Chemical process of decomposition
Encyclopedia
Decomposition
Decomposition
Decomposition is the process by which organic material is broken down into simpler forms of matter. The process is essential for recycling the finite matter that occupies physical space in the biome. Bodies of living organisms begin to decompose shortly after death...

 is a process that begins immediately after death and involves the destruction of soft tissue, leaving behind skeletonized remains. The chemical process of decomposition is complex and involves the breakdown of soft tissue, as the body passes through the sequential stages of decomposition
Decomposition
Decomposition is the process by which organic material is broken down into simpler forms of matter. The process is essential for recycling the finite matter that occupies physical space in the biome. Bodies of living organisms begin to decompose shortly after death...

. Autolysis and putrefaction
Putrefaction
Putrefaction is one of seven stages in the decomposition of the body of a dead animal. It can be viewed, in broad terms, as the decomposition of proteins, in a process that results in the eventual breakdown of cohesion between tissues and the liquefaction of most organs.-Description:In terms of...

 also play major roles in the disintegration of cells and tissues.

The human body is composed of approximately: 64% water
Water
Water is a chemical substance with the chemical formula H2O. A water molecule contains one oxygen and two hydrogen atoms connected by covalent bonds. Water is a liquid at ambient conditions, but it often co-exists on Earth with its solid state, ice, and gaseous state . Water also exists in a...

, 20% protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

, 10% fat
Fat
Fats consist of a wide group of compounds that are generally soluble in organic solvents and generally insoluble in water. Chemically, fats are triglycerides, triesters of glycerol and any of several fatty acids. Fats may be either solid or liquid at room temperature, depending on their structure...

, 1% carbohydrate
Carbohydrate
A carbohydrate is an organic compound with the empirical formula ; that is, consists only of carbon, hydrogen, and oxygen, with a hydrogen:oxygen atom ratio of 2:1 . However, there are exceptions to this. One common example would be deoxyribose, a component of DNA, which has the empirical...

, 5% minerals. The decomposition of soft tissue is characterized by the breakdown of these macromolecules, and thus a large proportion of the decomposition products should reflect the amount of protein and fat content initially present in the body. As such, the chemical process of decomposition involves the breakdown of proteins, carbohydrates, lipids, nucleic acids, and bone.

Protein degradation

Proteins make up a variety of different tissues within the body, which may be classified as soft or hard tissue proteins. As such, proteins within the body are not degraded at a uniform rate.

Proteolysis

Proteolysis
Proteolysis
Proteolysis is the directed degradation of proteins by cellular enzymes called proteases or by intramolecular digestion.-Purposes:Proteolysis is used by the cell for several purposes...

 is the process that breaks down proteins. It is regulated by moisture, temperature, and bacteria. This process does not occur at a uniform rate and thus some proteins are degraded during early decomposition, while others are degraded during later stages of decomposition. During the early stages of decomposition, soft tissue proteins are broken down. These include proteins that:
  • line the gastrointestinal tract
    Gastrointestinal tract
    The human gastrointestinal tract refers to the stomach and intestine, and sometimes to all the structures from the mouth to the anus. ....

     and pancreatic epithelium
    Pancreas
    The pancreas is a gland organ in the digestive and endocrine system of vertebrates. It is both an endocrine gland producing several important hormones, including insulin, glucagon, and somatostatin, as well as a digestive organ, secreting pancreatic juice containing digestive enzymes that assist...

  • form the brain
    Brain
    The brain is the center of the nervous system in all vertebrate and most invertebrate animals—only a few primitive invertebrates such as sponges, jellyfish, sea squirts and starfishes do not have one. It is located in the head, usually close to primary sensory apparatus such as vision, hearing,...

    , liver
    Liver
    The liver is a vital organ present in vertebrates and some other animals. It has a wide range of functions, including detoxification, protein synthesis, and production of biochemicals necessary for digestion...

    , and kidneys


During later stages of decomposition, more resistant tissue proteins are degraded by the effects of putrefaction. These include:
  • reticulin
  • muscle
    Muscle
    Muscle is a contractile tissue of animals and is derived from the mesodermal layer of embryonic germ cells. Muscle cells contain contractile filaments that move past each other and change the size of the cell. They are classified as skeletal, cardiac, or smooth muscles. Their function is to...

     protein
  • collagen
    Collagen
    Collagen is a group of naturally occurring proteins found in animals, especially in the flesh and connective tissues of mammals. It is the main component of connective tissue, and is the most abundant protein in mammals, making up about 25% to 35% of the whole-body protein content...

     (a hard tissue protein), which survives even longer than the former tissue proteins


Keratin
Keratin
Keratin refers to a family of fibrous structural proteins. Keratin is the key of structural material making up the outer layer of human skin. It is also the key structural component of hair and nails...

 is a protein which is found in skin, hair, and nails. It is most resistant to the enzymes involved in proteolysis and must be broken down by special keratinolytic microorganisms. This is the reason that hair and nails are commonly found with skeletal remains.

