Biomolecules, Nucleic Acids, and DNA Dynamics

Vocabulary flashcards covering key terms, structures, bond types, physical properties, and denaturation dynamics of biomolecules and nucleic acids.

Residue

A single monomer unit incorporated into a polymer chain.

Peptide bond

The covalent bond linking amino acid monomers together to form protein polymers.

Phosphodiester bond

The covalent bond linking nucleotide residues together between their $3'$ and $5'$ positions to form nucleic acid polymers.

Glycosidic bond

The covalent bond linking monosaccharides together to form polysaccharide polymers.

Hydrophobic effect

The phenomenon where water minimizes its contact with non-polar substances, causing non-polar molecules to aggregate together.

Amphipathic molecule

A molecule in which most of the structure is non-polar with a few polar regions, such as membrane lipids.

Amphiphilic molecule

A molecule in which most of the structure is polar with a few non-polar regions, such as fatty acids.

Nucleoside

A molecule composed of a purine or pyrimidine base covalently linked to a pentose sugar ring.

Phosphoester bond

A chemical bond formed by linking a phosphate group to a hydroxyl group via a dehydration/condensation reaction.

Phosphoanhydride bond

A high-energy chemical bond formed by linking two phosphate groups together.

5' end

The terminal end of a nucleic acid strand where the $5'$ carbon of the pentose sugar is not involved in a phosphodiester bond.

3' end

The terminal end of a nucleic acid strand where the $3'$ carbon of the pentose sugar is not involved in a phosphodiester bond.

Hydrolase

An enzyme class that catalyzes the cleavage of chemical bonds using water.

Alkaline Hydrolysis of RNA

The random and destructive cleavage of RNA phosphodiester bonds at high pH, caused by the removal of a hydrogen from the $2'-OH$ group which then attacks the phosphorus atom.

A260

Absorbance measured at a wavelength of $260\,nm$, used to determine the concentration of nucleic acids in solution.

A260/A280 ratio

The ratio of absorbance at $260\,nm$ to $280\,nm$ used to assess nucleic acid purity, yielding a value of $1.8 - 1.95$ for pure DNA.

B-form DNA

The default secondary structure of DNA, characterized by antiparallel strands in a right-handed double helix stabilized by base stacking and hydrogen bonding.

Chargaff's rule

The rule stating that in double-stranded DNA or RNA, $A=T$ (or $A=U$) and $G=C$, meaning total purines equal total pyrimidines ($A+G = T+C$).

Tm (Melting Temperature)

The melting midpoint temperature at which half of a nucleic acid sample is double-stranded ($ds$) and half is single-stranded ($ss$).

Hyperchromicity

The increase in UV absorbance at $260\,nm$ observed when double-stranded DNA denatures into single-stranded DNA.

Hypochromicity

The decrease in UV absorbance at $260\,nm$ observed when single-stranded DNA renatures into double-stranded DNA.

Nucleation

The initial, slow step of DNA renaturation where complementary strands align correctly as temperature drops.

Zippering

The rapid second step of DNA renaturation where hydrogen bonds quickly form along aligned complementary strands to restore the double helix.

Degradation (Nucleic Acids)

The permanent cleavage of covalent bonds in nucleic acids (e.g., RNA at $pH\,10$ or alkaline conditions) that prevents strands from reforming.

Denaturation (Nucleic Acids)

The separation of double-stranded nucleic acids into single strands by breaking non-covalent bonds (e.g., via heat), which can be reversed through renaturation.

pKa

The negative logarithm of the acid dissociation constant ($pKa = -\log(Ka)$), representing the pH at which an acid is $50\%$ protonated and $50\%$ deprotonated.

Nicotinamide electron carriers

Coenzymes such as $NAD^+$ and $NADP^+$ that undergo reversible reduction at their nitrogenous base to pick up a proton ($H^+$) and electrons during metabolic reactions.