Biochemistry: Metabolism of Carbohydrates, Lipids, and Nitrogen

Comprehensive vocabulary flashcards covering the citric acid cycle, electron transport and oxidative phosphorylation, lipid classification and membrane structure, fatty acid and cholesterol metabolism, and nitrogen assimilation and neurotransmitter synthesis.

Citrate Synthase

The enzyme that catalyzes the first step of the citric acid cycle, condensing two-carbon acetyl-CoA with four-carbon oxaloacetate to form six-carbon citrate.

Aconitase

The enzyme that reversibly catalyzes the isomerization of citrate into isocitrate in the citric acid cycle.

Isocitrate Dehydrogenase

The enzyme that oxidatively decarboxylates isocitrate to $\alpha$-ketoglutarate and $\text{CO}_2$ while reducing $\text{NAD}^+$ to $\text{NADH}$; stimulated allosterically by $\text{ADP}$ and $\text{NAD}^+$ and inhibited by $\text{ATP}$ and $\text{NADH}$.

$\alpha$-Ketoglutarate Dehydrogenase Complex

A multienzyme complex requiring $\text{CoASH}$ and $\text{NAD}^+$ that converts $\alpha$-ketoglutarate to succinyl-CoA and $\text{CO}_2$; inhibited by succinyl-CoA, $\text{NADH}$, $\text{ATP}$, and $\text{GTP}$.

Succinate Thiokinase

The enzyme that catalyzes the cleavage of the high-energy thioester bond in succinyl-CoA to form succinate, coupled directly to the synthesis of $\text{GTP}$ (or $\text{ATP}$ in some organisms).

Succinate Dehydrogenase

An inner mitochondrial membrane-bound enzyme containing covalently bound $\text{FAD}$ and iron-sulfur centers that oxidizes succinate to fumarate while reducing ubiquinone ($\text{UQ}$); also functions as Complex II of the electron transport chain.

Fumarase

An enzyme (also known as fumarate hydratase) that catalyzes the reversible, stereospecific hydration of fumarate to form $L$-malate.

Malate Dehydrogenase

The enzyme that catalyzes the endergonic oxidation of $L$-malate to oxaloacetate, producing one molecule of $\text{NADH}$ to complete the citric acid cycle.

Amphibolic Pathway

A metabolic pathway that functions in both catabolism (oxidizing acetyl-CoA to $\text{CO}_2$ to conserve energy as $\text{NADH}$ and $\text{FADH}_2$) and anabolism (supplying metabolic intermediates as biosynthetic precursors).

Citrate Lyase

The cytoplasmic enzyme that cleaves citrate transported out of the mitochondria back into acetyl-CoA and oxaloacetate, supplying acetyl-CoA for fatty acid and lipid biosynthesis.

Glyoxylate Cycle

A modified version of the citric acid cycle occurring in glyoxysomes of plants and the cytoplasm of bacteria and algae that converts two molecules of acetyl-CoA into one molecule of oxaloacetate, bypassing both decarboxylation reactions.

Isocitrate Lyase

An enzyme unique to the glyoxylate cycle that cleaves isocitrate into succinate and glyoxylate.

Malate Synthase

An enzyme unique to the glyoxylate cycle that condenses glyoxylate with a second molecule of acetyl-CoA to form malate.

Complex I (NADH Dehydrogenase Complex)

A large inner mitochondrial membrane complex consisting of over two dozen polypeptides, one $\text{FMN}$, and seven iron-sulfur centers that transfers electrons from $\text{NADH}$ to ubiquinone ($\text{UQ}$) coupled with proton translocation.

Complex III (Cytochrome $bc_1$ Complex)

A respiratory chain complex composed of two $b$-type cytochromes, cytochrome $c_1$, and an iron-sulfur center that transfers electrons from reduced ubiquinone ($\text{UQH}_2$) to cytochrome $c$ via the Q cycle.

Complex IV (Cytochrome Oxidase)

The terminal electron transport complex containing cytochromes $a$ and $a_3$ and two copper centers ($\text{Cu}_\text{A}$ and $\text{Cu}_\text{B}$) that catalyzes the four-electron reduction of molecular oxygen ($\text{O}_2$) to two molecules of $\text{H}_2\text{O}$.

Chemiosmotic Coupling Theory

The mechanism proposed by Peter Mitchell in $1961$ in which the free energy released during electron transport pumps protons out of the mitochondrial matrix into the intermembrane space, creating an electrochemical gradient (proton motive force) that drives $\text{ATP}$ synthesis.

