Catabolism

Catabolism (from Greek κάτω kato, "downward" and βάλλειν ballein, "to throw") is the set of metabolic pathways that breaks down molecules into smaller units that are either oxidized to release energy or used in other anabolic reactions.[1] Catabolism breaks down large molecules (such as polysaccharides, lipids, nucleic acids and proteins) into smaller units (such as monosaccharides, fatty acids, nucleotides, and amino acids, respectively).

Cells use the monomers released from breaking down polymers to either construct new polymer molecules, or degrade the monomers further to simple waste products, releasing energy. Cellular wastes include lactic acid, acetic acid, carbon dioxide, ammonia, and urea. The creation of these wastes is usually an oxidation process involving a release of chemical free energy, some of which is lost as heat, but the rest of which is used to drive the synthesis of adenosine triphosphate (ATP). This molecule acts as a way for the cell to transfer the energy released by catabolism to the energy-requiring reactions that make up anabolism. (Catabolism is seen as destructive metabolism and anabolism as constructive metabolism). Catabolism therefore provides the chemical energy necessary for the maintenance and growth of cells. Examples of catabolic processes include glycolysis, the citric acid cycle, the breakdown of muscle protein in order to use amino acids as substrates for gluconeogenesis, the breakdown of fat in adipose tissue to fatty acids, and oxidative deamination of neurotransmitters by monoamine oxidase.

Catabolic hormones

There are many signals that control catabolism. Most of the known signals are hormones and the molecules involved in metabolism itself. Endocrinologists have traditionally classified many of the hormones as anabolic or catabolic, depending on which part of metabolism they stimulate. The so-called classic catabolic hormones known since the early 20th century are cortisol, glucagon, and adrenaline (and other catecholamines). In recent decades, many more hormones with at least some catabolic effects have been discovered, including cytokines, orexin (also known as hypocretin), and melatonin.

Catabolism schematic
Schematical diagram

See also

References

  1. ^ de Bolster, M.W.G. (1997). "Glossary of Terms Used in Bioinorganic Chemistry: Catabolism". International Union of Pure and Applied Chemistry. Archived from the original on 2017-01-21. Retrieved 2007-10-30.

External links

2-hydroxyphytanoyl-CoA lyase

2-Hydroxyphytanoyl-CoA lyase is a peroxisomal enzyme involved in the catabolism of phytanoic acid by α-oxidation. It requires thiamine diphosphate (ThDP) as cofactor.It is classified under EC number 4.1.

Amino acid

Amino acids are organic compounds containing amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) specific to each amino acid. The key elements of an amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), although other elements are found in the side chains of certain amino acids. About 500 naturally occurring amino acids are known (though only 20 appear in the genetic code) and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid residues form the second-largest component (water is the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis.

In biochemistry, amino acids having both the amine and the carboxylic acid groups attached to the first (alpha-) carbon atom have particular importance. They are known as 2-, alpha-, or α-amino acids (generic formula H2NCHRCOOH in most cases, where R is an organic substituent known as a "side chain"); often the term "amino acid" is used to refer specifically to these. They include the 22 proteinogenic ("protein-building") amino acids, which combine into peptide chains ("polypeptides") to form the building-blocks of a vast array of proteins. These are all L-stereoisomers ("left-handed" isomers), although a few D-amino acids ("right-handed") occur in bacterial envelopes, as a neuromodulator (D-serine), and in some antibiotics.Twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as "standard" amino acids. The other two ("non-standard" or "non-canonical") are selenocysteine (present in many prokaryotes as well as most eukaryotes, but not coded directly by DNA), and pyrrolysine (found only in some archea and one bacterium). Pyrrolysine and selenocysteine are encoded via variant codons; for example, selenocysteine is encoded by stop codon and SECIS element. N-formylmethionine (which is often the initial amino acid of proteins in bacteria, mitochondria, and chloroplasts) is generally considered as a form of methionine rather than as a separate proteinogenic amino acid. Codon–tRNA combinations not found in nature can also be used to "expand" the genetic code and form novel proteins known as alloproteins incorporating non-proteinogenic amino acids.Many important proteinogenic and non-proteinogenic amino acids have biological functions. For example, in the human brain, glutamate (standard glutamic acid) and gamma-amino-butyric acid ("GABA", non-standard gamma-amino acid) are, respectively, the main excitatory and inhibitory neurotransmitters. Hydroxyproline, a major component of the connective tissue collagen, is synthesised from proline. Glycine is a biosynthetic precursor to porphyrins used in red blood cells. Carnitine is used in lipid transport.

Nine proteinogenic amino acids are called "essential" for humans because they cannot be produced from other compounds by the human body and so must be taken in as food. Others may be conditionally essential for certain ages or medical conditions. Essential amino acids may also differ between species.Because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, feed, and food technology. Industrial uses include the production of drugs, biodegradable plastics, and chiral catalysts.

