DNA Structure and Replication Study Guide

Comprehensive vocabulary flashcards covering the molecular structure of nucleic acids, chemical bonding, structural dimensions, replication models, and the complete enzymatic machinery of prokaryotic and eukaryotic DNA replication.

Nucleotide

The monomer subunit of nucleic acids, consisting of a five-carbon sugar, a phosphate group, and a nitrogenous base.

Purines

A class of nitrogenous bases with a double-ring structure, which includes adenine and guanine.

Pyrimidines

A class of nitrogenous bases with a single-ring structure, which includes cytosine, thymine (found only in DNA), and uracil (found only in RNA).

Phosphodiester bond

The chemical linkage that joins the $5'$ phosphate group of one nucleotide to the $3'$ hydroxyl group of the next nucleotide, forming the sugar-phosphate backbone of a nucleic acid.

Complementary base pairing

The specific pairing of nitrogenous bases via hydrogen bonding, where the sequence of one strand dictates the complementary sequence of the opposite strand.

DNA double helix dimensions

The physical measurements of a DNA molecule, featuring a diameter of $2\,\text{nm}$, an interval of $0.34\,\text{nm}$ between adjacent base pairs, and a full turn length of $3.4\,\text{nm}$.

Major and minor grooves

The alternating larger and smaller spiral indentations along the outer surface of the twisted DNA double helix.

Semiconservative replication

The mechanism of DNA replication, supported by the Meselson and Stahl experiment, in which each newly formed DNA molecule contains one original parent strand and one newly synthesized strand.

Conservative replication

A theoretical model of DNA replication where the two original parent strands remain together, producing a completely separate, newly synthesized double helix.

Dispersive replication

A theoretical model of DNA replication in which parental and newly synthesized segments of DNA are interspersed within both strands of the daughter duplexes.

DNA helicase

An enzyme that unwinds the DNA double helix at the replication fork using energy supplied by $\text{ATP}$.

Single-strand binding protein (SSB)

A protein that binds to and stabilizes single-stranded DNA regions to prevent the reformation of the double helix during replication.

DNA gyrase

A topoisomerase enzyme that relieves torsional strain and prevents supercoiling ahead of the advancing replication fork.

Primase

An enzyme that synthesizes short RNA primers approximately $10\text{ to }20$ nucleotides in length to initiate DNA synthesis.

RNA primer

A short sequence of approximately $10\text{ to }20$ RNA nucleotides synthesized by primase that provides the initial $3'\text{-OH}$ group required for DNA polymerase activity.

DNA polymerase III

The main replication enzyme that synthesizes new DNA strands in the $5'\text{ to }3'$ direction by sequentially adding free deoxynucleotide triphosphates.

DNA polymerase I

An enzyme that removes RNA primers and fills the resulting gaps with DNA nucleotides during replication and repair.

DNA ligase

An enzyme that joins the ends of adjacent DNA segments, such as Okazaki fragments, by sealing nicks in the phosphodiester backbone.

Leading strand

The continuously synthesized DNA strand that elongates toward the replication fork in the $5'\text{ to }3'$ direction.

Lagging strand

The discontinuously synthesized DNA strand that elongates away from the replication fork in the $5'\text{ to }3'$ direction.

Okazaki fragment

A short segment of newly synthesized DNA on the lagging strand, approximately $100\text{ to }1000$ nucleotides long.

Replisome

A macromolecular assembly of enzymes and proteins that carries out DNA replication, composed of the primosome and two DNA polymerase III complexes.

Primosome

A functional subcomplex of the replisome consisting of primase, helicase, and accessory proteins.

$\beta$ clamp (sliding clamp)

A ring-shaped protein structure that tethers DNA polymerase III to the template strand to ensure efficient, continuous DNA synthesis.

Chromatin

The complex of DNA and associated proteins that composes eukaryotic chromosomes.

Histones

Basic proteins around which eukaryotic DNA winds like 'beads on a string' to form nucleosomes.

Nucleosome

The repeating structural subunit of chromatin, consisting of DNA wrapped around a core of histone proteins.

Bidirectional replication

A replication process that proceeds outward in both directions from an origin of replication, seen in circular prokaryotic DNA and eukaryotic replication bubbles.