Nucleic Acids: Structure, Function, and DNA Replication

Vocabulary practice flashcards covering nucleic acid chemical structures, base pairing geometry, B-DNA characteristics, RNA stability differences, and the enzymatic mechanisms of DNA replication.

Deoxyribonucleic Acid (DNA)

A stable, double-helical nucleic acid polymer that acts as the store of genetic information and provides the instructions for making proteins.

Ribonucleic Acid (RNA)

An unbranched polymer of ribonucleotides produced through transcription that is smaller and less stable than DNA, acting as a template for protein synthesis.

Phosphoric Acid

The inorganic acid component of a nucleotide that provides nucleic acids with their acidic properties.

Deoxyribose

The five-carbon pentose sugar found in DNA nucleotides that lacks a hydroxyl group at the $2'$ carbon position.

Ribose

The five-carbon pentose sugar found in RNA nucleotides that contains a reactive hydroxyl ($\text{-OH}$) group at the $2'$ carbon position.

Purines

A class of nitrogenous bases with a double-ring chemical structure, consisting of adenine (A) and guanine (G) in both DNA and RNA.

Pyrimidines

A class of nitrogenous bases with a single-ring chemical structure, consisting of cytosine (C), thymine (T; DNA only), and uracil (U; RNA only).

Nucleoside

A structural unit composed solely of a nitrogenous base covalently linked to a pentose sugar via an N-glycosidic bond.

Nucleotide

A monomeric subunit of nucleic acids consisting of a nucleoside covalently attached to one or more phosphate groups via a phosphoester bond.

Photo 51

The iconic X-ray diffraction photograph of DNA captured by Rosalind Franklin and Raymond Gosling that revealed the helical structure of DNA.

Phosphodiester Bond

The covalent linkage formed between the $3'$ hydroxyl group of one nucleotide's sugar and the $5'$ phosphate group of the adjacent nucleotide, forming the sugar-phosphate backbone.

B-DNA

The predominant right-handed conformation of the DNA double helix in aqueous solution, featuring a hydrophobic core, hydrophilic backbone, a base-pair spacing of $0.34\,\text{nm}$, and major and minor grooves.

Base Stacking

Non-covalent stabilizing forces in the interior of the double helix driven by hydrophobic interactions and mutual attraction between the aromatic rings of adjacent bases.

Base Pairing Geometry

The spatial arrangement where purine-to-pyrimidine pairing maintains a uniform distance of $1.1\,\text{nm}$ between glycosidic bonds across the helix; non-standard pairings distort this distance.

Major Groove

The wider and more accessible spiral indentation along the DNA double helix that displays distinct chemical groups (hydrogen bond donors, acceptors, non-polar hydrogens, and methyl groups) allowing proteins to read sequence without unwinding the helix.

Minor Groove

The narrower spiral groove on the surface of the DNA double helix that is accessible to DNA-binding proteins.

Cytosine Deamination

A spontaneous chemical reaction where cytosine reacts with water ($\text{H}_2\text{O}$) to form uracil and release ammonia ($\text{NH}_3$); because DNA normally utilizes thymine instead of uracil, repair systems can identify and excise inappropriately formed uracil.

2'-3'-Cyclic Monophosphate

The intermediate formed during internal cleavage of RNA when the $2'$ hydroxyl group acts as an internal nucleophile attacking the phosphodiester backbone, explaining why RNA is intrinsically less stable than DNA.

Half-Life of DNA

The calculated persistence time of DNA, determined by palaeogeneticist Morten Allentoft using bones of extinct moa birds to be $521\,\text{years}$.

Semi-Conservative Replication

The mechanism of DNA synthesis in which the parent double helix unwinds and each original strand serves as a template, producing two daughter double helices each made of one original strand and one newly formed strand.

Pyrophosphate Hydrolysis

The exergonic cleavage of pyrophosphate ($\text{PP}_i$) into two inorganic phosphates ($2\,\text{P}_i$) by water ($\text{H}_2\text{O}$), driving the thermodynamic equilibrium of DNA polymerization forward.

DNA Helicase

An enzyme at the replication fork that unwinds and separates double-stranded DNA by breaking the hydrogen bonds holding the nitrogenous base pairs together.

Topoisomerase

An enzyme (also known as DNA gyrase) that relieves torsional strain generated ahead of the replication fork by making transient cuts in the DNA backbone and subsequently resealing them.

Single-Stranded DNA Binding Proteins

Proteins that stabilize unwound single DNA strands at the replication fork to prevent them from prematurely reannealing.

DNA Primase

A specialised RNA polymerase that initiates synthesis by creating a complementary RNA primer approximately $5\text{--}10\,\text{nucleotides}$ long, supplying the necessary free $3'\text{-OH}$ group for DNA polymerase.

DNA Polymerase III

The primary prokaryotic replication enzyme that adds deoxyribonucleotides onto the free $3'\text{-OH}$ end of a growing strand at approximately $1000\,\text{nucleotides per second}$.

DNA Polymerase I

The prokaryotic enzyme responsible for excising RNA primers and filling the resulting gaps with DNA nucleotides during replication.

DNA Ligase

An enzyme that seals single-strand nicks in the phosphodiester backbone by joining adjacent fragments on the lagging strand.

Sliding Clamp

A ring-like protein complex that encircles the DNA double helix to anchor DNA polymerase to the template strand and improve processivity.

Leading Strand

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

Lagging Strand

The newly synthesized DNA strand that runs antiparallel to the fork's movement and must be produced discontinuously as a series of short segments.

Okazaki Fragments

The short stretches of DNA produced discontinuously on the lagging template strand by DNA polymerase III before being joined together.

3'-to-5' Exonuclease Activity

The proofreading function of DNA polymerase that identifies a misplaced $3'\text{-OH}$ group from a mismatched nucleotide and excises the erroneous base to maintain a low error rate of $10^{-8}$ to $10^{-10}$.

Strand Slippage

A replication error mechanism where looping out of the newly synthesized strand inserts an extra nucleotide, or looping out of the template strand causes an omission, resulting in a frameshift.

Origin of Replication (ori)

The specific DNA sequence where replication bubbles form; bacterial circular chromosomes possess a single origin, whereas eukaryotic chromosomes feature multiple origins to complete replication in approximately $7\,\text{hours}$.