex-specific chromosomes XX or XY in human cells).

Cell Cycle

A series of regulated events through which a cell grows, replicates its DNA, and divides into two daughter cells.

Semi-Conservative Replication

The mechanism of DNA replication in which parental strands separate and each serves as a template for synthesizing a new complementary daughter strand.

Origins of Replication (ORI)

Specific regions scattered across chromosomes (approx. 30,000–50,000 in human cells) where double-stranded DNA melts to initiate replication.

Origin Recognition Complex (ORC)

A six-subunit protein complex bound to origins of replication throughout the cell cycle that serves as a platform for recruiting replication proteins.

MCM DNA Helicase

A helicase complex recruited by ORC that unwinds and opens the DNA double helix bidirectionally at replication forks.

DNA Polymerase

The principal enzyme that synthesizes new DNA strands in the 5' to 3' direction, requiring a primer and possessing 3' to 5' exonuclease proofreading activity.

Leading Strand

The DNA strand oriented 3' to 5' relative to replication fork movement, synthesized continuously in the 5' to 3' direction.

Lagging Strand

The DNA strand oriented 5' to 3' relative to replication fork movement, synthesized discontinuously in short segments away from the fork.

Okazaki Fragments

Short DNA segments synthesized discontinuously on the lagging strand during replication.

DNA Primase

An enzyme that synthesizes short RNA primers necessary to provide a free 3'-OH group for DNA polymerase initiation.

DNA Ligase

An enzyme that joins Okazaki fragments on the lagging strand by sealing phosphodiester backbone nicks.

DNA Topoisomerase I

An ATP-independent enzyme that creates single-strand nicks to relieve torsional tension and supercoiling upstream of the replication fork.

DNA Topoisomerase II

An ATP-dependent enzyme that relieves supercoiling and torsional strain ahead of the replication fork by making double-strand cuts.

Single-Strand DNA-binding (SSB) Proteins

Proteins that bind to exposed single-stranded DNA to prevent re-annealing and secondary structure formation during replication.

End Replication Problem

The inability of conventional replication machinery to complete synthesis at the extreme 5' end of the lagging strand, leaving an approx. 100 bp gap per cell division.

Telomeres

Repetitive DNA sequences (such as AGGGTTA) at chromosome ends that shield coding DNA from degradation during successive divisions.

Telomerase

An enzyme complex active in stem and cancer cells that uses an internal RNA template to reverse transcribe and extend telomeric DNA ends.

Senescence

Permanent growth arrest and cell death reached after approximately 50–70 cell divisions as telomeres progressively shorten.

HeLa Cells

An immortal human cell line derived in 1951 from cervical cancer cells taken from Henrietta Lacks.

Basal Mutation Rate

The natural background mutation rate occurring during cell division, measured at approximately $1 \times 10^{-8}$ per nucleotide per cell division.

Depurination

An endogenous DNA lesion resulting from the spontaneous loss of a purine base (A or G), leaving an abasic site.

Ionizing Radiation

High-energy radiation (X-rays, gamma rays, particles) causing single- and double-strand breaks and oxidative DNA damage.

Non-Ionizing Radiation

Electromagnetic radiation (specifically UV light) causing single-strand breaks and base modifications such as thymine dimers.

DNA Mutation

A permanent, rare sequence alteration present in less than 1% of a given population (such as cystic fibrosis - mutation in CFTR)

DNA Polymorphism

A common genetic sequence variation present in greater than 1% of a population (such as ABO blood group alleles).

Point Mutation

A small-scale mutation involving a substitution, insertion, or deletion of a single base pair.

Silent Mutation

A point mutation in a coding region that changes a codon to a synonymous codon, resulting in no change to the amino acid sequence.

Missense Mutation

A point mutation that alters a codon to code for a different amino acid.

Nonsense Mutation

A point mutation that converts an amino acid codon into a stop codon, producing a truncated protein.

Indels

Small-scale insertion or deletion mutations of base pairs in a DNA sequence.

Frameshift Mutation

A mutation caused by indels not divisible by 3, altering the reading frame and resulting in an altered amino acid sequence and premature stop codon.

Splicing Mutation

A mutation that affects pre-mRNA processing, leading to consequences such as exon skipping, intron retention, or creation of cryptic splice sites.

Chromosomal Rearrangements

Large-scale structural alterations spanning kilobases to whole chromosomes, including deletions, duplications, translocations, and inversions.

Philadelphia Chromosome

An abnormal chromosome created by a reciprocal translocation between chromosomes 9 and 22, producing the BCR::ABL fusion gene seen in Chronic Myeloid Leukemia (CML).

BCR::ABL fusion gene leads to what

Uncontrolled proliferation

Charcot-Marie-Tooth Disease

A hereditary peripheral neuropathy caused by a duplication of the PMP22 gene on chromosome 17, leading to myelin destabilization.

Sickle Cell Anemia

A disease caused by a missense mutation (Glu to Val) in the beta-globin gene, causing HbS polymerization under hypoxia and erythrocyte sickling.

Cystic Fibrosis

A disease caused by mutations in the CFTR gene that impair chloride ion transport and lead to thick mucus build-up in airways.

DNA Mismatch Repair (MMR)

A post-replication repair pathway mediated by MSH2, MSH6, MLH1, and PMS2 that corrects base mismatches resulting from DNA polymerase errors.

Lynch Syndrome

Hereditary non-polyposis colorectal cancer caused by germline mutations in MMR genes (MLH1, MSH2, MSH6, PMS2), causing high risks of colorectal and endometrial cancers.

Base Excision Repair (BER)

A repair pathway initiated by PARP1 and DNA glycosylases that removes small non-distorting lesions like abasic sites, uracil from deamination, and oxidized bases.

Synthetic Lethality

A therapeutic principle where blocking BER using PARP inhibitors in BRCA1/2-deficient cancer cells (lacking homologous recombination) leads to cell death.

Nucleotide Excision Repair (NER)

A pathway involving over 40 proteins (including XPA–XPE and POLH) that removes bulky, helix-distorting DNA lesions such as UV-induced thymine dimers.

Xeroderma Pigmentosum (XP)

A hereditary condition caused by deficiencies in NER proteins, leading to extreme UV sensitivity and markedly elevated skin cancer incidence.

Homologous Recombination (HR)

A high-fidelity double-strand break repair pathway active in S and G2 phases that uses the sister chromatid template to repair DNA without nucleotide loss.

Non-Homologous End-Joining (NHEJ)

An error-prone double-strand break repair pathway active throughout the cell cycle that uses Ku70/80, DNA-PKcs, and LIG4 to directly ligate ends, causing loss of DNA.

Double-Strand Break Repair (DSBR)

The overarching repair pathways (Homologous Recombination and Non-Homologous End-Joining) responsible for fixing severe lesions across both DNA strands caused by ionizing radiation, ROS, or replication collapse.

BRCA1

A tumor suppressor protein that functions in double-strand break sensing, end resection, and recruitment of repair factors for homologous recombination.

BRCA2

A tumor suppressor protein in the homologous recombination pathway that promotes homologous pairing and strand invasion.