Bilirubin

Bilirubin is a yellow compound that occurs in the normal catabolic pathway that breaks down heme in vertebrates. This catabolism is a necessary process in the body's clearance of waste products that arise from the destruction of aged red blood cells. First the hemoglobin gets stripped of the heme molecule which thereafter passes through various processes of porphyrin catabolism, depending on the part of the body in which the breakdown occurs. For example, the molecules excreted in the urine differ from those in the feces. The production of biliverdin from heme is the first major step in the catabolic pathway, after which the enzyme biliverdin reductase performs the second step, producing bilirubin from biliverdin.

Bilirubin is excreted in bile and urine, and elevated levels may indicate certain diseases. It is responsible for the yellow color of bruises and the yellow discoloration in jaundice. Its subsequent breakdown products, such as stercobilin, cause the brown color of faeces. A different breakdown product, urobilin, is the main component of the straw-yellow color in urine.

It has also been found in plants.

Biological process

Biological processes are the processes vital for a living organism to live. Biological processes are made up of many chemical reactions or other events that are involved in the persistence and transformation of life forms. Metabolism and homeostasis are examples.

Regulation of biological processes occurs when any process is modulated in its frequency, rate or extent. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. Mamel

Homeostasis: regulation of the internal environment to maintain a constant state; for example, sweating to reduce temperature

Organization: being structurally composed of one or more cells – the basic units of life

Metabolism: transformation of energy by converting chemicals and energy into cellular components (anabolism) and decomposing organic matter (catabolism). Living things require energy to maintain internal organization (homeostasis) and to produce the other phenomena associated with life.

Growth: maintenance of a higher rate of anabolism than catabolism. A growing organism increases in size in all of its parts, rather than simply accumulating matter.

Adaptation: the ability to change over time in response to the environment. This ability is fundamental to the process of evolution and is determined by the organism's heredity, diet, and external factors.

Response to stimuli: a response can take many forms, from the contraction of a unicellular organism to external chemicals, to complex reactions involving all the senses of multicellular organisms. A response is often expressed by motion; for example, the leaves of a plant turning toward the sun (phototropism), and chemotaxis.

Reproduction: the ability to produce new individual organisms, either asexually from a single parent organism or sexually from two parent organisms.

Interaction between organisms. the processes by which an organism has an observable effect on another organism of the same or different species.

Also: cellular differentiation, fermentation, fertilisation, germination, tropism, hybridisation, metamorphosis, morphogenesis, photosynthesis, transpiration.

Carbohydrate catabolism

Digestion is the breakdown of carbohydrates to yield an energy rich compound called ATP. The production of ATP is achieved through the oxidation of glucose molecules. In oxidation, the electrons are stripped from a glucose molecule to reduce NAD+ and FAD. NAD+ and FAD possess a high energy potential to drive the production of ATP in the electron transport chain. ATP production occurs in the mitochondria of the cell. There are two methods of producing ATP: aerobic and anaerobic.

In aerobic respiration, oxygen is required. Oxygen plays a key role as it increases ATP production from 4 ATP molecules to about 30 ATP molecules.

In anaerobic respiration, oxygen is not required. When oxygen is absent, the generation of ATP continues through fermentation.There are two types of fermentation: alcohol fermentation and lactic acid fermentation.

There are several different types of carbohydrates: polysaccharides (e.g., starch, amylopectin, glycogen, cellulose), monosaccharides (e.g., glucose, galactose, fructose, ribose) and the disaccharides (e.g., sucrose, maltose, lactose).

Glucose reacts with oxygen in the following redox reaction, C6H12O6 + 6O2 → 6CO2 + 6H2O, Carbon dioxide and water are waste products, and the overall reaction is exothermic.

The breakdown of glucose into energy in the form of molecules of ATP is therefore one of the most important biochemical pathways found in living organisms.

Carboxypeptidase

A carboxypeptidase (EC number 3.4.16 - 3.4.18) is a protease enzyme that hydrolyzes (cleaves) a peptide bond at the carboxy-terminal (C-terminal) end of a protein or peptide. (Contrast with an aminopeptidase, which cleaves peptide bonds at the other end of the protein.) Humans, animals, and plants contain several types of carboxypeptidases that have diverse functions ranging from catabolism to protein maturation.

Cysteine metabolism

Cysteine metabolism refers to the biological pathways that consume or create cysteine. The pathways of different amino acids and other metabolites interweave and overlap to creating complex systems.

