Molecular Genetics, DNA Replication, PCR, and Cell Division

Vocabulary practice flashcards covering the molecular basis of inheritance, DNA structure and replication, PCR methodology, the cell cycle, mitosis, meiosis, and gametogenesis.

Transformation

A change in genotype and phenotype resulting from the assimilation of external, foreign DNA by a cell, first demonstrated in bacteria by Frederick Griffith.

Bacteriophage

A virus that infects bacteria by attaching to the cell surface, piercing the cell wall with an internal needle-like structure, and injecting its genetic material while leaving its protein coat outside.

Hershey-Chase Experiment

A landmark $1952$ study using bacteriophages tagged with radioactive sulfur (to label proteins) and radioactive phosphorus (to label DNA), establishing that DNA is the molecule of inheritance injected into bacterial host cells.

Chargaff's Rules

The biochemical findings stating that DNA base composition varies between species, and that within any species, the percentage of adenine roughly equals thymine ($A = T$) and guanine roughly equals cytosine ($G = C$).

Photo 51

An X-ray diffraction image of DNA taken by Rosalind Franklin under Maurice Wilkins, revealing an "X" pattern characteristic of a helical structure, layer lines showing turns every $34\,\text{\AA}$, and base pair spacing of $3.4\,\text{\AA}$.

Double Helix

The structural model of DNA synthesized by James Watson and Francis Crick in $1953$, comprising two antiparallel polynucleotide chains wound around a central axis, held together by complementary base pairs.

Antiparallel

The arrangement of the two complementary sugar-phosphate backbones in a DNA double helix, running in opposite directions with one oriented $5' \rightarrow 3'$ and the other $3' \rightarrow 5'$.

Semiconservative Model

The replication mechanism demonstrated by Meselson and Stahl wherein each of the two replicated double-stranded DNA molecules consists of one conserved parental strand and one newly synthesized daughter strand.

Origin of Replication

A specific sequence of nucleotides where DNA replication initiates, occurring as a single site on circular bacterial chromosomes and at multiple sites along eukaryotic linear chromosomes.

Replication Fork

A Y-shaped region where the parental DNA double helix is unwound and separated into single strands to allow replication to proceed bidirectionally.

Helicase

An enzyme that unzips double-stranded DNA by breaking the hydrogen bonds between complementary nitrogenous bases at the replication fork.

Topoisomerase

An enzyme that relieves torsional strain ahead of the replication fork by swiveling, breaking, and rejoining DNA strands to prevent excessive supercoiling during unwinding.

Primase

An RNA polymerase enzyme that synthesizes a short complementary RNA primer on a single-stranded DNA template to provide a free $3'\text{-OH}$ group for DNA polymerase.

DNA Polymerase III

The primary prokaryotic replication enzyme that adds deoxynucleotides to the $3'$ end of a growing DNA strand complementary to the template strand.

DNA Polymerase I

The enzyme that hydrolyzes and removes RNA primers from the newly synthesized strand and replaces them with corresponding DNA nucleotides.

DNA Ligase

An enzyme that catalyzes the formation of covalent phosphodiester bonds to join the sugar-phosphate backbones of adjacent Okazaki fragments and DNA repair patches.

Leading Strand

The continuously synthesized daughter DNA strand elongation toward the replication fork in the obligatory $5' \rightarrow 3'$ direction.

Lagging Strand

The discontinuously synthesized daughter DNA strand that elongates away from the replication fork as a series of short segments.

Okazaki Fragments

The short discontinuous segments of newly synthesized DNA produced on the lagging strand template during DNA replication.

Nucleoside Triphosphate

The precursor monomer for DNA synthesis (such as dATP, dCTP, dGTP, dTTP) that delivers a nucleotide along with high-energy bonds; the cleavage of two phosphate groups as pyrophosphate ($\text{PP}_i$) powers the polymerization reaction.

Thymine Dimer

A covalent linkage formed between two adjacent thymine bases on a DNA strand, induced by ultraviolet (UV) radiation, which buckles the DNA backbone and disrupts replication.

Nucleotide Excision Repair

A DNA repair pathway wherein a nuclease cuts out damaged nucleotides (such as thymine dimers), DNA polymerase synthesizes a replacement patch using the intact strand as a template, and DNA ligase seals the nick.

