DNA Replication and DNA Structure

Comprehensive vocabulary flashcards covering nucleic acid composition, DNA structure, prokaryotic DNA replication enzymes and steps, and eukaryotic chromosome packaging levels.

Nucleotide

The monomer building block of nucleic acids, composed of a 5-carbon pentose sugar, a phosphate group, and a nitrogenous base.

Ribonucleotide (NTP)

A nucleotide containing the five-carbon sugar ribose, used as a building block for RNA.

Deoxyribonucleotide (dNTP)

A nucleotide containing the five-carbon sugar deoxyribose, used as a building block for DNA.

Purines

Nitrogenous bases characterized by a two-ring structure; examples include Adenine ($A$) and Guanine ($G$).

Pyrimidines

Nitrogenous bases characterized by a single-ring structure; examples include Cytosine ($C$), Thymine ($T$), and Uracil ($U$).

Phosphodiester Bond

The linkage connecting adjacent nucleotides along the same strand, spanning between the $5'$ phosphate group of one nucleotide and the $3'\text{--OH}$ group of the next.

Antiparallel

The arrangement of the two complementary strands in a double-stranded DNA molecule, running oriented in opposite directions ($5' \rightarrow 3'$ relative to $3' \rightarrow 5'$).

Complementary Base Pairs

Specific pairs of nitrogenous bases on opposite strands held together by hydrogen bonds, where Adenine pairs with Thymine ($A\text{--}T$) and Guanine pairs with Cytosine ($G\text{--}C$).

Semiconservative Replication

The model of DNA replication in which each parental strand serves as a template for a newly synthesized daughter strand, resulting in two molecules each with one old and one new strand.

Origin of Replication (ORI)

The specific sequence or site where double-stranded DNA opens up and bidirectional replication begins.

Replication Fork

The Y-shaped region where parental strands of DNA are actively unwound and new strands are synthesized in both directions from the origin.

Helicase

An enzyme that unwinds double-stranded DNA during replication.

Topoisomerase (Gyrase)

An enzyme that unwinds DNA and relieves supercoiling strain by introducing temporary single-stranded nicks/cuts, allowing it to swivel and unkink before repairing the break.

Single-Stranded DNA Binding Proteins (ssBP)

Proteins that bind to exposed single-stranded DNA to stabilize it and prevent it from reforming a double helix.

Primase

An enzyme that synthesizes short RNA primers from scratch on the template DNA strand to provide a free $3'\text{--OH}$ for DNA polymerase.

RNA Primer

A short sequence of RNA that acts as a starting point onto which deoxyribonucleotides (dNTPs) can be added during DNA replication.

DNA Polymerase III

The primary enzyme in prokaryotic replication that synthesizes DNA in the $5' \rightarrow 3'$ direction on both leading and lagging strands, possessing $3' \rightarrow 5'$ exonuclease proofreading activity.

Proofreading

The $3' \rightarrow 5'$ exonuclease activity of DNA polymerase that identifies and excises mismatched bases during synthesis.

Leading Strand

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

Lagging Strand

The DNA strand synthesized discontinuously in the $5' \rightarrow 3'$ direction away from the replication fork, formed as a sequence of short segments.

Okazaki Fragments

Short pieces of newly synthesized DNA made discontinuously on the lagging strand by DNA Polymerase III.

DNA Polymerase I

The enzyme that removes RNA primers and fills the resulting gaps with DNA nucleotides, additionally possessing proofreading activity.

DNA Ligase

An enzyme that catalyzes the final phosphodiester bond connecting adjacent DNA fragments together without adding any new nucleotides.

Chromatin

A complex of DNA and protein in its less folded, uncondensed state, representing the predominant form of DNA throughout most of the cell cycle.

Chromosome

A complex of DNA and protein in its most tightly packed, condensed form, visible primarily during mitosis and meiosis.

Nucleosome

The basic structural repeating unit of chromatin ($10\text{ nm}$ fiber or 'beads on a string') consisting of $146\text{ bp}$ of DNA wrapped $1.65$ turns around a core of histone proteins.

Histone Core Octamer

The protein core of a nucleosome composed of eight histone proteins: two each of H2A, H2B, H3, and H4.

Linker DNA

A stretch of DNA roughly $100\text{--}200\text{ bp}$ in length connecting adjacent nucleosomes.

Histone H1

A specific histone protein that associates with the linker DNA region outside the nucleosome core particle.

30 nm Fiber

The third level of chromatin packing formed by the zigzag folding of the nucleosome string.

Radial Loop Domains

The fourth level of chromatin packing ($300\text{ nm}$ fiber) formed by loops of the $30\text{ nm}$ fiber anchored to scaffold proteins in the nuclear matrix.