Biochemical Interactions and Water Chemistry

Vocabulary flashcards covering biochemical concepts including water properties, noncovalent interactions, molecular structures, and functional groups based on lecture notes.

Hydrophilic

Describing polar or charged molecules that interact favorably with water.

Hydrophobic

Describing nonpolar molecules that avoid interaction with water.

Hydrophobic Effect

An entropy-driven phenomenon where nonpolar molecules aggregate together, causing an increase in the entropy of $H_2O$; drives protein folding, lipid micelle and bilayer formation, steroid binding, and protein-protein interactions.

Hydrogen Bonding

A directional interaction formed when a hydrogen atom covalently bonded to O, N, or F interacts with an electronegative atom; it is weak individually, strong collectively, essential for protein secondary structure and DNA base pairing, and has a relative strength of $20$.

Hydration Shell

A surrounding cluster of water molecules that hydrates and stabilizes dissolved ionic solutes, such as $Na^+$ and $Cl^-$, and polar solutes.

Ionic Interactions

Electrostatic interactions between permanently charged species with a relative strength of $86$, making them the strongest noncovalent interaction.

Salt Bridge

An ionic interaction formed between oppositely ionized amino acid side chains, such as Asp/Glu ($-COO^-$) and Lys/Arg ($-NH_3^+$).

Van der Waals Interactions

Weak noncovalent interactions occurring between all atoms—including dipole-dipole, dipole-induced dipole, and induced dipole-induced dipole—with a relative strength of $0.3$; important for DNA base stacking, molecular complementarity, and protein packing.

Dipole Interactions

Noncovalent interactions between dipoles with a relative strength of $9.3$.

Amphiphilic (Amphipathic)

Molecules containing both hydrophilic and hydrophobic parts that spontaneously form micelles, bilayers, and vesicles driven by the hydrophobic effect.

Hemiacetal

A functional group formed when an aldehyde reacts with an alcohol, producing a carbon bonded to an OH, OR, H, and R group; formed when monosaccharides like glucose cyclize into $\text{α}$ and $\text{β}$ anomers.

Phosphodiester Bond

A structure containing two ester groups that links two sugars via a phosphate group in DNA and RNA backbones, stabilized by water through hydration and ionic interactions.