Biochemistry I: Foundations, Water Chemistry, Amino Acids, and Thermodynamics

Vocabulary flashcards covering core biochemistry topics including history, water chemistry, noncovalent interactions, acids and bases, amino acids, peptide structure, and biological thermodynamics.

Vitalism

The historical doctrine proposing that biological phenomena are governed by a unique vital force, which was disproved when Friedrich Wöhler synthesized organic urea from inorganic ammonium cyanate in $1828$.

Path Dependence

The evolutionary concept wherein the historical development of a biological system or biochemical pathway strongly constrains and influences its current structure and future outcomes.

Exaptation

An evolutionary process where a biological trait or structure originally developed for one specific function is co-opted for an entirely new purpose, such as proto-feathers in the dinosaur Beipiaosaurus inexpectus.

Enzyme

A biological macromolecular catalyst, named from the German enzym and Greek en-zymon ("in-leaven") by Wilhelm Kühne in $1877$.

Chirality

A geometric property of asymmetry in which a molecule cannot be superimposed on its mirror image.

Heat of Vaporization

The amount of thermal energy required to convert a defined quantity of a liquid into a gas at its boiling point under $1,atm$ of pressure.

Dielectric Constant ($\epsilon$)

A physical measure of a solvent's capacity to attenuate electrostatic interactions between charged ions, equal to $79$ for water and $5$ for benzene.

Adhesive Interactions

Favorable attractive noncovalent forces that occur between distinct and different molecular substances.

Cohesive Interactions

Favorable attractive noncovalent forces that occur between identical molecular substances.

van der Waals Contact Distance

The specific internuclear distance between two nonbonded atoms where attractive dispersion forces and repulsive electron-cloud steric forces reach optimal equilibrium.

Amphiphile

A molecule that simultaneously contains distinct hydrophilic (polar or charged) and hydrophobic (nonpolar) functional domains.

Morse Equation

The mathematical equation $\pi = i M R T$ used to compute osmotic pressure ($\pi$) from the van 't Hoff factor ($i$), molarity ($M$), gas constant ($R$), and absolute temperature ($T$).

Henderson-Hasselbalch Equation

The buffer relationship $\text{pH} = pK_a + \log\left(\frac{[\text{A}^-]}{[\text{HA}]}\right)$ that defines the pH of a solution containing a weak acid and its conjugate base.

Zwitterion

A neutral dipolar molecule carrying equal numbers of positively and negatively charged functional groups simultaneously.

Isoelectric Point ($pI$)

The specific pH condition at which a molecule or peptide possesses zero net electrical charge.

Inductive Effect

The redistribution of electron density through covalent bonds caused by electronegative atoms that lowers adjacent group $pK_a$ values by stabilizing conjugate bases.

Peptide Bond

A planar, rigid covalent amide bond formed via a condensation reaction between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of another.

Cystine

The dimeric amino acid generated through the oxidation of two cysteine residues to form a covalent disulfide linkage.

Beer-Lambert Law

The linear physical relationship $A = \epsilon c l$ that equates light absorbance ($A$) to molar absorptivity ($\epsilon$), solute concentration ($c$), and path length ($l$).

Bioenergetics

The quantitative thermodynamic study of energy transductions, conversions, and flows occurring within living organisms.

Enthalpy ($H$)

A thermodynamic state function defined as $H = U + pV$, representing the total internal energy plus the energy required to make room for its pressure and volume.

Entropy ($S$)

A fundamental thermodynamic property measuring the molecular disorder or number of microscopic arrangements ($W$) of a system, expressed as $S = k_B \ln(W)$.

Exergonic Reaction

A spontaneous chemical transformation characterized by a negative change in Gibbs free energy ($\Delta G < 0$), releasing usable energy to do work.

Mass Action Ratio ($Q$)

The calculated ratio of product concentrations raised to their stoichiometric coefficients divided by reactant concentrations at any specified non-equilibrium point in a reaction.

Phosphotransfer Potential

The standard Gibbs free energy change ($\Delta G'^\circ$) associated with the hydrolytic liberation of a phosphate group from a phosphorylated molecule.

Standard Reduction Potential ($E'^\circ$)

A quantitative measure in volts of the relative affinity of an oxidized chemical species for electrons compared to a standard hydrogen reference electrode.

Chemotroph

An organism that derives its metabolic energy from the chemical oxidation of organic or inorganic fuels.

Vitalism

The historical doctrine proposing that biological phenomena are governed by a unique vital force, which was disproved when Friedrich Wöhler synthesized organic urea from inorganic ammonium cyanate in $1828$.

Path Dependence

The evolutionary concept wherein the historical development of a biological system or biochemical pathway strongly constrains and influences its current structure and future outcomes.

Exaptation

An evolutionary process where a biological trait or structure originally developed for one specific function is co-opted for an entirely new purpose, such as proto-feathers in the dinosaur Beipiaosaurus inexpectus.

Enzyme

A biological macromolecular catalyst, named from the German enzym and Greek en-zymon ("in-leaven") by Wilhelm Kühne in $1877$.

Chirality

A geometric property of asymmetry in which a molecule cannot be superimposed on its mirror image.

Heat of Vaporization

The amount of thermal energy required to convert a defined quantity of a liquid into a gas at its boiling point under $1\,\text{atm}$ of pressure.