Telomeres

Non-coding repetitive nucleotide sequences ($\text{TTAGGG}$ in humans) located at the ends of linear eukaryotic chromosomes that protect genomic integrity and progressively shorten with each cell division cycle.

Telomerase

An enzyme that extends and maintains telomeres by adding repetitive sequences to chromosome ends; normally active in germ cells and embryos, but silenced in somatic cells and reactivated in many cancer cells.

Nucleosome

The fundamental subunit of chromatin packaging, consisting of DNA wrapped around an octamer of histone proteins, appearing as "beads on a string" with a diameter of approximately $10\,\text{nm}$.

Heterochromatin

Highly condensed, tightly packed regions of interphase chromatin that are transcriptionally silent and inaccessible to gene expression machinery.

Euchromatin

Loosely packed, less condensed chromatin regions that are transcriptionally active and accessible to RNA polymerases and transcription factors.

Epigenetics

The study of heritable modifications in gene expression and function that occur without alterations to the underlying nucleotide sequence of DNA.

X-Inactivation

The random transcriptional silencing of one of the two X chromosomes in mammalian female embryonic cells, condensing it into a Barr body to achieve dosage compensation.

Thermus aquaticus

An extremophilic bacterium isolated by Thomas Brock and Hudson Freeze from a hot spring in Yellowstone National Park, surviving optimally between $60\text{--}70\,^{\circ}\text{C}$ and up to $80\,^{\circ}\text{C}$.

Taq Polymerase

A thermostable DNA polymerase isolated from Thermus aquaticus that remains catalytic at high temperatures ($72\,^{\circ}\text{C}$) without denaturing during PCR thermal cycles.

Polymerase Chain Reaction (PCR)

An in vitro enzymatic method invented by Kary Mullis in $1983$ that exponentially amplifies a specific target DNA region through repeating cycles of denaturation, primer annealing, and extension.

Denaturation (in PCR)

The first step of a PCR cycle, typically executed at approximately $95\,^{\circ}\text{C}$, which breaks the hydrogen bonds between complementary strands to yield single-stranded DNA templates.

Annealing (in PCR)

The second step of a PCR cycle, typically conducted at $50\text{--}60\,^{\circ}\text{C}$ (often around $55\,^{\circ}\text{C}$), allowing oligonucleotide primers to hybridize specifically to complementary flanking sequences on the single-stranded template.

Extension (in PCR)

The third step of a PCR cycle, conducted at the optimal operating temperature of Taq polymerase ($\approx 72\,^{\circ}\text{C}$), where the enzyme synthesizes new complementary DNA strands from the primers.

Thermal Cycler

An automated laboratory instrument programmed to rapidly alternate temperatures across repeated cycles to automate the denaturation, annealing, and extension steps of PCR.

Quantitative Real-Time PCR (qPCR)

A PCR variant employing fluorescent dyes or probes to quantify target DNA or RNA molecules in real time as amplification progresses, commonly used for pathogen load testing and GMO detection.

Reverse Transcription PCR (RT-PCR)

A technique that uses reverse transcriptase to synthesize complementary DNA (cDNA) from an RNA template, followed by standard PCR amplification of the resulting cDNA.

Cell Cycle

The orderly series of events extending from the birth of a eukaryotic somatic cell through division into two daughter cells, subdivided into interphase ($G_1$, $S$, $G_2$) and the mitotic ($M$) phase.

Interphase

The non-dividing growth phase of the cell cycle comprising $G_1$, $S$, and $G_2$, accounting for the vast majority of a somatic cell's lifespan.

G0 Phase

A specialized non-dividing, quiescent state entered by differentiated cells (such as neurons and mature muscle cells) that exit the cell cycle in early $G_1$.

Mitosis

The division of a eukaryotic somatic cell nucleus into two genetically identical daughter nuclei, consisting of prophase, metaphase, anaphase, and telophase.

Cytokinesis

The physical division of the cytoplasm following nuclear division, yielding two distinct daughter cells through cleavage furrow constriction in animal cells.

Centromere

The specialized, constricted chromosomal region composed of constitutive heterochromatin where two sister chromatids are joined and where kinetochores assemble to bind mitotic spindle microtubules.

Centrosome

A cytoplasmic organelle functioning as the primary microtubule-organizing center of animal cells; during prophase, two centrosomes migrate to opposite poles to construct the mitotic spindle.

