BIOL1010 Week 1 - Biochemistry and Biophysics Vocabulary Flashcards

Vocabulary flashcards covering key terms, functional groups, atomic bonding valencies, chemical bond lengths, and non-covalent interactions from Lecture 1.

Protonated amine group ($\text{-NH}_3^+$)

A positively charged functional group on biological molecules formed when nitrogen accepts a proton and forms $4$ bonds.

Ionized carboxyl group ($\text{-COO}^-$)

A negatively charged functional group on biological molecules resulting from the loss of a proton from a carboxyl group, featuring charge delocalization between two oxygen atoms.

Carboxyl group (un-ionized)

A functional group consisting of a carbonyl group single-bonded to a hydroxyl group ($\text{-COOH}$).

Ångstrom ($\text{\text{Å}}$)

A unit of length equal to $10^{-10}\,\text{m}$, which is approximately the length of chemical bonds.

Single bond

A strong covalent bond between two atoms that allows free rotation.

Double bond

A covalent bond between atoms that does not allow rotation.

Conformation

The specific spatial arrangement or structural folding of a macromolecule made possible by freely-rotating single bonds.

Ionic bond

A non-covalent interaction resulting from the electrostatic attraction between opposite charges that is nondirectional.

Hydrogen bond

A directional and length-constrained non-covalent interaction where a partially positively charged H bond donor shares a proton with a partially negatively charged H bond acceptor.

Hydrophobic interaction

A non-covalent interaction within a macromolecule driven by maximizing the hydrogen bonding of surrounding water molecules.

van der Waals interactions

Non-covalent interactions occurring between nonpolar surfaces due to synchronized transient electric dipoles.

Substrate

A specific molecule that biological macromolecules reversibly bind to via non-covalent interactions.

Elemental bonding stability rules

Hydrogen forms $1$ bond; Oxygen forms $2$ bonds; Sulfur forms $2$ bonds; Nitrogen forms $3$ bonds (or $4$ with a positive charge); Carbon forms $4$ bonds; Phosphorus forms $5$ bonds.

Amine group

A nitrogen-containing functional group that usually forms $3$ bonds to be stable, but can take on a positive charge and form $4$ bonds.

Polar

Describing molecules or chemical groups that possess partial or full electrical charges.

Non-polar

Describing molecules or surfaces that lack net or partial charges and interact primarily through synchronized transient dipoles.

Hydrophilic

Describing polar or charged groups that interact favorably with water through hydrogen bonding or ionic interactions.

Hydrophobic

Describing nonpolar molecules or surfaces that do not interact favorably with water, causing water to organize around them.

Space-filling model

A three-dimensional molecular representation that illustrates the physical space occupied by constituent atoms and their electron clouds.