Chemistry of Life and DNA Replication

Comprehensive practice flashcards detailing the chemical elements of life, atomic bonding, water dynamics, and the enzymes, models, and experiments underlying DNA replication.

SPONCH elements

The six primary chemical elements that compose the human body: Sulfur, Phosphorus, Oxygen (which makes up the majority at $65\%$), Nitrogen, Carbon, and Hydrogen.

Electronegativity

The measure of how strongly atomic nuclei attract shared electrons, determined by proton count and the valence shell's distance from the nucleus; it increases moving up and to the right on the periodic table ($\text{O} > \text{N} > \text{S}, \text{C}, \text{H}, \text{P}$).

Nonpolar covalent bond

A covalent bond formed by the equal sharing of electrons between atoms, resulting in an electrically neutral molecule without partial charges (e.g., C-H and C-C bonds).

Polar covalent bond

A covalent bond in which electrons are shared unequally and pulled closer to the more electronegative atom, producing partial charges across the molecule (e.g., H-O, C-O, and H-N bonds).

Ionic bond

A chemical bond resulting from the complete transfer of one or more valence electrons from one atom to another, producing full positive and negative charges; these bonds dissociate in aqueous environments where covalent bonds are stronger.

Van der Waals' forces

Transient, weak attractions between nonpolar atoms or molecules caused by momentary fluctuations in electron density that create short-lived partial charges.

Cohesion

The property of water molecules adhering to one another through hydrogen bonding, which creates a high surface tension.

Adhesion

The property of water molecules to form attractions and adhere to other surfaces.

Water density anomaly

The property where water is denser as a liquid than as a solid because hydrogen bonds organize ice into an open crystalline lattice, preventing Earth's oceans from freezing solid.

Amphipathic molecules

Molecules possessing both hydrophilic (charged/polar) and hydrophobic (uncharged/nonpolar) regions, enabling the formation of selectively permeable cell membranes.

Chargoff's Rule

The base-pairing regularity in DNA stating that the amount of cytosine equals guanine ($\text{C} = \text{G}$) and adenine equals thymine ($\text{A} = \text{T}$) to maintain double-helix width and hydrogen bonding in an anti-parallel configuration.

Hershey-Chase Experiment

An experiment by Alfred Hershey and Martha Chase that demonstrated DNA is the genetic material by using bacteriophages labeled with radioactive sulfur ($^{35}\text{S}$) for proteins and radioactive phosphorus ($^{32}\text{P}$) for DNA; after centrifugation, only $^{32}\text{P}$ entered the bacterial cell pellet and passed to offspring.

Semiconservative replication

The confirmed mechanism of DNA replication in which parental strands separate and each acts as a template for synthesizing a new strand, yielding two daughter duplexes each composed of one original strand and one newly synthesized strand.

Conservative replication

A disproven replication hypothesis proposing that the original parental strands remain fully associated with each other while directing the synthesis of a completely new double helix.

Dispersive replication

A disproven replication hypothesis stating that parental DNA strands are cut into fragments and randomly interspersed with newly synthesized DNA segments throughout both daughter strands.

Meselson & Stahl Experiment

The experiment confirming semiconservative replication by culturing E. coli in heavy $^{15}\text{N}$ medium, shifting them to light $^{14}\text{N}$ medium, and using CsCl density ultracentrifugation to observe density shifts across four successive generations.

Replication origin

Specific AT-rich regions where DNA replication initiates; their $2$ hydrogen bonds make them easier to separate, and human eukaryotic genomes contain approximately $10{,}000$ of these sites.

Topoisomerase

An enzyme that uncoils the DNA double helix ahead of the replication fork to release torsional tension and prevent the strand from bunching up.

Helicase

An enzyme that unzips and separates the two complementary parental DNA strands by breaking hydrogen bonds, forming the replication fork.

Single-strand binding proteins

Proteins that bind to exposed single strands of template DNA behind the helicase to prevent them from re-annealing.

Primase

An RNA polymerase that synthesizes a short RNA primer complementary to the template strand, providing the free $3'$ hydroxyl group required for DNA polymerases to initiate elongation.

DNA Polymerase III

The primary enzyme responsible for synthesizing new DNA strands in the $5'$ to $3'$ direction from a primer, possessing intrinsic $3'$ to $5'$ proofreading exonuclease activity.

Sliding clamp

A ring-shaped protein complex that encircles the DNA and tethers DNA Polymerase III to the template, preventing it from dissociating during strand synthesis.

Leading strand

The newly synthesized DNA strand that is extended continuously in the $5'$ to $3'$ direction toward the opening replication fork.

Lagging strand

The newly synthesized DNA strand oriented away from the fork that must be synthesized discontinuously in the $5'$ to $3'$ direction using multiple RNA primers.

Okazaki fragments

Short stretches of newly synthesized DNA separated by RNA primers along the lagging strand during discontinuous DNA replication.

DNA Polymerase I

The enzyme that excises RNA primers from synthesized DNA strands and replaces them with DNA nucleotides.

DNA ligase

An enzyme that seals phosphodiester backbone gaps between adjacent Okazaki fragments after primer removal and gap filling, producing a continuous DNA strand.

Replication fork

The Y-shaped active region within a replication bubble where parental DNA is unwound by helicase and both leading and lagging daughter strands are simultaneously synthesized.

Telomerase

A ribonucleoprotein enzyme that adds repetitive non-coding DNA sequences to the ends of chromosomes to prevent loss of essential genetic code; activated in approximately $85\%$ of cancers.

Proofreading

The enzymatic self-correction mechanism of DNA Polymerase III that removes mismatched nucleotides by moving backwards in the $3'$ to $5'$ direction, reducing replication error rates from $1/100{,}000$ to $1/1{,}000{,}000$.