Catabolism in the context of Biliverdin

Fermentation is a type of anaerobic metabolism that harnesses the redox potential of the reactants to make adenosine triphosphate (ATP) and organic end products. Organic molecules, such as glucose or other sugars, are catabolized and their electrons are transferred to other organic molecules (cofactors, coenzymes, etc.). Anaerobic glycolysis is a related term used to describe the occurrence of fermentation in organisms (usually multicellular organisms such as animals) when aerobic respiration cannot keep up with the ATP demand, due to insufficient oxygen supply or anaerobic conditions.

Fermentation is important in several areas of human society. Humans have used fermentation in the production and preservation of food for 13,000 years. It has been associated with health benefits, unique flavor profiles, and making products have better texture. Humans and their livestock also benefit from fermentation from the microbes in the gut that release end products that are subsequently used by the host for energy. Perhaps the most commonly known use for fermentation is at an industrial level to produce commodity chemicals, such as ethanol and lactate. Ethanol is used in a variety of alcoholic beverages (beers, wine, and spirits) while lactate can be neutralized to lactic acid and be used for food preservation, curing agent, or a flavoring agent.

An essential amino acid, or indispensable amino acid, is an amino acid that cannot be synthesized from scratch by the organism fast enough to supply its demand, and must therefore come from the diet. Of the 21 amino acids common to all life forms, the nine amino acids humans cannot synthesize are valine, isoleucine, leucine, methionine, phenylalanine, tryptophan, threonine, histidine, and lysine.

Six other amino acids are considered conditionally essential in the human diet, meaning their synthesis can be limited under special pathophysiological conditions, such as prematurity in the infant or individuals in severe catabolic distress. These six are arginine, cysteine, glycine, glutamine, proline, and tyrosine. Six amino acids are non-essential (dispensable) in humans, meaning they can be synthesized in sufficient quantities in the body. These six are alanine, aspartic acid, asparagine, glutamic acid, serine, and selenocysteine (considered the 21st amino acid). Pyrrolysine (considered the 22nd amino acid), which is proteinogenic only in certain microorganisms, is not used by and therefore non-essential for most organisms, including humans.

Digestion is the breakdown of large insoluble food compounds into small water-soluble components so that they can be absorbed into the blood plasma. In certain organisms, these smaller substances are absorbed through the small intestine into the blood stream. Digestion is a form of catabolism that is often divided into two processes based on how food is broken down: mechanical and chemical digestion. The term mechanical digestion refers to the physical breakdown of large pieces of food into smaller pieces which can subsequently be accessed by digestive enzymes. Mechanical digestion takes place in the mouth through mastication and in the small intestine through segmentation contractions. In chemical digestion, enzymes break down food into the small compounds that the body can use.

In the human digestive system, food enters the mouth and mechanical digestion of the food starts by the action of mastication (chewing), a form of mechanical digestion, and the wetting contact of saliva. Saliva, a liquid secreted by the salivary glands, contains salivary amylase, an enzyme which starts the digestion of starch in the food. The saliva also contains mucus, which lubricates the food; the electrolyte hydrogencarbonate (HCO₃), which provides the ideal conditions of pH for amylase to work; and other electrolytes (Na, K, Cl). About 30% of starch is hydrolyzed into disaccharide in the oral cavity (mouth). After undergoing mastication and starch digestion, the food will be in the form of a small, round slurry mass called a bolus. It will then travel down the esophagus and into the stomach by the action of peristalsis. Gastric juice in the stomach starts protein digestion. Gastric juice mainly contains hydrochloric acid and pepsin. In infants and toddlers, gastric juice also contains rennin to digest milk proteins. As the first two chemicals may damage the stomach wall, mucus and bicarbonates are secreted by the stomach. They provide a slimy layer that acts as a shield against the damaging effects of chemicals like concentrated hydrochloric acid while also aiding lubrication. Hydrochloric acid provides acidic pH for pepsin. At the same time protein digestion is occurring, mechanical mixing occurs by peristalsis, which is waves of muscular contractions that move along the stomach wall. This allows the mass of food to further mix with the digestive enzymes. Pepsin breaks down proteins into peptides or proteoses, which are further broken down into dipeptides and amino acids by enzymes in the small intestine. Studies suggest that increasing the number of chews per bite increases relevant gut hormones and may decrease self-reported hunger and food intake.