Proteolysis products

In general, proteolysis breaks down proteins into,:
  • proteoses
  • peptones
  • polypeptides
  • amino acids


Continuing proteolysis leads to the production of phenolic substances
Phenols
In organic chemistry, phenols, sometimes called phenolics, are a class of chemical compounds consisting of a hydroxyl group bonded directly to an aromatic hydrocarbon group...

. In addition, the following gases will also be produced:
  • carbon dioxide
    Carbon dioxide
    Carbon dioxide is a naturally occurring chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom...

  • hydrogen sulphide, which is highly toxic
  • ammonia
    Ammonia
    Ammonia is a compound of nitrogen and hydrogen with the formula . It is a colourless gas with a characteristic pungent odour. Ammonia contributes significantly to the nutritional needs of terrestrial organisms by serving as a precursor to food and fertilizers. Ammonia, either directly or...

  • methane
    Methane
    Methane is a chemical compound with the chemical formula . It is the simplest alkane, the principal component of natural gas, and probably the most abundant organic compound on earth. The relative abundance of methane makes it an attractive fuel...



Sulfur containing amino acids, such as cysteine
Cysteine
Cysteine is an α-amino acid with the chemical formula HO2CCHCH2SH. It is a non-essential amino acid, which means that it is biosynthesized in humans. Its codons are UGU and UGC. The side chain on cysteine is thiol, which is polar and thus cysteine is usually classified as a hydrophilic amino acid...

, cystine
Cystine
Cystine is a dimeric amino acid formed by the oxidation of two cysteine residues that covalently link to make a disulfide bond. This organosulfur compound has the formula 2. It is a white solid, and melts at 247-249 °C...

, and methionine
Methionine
Methionine is an α-amino acid with the chemical formula HO2CCHCH2CH2SCH3. This essential amino acid is classified as nonpolar. This amino-acid is coded by the codon AUG, also known as the initiation codon, since it indicates mRNA's coding region where translation into protein...

, undergo bacterial decomposition to yield:
  • ammonia
  • thiols (decomposition gases known for their foul odours)
  • pyruvic acid
    Pyruvic acid
    Pyruvic acid is an organic acid, a ketone, as well as the simplest of the alpha-keto acids. The carboxylate ion of pyruvic acid, CH3COCOO−, is known as pyruvate, and is a key intersection in several metabolic pathways....

  • sulphides
  • hydrogen sulphide gas
    • Ferrous sulphide
      Iron sulfide
      Iron sulfide or Iron sulphide refers to a chemical compound of iron and sulfur with a wide range of stoechiometric formulae and different crystalline structures.-Natural minerals:By increasing order of stability:...

       will be produced if iron is present, which can be seen as a black precipitate


Two common decarboxylation
Decarboxylation
Decarboxylation is a chemical reaction that releases carbon dioxide . Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. The reverse process, which is the first chemical step in photosynthesis, is called carbonation, the addition of CO2 to...

 products of protein associated with decomposition are putrescine and cadaverine. These compounds are toxic and have distinctive, foul odours. It is believed that they are components of the characteristic odours of decomposition commonly detected by cadaver dogs
Cadaver Dogs
Cadaver Dogs are an Ohio based rock band formed in late 2009. Composed of Mat Franklin, Cole Walsh-Davis, and Alex "Lex Vegas" Mosie, all members of notable Ohio band Look Afraid, they have quickly made an impression on not only their home base of Columbus, OH but the entire mid-west music scene...

.

A summary of the protein degradation products can be found in Table 1 below.

Nitrogen release

Nitrogen
Nitrogen
Nitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless, and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere...

 is a component of amino acids and is released upon deamination
Deamination
Deamination is the removal of an amine group from a molecule. Enzymes which catalyse this reaction are called deaminases.In the human body, deamination takes place primarily in the liver, however glutamate is also deaminated in the kidneys. Deamination is the process by which amino acids are...

. It is typically released in the form of ammonia, which may be used by plants or microbes in the surrounding environment, converted to nitrate
Nitrate
The nitrate ion is a polyatomic ion with the molecular formula NO and a molecular mass of 62.0049 g/mol. It is the conjugate base of nitric acid, consisting of one central nitrogen atom surrounded by three identically-bonded oxygen atoms in a trigonal planar arrangement. The nitrate ion carries a...

, or can accumulate in soil (if the body is located on top of or within soil). It has been suggested that the presence of nitrogen in soil may enhance nearby plant growth.

