BC 212 Lecture 12: Nucleic Acid Structure

Vocabulary practice flashcards covering nucleic acid components, base pairing, helical structure, DNA compaction, and replication from BC 212 Lecture 12.

Nucleotide

The monomeric building block of nucleic acids, composed of three structural components: a heterocyclic amine nitrogenous base, a five-carbon monosaccharide sugar (ribose or deoxyribose), and one or more phosphate groups.

Nucleoside

A biomolecule consisting of a heterocyclic nitrogenous base joined to a five-carbon monosaccharide sugar (ribose or deoxyribose) via a condensation reaction, lacking an attached phosphate group.

2-Deoxyribose

A five-carbon monosaccharide sugar derived from ribose ($\text{C}_5\text{H}_{10}\text{O}_5$) that has undergone reduction at carbon-$2$, resulting in a hydrogen atom in place of a hydroxyl group.

Purines

A category of planar, aromatic heterocyclic amine bases consisting of a fused two-ring structure, which includes adenine (A) and guanine (G).

Pyrimidines

A category of planar, aromatic heterocyclic amine bases consisting of a single six-membered ring, which includes cytosine (C), thymine (T; specific to DNA), and uracil (U; specific to RNA).

Hydrogen Bond Donor

An electronegative atom (oxygen or nitrogen in nucleic acids) directly bonded to a hydrogen atom ($\text{O—H}$ or $\text{N—H}$) that interacts with an electronegative atom on a partnering base or molecule.

Hydrogen Bond Acceptor

An electronegative oxygen or nitrogen atom possessing an unshared lone pair of electrons capable of attracting a hydrogen atom covalently attached to a donor atom.

Phosphodiester Bond

The covalent link joining adjacent nucleotides in a polynucleotide chain, formed through a condensation reaction connecting the hydroxyl group on carbon-$3'$ of one sugar to the phosphate ester on carbon-$5'$ of the next sugar.

Phosphoanhydride Bond

A high-energy chemical linkage formed between two adjacent phosphate groups, present once in adenosine diphosphate ($\text{ADP}$) and twice in adenosine triphosphate ($\text{ATP}$).

Antiparallel

The orientation of the two complementary strands in a double-stranded DNA helix, wherein one strand runs in the $5' \rightarrow 3'$ direction and the complementary partner strand runs in the $3' \rightarrow 5'$ direction.

Base Stacking Energy

Attractive dispersion forces between the stacked, planar, aromatic electron clouds of adjacent nitrogenous base pairs that supply the primary stabilizing force for the DNA double helix.

Watson-Crick Base Pairs

Isosteric base pairings where adenine forms $2$ hydrogen bonds with thymine ($\text{A-T}$), and guanine forms $3$ hydrogen bonds with cytosine ($\text{G-C}$).

Major and Minor Grooves

Asymmetric spiral indentations on the exterior of the DNA double helix where outer edges of base pairs are accessible, presenting unique patterns of hydrogen-bond donors and acceptors recognized by sequence-specific proteins.

Salt Bridge (Protein-DNA Interaction)

An electrostatic non-covalent bond formed between basic, positively charged amino acid side chains (such as arginine, lysine, and histidine) on a protein and the negatively charged phosphate groups along the DNA backbone.

Histones

Basic eukaryotic nuclear proteins rich in positively charged arginine and lysine residues around which genomic DNA winds to establish compact chromatin structures.

Nucleosome

The fundamental repeating structural subunit of chromatin, comprising a length of double-stranded DNA wound around a core assembly of histone proteins, often described as 'beads on a string.'

Chromatin

The compact, orderly tangle of genomic DNA and associated histone proteins present inside the nucleus of non-dividing eukaryotic cells.

Chromosome

A single linear molecule of genomic DNA in a highly compacted state with structural proteins, visible under microscopy during eukaryotic cell division.

Centromere

The narrow, constricted locus of a chromosome that serves as a central structural region during eukaryotic cellular division.

Telomeres

The specialized nucleoprotein capping structures situated at the terminal ends of linear eukaryotic chromosomes.

Gene

A discrete linear segment of DNA that encodes the genetic instructions necessary to direct the synthesis of a single polypeptide chain.

Chargaff's Rules

The biochemical principle establishing that double-stranded DNA contains an equimolar proportion of adenine to thymine ($\%A = \%T$) and guanine to cytosine ($\%G = \%C$).

Reverse Complement

The sequence of a complementary antiparallel nucleic acid strand written in the standard $5' \rightarrow 3'$ convention by pairing complementary bases ($\text{A}$ with $\text{T}$ or $\text{U}$, and $\text{G}$ with $\text{C}$) and reversing the linear order.

Semiconservative Replication

The mode of DNA copying wherein each parental double-stranded molecule unwinds to serve as templates, generating two daughter duplexes that each retain one parental (old) strand and one newly formed strand.

Central Dogma

The core paradigm describing the directional flow of biological sequence information: replication ($\text{DNA} \rightarrow \text{DNA}$), transcription ($\text{DNA} \rightarrow \text{RNA}$), and translation ($\text{RNA} \rightarrow \text{protein}$), each proceeding through initiation, elongation, and termination phases.

Mutagen

An environmental agent or chemical substance—such as ionizing radiation (UV, X-rays), reactive oxygen species (ROS), or methylating agents—capable of causing alterations in DNA sequence.

Cytosine Deamination

A spontaneous oxidative alteration occurring approximately $100$ times per cell each day that converts cytosine to uracil, changing its hydrogen-bonding characteristics to pair with adenine instead of guanine.