Insulin (/ˈɪn.sjʊ.lɪn/ ; from Latin insula 'island') is a peptide hormone produced by beta cells of the pancreatic islets encoded in humans by the insulin (INS) gene. It is the main anabolic hormone of the body. It regulates the metabolism of carbohydrates, fats, and protein by promoting the absorption of glucose from the blood into cells of the liver, fat, and skeletal muscles. In these tissues the absorbed glucose is converted into either glycogen, via glycogenesis, or fats (triglycerides), via lipogenesis; in the liver, glucose is converted into both. Glucose production and secretion by the liver are strongly inhibited by high concentrations of insulin in the blood. Circulating insulin also affects the synthesis of proteins in a wide variety of tissues. It is thus an anabolic hormone, promoting the conversion of small molecules in the blood into large molecules in the cells. Low insulin in the blood has the opposite effect, promoting widespread catabolism, especially of reserve body fat.

Beta cells are sensitive to blood sugar levels so that they secrete insulin into the blood in response to high level of glucose, and inhibit secretion of insulin when glucose levels are low. Insulin production is also regulated by glucose: high glucose promotes insulin production while low glucose levels lead to lower production. Insulin enhances glucose uptake and metabolism in the cells, thereby reducing blood sugar. Their neighboring alpha cells, by taking their cues from the beta cells, secrete glucagon into the blood in the opposite manner: increased secretion when blood glucose is low, and decreased secretion when glucose concentrations are high. Glucagon increases blood glucose by stimulating glycogenolysis and gluconeogenesis in the liver. The secretion of insulin and glucagon into the blood in response to the blood glucose concentration is the primary mechanism of glucose homeostasis.

Anabolism (/əˈnæbəlɪzəm/ ə-NAB-ə-liz-əm) is the set of metabolic pathways that construct macromolecules like DNA or RNA from smaller units. These reactions require energy, known also as an endergonic process. Anabolism is the building-up aspect of metabolism, whereas catabolism is the breaking-down aspect. Anabolism is usually synonymous with biosynthesis.

Biosynthesis, i.e., chemical synthesis occurring in biological contexts, is a term most often referring to multi-step, enzyme-catalyzed processes where chemical substances absorbed as nutrients (or previously converted through biosynthesis) serve as enzyme substrates, with conversion by the living organism either into simpler or more complex products. Examples of biosynthetic pathways include those for the production of amino acids, lipid membrane components, and nucleotides, but also for the production of all classes of biological macromolecules, and of acetyl-coenzyme A, adenosine triphosphate, nicotinamide adenine dinucleotide and other key intermediate and transactional molecules needed for metabolism. Thus, in biosynthesis, any of an array of compounds, from simple to complex, are converted into other compounds, and so it includes both the catabolism and anabolism (building up and breaking down) of complex molecules (including macromolecules). Biosynthetic processes are often represented via charts of metabolic pathways. A particular biosynthetic pathway may be located within a single cellular organelle (e.g., mitochondrial fatty acid synthesis pathways), while others involve enzymes that are located across an array of cellular organelles and structures (e.g., the biosynthesis of glycosylated cell surface proteins).

Apolipoprotein E (Apo-E) is a protein involved in the metabolism of fats in the body of mammals. A subtype is implicated in Alzheimer's disease and cardiovascular diseases. It is encoded in humans by the gene APOE.

Apo-E belongs to a family of fat-binding proteins called apolipoproteins. In the circulation, it is present as part of several classes of lipoprotein particles, including chylomicron remnants, VLDL, IDL, and some HDL. Apo-E interacts significantly with the low-density lipoprotein receptor (LDLR), which is essential for the normal processing (catabolism) of triglyceride-rich lipoproteins. In peripheral tissues, Apo-E is primarily produced by the liver and macrophages, and mediates cholesterol metabolism. In the central nervous system, Apo-E is mainly produced by astrocytes and transports cholesterol to neurons via Apo-E receptors, which are members of the low density lipoprotein receptor gene family. Apo-E is the principal cholesterol carrier in the brain. Apo-E qualifies as a checkpoint inhibitor of the classical complement pathway by complex formation with activated C1q.

