BCHE307 Fall 2025 Review: Chapter 2 Water & Chapter 3 Amino Acids

Flashcards covering key concepts from Chapter 2 (Water) and Chapter 3 (Amino Acids) for BCHE307, Fall 2025, including definitions related to weak bonds, pH calculations, buffers, amino acid structure, polypeptide properties, and protein purification methods.

Hydrogen bonds (in liquid water)

Fleeting bonds that are constantly breaking and regrouping, much weaker than covalent bonds, and account for water's anomalously high boiling point.

Hydrophobic effect

The tendency of nonpolar molecules to aggregate and minimize their exposure to water in an aqueous environment by clumping together.

Hydronium ion

The species (H3O+) primarily responsible for the acidic properties of aqueous solutions.

pH of a strong base solution

Calculated by finding pOH from the hydroxide concentration and then subtracting from 14 (e.g., for 0.001 M NaOH, pH = 11).

Lowest pH in aqueous solution

Achieved with the highest concentration of a strong acid (e.g., 0.1 M HCl).

Relationship between pH difference and [H+] concentration

Each pH unit represents a 10-fold difference in [H+]; a 4 pH unit difference means a 10,000 times difference in [H+].

Buffer solution (at pH = pKa)

A solution where the concentrations of the weak acid and its conjugate base (salt) are equal.

Henderson-Hasselbalch equation

Relates the pH of a solution to the pKa and the concentrations of the weak acid and its conjugate base.

Effect on acetate buffer when NaOH is added

If starting at pH=pKa, the ratio of acetic acid to sodium acetate in the buffer falls due to the conversion of acid to conjugate base.

Sulfur-containing amino acids

Cysteine and Methionine are the two standard amino acids that contain sulfur atoms.

Isoelectric pH of a polypeptide

The pH at which the total net charge of the polypeptide is zero.

Peptide bond formation

An example of a condensation reaction, where water is removed.

Peptide bonds in a pentapeptide

A peptide composed of 'n' amino acids will have 'n-1' peptide bonds; for a pentapeptide, there are four peptide bonds.

Amino acid with three pKa values

Histidine is an amino acid that has three pKa values due to its ionizable R-group.

Charge of neutral R group amino acids at pH below pI

At any pH below the isoelectric point (pI), the population of amino acids in solution will have a net positive charge.

Aromatic amino acid UV absorption

On a molar basis, tryptophan absorbs more ultraviolet light (at 280 nm) than tyrosine.

Affinity chromatography

A protein purification technique that purifies proteins by binding them to a specific ligand that interacts with the target protein.

Micromolar (μM) to Nanomolar (nM) conversion

1 μM equals 1000 nM; thus, 4.20 μM is 4.2 x 10^3 nM.

Functional group in propanol

Propanol contains an alcohol functional group.

Conjugate acid of NH3

The conjugate acid of ammonia (NH3) is ammonium (NH4+).

Phospholipid self-assembly in water

Phospholipids spontaneously form micelles or bilayers in aqueous environments primarily due to the hydrophobic effect, which drives nonpolar tails away from water.

Alanine's titration curve

Alanine acts as a good buffer near its two pKa values (for the carboxyl and amino groups).

pH calculation for a buffer solution

Solved using the Henderson-Hasselbalch equation: pH = pKa + log([conjugate base]/[weak acid]).

Isoelectric point (pI) calculation for a polypeptide with multiple ionizable groups

Determined by averaging the pKa values of the groups that bracket the neutral form, ensuring the net charge is zero (e.g., for Ile-His-Phe-Lys-Ala-Thr-Glu, pI = (pKR[His] + pKa[N-terminus] + pKR[Lys] + pKa[C-terminus]) / relevant pKa values).