Metaphase Plate

The imaginary plane equidistant between the two spindle poles along which duplicate chromosome pairs align during metaphase.

Cleavage Furrow

A shallow contractile groove that forms in the plasma membrane near the old metaphase plate in animal cells during telophase, pinching the cytoplasm into two daughter cells.

Binary Fission

The simple form of asexual cell division utilized by prokaryotic cells such as bacteria, which lack a nucleus and multiple linear chromosomes.

Homologous Chromosomes

A pair of chromosomes (one maternal and one paternal) of the same size and centromere location that carry the same genes arranged in the same order, but may contain different alleles.

Diploid (2n)

A cell or organism containing two complete sets of chromosomes, one inherited from each parent; in humans, somatic cells are diploid with $2n = 46$.

Haploid (n)

A cell containing only a single set of chromosomes; in humans, mature gametes (sperm and egg) are haploid with $n = 23$.

Meiosis

A specialized two-division cell cycle (Meiosis I and Meiosis II) occurring in germ-line cells that reduces chromosome ploidy from diploid ($2n$) to haploid ($n$) to produce genetically diverse gametes.

Synapsis

The precise physical pairing and side-by-side lateral attachment of duplicated homologous chromosomes along their entire length during prophase I of meiosis.

Tetrad

The four-chromatid structure formed by the synapsis of a pair of homologous, replicated chromosomes during prophase I of meiosis.

Crossing Over

The reciprocal exchange of genetic material between non-sister chromatids of homologous chromosomes during prophase I, generating hybrid recombinant chromosomes.

Independent Assortment

The random and independent orientation and separation of maternal and paternal homologous chromosome pairs along the metaphase plate during metaphase I of meiosis.

Spermatogenesis

The continuous developmental process occurring within the seminiferous tubules of male testes from puberty until death that yields four functional, mature spermatozoa from each primary spermatocyte.

Seminiferous Tubules

Tightly coiled tubular structures within the testes where spermatogonial stem cells reside and undergo spermatogenesis.

Spermatogonia

Diploid stem cells located near the outer basement membrane of seminiferous tubules that divide mitotically to produce primary spermatocytes and replenish the stem cell population.

Primary Spermatocyte

A diploid germ cell ($2n$) formed by mitosis of a spermatogonium that undergoes meiosis I to produce two haploid secondary spermatocytes.

Secondary Spermatocyte

A haploid cell ($n$) produced at the completion of meiosis I during male gametogenesis that enters meiosis II to produce two spermatids.

Spermatids

Four haploid, immature gametes produced at the conclusion of meiosis II that undergo morphological differentiation (spermiogenesis) into flagellated mature sperm.

Oogenesis

The gametogenic process in female ovaries producing functional haploid ova, beginning during fetal development and characterized by prolonged arrests and asymmetric cytokinesis.

Oogonia

Diploid female germ stem cells in the embryonic ovary that divide by mitosis to form primary oocytes before birth.

Primary Oocyte

A diploid female germ cell formed before birth that begins meiosis I but becomes developmentally arrested in prophase I until stimulated during puberty.

Secondary Oocyte

A haploid female germ cell produced after meiosis I along with a polar body, which begins meiosis II and becomes arrested in metaphase II until fertilization occurs.

Polar Body

A small, nonfunctional haploid cell produced during the asymmetric cytoplasmic divisions of female meiosis that receives minimal cytoplasm and eventually degenerates.

Graafian Follicle

A fluid-filled, mature ovarian follicle containing a secondary oocyte arrested in metaphase II that bulges on the ovarian surface prior to ovulation.

Ovulation

The event in which a mature Graafian follicle ruptures at the surface of the ovary, releasing the secondary oocyte into the oviduct.

Gene

A discrete physical unit of heredity consisting of a specific sequence of DNA nucleotides occupying a definite locus on a chromosome that codes for a polypeptide.

Allele

Any of the alternative nucleotide sequence variants of a specific gene that can occur at a given chromosomal locus.

Genotype

The specific genetic or allelic makeup of an individual organism at one or more gene loci.

Phenotype

The observable biochemical, physiological, and physical characteristics of an organism, determined by its genotype interacting with environmental factors.

Homozygous

The state of possessing two identical alleles at a given gene locus on homologous chromosomes.

Heterozygous

The state of possessing two different alleles at a given gene locus on homologous chromosomes.