Biochemical Energy Production and the Common Metabolic Pathway

Vocabulary practice flashcards defining core terms, enzymes, coenzymes, structural concepts, and pathways of cellular metabolism and biochemical energy production.

Metabolism

The sum total of all the biochemical reactions that take place in a living organism.

Catabolism

All metabolic reactions in which large biochemical molecules are broken down to smaller ones, usually accompanied by the release of energy.

Anabolism

All metabolic reactions in which small biochemical molecules are joined together to form larger ones, usually requiring the input of energy.

Metabolic Pathway

A series of consecutive biochemical reactions used to convert a starting material into an end product.

Linear Metabolic Pathway

A metabolic pathway in which a series of consecutive reactions generates a final product.

Cyclic Metabolic Pathway

A metabolic pathway in which a series of consecutive reactions regenerates the starting reactant.

Prokaryotic Cell

A cell that lacks a membrane-bound nucleus and possesses DNA in a central nucleoid region, found only in bacteria.

Eukaryotic Cell

A cell found in higher organisms in which the genetic material (DNA) is contained within a membrane-enclosed nucleus.

Cytoplasm

The water-based cellular material of a eukaryotic cell that lies between the cellular nucleus and the outer membrane.

Organelle

A minute structure within the cytoplasm of a cell that carries out a specialized cellular function.

Cytosol

The water-based fluid portion of the cytoplasm of a cell that surrounds the organelles.

Lysosome

A cytoplasmic organelle containing hydrolytic enzymes active at an optimum pH of $4.8$ that degrades proteins, polysaccharides, and foreign invaders.

Mitochondrion

A sausage-shaped eukaryotic organelle surrounded by a permeable outer membrane and an impermeable inner membrane that generates most of the cellular energy.

Cristae

The inward folds of the inner mitochondrial membrane that extend into the central matrix.

Mitochondrial Matrix

The interior compartment of a mitochondrion enclosed by the inner mitochondrial membrane, housing most citric acid cycle enzymes.

Intermembrane Space

The region of a mitochondrion located between the freely permeable outer membrane and the impermeable inner membrane.

ATP Synthase Complex

Small spherical enzyme knobs attached to the cristae on the matrix side of the inner mitochondrial membrane that synthesize ATP from ADP and inorganic phosphate.

Phosphoanhydride Bond

The chemical bond formed when two phosphate groups react with one another accompanied by the loss of a water molecule.

Phosphoryl Group

The functional group derived from a phosphate ion when it becomes incorporated into another molecule, having the formula $\text{PO}_3^{2-}$.

Flavin Adenine Dinucleotide (FAD)

A metabolic redox coenzyme consisting of ribitol, flavin (riboflavin/vitamin $B_2$), and an activating ADP subunit that acts as an oxidizing agent by accepting two electrons and two protons.

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

A metabolic redox coenzyme containing a nicotinamide ring with a positively charged nitrogen atom that serves as an oxidizing agent by accepting two electrons and one proton to form $\text{NADH}$.

Coenzyme A ($\text{CoA-SH}$)

A metabolic coenzyme composed of 2-aminoethanethiol, pantothenic acid (vitamin $B_5$), and phosphorylated ADP that transfers acetyl groups via its terminal sulfhydryl group.

Acetyl Group

The two-carbon acyl functional group ($\text{CH}_3\text{--C(=O)--}$) derived from acetic acid after removing the $-\text{OH}$ group from the carboxyl carbon.

High-Energy Compound

A compound containing strained bonds that liberates a greater-than-normal amount of free energy upon hydrolysis, generally exceeding $6.0\,\text{kcal/mol}$.

Free Energy

The portion of energy released by a chemical reaction that is actually available to perform work or drive energy-requiring biochemical processes at a given temperature and pressure.

Digestion

The first stage of biochemical energy production, an extracellular process occurring in the mouth, stomach, and small intestine that breaks dietary macromolecules into transportable monomers.

Common Metabolic Pathway

The sum total of the biochemical reactions of the citric acid cycle, the electron transport chain, and oxidative phosphorylation that process products from all classes of food.

