Biochemistry I: Introduction to Metabolism & Energy Transformations

Vocabulary flashcards covering the core principles of metabolic energy transformations, carbon oxidation states, electron carriers (NADH, FADH2, NADPH), membrane potential thermodynamics, and the phosphoryl transfer hierarchy from Biochemistry I (BCHM 451).

Core Metabolic Transformation Flowchart

The pathway of biological energy conversion: Reduced Carbon Fuels (glucose, fatty acids) $\rightarrow$ High-Energy Electrons ($\text{NADH}$, $\text{FADH}_2$) $\rightarrow$ Electrochemical Gradient (proton-motive force across the inner mitochondrial membrane) $\rightarrow$ Chemical Bonds ($\text{ATP}$ synthesis via $\text{ATP}$ Synthase).

Carbon Oxidation State

The chemical degree of reduction of carbon in metabolic fuels; a higher proportion of $\text{C–H}$ and $\text{C–C}$ bonds and fewer $\text{C–O}$ bonds yields greater stored free energy ($\Delta G^{\circ\prime}$ is more negative) upon complete oxidation to $\text{CO}_2$.

Single-Carbon Oxidation Levels

The hierarchical sequence of single-carbon compounds from most reduced (highest energy) to fully oxidized (lowest energy): Methane ($\text{CH}_4$, $-820\,\text{kJ}\cdot\text{mol}^{-1}$), Methanol ($\text{CH}_3\text{OH}$, $-703\,\text{kJ}\cdot\text{mol}^{-1}$), Formaldehyde ($\text{CH}_2\text{O}$, $-523\,\text{kJ}\cdot\text{mol}^{-1}$), Formic Acid ($\text{HCOOH}$, $-285\,\text{kJ}\cdot\text{mol}^{-1}$), and Carbon Dioxide ($\text{CO}_2$, $0\,\text{kJ}\cdot\text{mol}^{-1}$).

Energy Density of Fats vs. Carbohydrates

Triglycerides/fats are more energy-rich per gram than carbohydrates because fats are composed of long, saturated hydrocarbon chains ($-\text{CH}_2-$) where carbon is almost fully reduced, whereas glucose carbons are already partially oxidized with hydroxyl ($-\text{OH}$) groups, liberating fewer electrons and less free energy.

Controlled Combustion

The stepwise oxidation of fuel molecules by enzymes under aerobic cellular respiration, which captures energy in metabolic intermediate carriers rather than releasing it all at once as explosive heat.

Catabolism

Degradative metabolic pathways that break down fuels (fats, carbohydrates $+$ $\text{O}_2$) into simple end products ($\text{CO}_2$, $\text{H}_2\text{O}$) to capture free energy.

Anabolism

Biosynthetic metabolic pathways that consume energy ($\text{ATP}$ and reducing power) to assemble complex cellular macromolecules from simpler precursor molecules.

Activated Electron Carriers

Intermediate coenzymes ($\text{NAD}^+$ and $\text{FAD}$) that collect high-energy electrons extracted from carbon fuels to preserve reducing power and sequentially deliver them to the electron transport chain, rather than transferring them directly to $\text{O}_2$.

Hydride Transfer

The mechanism of electron pickup by $\text{NAD}^+$, where its nicotinamide ring (derived from niacin/vitamin $\text{B}_3$) accepts a hydride ion ($\text{H}:^-$, containing $1$ proton and $2$ electrons) to form $\text{NADH}$, while releasing a second proton ($\text{H}^+$) into solution.

Flavin Adenine Dinucleotide (FAD)

An electron carrier derived from riboflavin/vitamin $\text{B}_2$ that accepts $2$ electrons and $2$ protons ($2\,e^- + 2\,\text{H}^+$) at its isoalloxazine ring to form $\text{FADH}_2$.

NADPH

A dinucleotide electron carrier distinguished by an extra $2^\prime$-phosphate on its adenosine ribose; unlike $\text{NADH}$ (which serves in catabolic $\text{ATP}$ synthesis), it acts almost exclusively as reducing power for anabolic biosynthesis.

Kinetic Stability (Metabolic Carriers)

The property of reduced electron carriers and $\text{ATP}$ characterized by large transition state activation barriers that prevent spontaneous reaction with $\text{O}_2$ or $\text{H}_2\text{O}$ without enzymes, allowing precise cellular regulation of energy flow.

