Biochemistry Basics - Dr. Paul Rosevear Lecture Flashcards

Comprehensive vocabulary flashcards covering fundamental biochemical concepts, water properties, chemical reactions, carbohydrate stereochemistry, and membrane lipid dynamics from Dr. Paul Rosevear's lecture notes.

Hydrogen Bond

A strong dipole-dipole or charge-dipole interaction between a proton donor (acid) and a proton acceptor (base), typically involving electronegative atoms such as nitrogen and oxygen.

Van der Waals Interactions

Interactions comprised of an attractive component (London dispersion) that depends on polarizability and a repulsive component (steric repulsion) that depends on atomic size.

Water Ionization Constant ($K_w$)

The equilibrium constant expression defined as $K_w = [\text{H}_3\text{O}^+][\text{OH}^-]$, which equals $1.011 \times 10^{-14}$ at $25\,^{\circ}\text{C}$.

pH

A logarithmic measure of the hydroxonium ion concentration defined by the expression $\text{pH} = -\log_{10}([\text{H}_3\text{O}^+])$.

pKa

The negative logarithm of the acid dissociation constant ($-\log_{10}(K_a)$), where a larger value indicates a weaker acid and less dissociation.

Buffer

A solution consisting of a weak acid and its conjugate base that resists changes in pH upon the addition of $\text{H}^+$ or $\text{OH}^-$ ions.

Hydrophobic Effect

The aggregation of nonpolar molecules in aqueous solution, which releases ordered water molecules back into bulk solvent and increases system entropy ($\Delta S$).

Valence

The characteristic number of covalent bonds that an atom of a specific element can form based on its shared electron pairs.

Ionization

The generation of positive or negative charges on a molecule, such as negative charges from dissociating protons off oxygen/sulfur groups or positive charges from acquiring protons on nitrogen groups.

Nucleophile

An electron-rich group, often the conjugate base of a weak acid (such as hydroxyl, sulfhydryl, amino, or imidazole groups), that donates an electron pair to an electrophile.

Electrophile

An electron-deficient species that may carry a positive charge, possess an unfilled valence electron shell, or contain an electronegative atom.

Acyl Group Transfer

A reaction involving the addition of a nucleophile to the electrophilic carbon of an acyl compound to form a tetrahedral intermediate, followed by expulsion of the leaving group.

Phosphoryl Group Transfer

A reaction involving the addition of a nucleophile to the electrophilic phosphorus atom of a tetrahedral phosphoryl group, forming a trigonal bipyramidal intermediate and resulting in inversion of configuration.

Aldose

A monosaccharide carbohydrate in which the carbonyl group is located at position $\text{C1}$ as an aldehyde.

Ketose

A monosaccharide carbohydrate in which the carbonyl group is located at a carbon position other than $\text{C1}$ (such as $\text{C2}$) as a ketone.

Enantiomers

Stereoisomers that are non-superimposable complete mirror images of each other, differing in absolute configuration at every single chiral center.

Diastereomers

Stereoisomers that are not mirror images of one another and possess distinct physical and chemical properties.

Epimers

Monosaccharides that differ in chemical configuration around only one specific chiral carbon atom, such as glucose and mannose at $\text{C-2}$.

Mutarotation

The interconversion between $\alpha$ and $\beta$ anomeric ring forms of a monosaccharide in solution via an open-chain intermediate.

Glycosidic Bond

A covalent linkage formed when the anomeric hydroxyl of a cyclic monosaccharide reacts with a hydroxyl group of another molecule, splitting out water.

Sialic Acid

A $9$-carbon monosaccharide attached to the termini of cell-surface glycans that acts as a receptor for pathogens like SARS-CoV-2.

Saturated Fatty Acid

A fatty acid containing no carbon-carbon double bonds, allowing maximum flexibility and tight molecular packing.

Unsaturated Fatty Acid

A fatty acid containing one or more carbon-carbon double bonds (typically in the cis configuration), which introduces kinks that hinder tight packing and lower the melting temperature.

Fluid Mosaic Model

The structural model proposed by Singer and Nicolson wherein globular integral membrane proteins freely diffuse laterally within a phospholipid and cholesterol bilayer.