Citric Acid Cycle

A series of eight biochemical reactions in the mitochondrial matrix where the acetyl portion of acetyl CoA is oxidized to two $\text{CO}_2$ molecules while generating three $\text{NADH}$, one $\text{FADH}_2$, and one $\text{GTP}$.

Synthase

An enzyme that catalyzes the formation of a new covalent bond during a biochemical reaction without the direct expenditure of an ATP molecule.

Synthetase

An enzyme that catalyzes the linking of two molecules using energy derived from breaking a high-energy phosphate bond.

Aconitase

The enzyme that catalyzes the isomerization of achiral citrate to chiral isocitrate via dehydration to cis-aconitate followed by hydration.

Isocitrate Dehydrogenase

The enzyme catalyzing Step 3 of the citric acid cycle, which oxidizes isocitrate to oxalosuccinate and decarboxylates it to form $\alpha\text{-ketoglutarate}$, $\text{CO}_2$, and $\text{NADH}$.

$\alpha\text{-Ketoglutarate}$ Dehydrogenase Complex

A multienzyme complex containing thiamin pyrophosphate (TPP) and $\text{Mg}^{2+}$ that oxidatively decarboxylates $\alpha\text{-ketoglutarate}$ to succinyl CoA, $\text{CO}_2$, and $\text{NADH}$.

Succinyl-CoA Synthetase

The enzyme that cleaves the high-energy thioester bond in succinyl CoA to generate succinate while phosphorylating GDP to GTP.

Succinate Dehydrogenase

An integral inner mitochondrial membrane enzyme that oxidizes succinate to trans-fumarate while reducing FAD to $\text{FADH}_2$.

Fumarase

The stereospecific enzyme that catalyzes the hydration of the trans double bond of fumarate to produce exclusively L-malate.

Malate Dehydrogenase

The enzyme that oxidizes the secondary alcohol group of L-malate to regenerate oxaloacetate while producing $\text{NADH} + \text{H}^+$.

Electron Transport Chain

A sequence of four protein complexes and mobile carriers located on the inner mitochondrial membrane that transfers electrons from $\text{NADH}$ and $\text{FADH}_2$ to molecular oxygen to form water.

Coenzyme Q ($\text{CoQ}$)

A lipid-soluble mobile electron carrier in the inner mitochondrial membrane that shuttles electrons from Complexes I and II to Complex III.

Cytochrome c Oxidase

Complex IV of the electron transport chain, which transfers electrons from cytochrome c to molecular oxygen, reducing oxygen to water.

Oxidative Phosphorylation

The biochemical process by which ATP is synthesized from ADP and inorganic phosphate using the electrochemical proton gradient established by the electron transport chain.

Coupled Reactions

Pairs of biochemical reactions that occur concurrently so that the energy released by one reaction is utilized to drive the other energy-requiring reaction.

Chemiosmotic Coupling

The mechanism linking electron transport to ATP synthesis, wherein protons pumped across the inner mitochondrial membrane establish an electrochemical gradient that powers ATP synthase.

Thermogenin

An inner mitochondrial membrane uncoupling protein abundant in brown fat that acts as a proton channel, allowing protons to bypass ATP synthase and release energy as heat.

Irisin

An exercise-induced hormone discovered in 2013 that triggers white fat cells to adopt the heat-producing, uncoupled characteristics of brown fat cells.

Amygdalin

A natural cyanoglycoside consisting of two D-glucose units joined by a $\beta(1\rightarrow 6)$ linkage, found in apricot and peach pits, that releases toxic hydrogen cyanide (HCN) upon enzymatic hydrolysis.

Phytochemicals

Biologically active plant chemicals that provide color, hormonal, and defensive functions in plants and serve largely as dietary antioxidants in humans.

Quercetin

The most widespread dietary flavonoid antioxidant, concentrated heavily in onions and apple peel, capable of scavenging free radicals and inhibiting certain bacterial strains.

Reactive Oxygen Species (ROS)

Highly reactive chemical species—including hydrogen peroxide ($\text{H}_2\text{O}_2$), superoxide ion ($\text{O}_2^{\bullet -}$), and hydroxyl radical ($\text{OH}^\bullet$)—formed from less than $10\%$ of cellular oxygen consumption to help destroy invading pathogens.