Gene Expression Foundations: Nucleic Acid Architecture and DNA Copying

Nucleic acids

Biological polymers (DNA and RNA) that store, transmit, and help use genetic information; their structure helps explain accurate replication and reliable gene expression.

Nucleotide

The monomer of DNA/RNA, consisting of a phosphate group, a 5-carbon sugar (deoxyribose or ribose), and a nitrogenous base (A, G, C, T, or U).

Deoxyribose

The 5-carbon sugar in DNA; lacks an -OH on the 2′ carbon (has -H instead), making DNA more stable for long-term information storage.

Ribose

The 5-carbon sugar in RNA; has an -OH on the 2′ carbon, making RNA generally more reactive and less stable than DNA.

Purines vs. pyrimidines

Two base size classes: purines (two-ring) are adenine (A) and guanine (G); pyrimidines (one-ring) are cytosine (C), thymine (T), and uracil (U).

Phosphodiester bond

A covalent bond linking the phosphate of one nucleotide to the sugar of the next, forming the nucleic acid chain.

Sugar-phosphate backbone

The repeating structural framework of a DNA/RNA strand made of alternating sugars and phosphates; bases project outward from this backbone.

5′ and 3′ ends (directionality)

The two distinct ends of a nucleic acid strand: the 5′ end often has a free phosphate, and the 3′ end has a free -OH; DNA polymerase can add nucleotides only to the 3′ end (synthesizing 5′→3′).

Complementary base pairing

Specific base-pair rules that guide accurate copying: in DNA, A pairs with T and C pairs with G; in RNA, A pairs with U and C pairs with G.

Antiparallel strands

The orientation of DNA’s two strands running in opposite directions: one 5′→3′ and the other 3′→5′.

Double helix

The typical structure of DNA: two antiparallel strands coiled around each other, stabilized by hydrogen bonds between complementary bases.

Chromatin

Eukaryotic DNA packaged with proteins; packaging level affects DNA accessibility (more open chromatin is generally more accessible for transcription).

Semiconservative replication

Model of DNA replication in which each daughter DNA molecule contains one original (parental) strand and one newly synthesized strand.

Origin of replication

A specific DNA sequence where replication begins; typically one origin in many prokaryotes and many origins per chromosome in eukaryotes.

Replication fork

A Y-shaped region where DNA is unwound and new strands are synthesized.

Helicase

Enzyme that unwinds the DNA double helix by breaking hydrogen bonds between base pairs, creating single-stranded templates.

Single-strand binding proteins

Proteins that stabilize separated DNA strands during replication, preventing them from re-annealing or forming secondary structures.

Topoisomerase

Enzyme that relieves torsional strain (supercoiling) ahead of the replication fork by temporarily cutting DNA, allowing it to untwist, then rejoining it.

Primase

Enzyme that synthesizes a short RNA segment complementary to the DNA template to provide a starting point for DNA polymerase.

RNA primer

A short RNA sequence made by primase that provides a free 3′-OH group required for DNA polymerase to begin DNA synthesis.

DNA polymerase

Enzyme that builds new DNA by adding nucleotides to the 3′ end (synthesizing 5′→3′) using a template strand; many DNA polymerases also proofread mismatches.

Leading strand

The new DNA strand synthesized continuously in the same direction that the replication fork moves.

Lagging strand

The new DNA strand synthesized discontinuously away from the replication fork as short segments, due to the 5′→3′ synthesis rule and antiparallel templates.

Okazaki fragments

Short DNA segments made on the lagging strand; each starts with an RNA primer and later the fragments are joined to form a continuous strand.

DNA ligase

Enzyme that seals breaks in the sugar-phosphate backbone by forming phosphodiester bonds; crucial for joining Okazaki fragments on the lagging strand.