Dielectric Constant ($\epsilon$)

A physical measure of a solvent's capacity to attenuate electrostatic interactions between charged ions, equal to $79$ for water and $5$ for benzene.

Adhesive Interactions

Favorable attractive noncovalent forces that occur between distinct and different molecular substances.

Cohesive Interactions

Favorable attractive noncovalent forces that occur between identical molecular substances.

van der Waals Contact Distance

The specific internuclear distance between two nonbonded atoms where attractive dispersion forces and repulsive electron-cloud steric forces reach optimal equilibrium.

Amphiphile

A molecule that simultaneously contains distinct hydrophilic (polar or charged) and hydrophobic (nonpolar) functional domains.

Morse Equation

The mathematical equation $\pi = iMRT$ used to compute osmotic pressure ($\pi$) from the van 't Hoff factor ($i$), molarity ($M$), gas constant ($R$), and absolute temperature ($T$).

Henderson-Hasselbalch Equation

The buffer relationship $\text{pH} = pK_a + \log\left(\frac{[\text{A}^-]}{[\text{HA}]}\right)$ that defines the pH of a solution containing a weak acid and its conjugate base.

Zwitterion

A neutral dipolar molecule carrying equal numbers of positively and negatively charged functional groups simultaneously.

Isoelectric Point ($pI$)

The specific pH condition at which a molecule or peptide possesses zero net electrical charge.

Inductive Effect

The redistribution of electron density through covalent bonds caused by electronegative atoms that lowers adjacent group $pK_a$ values by stabilizing conjugate bases.

Peptide Bond

A planar, rigid covalent amide bond formed via a condensation reaction between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of another.

Cystine

The dimeric amino acid generated through the oxidation of two cysteine residues to form a covalent disulfide linkage.

Beer-Lambert Law

The linear physical relationship $A = \epsilon c l$ that equates light absorbance ($A$) to molar absorptivity ($\epsilon$), solute concentration ($c$), and path length ($l$).

Bioenergetics

The quantitative thermodynamic study of energy transductions, conversions, and flows occurring within living organisms.

Enthalpy ($H$)

A thermodynamic state function defined as $H = U + pV$, representing the total internal energy plus the energy required to make room for its pressure and volume.

Entropy ($S$)

A fundamental thermodynamic property measuring the molecular disorder or number of microscopic arrangements ($W$) of a system, expressed as $S = k_B \log(W)$.

Exergonic Reaction

A spontaneous chemical transformation characterized by a negative change in Gibbs free energy ($\Delta G < 0$), releasing usable energy to do work.

Mass Action Ratio ($Q$)

The calculated ratio of product concentrations raised to their stoichiometric coefficients divided by reactant concentrations at any specified non-equilibrium point in a reaction.

Phosphotransfer Potential

The standard Gibbs free energy change ($\Delta G'^\circ$) associated with the hydrolytic liberation of a phosphate group from a phosphorylated molecule.

Standard Reduction Potential ($E'^\circ$)

A quantitative measure in volts of the relative affinity of an oxidized chemical species for electrons compared to a standard hydrogen reference electrode.

Chemotroph

An organism that derives its metabolic energy from the chemical oxidation of organic or inorganic fuels.

Hydrophobic Effect

The thermodynamic driving force causing nonpolar molecules to aggregate in aqueous solution to minimize contact with water, thereby increasing overall system entropy by releasing structured water molecules.

Ion Product of Water ($K_w$)

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

Essential Amino Acids

The group of nine amino acids that cannot be synthesized de novo by an organism in adequate amounts and must be obtained through dietary sources.

Racemization

The chemical process in which optically active L-amino acids spontaneously convert into a mixture of L- and D-enantiomers over time.

Primary Structure

The specific linear covalent sequence of amino acids linked together by peptide bonds from the N-terminus to the C-terminus of a protein.

First Law of Thermodynamics

The physical principle asserting that total energy in a closed system is conserved, expressed as $\Delta U = q + w$, meaning energy can change forms but cannot be created or destroyed.

Second Law of Thermodynamics

The fundamental law stating that the total entropy of an isolated system always increases in any spontaneous process ($\Delta S_{\text{universe}} > 0$).

Reaction Coupling

The thermodynamic strategy of pairing an endergonic process ($\Delta G > 0$) with a strongly exergonic process ($\Delta G < 0$) so that the overall combined free energy change is negative.

Thioester

A high-energy functional group formed by the linkage of a carboxylic acid to a thiol, which lacks resonance stabilization and releases significant free energy upon hydrolysis.

Nicotinamide Adenine Dinucleotide ($\text{NAD}^+$)

A central electron carrier coenzyme that accepts two electrons and one proton during metabolic oxidation reactions to form reduced $\text{NADH}$.

Flavin Adenine Dinucleotide ($\text{FAD}$)

A flavin-containing electron transfer coenzyme derived from riboflavin ($\text{Vitamin B}_2$) that accepts two electrons and two protons to form fully reduced $\text{FADH}_2$.

Polyprotic Acid

An acid capable of donating more than one proton per molecule in successive ionization steps, featuring distinct $pK_a$ values for each dissociation step.

Partition Coefficient ($\log P_{\text{oct/water}}$)

A physical metric representing the ratio of solute concentrations between octanol and water, serving as a quantitative measure of molecular hydrophobicity.