Biochemistry - Water, Weak Interactions, and Buffers

Vocabulary practice flashcards covering fundamental biochemistry concepts, chemical properties of water, weak noncovalent interactions, ionization, and biological buffer systems.

Biochemistry

The branch of science that explores the chemical processes within and related to living organisms.

Macroelements

Essential inorganic mineral elements required by living organisms in large amounts, including $\text{Na}$, $\text{K}$, $\text{Ca}$, $\text{Mg}$, $\text{Cl}$, $\text{P}$, and $\text{S}$.

Trace Elements

Inorganic mineral elements required by organisms in minute quantities, including $\text{Fe}$, $\text{Zn}$, $\text{Cu}$, $\text{Mn}$, $\text{I}$, $\text{Se}$, $\text{Co}$, and $\text{Mo}$.

Supramolecular Complexes

Level 3 biological assemblies formed from macromolecules, such as chromosomes (composed of DNA and proteins), plasma membranes, and cell walls.

Hydrogen Bond (Water)

An electrostatic attraction between the partially positive hydrogen ($\delta^+$) of one $\text{H}_2\text{O}$ molecule and the partially negative oxygen ($\delta^-$) of an adjacent $\text{H}_2\text{O}$ molecule, allowing each water molecule to form up to 4 hydrogen bonds simultaneously.

Proton Hopping

The rapid transfer of protons ($\text{H}^+$) along hydrogen-bonded networks of water molecules as hydronium ions ($\text{H}_3\text{O}^+$), rather than through physical diffusion of free protons.

Cohesion

The electrostatic attraction among molecules of the same substance, which makes water molecules stick to one another and generates surface tension.

Adhesion

The electrostatic attraction among molecules of different substances, enabling water molecules to stick to polar or charged surfaces like glass walls and plant xylem.

Specific Heat

The amount of energy required to raise the temperature of $1\,\text{g}$ of a substance by $1^\circ\text{C}$. Water has a high specific heat of $1.0\,\text{cal/g/}^\circ\text{C}$ ($4.184\,\text{J/g/}^\circ\text{C}$), which resists rapid thermal changes.

Density Anomaly of Water

The physical property where liquid water reaches maximum density at approximately $4^\circ\text{C}$. Below this temperature and upon freezing, molecules form an open 3D crystal lattice holding each molecule to 4 neighbors, leaving more space between molecules and causing ice to float.

Hydrophobic Effect

The thermodynamic tendency of nonpolar groups to cluster together in aqueous solutions, driven by the release of highly ordered water molecules surrounding nonpolar groups back into the bulk solvent, thereby increasing solvent entropy and lowering Gibbs free energy.

Amphipathic Molecule

A compound containing both polar (hydrophilic) and nonpolar (hydrophobic) regions, such as phosphatidylcholine and phenylalanine.

Micelle

A stable aggregate formed by amphipathic compounds in water where nonpolar hydrophobic alkyl tails are sequestered inward from the solvent and polar hydrophilic heads face outward to interact with water.

van der Waals Interactions

Weak, transient dipole-dipole attractions occurring between any two atoms in close proximity, which collectively provide significant stabilization when large surface areas interact.

Cell Turgor

Internal hydrostatic pressure in plant cells that maintains cellular shape, keeps leaves expanded for light capture and gas exchange, and allows roots to push through soil.

Hydrolysis

A biochemical reaction in which water serves as a reactant to cleave a covalent bond within a molecule according to the general equation: $\text{AB} + \text{H}_2\text{O} \rightarrow \text{A-H} + \text{B-OH}$.

Condensation Reaction

A biochemical synthesis reaction in which two molecules are linked together with the release of a water molecule as a product according to the equation: $\text{A-H} + \text{B-OH} \rightarrow \text{AB} + \text{H}_2\text{O}$.

Ion Product of Water ($K_w$)

The equilibrium constant product for the autoionization of water, defined as $K_w = [\text{H}^+][\text{OH}^-] = 1.0 \times 10^{-14}\,\text{M}^2$ at $25^\circ\text{C}$.

pH

A logarithmic measure of hydronium ion concentration defined as $\text{pH} = -\log_{10}[\text{H}^+]$, where a change of $1.0\,\text{pH unit}$ represents a 10-fold difference in $[\text{H}^+]$.

Acid Dissociation Constant ($K_a$)

The equilibrium constant for the dissociation of a weak acid ($\text{HA} \rightleftharpoons \text{H}^+ + \text{A}^-$), defined as $K_a = \frac{[\text{H}^+][\text{A}^-]}{[\text{HA}]}$, where smaller $K_a$ values (larger $\text{p}K_a$) indicate weaker acids.

Buffer

An aqueous solution consisting of a weak acid and its conjugate base (or a weak base and its conjugate acid) that resists significant changes in pH upon addition of small quantities of acid or base.

Henderson–Hasselbalch Equation

An equation relating pH, $\text{p}K_a$, and the molar ratio of conjugate base to weak acid in a buffer solution: $\text{pH} = \text{p}K_a + \log\left(\frac{[\text{A}^-]}{[\text{HA}]}\right)$.

Midpoint (Half-Equivalence Point)

The point during titration of a weak acid where exactly $0.5$ equivalents of strong base have been added, resulting in equal concentrations of weak acid and conjugate base ($[\text{HA}] = [\text{A}^-]$), $\text{pH} = \text{p}K_a$, and maximum buffering capacity.

Effective Buffering Region

The pH range spanning approximately $1.0\,\text{pH unit}$ on either side of the weak acid's $\text{p}K_a$ ($\text{pH} = \text{p}K_a \pm 1.0$), corresponding to base-to-acid ratios between $1:10$ and $10:1$.

Phosphate Buffer System

An intracellular buffer system consisting of the conjugate pair $\text{H}_2\text{PO}_4^- / \text{HPO}_4^{2-}$, with a $\text{p}K_a$ of $6.86$, making it effective near cytosolic pH ($\sim 7.2$).

Carbonic Acid–Bicarbonate Buffer System

The primary extracellular buffer system in blood plasma that maintains physiological pH near $7.4$ through coupled equilibria between gaseous $\text{CO}_2$ in lung air space, dissolved $\text{CO}_2$, carbonic acid ($\text{H}_2\text{CO}_3$), and bicarbonate ($\text{HCO}_3^-$).

Histidine Imidazole Group

An ionizable nitrogen-containing side chain in protein structures with a $\text{p}K_a \approx 6.0$ that can reversibly accept or donate protons, allowing proteins to contribute significantly to intracellular and plasma buffering.

Acidosis and Alkalosis

Clinical disorders involving blood pH imbalance, where acidosis refers to an abnormally decreased blood pH and alkalosis refers to an abnormally elevated blood pH.