Biochemistry Lecture: Thermodynamics, Ionization, and Acid-Base Chemistry

Vocabulary flashcards covering hydrophobic interactions, water structure, ionization constants, pH scale, and acid-base buffer principles based on the transcript.

Water cage

An ordered structure formed by water molecules surrounding a non-polar or hydrophobic solute, which carries a high entropic cost.

Amphipathic molecule

A molecule containing both a hydrophilic (charged or polar) portion and a hydrophobic portion within its structure.

Phenylalanine

An amphipathic amino acid that features a phenyl ring as its hydrophobic portion alongside hydrophilic groups.

Micelle

A spherical structure formed by amphipathic molecules in aqueous solution, where polar groups face the outer surface to interact with water and hydrophobic tails cluster into the interior.

Acid

Any molecule capable of releasing a hydrogen atom or proton ($H^+$).

Base

Any molecule capable of accepting or grabbing a proton ($H^+$) when needed.

Proton jump

The rapid transfer of delocalized protons ($H^+$) through a hydrogen bonding network by grabbing protons from neighboring water molecules.

Molarity of pure water

The molar concentration of water, which is $55.5$\,M.

$$K_w$$

The ion product constant of water, defined as $K_w = [H^+][OH^-]$, which equals $10^{-14}$ under standard state conditions.

pH

A logarithmic scale representing hydrogen ion concentration, defined as $\text{pH} = -\text{log}([H^+])$, where neutral water has a value of $7$ at standard state.

Neutral water pH at $40^\text{o}$

The pH value of neutral water at $40^\text{o}\text{C}$, which is $6.7$ due to the endothermic shift in water ionization at elevated temperature.

Neutral water pH at $0^\text{o}$

The pH value of neutral water at $0^\text{o}\text{C}$, which is $7.47$.

$$K_a$$

The acid dissociation constant defined as the equilibrium concentration of products divided by reactants, or $K_a = \frac{[H^+][A^-]}{[HA]}$.

Henderson-Hasselbalch equation

A mathematical rearrangement of the $K_a$ equilibrium expression used to calculate the pH of buffers composed of weak acids.