Submitochondrial Particles

Vesicles formed upon physical disruption of mitochondria whose inner membrane fragments reseal in an inside-out orientation, exposing the catalytic $F_1$ spheres toward the external medium.

ATP Synthase

A lollipop-shaped multisubunit enzyme composed of a membrane-embedded proton-conducting rotor ($F_0$ consisting of subunits $a_1b_2c_{12}$) and a catalytic stator head ($F_1$ consisting of subunits $\alpha_3\beta_3\gamma\delta\epsilon$) that drives $\text{ATP}$ synthesis from $\text{ADP}$ and $\text{P}_\text{i}$ as protons flow across the membrane.

Antimycin A

A specific metabolic inhibitor that blocks the respiratory electron transport chain by preventing electron transfer from the $b$ cytochromes in Complex III.

Fatty Acids

Monocarboxylic acids with variable-length unbranched hydrocarbon chains, predominantly possessing an even number of carbon atoms, that react with alcohols to form esters.

Triacylglycerols

Neutral, nonpolar fats consisting of three fatty acid chains esterified to a single glycerol molecule, releasing $9.3\,\text{kcal/mole}$ upon complete oxidation (compared to $4.1\,\text{kcal/mole}$ for glycogen).

Wax Esters

Complex mixtures of nonpolar lipids formed by esterifying long-chain fatty acids with long-chain alcohols, such as melissyl cerotate ($\text{CH}_3(\text{CH}_2)_{24}\text{COO}(\text{CH}_2)_{29}\text{CH}_3$) found in carnauba wax.

Phosphatidic Acid

The simplest phosphoglyceride, composed of glycerol-3-phosphate esterified with two fatty acids, serving as the common biosynthetic precursor for all other phosphoglycerides.

Ceramide

A sphingolipid core structure consisting of a fatty acid linked via an amide bond to the amino alcohol sphingosine, serving as the metabolic precursor for sphingomyelins and glycolipids.

Sphingomyelin

A major animal membrane phospholipid consisting of a ceramide unit esterified at the 1-hydroxyl group to phosphorylcholine or phosphorylethanolamine, concentrated in the myelin sheath of nerves.

Isoprenoids

A large and diverse class of biomolecules composed of repeating branched five-carbon isoprene units biosynthesized from isopentenyl pyrophosphate ($\text{IPP}$).

Terpenes

Isoprenoid compounds classified according to their number of five-carbon isoprene units: monoterpenes ($2$ units), sesquiterpenes ($3$ units), diterpenes ($4$ units), triterpenes ($6$ units), tetraterpenes ($8$ units), and polyterpenes ($3000\text{ to }6000$ units).

Mixed Terpenoids

Biomolecules composed of nonterpene groups covalently attached to isoprenoid chains, including Vitamin E, ubiquinone, Vitamin K, and plant cytokinins.

Cholesterol

A $27$-carbon steroid alcohol containing four fused rings that modulates eukaryotic cell membrane fluidity and serves as the precursor for steroid hormones, vitamin D, and bile salts.

Plasma Lipoproteins

Spherical complexes consisting of a hydrophobic core of cholesteryl esters and triacylglycerols enclosed by a monolayer of amphipathic phospholipids, unesterified cholesterol, and apolipoproteins that transport lipids through the bloodstream.

Fluid Mosaic Model

The model of biological membranes describing them as dynamic, two-dimensional fluid lipid bilayers within which integral and peripheral membrane proteins float and execute biological tasks.

Membrane Self-Sealing

The property of lipid bilayers to rapidly close punctures because exposed hydrophobic fatty acid chains spontaneously orient away from water to reform a continuous bilayer with hydrophilic polar head groups on the surface.

Lipogenesis

The biochemical pathway of triacylglycerol synthesis in liver or adipose tissue, occurring via the sequential acylation of glycerol-3-phosphate or dihydroxyacetone phosphate ($\text{DHAP}$) with three acyl-CoA molecules.

Phosphatidic Acid Phosphatase

The enzyme in lipogenesis that removes the phosphate group from phosphatidic acid to produce diacylglycerol ($\text{DAG}$), which can then be acylated to form a triacylglycerol.

Lipolysis

The hormone-stimulated enzymatic breakdown of triacylglycerols in adipocytes into free fatty acids and glycerol, mediated by cyclic $\text{AMP}$ ($\text{cAMP}$) activation of protein kinase and triacylglycerol lipase.

