Catabolism: Principles and Types

• This text is study note for catabolism

Metabolism and Nutrition

• Metabolism involves all the chemical transformations within an organism's cells, a coordinated cellular activity with interconnected chemical reactions known as metabolic pathways.
• Metabolism has two key processes: catabolism and anabolism, which occur simultaneously within cells.

Catabolism: Principles

• Catabolism is the step involving the breaking down of organic compounds through oxidation into simpler molecules, generating energy for cellular work and anabolism with two processes: respiration and fermentation
• Respiration involves the complete oxidation of an organic molecule, differentiated by the final electron acceptor, with two variants:

Aerobic respiration

• Aerobic respiration uses molecular oxygen as the final electron acceptor, which is reduced to water.

Anaerobic respiration

• Anaerobic respiration uses an inorganic molecule (e.g., sulfates or nitrates) as the final electron acceptor, utilized by certain bacteria and presenting lower energy efficiency than aerobic respiration.

Fermentation

• Fermentation involves partial oxidation of organic molecules.
• Anabolism is the process of biosynthesis where simple molecules are reduced to form complex ones.
• Biomolecules synthesized during anabolism are used for growth, cellular renewal, and storage for later catabolism.

Types of Metabolism

• Organisms can have different types of nutrition based on their carbon and energy sources.
• Based on carbon source, organisms are divided into autotrophs (using inorganic compounds like CO2) and heterotrophs (using organic molecules).
• Based on energy source, organisms are classified as phototrophs (using light) and chemotrophs (using chemical compounds).
• Photoautotrophs use CO2 as a carbon source and light as an energy source, like photosynthetic bacteria and plants.
• Chemoautotrophs use CO2 as a carbon source and inorganic compounds as an energy source, like certain bacteria and archaea.
• Photoheterotrophs use organic molecules as a carbon source and light as an energy source, like nonsulfur red and green bacteria.
• Chemoheterotrophs use organic molecules as both carbon and energy sources, like heterotrophic prokaryotes, protozoa, chromists, fungi, and animals.

Catabolism: General Information

• Catabolism involves degradative oxidation reactions requiring initial organic compounds and a final electron acceptor.
• End Result: producing ATP for anabolic processes.

ATP and NADH

• Catabolic reactions are powered by the chemical energy from biomolecules such as NADH, NADPH, and FADH2, which supply redox energy.
• Oxidation-reduction reactions are central to catabolism, happening simultaneously and paired:
  • Oxidation involves a compound losing electrons (and sometimes hydrogens).
  • Reduction involves a compound gaining electrons (and sometimes hydrogens).
  • During catabolism, substrate oxidation is linked to the reduction of coenzymes NAD+ and FAD into NADH and FADH2.
  • Anabolism requires the electrons from the reduced coenzymes NADH and FADH2, synthesized during catabolic reactions.
• Nucleotide triphosphates, like ATP, store significant energy in the bonds between their phosphate groups.
• ATP synthesis is energetically unfavorable and relies on energy coupling from catabolic reactions, while ATP reserves last briefly, requiring continuous synthesis.
• ATP hydrolysis, is used to power endergonic reactions.

Synthesis of ATP

• ATP synthesis occurs through:
  • Oxidative phosphorylation is coupled with the mitochondrial electron transport chain and the light phase of photosynthesis.
  • ATP synthases (ATPases) facilitate ATP synthesis by using the energy from H⁺ flow down its gradient to phosphorylate ADP.
  • Substrate-level phosphorylation, ATP is synthesized through direct coupling with highly exergonic catabolic reactions, such as those in glycolysis and the Krebs cycle, and it’s the only method in anaerobic conditions.

General Scheme of Catabolism

• Catabolism involves different catabolic rection inside of a cell.

Glucose Catabolism

• Glucose, the primary monosaccharide, is mostly used to get energy from catabolic paths
• Energy from glucose is obtained through respiration or fermentation, both starting with glycolysis but diverging afterward.

