BIOCHEMISTRY (BIOENERGETICS)

Metabolism

The chemical processes used to synthesize complex molecules from basic precursor molecules (anabolism) and to break down complex molecules into less complex components (catabolism).

Anabolism

The process by which living organisms build complex molecules from simpler ones. It requires energy and is an endergonic process.

Catabolism

The process by which living organisms break down complex molecules into simpler ones. It releases energy and is an exergonic process.

ΔG (Change in Gibbs free energy)

A criterion used to predict whether a chemical reaction will be spontaneous. It measures the change in total free energy of a system as a result of a particular reaction.

ΔG°' (Change in Gibbs free energy under standard conditions)

The change in Gibbs free energy when all components of a reaction are present at their standard states.

Exergonic reaction

A reaction that releases Gibbs free energy, has a negative value for ΔG, and occurs spontaneously.

Endergonic reaction

A reaction that requires an input of Gibbs free energy, has a positive value for ΔG, and does not occur spontaneously.

Energy charge

The ratio of cellular ATP relative to AMP and ADP. Cells maintain the energy charge within a narrow range to determine whether ATP needs to be synthesized or is abundant and ready to be used.

Glycolysis

The first stage of cellular respiration that occurs in both aerobic and anaerobic conditions. It involves the breakdown of glucose into pyruvate, producing ATP and NADH.

Glycolytic pathway

The pathway consisting of three stages (priming, splitting, and oxidoreduction-phosphorylation) in glycolysis. Each stage involves specific enzymatic reactions.

TCA cycle

The tricarboxylic acid cycle, also known as the citric acid cycle or Krebs cycle. It is a series of enzyme-catalyzed reactions that occur in the presence of oxygen and oxidize acetyl CoA to produce CO2.

Acetyl CoA

A high-energy molecule that transfers acetyl groups in a similar way to ATP transferring phosphoryl groups.

Oxidative phosphorylation

The synthesis of ATP from ADP and Pi during the transport of electrons from NADH and FADH2 to oxygen.

Regulation of metabolism

The control of metabolic processes in living organisms. Prokaryotes regulate metabolism at the level of DNA transcription, while eukaryotes use enzyme control, differentiation of anabolic and catabolic pathways, and physical separation of metabolic pathways.

Energy requirements for metabolism

The energy needed for all metabolic processes in the human body, obtained through the oxidation of carbohydrates, fats, and proteins in food. Complex molecules are catabolized into simpler ones, which are then catabolized to common metabolic intermediates.

ATP

the main source of free energy in biochemical reactions. It is constantly being recycled to transmit free energy from one reaction to another.

Glycolysis

The process through which each glucose molecule is converted to two molecules of pyruvate.

Oxidative decarboxylation

The process in which two pyruvate molecules yield two CO2 molecules.

TCA cycle

The cycle in which two acetyl CoA molecules yield four CO2 molecules.

Pyruvate dehydrogenase

The enzyme that catalyzes the oxidative decarboxylation of pyruvate to CO2 and acetyl CoA.

NADH

The reduced form of NAD, located in the matrix of mitochondria.

Pyruvate dehydrogenase complex

A complex enzyme that contains three catalytic subunits:pyruvate dehydrogenase, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase.

Cofactors

Additional requirements for pyruvate dehydrogenase, including CoA and NAD.

Pyruvate dehydrogenase regulation

The activity of pyruvate dehydrogenase is inhibited by elevated concentrations of NADH, acetyl CoA, and GTP, and is activated by AMP.

Phosphorylation

In mammals, pyruvate dehydrogenase is inhibited via phosphorylation, a covalent modification.

TCA cycle intermediates

The TCA cycle has no ultimate products, but the intermediates serve as building blocks for other biosynthetic reactions.

Citrate Synthase

The enzyme that catalyzes the condensation of acetyl CoA and oxaloacetate to form citrate.

Aconitase

The enzyme that catalyzes the isomerization of citrate to isocitrate via the enzyme-bound intermediate, cis-aconitate.

Isocitrate dehydrogenase

The enzyme that catalyzes the oxidative decarboxylation of isocitrate to alpha-ketoglutarate and CO2.

Alpha-ketoglutarate dehydrogenase

The enzyme that oxidatively decarboxylates alpha-ketoglutarate to CO2 and succinate.

