Lecture 12: Structure and Function of Nucleic Acids

Vocabulary practice flashcards covering nucleic acid monomers, pentose sugar differences, phosphodiester linkages, directionality, helical geometry, stabilizing interactions, and levels of DNA structure.

Nucleoside

A structural unit of nucleic acids consisting exclusively of a pentose sugar (ribose or deoxyribose) bonded covalently to a nitrogenous base, lacking any phosphate groups.

Nucleotide

The monomer building block of nucleic acids, consisting of a pentose sugar, a nitrogenous base, and one to three phosphate groups.

Deoxyribose

The five-carbon pentose sugar found in DNA that lacks a hydroxyl group at the $2'$ carbon position, having a hydrogen atom ($-\text{H}$) instead.

Ribose

The five-carbon pentose sugar found in RNA that contains a reactive hydroxyl group ($-\text{OH}$) at the $2'$ carbon position.

Phosphodiester Bond

The covalent linkage formed between adjacent nucleotides connecting the $3'$ carbon of one pentose sugar to the $5'$ carbon of the next through a phosphate group.

$5'$ End

The terminal end of a nucleic acid strand that terminates with an exposed, unlinked phosphate group attached to the $5'$ carbon of the terminal pentose sugar.

$3'$ End

The terminal end of a nucleic acid strand that terminates with an exposed, unlinked hydroxyl group ($-\text{OH}$) on the $3'$ carbon of the terminal pentose sugar.

Antiparallel

The relative structural orientation of double-stranded DNA in which one strand runs in the $5' \rightarrow 3'$ direction while its complementary paired strand runs in the $3' \rightarrow 5'$ direction.

$5' \rightarrow 3'$ Polymerization

The intrinsic direction of nucleic acid synthesis wherein each new incoming nucleotide monomer is added covalently to the exposed $3'$ hydroxyl group ($-\text{OH}$) of the growing strand.

Sugar-Phosphate Backbone

The hydrophilic outer structural framework of a DNA or RNA strand composed of repeating alternating pentose sugars and negatively charged, polar phosphate groups.

Base-Stacking Attraction

Non-covalent hydrophobic and van der Waals interactions between planar nitrogenous bases stacked parallel to each other inside the double helix, providing critical stability to the DNA molecule.

Major Groove

The wider groove of the DNA double helix where nitrogenous base edges are more accessible for sequence-specific recognition and binding by proteins, such as the transcription factor $E2F8$.

Minor Groove

The narrower spiral groove across the DNA double helix formed where the sugar-phosphate backbones are positioned closer together.

Chargaff's Base-Pairing Rules

The geometric principle of nucleic acid structure specifying that a two-ring purine must always pair with a one-ring pyrimidine ($A$ with $T$ via two hydrogen bonds; $G$ with $C$ via three hydrogen bonds) to maintain a constant helical diameter.

Photo 51

The historic X-ray diffraction photograph of DNA captured by Rosalind Franklin at King's College London in 1953, which disclosed the helical geometry of DNA to James Watson, Francis Crick, and Maurice Wilkins.

Primary Structure of DNA

The linear sequence of nucleotide bases covalently linked along a single strand of DNA.

Secondary Structure of DNA

The regular double-helical conformation formed by the spontaneous association of two antiparallel complementary DNA strands held together by hydrogen bonds and base-stacking interactions.

Tertiary Structure of DNA

The higher-order three-dimensional compaction and folding of the double helix into organized complexes, such as nucleosomes and condensed eukaryotic chromatin fibers.

Thymine

A pyrimidine nitrogenous base utilized in DNA that pairs with adenine and is distinguished structurally from uracil by the presence of a methyl group ($-\text{CH}_3$).

Uracil

A pyrimidine nitrogenous base utilized in RNA that pairs with adenine and is distinguished structurally from thymine by having a hydrogen atom ($-\text{H}$) in place of a methyl group.

DNA Helical Repeat

The structural measurement of the B-DNA double helix consisting of $10$ base pairs per complete helical turn, spanning an axial distance of $3.4\,\text{nm}$ ($0.34\,\text{nm}$ between adjacent base pairs) with a total diameter of $2\,\text{nm}$ ($20\,\text{Å}$).