Fatty acid metabolism

Fatty acid metabolism consists of catabolic processes that generate energy, and anabolic processes that create biologically important molecules (triglycerides, phospholipids, second messengers, local hormones and ketone bodies).Fatty acids are a family of molecules classified within the lipid macronutrient class. One role of fatty acids in animal metabolism is energy production, captured in the form of adenosine triphosphate (ATP). When compared to other macronutrient classes (carbohydrates and protein), fatty acids yield the most ATP on an energy per gram basis, when they are completely oxidized to CO2 and water by beta oxidation and the citric acid cycle. Fatty acids (mainly in the form of triglycerides) are therefore the foremost storage form of fuel in most animals, and to a lesser extent in plants. In addition, fatty acids are important components of the phospholipids that form the phospholipid bilayers out of which all the membranes of the cell are constructed (the cell wall, and the membranes that enclose all the organelles within the cells, such as the nucleus, the mitochondria, endoplasmic reticulum, and the Golgi apparatus). Fatty acids can also be cleaved, or partially cleaved, from their chemical attachments in the cell membrane to form second messengers within the cell, and local hormones in the immediate vicinity of the cell. The prostaglandins made from arachidonic acid stored in the cell membrane, are probably the most well known group of these local hormones.

Galactolysis

Galactolysis refers to the catabolism of galactose.

In the liver, galactose is converted through the Leloir pathway to glucose 6-phosphate in the following reactions:

galacto- uridyl phosphogluco-

kinase transferase mutase

gal --------> gal 1 P ------------------> glc 1 P -----------> glc 6 P

^ \

/ v

UDP-glc UDP-gal

^ /

\___________/

epimerase

Glutamate formimidoyltransferase

Glutamate formimidoyltransferase is a methyltransferase enzyme which uses tetrahydrofolate as part of histidine catabolism. It catalyses two reactions:

5-formimidoyltetrahydrofolate + L-glutamate <=> tetrahydrofolate + N-formimidoyl-L-glutamate

5-formyltetrahydrofolate + L-glutamate <=> tetrahydrofolate + N-formyl-L-glutamateIt is classified under EC 2.1.2.5 and in mammals is found as part of a bifunctional enzyme that also has formimidoyltetrahydrofolate cyclodeaminase activity.

HMOX1

HMOX1 (heme oxygenase (decycling) 1) is a human gene that encodes for the enzyme heme oxygenase 1 (EC 1.14.99.3). Heme oxygenase mediates the first step of heme catabolism, it cleaves heme to form biliverdin.

Heme oxygenase, an essential enzyme in heme catabolism, cleaves heme to form biliverdin, carbon monoxide, and ferrous iron. The biliverdin is subsequently converted to bilirubin by biliverdin reductase. Heme oxygenase activity is induced by its substrate heme and by various nonheme substances. Heme oxygenase occurs as 2 isozymes, an inducible heme oxygenase-1 and a constitutive heme oxygenase-2. HMOX1 and HMOX2 belong to the heme oxygenase family.The HMOX gene is located on the long (q) arm of chromosome 22 at position 12.3, from base pair 34,101,636 to base pair 34,114,748.

In vivo

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. This is not to be confused with experiments done in vitro ("within the glass"), i.e., in a laboratory environment using test tubes, Petri dishes, etc. 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).The English microbiologist Professor Harry Smith and his colleagues in the mid-1950s found that sterile filtrates of serum from animals infected with Bacillus anthracis were lethal for other animals, whereas extracts of culture fluid from the same organism grown in vitro were not. This discovery of anthrax toxin through the use of in vivo experiments had a major impact on studies of the pathogenesis of infectious disease.

The maxim in vivo veritas ("in a living thing [there is] truth") is used to describe this type of testing and is a play on in vino veritas, ("in wine [there is] truth"), a well-known proverb.

L-threonine dehydrogenase

L-Threonine dehydrogenase is an enzyme that facilitates the catabolism of threonine. It catalyses its conversion to glycine via 2-amino-3-ketobutyrate with concomitant reduction of NAD+.

Lysine

Lysine (symbol Lys or K) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated −NH3+ form under biological conditions), an α-carboxylic acid group (which is in the deprotonated −COO− form under biological conditions), and a side chain lysyl ((CH2)4NH2), classifying it as a basic, charged (at physiological pH), aliphatic amino acid. It is encoded by the codons, AAA and AAG. Like almost all other amino acids, the α-carbon is chiral and lysine may refer to either enantiomer or a racemic mixture of both. For the purpose of this article, lysine will refer to the biologically active enantiomer L-lysine, where the α-carbon is in the S configuration.

The human body cannot synthesize lysine, so it is essential in humans and must be obtained from the diet. In organisms that synthesise lysine, it has two main biosynthetic pathways, the diaminopimelate and α-aminoadipate pathways, which employ different enzymes and substrates and are found in different organisms. Lysine catabolism occurs through one of several pathways, the most common of which is the saccharopine pathway.