A peroxisome (/pəˈrɒksɪˌsoʊm/) is a membrane-bound organelle, a type of microbody, found in the cytoplasm of virtually all eukaryotic cells. Peroxisomes are oxidative organelles. Frequently, molecular oxygen serves as a co-substrate, from which hydrogen peroxide (H₂O₂) is then formed. Peroxisomes owe their name to hydrogen peroxide-generating and scavenging activities. They perform key roles in lipid metabolism and the reduction of reactive oxygen species.

Peroxisomes are involved in the catabolism of very long chain fatty acids, branched chain fatty acids, bile acid intermediates (in the liver), D-amino acids, and polyamines. Peroxisomes also play a role in the biosynthesis of plasmalogens: ether phospholipids critical for the normal function of mammalian brains and lungs. Peroxisomes contain approximately 10% of the total activity of two enzymes (Glucose-6-phosphate dehydrogenase and 6-Phosphogluconate dehydrogenase) in the pentose phosphate pathway, which is important for energy metabolism. It is debated whether peroxisomes are involved in isoprenoid and cholesterol synthesis in animals. Other peroxisomal functions include the glyoxylate cycle in germinating seeds ("glyoxysomes"), photorespiration in leaves, glycolysis in trypanosomes ("glycosomes"), and methanol and amine oxidation and assimilation in some yeasts.

Carbohydrate metabolism is the whole of the biochemical processes responsible for the metabolic formation, breakdown, and interconversion of carbohydrates in living organisms.

Carbohydrates are central to many essential metabolic pathways. Plants synthesize carbohydrates from carbon dioxide and water through photosynthesis, allowing them to store energy absorbed from sunlight internally. When animals and fungi consume plants, they use cellular respiration to break down these stored carbohydrates to make energy available to cells. Both animals and plants temporarily store the released energy in the form of high-energy molecules, such as adenosine triphosphate (ATP), for use in various cellular processes.

Studies that are in vivo (Latin for "within the living"; often not italicized in English) are those in which the effects of various biological entities are tested on whole, living organisms or cells, usually animals, including humans, and plants, as opposed to a tissue extract or dead organism.

Examples of investigations in vivo include: the pathogenesis of disease by comparing the effects of bacterial infection with the effects of purified bacterial toxins; the development of non-antibiotics, antiviral drugs, and new drugs generally; and new surgical procedures. Consequently, animal testing and clinical trials are major elements of in vivo research. In vivo testing is often employed over in vitro because it is better suited for observing the overall effects of an experiment on a living subject. In drug discovery, for example, verification of efficacy in vivo is crucial, because in vitro assays can sometimes yield misleading results with drug candidate molecules that are irrelevant in vivo (e.g., because such molecules cannot reach their site of in vivo action, for example as a result of rapid catabolism in the liver).

Coenzyme A (CoA, SHCoA, CoASH) is a coenzyme, notable for its role in the synthesis and oxidation of fatty acids, and the oxidation of pyruvate in the citric acid cycle. All genomes sequenced to date encode enzymes that use coenzyme A as a substrate, and around 4% of cellular enzymes use it (or a thioester) as a substrate. In humans, CoA biosynthesis requires cysteine, pantothenate (vitamin B₅), and adenosine triphosphate (ATP).

In its acetyl form, coenzyme A is a highly versatile molecule, serving metabolic functions in both the anabolic and catabolic pathways. Acetyl-CoA is utilised in the post-translational regulation and allosteric regulation of pyruvate dehydrogenase and carboxylase to maintain and support the partition of pyruvate synthesis and degradation.

Septic drain fields, also called leach fields or leach drains, are subsurface wastewater disposal facilities used to remove contaminants and impurities from the liquid that emerges after anaerobic digestion in a septic tank. Organic materials in the liquid are catabolized by a microbial ecosystem.

A septic drain field, a septic tank, and associated piping compose a septic system.