Electrochemical Proton Gradient

A stored proton-motive force across the inner mitochondrial membrane generated as exergonic redox flow in the Electron Transport Chain pumps protons ($\text{H}^+$) out of the mitochondrial matrix into the intermembrane space.

Free Energy of Ion Translocation Formula

$\Delta G = RT\ln\left(\frac{[\text{out}]}{[\text{in}]}\right) + nF\Delta V$, which calculates the combined thermodynamic contribution of the chemical concentration gradient ($\Delta\text{pH}$) and the electrical membrane potential ($\Delta V$), where $n$ is ion charge and $F$ is the Faraday constant.

Thermogenin (UCP-1)

An uncoupling protein found in brown adipose tissue (important for neonates and hibernators) that allows protons ($\text{H}^+$) to bypass $\text{ATP}$ synthase, dissipating the proton gradient directly as thermal heat for thermogenesis instead of producing $\text{ATP}$.

ATP Synthase

A rotary enzyme complex in the inner mitochondrial membrane that utilizes the flow of protons down their electrochemical gradient into the matrix to drive the phosphorylation of $\text{ADP}$ by $\text{P}_i$, storing energy in phosphoanhydride bonds.

High Exergonicity of ATP Hydrolysis

The large thermodynamic release of free energy ($\Delta G^{\circ\prime} \approx -30.5\,\text{kJ}\cdot\text{mol}^{-1}$) caused by electrostatic repulsion of the 4 negative charges on the triphosphate chain, resonance stabilization of free orthophosphate ($\text{P}_i$), and favorable entropy/hydration of the products.

Reaction Coupling

The thermodynamic pairing of an unfavorable endergonic step ($+\Delta G$) to exergonic $\text{ATP}$ hydrolysis ($-\Delta G$), producing a net negative free energy change that can shift the product-to-reactant equilibrium ratio by up to $10^8$ in vivo.

Hexokinase Net Free Energy Coupling

The coupled reaction where $\text{ATP}$ hydrolysis ($\Delta G^{\circ\prime} = -30.5\,\text{kJ}\cdot\text{mol}^{-1}$) drives glucose phosphorylation ($\Delta G^{\circ\prime} = +13.8\,\text{kJ}\cdot\text{mol}^{-1}$) to make the overall formation of Glucose-6-P favorable ($\Delta G^{\circ\prime} = -16.7\,\text{kJ}\cdot\text{mol}^{-1}$).

Thioester Bond

A high-energy $\text{C–S}$ bond linking an acetyl unit to coenzyme A in Acetyl-CoA ($\Delta G^{\circ\prime} = -31.5\,\text{kJ}\cdot\text{mol}^{-1}$); the absence of significant double-bond resonance between sulfur and carbonyl carbon endows it with high acetyl-transfer potential.

Adenylate Energy Charge Regulation

Allosteric metabolic control whereby elevated $\text{ATP}$ inhibits catabolic pathways and activates anabolism, while elevated $\text{ADP}/\text{AMP}$ indicates energy depletion and stimulates catabolic fuel breakdown.

Phosphoenolpyruvate (PEP)

A high-energy glycolytic intermediate with a standard free energy of hydrolysis of $\Delta G^{\circ\prime} = -61.9\,\text{kJ}\cdot\text{mol}^{-1}$, which is higher than $\text{ATP}$ and allows direct phosphoryl transfer to $\text{ADP}$.

1,3-Bisphosphoglycerate (1,3-BPG)

A glycolytic intermediate possessing a $\Delta G^{\circ\prime}$ of hydrolysis of $-49.4\,\text{kJ}\cdot\text{mol}^{-1}$ (higher than $\text{ATP}$) that directly couples carbon fuel oxidation to $\text{ATP}$ synthesis.

Phosphocreatine

An energy reservoir molecule with a free energy of hydrolysis of $\Delta G^{\circ\prime} = -43.1\,\text{kJ}\cdot\text{mol}^{-1}$ that rapidly recharges $\text{ATP}$ from $\text{ADP}$ in active muscle tissue.

Glucose 6-Phosphate (G-6-P)

A phosphorylated hexose with a standard free energy of hydrolysis of $\Delta G^{\circ\prime} = -13.8\,\text{kJ}\cdot\text{mol}^{-1}$ (lower than $\text{ATP}$) that traps glucose intracellularly for catabolic or storage pathways.