BIOL 1000 - DNA Structure, Chromatin Packaging, and DNA Replication

Vocabulary practice flashcards covering chromatin structure, nucleotide anatomy, complementary base pairing, and the initiation and mechanics of DNA replication.

Chromatin

The structural complex consisting of DNA and its associated proteins, which include both histone and non-histone proteins.

Euchromatin

Loosely packed regions of chromosomes where genes are active and transcription is actively occurring.

Heterochromatin

Densely packed chromosomal masses containing inactive genes that are not undergoing transcription.

Nucleosome Octamer

The core protein complex in a nucleosome composed of two copies each of four histones: H2A, H2B, H3, and H4, surrounded by wrapped DNA and projecting histone tails.

Histone H1

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

Solenoid (30 nm Chromatin Fibre)

A higher-order coiled chromatin structure measuring $30\text{ nm}$ in thickness that forms when histone H1 binds to nucleosomes.

Nucleotide

The fundamental monomer of nucleic acids, consisting of three components: a nitrogenous base, a 5-carbon pentose sugar, and a phosphate group.

1' Carbon of Pentose Sugar

The specific carbon atom on the nucleotide sugar ring that forms a covalent bond with the nitrogen atom of the nitrogenous base.

5' Carbon of Pentose Sugar

The carbon atom located outside the pentose furanose ring that is covalently bonded to the phosphate group in a nucleotide.

Ribose

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

Deoxyribose

The five-carbon pentose sugar found in DNA nucleotides that possesses a hydrogen atom ($-\text{H}$) instead of a hydroxyl group at its 2' carbon.

Pyrimidines

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

Purines

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

Cytosine (C)

A pyrimidine base found in both DNA and RNA that forms complementary hydrogen bonds with guanine.

Thymine (T)

A pyrimidine base specific to DNA that forms complementary hydrogen bonds with adenine.

Uracil (U)

A pyrimidine base found in RNA that substitutes for thymine.

Phosphodiester Bond

The covalent linkage formed between the 3' hydroxyl ($-\text{OH}$) of one nucleotide sugar and the 5' phosphate group of an adjacent nucleotide through a condensation reaction that releases water.

5' End

The terminus of a polynucleotide strand that bears a free or unlinked phosphate group attached to the 5' carbon of the terminal sugar.

3' End

The terminus of a polynucleotide strand that features a free hydroxyl ($-\text{OH}$) group attached to the 3' carbon of the terminal pentose sugar.

Antiparallel Arrangement

The structural orientation of double-stranded DNA in which the two sugar-phosphate backbones run parallel but in opposite directions ($5' \rightarrow 3'$ on one strand and $3' \rightarrow 5'$ on the complementary strand).

Complementary Base Pairing

The specific pairing between bases in DNA stabilized by hydrogen bonds, pairing guanine with cytosine (G:C) and adenine with thymine (A:T).

Purine–Pyrimidine Steric Constraint

The geometric rule of the DNA double helix dictating that only purine-pyrimidine pairs fit properly within the backbones; purine-purine pairs provide not enough space, whereas pyrimidine-pyrimidine pairs leave too much space.

Deoxyribonucleoside Triphosphate (dNTP)

The high-energy monomer precursor used during DNA synthesis that provides both the incoming nucleotide and the energy for polymerization via release of pyrophosphate ($\text{P-P}$).

Direction of DNA Synthesis

The obligatory biochemical directionality ($5' \rightarrow 3'$) in which new DNA daughter strands are elongated by adding nucleotides exclusively to the free 3' hydroxyl group.

S Phase (DNA Synthesis)

The period within interphase of the cell cycle during which chromosomes replicate, with origins of replication activated strictly once.

Origin of Replication

A specific nucleotide sequence in a chromosome recognized by initiating proteins where the DNA strands separate and replication commences.

Bacterial Origin of Replication

The single unique initiation site on circular bacterial chromosomes from which bidirectional DNA replication proceeds.

Eukaryotic Origins of Replication

The hundreds to thousands of initiation sites found along eukaryotic linear chromosomes that activate once per S phase to allow faster complete genome duplication.

Replication Bubble

The unwound and separated region of double-stranded DNA formed at an origin of replication where DNA synthesis takes place bidirectionally.

Replication Fork

The Y-shaped region located at each end of a replication bubble where parental DNA strands are actively separated and unwound.