Phototrophs (from Ancient Greek φῶς, φωτός (phôs, phōtós) 'light' and τροφή (trophḗ) 'nourishment') are organisms that carry out photon capture to acquire energy. They use the energy from light to carry out various cellular metabolic processes. It is a common misconception that phototrophs are obligatorily photosynthetic. Many, but not all, phototrophs photosynthesize: they anabolically convert carbon dioxide into biomolecules to be utilized structurally (e.g. cellulose and membrane lipids), functionally (e.g. vitamins, nucleotides, and amino acids), or as a source for later catabolic processes (e.g. starches, sugars and fats). All phototrophs either use electron transport chains or direct proton pumping to establish an electrochemical gradient, which is utilized by ATP synthase to provide adenosine triphosphate (ATP) for the cell. Phototrophs can be either autotrophs or heterotrophs. If their electron and hydrogen donors are inorganic compounds (e.g., Na
₂S
₂O
₃, as in some purple sulfur bacteria, or H
₂S, as in some green sulfur bacteria) they can be also called lithotrophs, and so, some photoautotrophs are also called photolithoautotrophs. Examples of phototroph organisms are Rhodobacter capsulatus, Chromatium, and Chlorobium.

Lithotrophs are a diverse group of organisms using an inorganic substrate (usually of mineral origin) to obtain reducing equivalents for use in biosynthesis (e.g., carbon dioxide fixation) or energy conservation (i.e., ATP production) via aerobic or anaerobic respiration. While lithotrophs in the broader sense include photolithotrophs like plants, chemolithotrophs are exclusively microorganisms; no known macrofauna possesses the ability to use inorganic compounds as electron sources. Macrofauna and lithotrophs can form symbiotic relationships, in which case the lithotrophs are called "prokaryotic symbionts". An example of this is chemolithotrophic bacteria in giant tube worms; or plastids, which are organelles within plant cells that may have evolved from photolithotrophic cyanobacteria-like organisms. Chemolithotrophs belong to the domains Bacteria and Archaea. The term "lithotroph" was created from the Greek terms 'lithos' (rock) and 'troph' (consumer), meaning "eaters of rock". Many but not all lithoautotrophs are extremophiles.

The last universal common ancestor of life is thought to be a chemolithotroph. Different from a lithotroph is an organotroph, an organism which obtains its reducing agents from the catabolism of organic compounds.

The pentose phosphate pathway (also called the phosphogluconate pathway and the hexose monophosphate shunt or HMP shunt) is a metabolic pathway parallel to glycolysis. It generates NADPH and pentoses (five-carbon sugars) as well as ribose 5-phosphate, a precursor for the synthesis of nucleotides. While the pentose phosphate pathway does involve oxidation of glucose, its primary role is anabolic rather than catabolic. The pathway is especially important in red blood cells (erythrocytes). The reactions of the pathway were elucidated in the early 1950s by Bernard Horecker and co-workers.

There are two distinct phases in the pathway. The first is the oxidative phase, in which NADPH is generated, and the second is the non-oxidative synthesis of five-carbon sugars. For most organisms, the pentose phosphate pathway takes place in the cytosol; in plants, most steps take place in plastids.

Methanogens are anaerobic archaea that produce methane as a byproduct of their energy metabolism, i.e., catabolism. Methane production, or methanogenesis, is the only biochemical pathway for ATP generation in methanogens. All known methanogens belong exclusively to the domain Archaea, although some bacteria, plants, and animal cells are also known to produce methane. However, the biochemical pathway for methane production in these organisms differs from that in methanogens and does not contribute to ATP formation. Methanogens belong to various phyla within the domain Archaea. Previous studies placed all known methanogens into the superphylum Euryarchaeota. However, recent phylogenomic data have led to their reclassification into several different phyla. Methanogens are common in various anoxic environments, such as marine and freshwater sediments, wetlands, the digestive tracts of animals, wastewater treatment plants, rice paddy soil, and landfills. While some methanogens are extremophiles, such as Methanopyrus kandleri, which grows between 84 and 110 °C, or Methanonatronarchaeum thermophilum, which grows at a pH range of 8.2 to 10.2 and a Na concentration of 3 to 4.8 M, most of the isolates are mesophilic and grow around neutral pH.