Succinyl CoA synthetase

The enzyme that hydrolyzes the high-energy thioester bond of succinyl CoA to form succinate and CoA, releasing energy for substrate-level phosphorylation.

Succinate dehydrogenase

The enzyme that catalyzes the oxidation of succinate to fumarate.

Fumarase

The enzyme that catalyzes the hydration of fumarate to form malate.

Malate dehydrogenase

The enzyme that catalyzes the oxidation of malate to oxaloacetate, completing the cycle.

Glyoxylate cycle

An anabolic pathway that is a modified form of the TCA cycle and enables plants and bacteria to use acetate or other compounds to generate energy and provide biosynthetic products.

Respiratory chain

A series of enzymatic reactions that occur in aerobic organisms and transfer electrons, ultimately forming water.

Oxidative phosphorylation

The process in which ATP is produced as electrons are shuttled through the respiratory chain to molecular oxygen, forming water.

ATP synthetase/ATPase

The enzyme complex that links the movement of protons back into the mitochondrial matrix to the synthesis and release of ATP from ADP and Pi.

Energetics of oxidative phosphorylation

The complete oxidation of glucose to CO2 and water yields either 38 or 36 molecules of ATP, depending on how the NADH produced in glycolysis is transported into the mitochondria.

Respiratory chain components

The respiratory chain consists of different complexes, including proteins that act as enzymes in electron transfer and cytochromes, which are electron-transferring proteins with a heme prosthetic group.

NADH-CoQ reductase

The enzyme complex that catalyzes electron flow between NADH and CoQ, transferring electrons and acting as a proton pump.

Cytochrome reductase

The enzyme complex that catalyzes electron flow between CoQ and Cyt c, transferring electrons and acting as a proton pump.

Cytochrome oxidase

The enzyme complex that catalyzes electron flow between Cyt c and O2, forming H2O as the terminal electron acceptor.

CoQH2

The reduced compound of CoQ, formed when CoQ accepts electrons.

Ubiquinone

Another name for the oxidized form of CoQ.

Ubiquino

Another name for the reduced compound of CoQ, CoQH2.

Cyt b

A protein that transfers electrons to heme groups and donates electrons to QH, reducing to CoQH2. It acts as an electron recycling device in the respiratory chain.

Cytochrome oxidase complex

The third enzyme complex in the respiratory chain that transfers electrons from Cyt c to O2, forming H2O. It is responsible for the last proton pump.

Proton-motive force

The difference in electrical potential and pH between the matrix and intermembrane space of the mitochondria, generated by the movement of electrons through the respiratory chain. It drives the production of ATP.

Glycerol phosphate shuttle

A shuttle mechanism that transfers electrons from cytosolic NADH to FAD in the mitochondria, producing FADH2. It yields two molecules of ATP per NADH.

Malate aspartate shuttle

A shuttle mechanism that transfers electrons from cytosolic NADH to NADH-CoQ reductase in the mitochondria, producing NADH. It yields three molecules of ATP per NADH.

Respiratory control

The phenomenon where electrons are transferred in the respiratory chain only when ATP is needed. It regulates the rate of oxidative phosphorylation.

Chemiosmotic theory

Describes how the proton gradient between the mitochondrial matrix and intermembrane space leads to the production of ATP. It involves H+ pumping, pH gradient, and membrane electrical potential.

P:O ratio

The number of molecules of inorganic phosphate incorporated into ADP per atom of oxygen consumed. It is an index of oxidative phosphorylation.

Respiratory chain inhibitors

Compounds that block the H+ pumping sites in the respiratory chain. Examples include rotenone, amytal, antimycin A, cyanide, azide, and carbon monoxide.

Uncouplers

Substances that increase the H+ permeability of the inner mitochondrial membrane, dissipating the pH gradient required for ATP synthesis. Examples include 2,4-dinitrophenol and dicumarol.

net production in glycolysis

The net production in glycolysis is 2 ATP molecules, 2 NADH molecules, and 2 pyruvate molecules.

net production in TCA Cycle or Krebs Cycle

The net production in the TCA Cycle, also known as the Krebs Cycle, includes the following:

• 3 NADH molecules

• 1 FADH2 molecule

• 1 ATP molecule

• 2 CO2 molecules

These products are generated per one round of the TCA Cycle.