Aerobic Catabolism of Glucose

• Catabolism of glucose via aerobic respiration transfers electrons from glucose to CO2 and H2O, paired with ATP synthesis.
• This process includes glycolysis, the Krebs cycle, and the respiratory chain.
• Glycolysis occurs in the cytoplasm of both prokaryotic and eukaryotic cells, is a metabolic pathway that does not require oxygen.
• Glucose (6 carbon atoms) is oxidized to two pyruvate molecules (3 carbon atoms each), ATP, and reduced coenzymes (NADH).
• Glycolysis happens in two phases:
  • Preparatory Phase includes first 5 reactions which requires energy, supplied by two ATP molecules, to add phosphate groups to glucose allowing and scission into two molecules of glyceraldehyde 3-phosphate, which results in consuming two ATP molecules.
  • Benefit Phase includes the other 5 reactions, starting with two molecules of glyceraldehyde 3-phosphate. It leads to four molecules of ATP and two molecules of NADH + H+, with a net gain of two ATP molecules and two NADH + H+.
  • End Result: glucose turns into two molecules of pyruvic acid or pyruvate.
• Glycolysis Net result is: Glucose + 2 ADP + 2 Pi + 2 NAD -> 2 pyruvate + 2 ATP + 2 NADH + 2 H⁺ + 2 H2O
• Glycolysis yields net two ATP molecules per glucose molecule, produces two NADH molecules for ATP synthesis via the electron transport chain.
• For pyruvic acid or pyruvate can incorporate into Krebs cycle, it requires mitochondrial membranes transport to turn into acetyl-CoA.
• Pyruvate is transported into the mitochondrial matrix where oxidative decarboxylation occurs, catalyzed by pyruvate dehydrogenase, forming two NADH molecules.
• Krebs cycle oxidizes acetate completely into CO2, creates NADH and FADH2 for the mitochondrial electron transport chain and it requires 8 steps in the mitochondrial matrix of eukaryotes and the cytoplasm of prokaryotes.
• Acetyl-CoA (2 carbon atoms) combines with oxaloacetate (4 carbon atoms) to form citrate (6 carbon atoms).
• Carbons are released as CO2, regenerating oxaloacetate to continue process, one GTP molecule (convertible to ATP), 3 NADH, and 1 FADH2.
• Two pyruvic acids from glycolysis yield two acetyl-CoA molecules.
• Overall power yield is:
  • 2 GTP molecules
  • 6 NADH + H+ and 2 FADH2
  • 4 molecules of CO2
• Total oxaloacetate molecules are restored to begin a new cycle.

Electron Transport Chain

• Respiratory chain and oxidative phosphorylation are processes oriented to the ATP synthesis and work together, they occur in the plasma membrane of prokaryotes and the membrane of eukaryotes.
• Functions: regenerating oxidized forms of reduced coenzymes and and synthesizing ATP.
• Structure: formed by electronic transporters, are transmembrane porteins that carry metallic elements that creates an oxidation process that starts with coenzymes and results in oxygen molecules, creating water.
• Animal cells have 4 main complexes in its mitocondria:
  • Complex I (NADH-CoQ reductase or NADH dehydrogenase) transfers electrons from NADH to ubiquinone (coenzyme Q).
  • Malate-aspartate shuttle (in heart and liver) transports cytosolic NADH electrons to Complex I.
• Glycerol 3-phosphate shuttle (in skeletal muscle and brain) transfers electrons to ubiquinone, skipping Complex I.
• Complex II (succinate dehydrogenase) transfers electrons from FADH2 to ubiquinone.
• Complex III (ubiquinol-cytochrome c oxidoreductase) moves electrons from ubiquinone to cytochrome C.
• Complex IV (cytochrome oxidase) transfers electrons from cytochrome c to O2, producing water.
• O2 is the final e- acceptor which facilitates the oxidation of glucose with 90% of celular O2 consumption.
• Electron transport chain uses energy to pump protons (H+) across the inner mitochondrial membrane, building a electrochemical gradient, also know as proton motive force.
• Electrochemical gradient powers ATP phosphorylation.
• ATP synthase allows protons to enter mitocondrial matrix which dissipates the electrochemical gradient and facilitates the phosphorylation of ADP to ATP.
• Electrochemical gradient is formed thanks to the integrity of the mitocondrial membranes.

Energetic Performance of Aerobic Respiration

• Aerobic respiration of glucose is energy efficient that oxidates atoms to carbon dioaxide or CO2
• Oxidative phosphorylation yields three ATP molecules for each pair of electrons from NADH and two ATP molecules for electrons from FADH2.
  • Phase: Glycolysis, Location: Citoplasma, Reduced Coenzymes: 2NADH
  • Phase: Acetyil-CoA formation, Location: Mitocondria/Eucariota and Citoplasma/Procariota, Reduced Coenzymes 2NADH
  • Phase: Krebs Cycle, Location: Mitocondrial Matrix, Reduced Coenzymes: 6NADH 2FADH2
  • Result: 38 ATP
• Only two ATP and two GTP molecules come from substrate-level phosphorylation.

Anaerobic Catabolism: Fermentation

• Fermentation is anaerobic, with oxidation reactions in the absence of oxygen and being an unfinished oxidation of glucose.
• ATP synthesis happens in glucolysis (substrate level of phosphorylation)
• Gluclose fermentation begins with glucolysis. Power is generated in a form of NADH which created ATP.
• Glycolysis gets interrupted if NAD is not reducted.
• In fermentation the NADH that is reduced gets oxidated to NAD⁺, which turns into its reduction to pyruvate.
• It happens in two phases:
  • Oxidation- glucose is oxidated in pyruvate by glucolysis, consumption of NAD and production of ATP
  • Reduction- pyruvate gets reducted to produce the final products, NAD is regenerated.
• Most fermentations are completed bvy bacteria, some of them are strict anaerobic and they cannot tolerate oxygen while others are facultative.
• Major fermentations products are organic aides like acetyl aide. The most important fermentations are alcoholic and lacticacid fermentation.

Alcoholic Fermentation

• Pyruvate undergoes a breakdown to produce CO2 and acetaldehyde. Then it gest reduced with the NADH and as the end product ethanol is obtained.

Lactic Fermentation

• Pyruvate gets electrons from NADH that are converted in lactate which regenerating NAD. It is catalyzed by lactate dehydrogenase.
• Anaerobic bacteria does this in bacterium,