Biochemistry Fundamentals: Cellular Organization, Water Chemistry, Thermodynamics, and Amino Acids

Vocabulary practice flashcards covering cell organization, weak molecular forces, water ionization and buffering, thermodynamic laws, and the chemical, stereochemical, and spectroscopic properties of amino acids.

Biomolecules

Carbon compounds bonded with hydrogen, nitrogen, and oxygen that form stable covalent bonds through electron-pair sharing.

Inorganic Precursors

Low-molecular-weight molecules ($18 - 64\,\text{daltons}$)—such as carbon dioxide, water, ammonia, nitrogen ($\text{N}_2$), and nitrate ($\text{NO}_3^-$)—that serve as the fundamental starting units for biological molecules.

Metabolites

Intermediate compounds ($50 - 250\,\text{daltons}$), including pyruvate, citrate, succinate, glyceraldehyde-3-phosphate, fructose-1,6-bisphosphate, and 3-phosphoglyceric acid, formed during metabolic pathways.

Building Blocks

Intermediate molecular units ($100 - 350\,\text{daltons}$)—such as amino acids, nucleotides, monosaccharides, fatty acids, and glycerol—that polymerize to build biological macromolecules.

Macromolecules

Large cellular polymers ($10^3 - 10^9\,\text{daltons}$), including proteins, nucleic acids, polysaccharides, and lipids.

Supramolecular Complexes

High-order cellular structures ($10^6 - 10^9\,\text{daltons}$), such as ribosomes, cytoskeleton, and multienzyme complexes, formed by non-covalent associations of macromolecules.

Biomolecular Recognition

Specific interactions between biological molecules mediated by weak chemical forces, which confine living organisms to a narrow range of environmental conditions.

Van der Waals Interactions

Weak electrical interactions between atoms that possess bond energies ranging between $0.4\,\text{kJ/mol}$ and $40\,\text{kJ/mol}$.

Hydrogen Bonds

Non-covalent interactions ($12 - 30\,\text{kJ/mol}$) formed between a hydrogen atom covalently bound to an electronegative atom and a second electronegative atom.

Ionic Interactions

Attractive forces between oppositely charged functional groups with characteristic interaction energies of approximately $20\,\text{kJ/mol}$.

Hydrophobic Interactions

Thermodynamic associations ($<40\,\text{kJ/mol}$) that result from the tendency of water molecules to exclude non-polar groups.

Prokaryotes

Unicellular organisms, including bacteria and Archaea, bounded by a single plasma membrane and lacking a membrane-enclosed nucleus or internal organelles.

Eukaryotes

Cells that are $10^3 - 10^4$ times larger than prokaryotes and contain distinct membrane-bound organelles such as the nucleus, endoplasmic reticulum, Golgi apparatus, and mitochondria.

Viruses

Non-cellular, non-living supramolecular complexes consisting of nucleic acid encapsulated inside a protective protein coat that cannot self-replicate independently.

Ion Product of Water ($K_w$)

The equilibrium constant for water autoionization, defined by the relationship $K_w = 55.5\,K_{eq} = [\text{H}^+][\text{OH}^-] = 10^{-14}\,\text{M}^2$.

Acid Dissociation Constant ($K_a$)

The equilibrium constant characterizing the tendency of an acid to dissociate into a proton and its conjugate base in aqueous solution.

Henderson-Hasselbalch Equation

The mathematical formula $pH = pK_a + \log_{10}\left(\frac{[\text{A}^-]}{[\text{HA}]}\right)$, which relates pH to the $pK_a$ and the ratio of conjugate base to weak acid.

Buffer

A solution composed of an equivalent mixture of a weak acid and its conjugate base that resists changes in pH upon the addition of acid or base.

Isolated System

A thermodynamic system that cannot exchange either energy or matter with its surrounding environment.

Closed System

A thermodynamic system that is capable of exchanging energy, but not matter, with its surroundings.

Open System

A thermodynamic system that is capable of exchanging both energy and matter with its surroundings.

Standard Free Energy Change (Equilibrium)

The free energy change under standard-state conditions, related to the equilibrium constant by the equation $\Delta G^o = -RT\ln(K_{eq}) = -2.3RT\log_{10}(K_{eq})$.

Coupled Processes

The bioenergetic mechanism in which a thermodynamically unfavorable reaction is driven forward by coupling it directly to a highly exergonic, favorable reaction.

Zwitterion

A dipolar molecule carrying simultaneously localized positive and negative charges with a net electrical charge that can equal zero.

Isoelectric Point ($pI$)

The characteristic pH at which the net overall electrical charge of an amino acid or protein equals zero, calculated as $pI = \frac{pK_{a1} + pK_{a2}}{2}$.

CORN Law

A stereochemical mnemonic rule stating that viewing an amino acid along the $\text{H}-\text{C}_\alpha$ bond yields the L-enantiomer if the groups $\text{CO}$, $\text{R}$, and $\text{N}$ read clockwise, and the D-enantiomer if they read anticlockwise.

Beer-Lambert Law

A physical law expressed as $A = \varepsilon c l$, where $A$ is light absorbance, $\varepsilon$ is the molar extinction coefficient ($\text{M}^{-1}\,\text{cm}^{-1}$), $c$ is molar concentration ($\text{M}$), and $l$ is pathlength ($\text{cm}$).

Peptide Bond

An unbranched covalent linkage predominantly in the trans conformation formed between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of another via a dehydration reaction.