Biochemistry: Acids, Bases, and Amino Acids

Flashcards covering the chemical properties of acids and bases, the Henderson-Hasselbalch equation, and the structural and chemical characteristics of the 20 standard amino acids based on lecture notes.

Brønsted Acids

Entities that act as $H^+$ donors.

Brønsted Bases

Entities that act as $H^+$ acceptors.

Strong Acid

An acid that is completely ionized in water (e.g., $1M HCl \rightarrow 1M H^+ + 1M Cl^-$).

Weak Acid

An acid that is incompletely ionized in aqueous solutions, reaching an equilibrium between the acid and its conjugate base.

Acid Dissociation Constant ($K_a$)

The equilibrium constant for the dissociation of an acid, defined as $K_a = \frac{[H^+][A^-]}{[HA]}$.

$$pK_a$$

A measure of acid strength defined as the negative logarithm of the acid dissociation constant: $pK_a = -\tan(\text{log } K_a)$.

Henderson-Hasselbalch Equation

An equation used to calculate buffer properties, expressed as $pH = pK_a + \text{log} \frac{[A^-]}{[HA]}$.

Buffer

A solution that resists changes in $pH$ when additional acids or bases are added, established by the equilibrium between a weak acid and its conjugate base.

Le Châtelier’s Principle

A principle stating that if a dynamic equilibrium is disturbed, the position of the equilibrium shifts to counteract the change.

Zwitterionic

A state where a molecule, such as an amino acid at physiological $pH$, carries both positive and negative charges but has a net charge of zero.

Amphoteric

Molecules that can act as both an acid and a base.

Chiral Molecules

Molecules in which the \text{\alpha} carbon has 4 different groups attached, leading to two different stereoisomers.

Stereoisomers

Molecules that have the same atom-to-atom connections but different spatial orientations.

Enantiomers

Stereoisomers that are non-superimposable mirror images of one another.

Aliphatic

Effectively hydrocarbons that are not aromatic; they can be straight, branched, or cyclic, and are typically not planar ($sp^3$ hybridized).

Aromatic

Conjugated structures, such as benzene, that are flat ($sp^2$ hybridized).

Glycine

The only standard amino acid that is not chiral because its R-group is a hydrogen atom.

Proline

An amino acid featuring a secondary (2º) amine; it is exceptionally rigid and conformationally restricted.

Methionine

A hydrophobic, aliphatic amino acid that contains a thioether functional group.

Tryptophan

An aromatic amino acid that contains an Indole functional group and acts as a precursor for brain chemicals regulating mood.

Histidine

A basic amino acid containing an Imidazole functional group that can act as a conjugate acid at neutrality.

Isoelectric Point ($pI$)

The $pH$ at the equivalence point where a molecule has no net charge; it is calculated as $pI = \frac{pK_a \text{ below} + pK_a \text{ above}}{2}$.

Peptide Bonds

Amide bonds that link amino acids together in proteins by connecting the carboxyl group of one to the amino group of another.

Phenylketonuria (PKU)

A rare inherited genetic disorder caused by a lack of the enzyme phenylalanine hydroxylase, preventing the breakdown of phenylalanine.