Carnitine Shuttle

The carrier mechanism that transfers fatty acyl groups from cytosolic acyl-CoA to carnitine, allowing them to cross the impermeable inner mitochondrial membrane into the matrix for $\beta$-oxidation.

$\beta$-Oxidation

The cyclical four-reaction mitochondrial pathway (dehydrogenation, hydration, dehydrogenation, thiolysis) that repeatedly removes two-carbon fragments from acyl-CoA as acetyl-CoA, generating $\text{FADH}_2$ and $\text{NADH}$.

Acyl-CoA Dehydrogenase

The initial enzyme of mitochondrial $\beta$-oxidation that removes hydrogen atoms from the $\alpha$ and $\beta$ carbons of acyl-CoA to yield trans-enoyl-CoA and $\text{FADH}_2$.

Thiolase

The enzyme that catalyzes the terminal step of each $\beta$-oxidation cycle, cleaving $\beta$-ketoacyl-CoA using $\text{CoASH}$ to release acetyl-CoA and a fatty acyl-CoA shortened by two carbons.

Ketone Bodies

Acetoacetate, $\beta$-hydroxybutyrate, and acetone; water-soluble molecules synthesized in liver mitochondria from excess acetyl-CoA that serve as alternative metabolic fuels during fasting or uncontrolled diabetes.

HMG-CoA Reductase

The rate-limiting enzyme of cholesterol biosynthesis that catalyzes the $\text{NADPH}$-dependent reduction of $\beta$-hydroxy-$\beta$-methylglutaryl-CoA ($\text{HMG-CoA}$) to mevalonate.

Squalene Synthase

The enzyme that catalyzes the reductive head-to-head condensation of two molecules of farnesyl pyrophosphate to yield squalene using $\text{NADPH}$.

Bile Acids

Steroid derivatives produced in the liver from cholesterol (such as cholic acid and glycocholate) that act as amphipathic detergents in the small intestine to emulsify fats and facilitate fat-soluble vitamin absorption.

Nitrogen Fixation

The biological reduction of inert atmospheric dinitrogen ($\text{N}_2$) into bioavailable ammonia ($\text{NH}_3$), catalyzed by prokaryotic nitrogenase complexes at the expense of metabolic energy ($\text{ATP}$) and reducing equivalents.

Nitrogenase Complex

A two-protein bacterial enzyme complex composed of nitrogenase reductase (a $60\,\text{kD}$ iron protein dimer) and nitrogenase (a $240\,\text{kD}$ molybdenum-iron tetramer) that carries out the reaction $\text{N}_2 + 6\text{H}^+ + 6\text{e}^- \rightarrow 2\text{NH}_3$.

Leghemoglobin

An oxygen-binding hemoprotein synthesized in the root nodules of nitrogen-fixing legumes that sequesters molecular oxygen to shield the oxygen-labile nitrogenase complex from inactivation.

Essential Amino Acids

Amino acids that animals cannot synthesize de novo and must acquire from their diet: isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, and conditionally arginine and histidine.

Transamination

A reversible reaction catalyzed by aminotransferases (transaminases) in which the $\alpha$-amino group of an amino acid is transferred to an $\alpha$-keto acid, predominantly using the glutamate/$\alpha$-ketoglutarate pair.

Glutamate Dehydrogenase

The enzyme that catalyzes the reversible reductive amination of $\alpha$-ketoglutarate with free ammonium ($\text{NH}_4^+$) using $\text{NAD(P)H}$ to form glutamate.

Glutamine Synthetase

The enzyme that catalyzes the ATP-dependent amidation of glutamate with free ammonium ($\text{NH}_4^+$) to produce glutamine, a central nitrogen donor in metabolism.

Catecholamines

A class of tyrosine-derived amine neurotransmitters and hormones consisting of dopamine, norepinephrine (noradrenaline), and epinephrine (adrenaline).

$\gamma$-Aminobutyric Acid (GABA)

The primary inhibitory neurotransmitter in the vertebrate central nervous system, synthesized via the decarboxylation of glutamate catalyzed by glutamate decarboxylase.

Serotonin

A biogenic amine neurotransmitter (5-hydroxytryptamine) synthesized from tryptophan via 5-hydroxytryptophan that regulates mood, sleep, and feeding behaviors.

Histamine

A biogenic amine produced by the decarboxylation of histidine that acts as a neurotransmitter in the brain, stimulates gastric acid secretion, and mediates allergic and inflammatory responses.

Nitric Oxide

A short-lived gaseous signaling messenger synthesized from arginine that induces blood vessel vasodilation, suppresses platelet aggregation, and participates in macrophage immune destruction.