Lysine plays several roles in humans, most importantly proteinogenesis, but also in the crosslinking of collagen polypeptides, uptake of essential mineral nutrients, and in the production of carnitine, which is key in fatty acid metabolism. Lysine is also often involved in histone modifications, and thus, impacts the epigenome. The ε-amino group often participates in hydrogen bonding and as a general base in catalysis. The ε-ammonium group (NH3+) is attached to the fourth carbon from the α-carbon, which is attached to the carboxyl (C=OOH) group.Due to its importance in several biological processes, a lack of lysine can lead to several disease states including defective connective tissues, impaired fatty acid metabolism, anaemia, and systemic protein-energy deficiency. In contrast, an overabundance of lysine, caused by ineffective catabolism, can cause severe neurological issues.

Lysine was first isolated by the German biological chemist Ferdinand Heinrich Edmund Drechsel in 1889 from the protein casein in milk. He named it "lysin". In 1902, the German chemists Emil Fischer and Fritz Weigert determined lysine's chemical structure by synthesizing it.

Metabolic pathway

In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reactions catalyzed by enzymes. In most cases of a metabolic pathway, the product of one enzyme acts as the substrate for the next. However, side products are considered waste and removed from the cell. These enzymes often require dietary minerals, vitamins, and other cofactors to function.

Different metabolic pathways function based on the position within a eukaryotic cell and the significance of the pathway in the given compartment of the cell. For instance, the citric acid cycle, electron transport chain, and oxidative phosphorylation all take place in the mitochondrial membrane. In contrast, glycolysis, pentose phosphate pathway, and fatty acid biosynthesis all occur in the cytosol of a cell.There are two types of metabolic pathways that are characterized by their ability to either synthesize molecules with the utilization of energy (anabolic pathway) or break down of complex molecules by releasing energy in the process (catabolic pathway). The two pathways complement each other in that the energy released from one is used up by the other. The degradative process of a catabolic pathway provides the energy required to conduct a biosynthesis of an anabolic pathway. In addition to the two distinct metabolic pathways is the amphibolic pathway, which can be either catabolic or anabolic based on the need for or the availability of energy.Pathways are required for the maintenance of homeostasis within an organism and the flux of metabolites through a pathway is regulated depending on the needs of the cell and the availability of the substrate. The end product of a pathway may be used immediately, initiate another metabolic pathway or be stored for later use. The metabolism of a cell consists of an elaborate network of interconnected pathways that enable the synthesis and breakdown of molecules (anabolism and catabolism).

Methylococcaceae

The Methylococcaceae are a family of bacteria that obtain their carbon and energy from methane, called methanotrophs.They comprise the type I methanotrophs, in contrast to the Methylocystaceae or type II methanotrophs. They belong among the gamma subdivision of the Proteobacteria, and are typically given their own order.

The Methylococcaceae have internal membranes in the form of flattened discs, perpendicular to the cell wall. Methane is oxidized to give formaldehyde, which is fixed by a process called the RuMP cycle (Ribulose Monophosphate Cycle). Here formaldehyde is combined with sugar ribulose, producing hexulose. This, in turn, is broken down to produce glyceraldehyde, which is used to produce new ribulose and other organic compounds. Catabolism does not involve a complete citric acid cycle.Some species of the Methylococcaceae have formed with certain marine mussels endosymbiotic relationships.

Nucleic acid metabolism

Nucleic acid metabolism is the process by which nucleic acids (DNA and RNA) are synthesized and degraded. Nucleic acids are polymers of nucleotides. Nucleotide synthesis is an anabolic mechanism generally involving the chemical reaction of phosphate, pentose sugar, and a nitrogenous base. Destruction of nucleic acid is a catabolic reaction. Additionally, parts of the nucleotides or nucleobases can be salvaged to recreate new nucleotides. Both synthesis and degradation reactions require enzymes to facilitate the event. Defects or deficiencies in these enzymes can lead to a variety of diseases.

Protein catabolism

Protein catabolism is the breakdown of proteins into amino acids and simple derivative compounds, for transport into the cell through the plasma membrane and ultimately for the polymerization into new proteins via the use of ribonucleic acids (RNA) and ribosomes. Protein catabolism, which is the breakdown of macromolecules, is essentially a digestion process.

Protein catabolism is most commonly carried out by non-specific endo- and exo-proteases. However, specific proteases are used for cleaving of proteins for regulatory and protein trafficking purposes. One example is the subclass of proteolytic enzymes called oligopeptidase.

The amino acids produced by catabolism may be directly recycled to form new proteins, converted into different amino acids, or can undergo amino acid catabolism to be converted to other compounds via the Krebs cycle.

Pyrimidine metabolism

Pyrimidine biosynthesis occurs both in the body and through organic synthesis.

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