BIOL 1000 B Lecture 21: Chromatin Structure, DNA Organization, and Replication

Vocabulary practice flashcards covering chromatin structure, nucleotide anatomy, base pairing, the cell cycle, and DNA replication initiation based on Lecture 21.

Chromatin

The complex of DNA plus associated proteins, which includes both histone and non-histone proteins.

Euchromatin

Loosely packed regions of chromatin containing active genes where transcription is occurring.

Heterochromatin

Densely packed masses of chromatin where genes are inactive.

Nucleosome Octamer

A histone protein complex around which DNA wraps, composed of two molecules each of histones H2A, H2B, H3, and H4.

Histone H1

A linker histone whose binding causes nucleosomes to package into a coiled structure known as a solenoid or $30\,\text{nm}$ chromatin fibre.

Solenoid ($30\,\text{nm}$ Chromatin Fibre)

A higher-order coiled chromatin fibre formed through the packaging of nucleosomes facilitated by histone H1.

Nucleotide

The monomer building block of DNA and RNA, composed of a nitrogenous base, a pentose (5-carbon) sugar, and a phosphate group.

1' Carbon of Pentose Sugar

The specific carbon on the pentose sugar ring to which the nitrogenous base covalently bonds via a nitrogen atom.

5' Carbon of Pentose Sugar

The specific carbon on the pentose sugar to which the phosphate group is attached.

Pyrimidines

A class of single-ring nitrogenous bases consisting of cytosine (C), uracil (U) in RNA, and thymine (T) in DNA.

Purines

A class of double-ring nitrogenous bases that are larger than pyrimidines, consisting of adenine (A) and guanine (G).

Deoxyribose

The pentose sugar present in DNA nucleotides, characterized by having a hydrogen ($-\text{H}$) atom bonded to the 2' carbon.

Ribose

The pentose sugar present in RNA nucleotides, characterized by having a hydroxyl ($-\text{OH}$) group bonded to the 2' carbon.

3' Hydroxyl ($-\text{OH}$) Group

The chemical group attached to the 3' carbon of a nucleotide sugar that acts as the nucleophile for the addition of an incoming dNTP during DNA elongation.

Phosphodiester Bond

The covalent linkage formed between the 3' hydroxyl group of one nucleotide sugar and the 5' phosphate group of an adjacent nucleotide with the release of $H_2O$.

Antiparallel Strands

The structural orientation of double-stranded DNA where one strand runs in the $5' \rightarrow 3'$ direction and the complementary strand runs in the $3' \rightarrow 5'$ direction.

Complementary Base Pairing

Specific hydrogen bonding between nitrogenous bases inside the DNA double helix, pairing adenine with thymine (A:T) and guanine with cytosine (G:C).

Purine-Pyrimidine Base Pairing Geometry

The pairing arrangement that provides the correct spatial width inside the sugar-phosphate backbones, unlike purine-purine pairs (not enough space) or pyrimidine-pyrimidine pairs (too much space).

Deoxyribonucleoside Triphosphate (dNTP)

The monomer precursor substrate used in DNA replication that provides both the incoming nucleotide and the chemical energy for polymer synthesis upon cleaving a pyrophosphate ($P-P$).

Directionality of DNA Synthesis

The strict $5' \rightarrow 3'$ orientation in which new DNA strands are enzymatically synthesized by adding nucleotides exclusively to the free 3' end.

Interphase

The non-dividing phase of the cell cycle composed of $G_1$, S, and $G_2$ phases during which the cell grows and replicates its genetic material.

S Phase

The specific stage of interphase during which DNA synthesis (replication) takes place.

Mitotic (M) Phase

The phase of the cell cycle comprising mitosis and cytokinesis.

Cytokinesis

The division of the cytoplasm that occurs during the mitotic (M) phase to complete cell division.

Daughter Cells

Identical copies produced from a parent cell through cell division, each carrying the exact same heritable genetic material (DNA).

Origin of Replication

A specific nucleotide sequence along a chromosome where initiating proteins bind to start the DNA replication process.

Bacterial Origin of Replication

A single specific site on a circular bacterial chromosome where DNA replication initiates bidirectionally.

Eukaryotic Origins of Replication

Hundreds to thousands of initiation sites on eukaryotic chromosomes that are activated only once during the S phase to ensure DNA replicates exactly once.

Replication Bubble

The open structure formed when double-stranded DNA unwinds and separates at an origin of replication.

Replication Fork

The Y-shaped region where parent DNA strands separate, toward and away from which bidirectional synthesis proceeds.