In acidic soil conditions, ammonia will be converted to ammonium
Ammonium
The ammonium cation is a positively charged polyatomic cation with the chemical formula NH. It is formed by the protonation of ammonia...

 ions, which can be used by plants or microbes. Under alkaline conditions, some of the ammonium ions entering soil may be converted back to ammonia. Any remaining ammonium in the environment can undergo nitrification
Nitrification
Nitrification is the biological oxidation of ammonia with oxygen into nitrite followed by the oxidation of these nitrites into nitrates. Degradation of ammonia to nitrite is usually the rate limiting step of nitrification. Nitrification is an important step in the nitrogen cycle in soil...

 and denitrification
Denitrification
Denitrification is a microbially facilitated process of nitrate reduction that may ultimately produce molecular nitrogen through a series of intermediate gaseous nitrogen oxide products....

 to yield nitrate
Nitrate
The nitrate ion is a polyatomic ion with the molecular formula NO and a molecular mass of 62.0049 g/mol. It is the conjugate base of nitric acid, consisting of one central nitrogen atom surrounded by three identically-bonded oxygen atoms in a trigonal planar arrangement. The nitrate ion carries a...

 and nitrite
Nitrite
The nitrite ion has the chemical formula NO2−. The anion is symmetric with equal N-O bond lengths and a O-N-O bond angle of ca. 120°. On protonation the unstable weak acid nitrous acid is produced. Nitrite can be oxidised or reduced, with product somewhat dependent on the oxidizing/reducing agent...

. In the absence of nitrifying bacteria, or organisms capable of oxidizing ammonia, ammonia will accumulate in the soil.

Phosphorus release

Phosphorus
Phosphorus
Phosphorus is the chemical element that has the symbol P and atomic number 15. A multivalent nonmetal of the nitrogen group, phosphorus as a mineral is almost always present in its maximally oxidized state, as inorganic phosphate rocks...

 can be released from various components of the body, including proteins (especially those making up nucleic acids), sugar phosphate, and phospholipids. The route phosphorus takes once it is released is complex and relies on the pH of the surrounding environment. In most soils, phosphorus exists as insoluble inorganic complexes, associated with iron
Iron
Iron is a chemical element with the symbol Fe and atomic number 26. It is a metal in the first transition series. It is the most common element forming the planet Earth as a whole, forming much of Earth's outer and inner core. It is the fourth most common element in the Earth's crust...

, calcium
Calcium
Calcium is the chemical element with the symbol Ca and atomic number 20. It has an atomic mass of 40.078 amu. Calcium is a soft gray alkaline earth metal, and is the fifth-most-abundant element by mass in the Earth's crust...

, magnesium
Magnesium
Magnesium is a chemical element with the symbol Mg, atomic number 12, and common oxidation number +2. It is an alkaline earth metal and the eighth most abundant element in the Earth's crust and ninth in the known universe as a whole...

, and aluminum. Soil microorganisms can also transform insoluble organic complexes into soluble ones.

Carbohydrate degradation

Early in decomposition, carbohydrates will be broken down by microorganisms. The process begins with the breakdown of glycogen
Glycogen
Glycogen is a molecule that serves as the secondary long-term energy storage in animal and fungal cells, with the primary energy stores being held in adipose tissue...

 into glucose
Glucose
Glucose is a simple sugar and an important carbohydrate in biology. Cells use it as the primary source of energy and a metabolic intermediate...

 monomers. These sugar monomers can be completely decomposed to carbon dioxide and water or incompletely decomposed to various organic acids and alcohols, or other oxygenated species, such as ketones, aldehydes, esters and ethers.

Depending on the availability of oxygen in the environment, sugars will be decomposed by different organisms and into different products, although both routes may occur simultaneously. Under aerobic conditions, fungi and bacteria will decompose sugars into the following organic acids:
  • glucuronic acid
    Glucuronic acid
    Glucuronic acid is a carboxylic acid. Its structure is similar to that of glucose. However, glucuronic acid's sixth carbon is oxidized to a carboxylic acid...

  • citric acid
    Citric acid
    Citric acid is a weak organic acid. It is a natural preservative/conservative and is also used to add an acidic, or sour, taste to foods and soft drinks...

  • oxalic acid
    Oxalic acid
    Oxalic acid is an organic compound with the formula H2C2O4. This colourless solid is a dicarboxylic acid. In terms of acid strength, it is about 3,000 times stronger than acetic acid. Oxalic acid is a reducing agent and its conjugate base, known as oxalate , is a chelating agent for metal cations...



Under anaerobic conditions, bacteria will decompose sugars into:
  • lactic acid
    Lactic acid
    Lactic acid, also known as milk acid, is a chemical compound that plays a role in various biochemical processes and was first isolated in 1780 by the Swedish chemist Carl Wilhelm Scheele. Lactic acid is a carboxylic acid with the chemical formula C3H6O3...

  • butyric acid
    Butyric acid
    Butyric acid , also known under the systematic name butanoic acid, is a carboxylic acid with the structural formula CH3CH2CH2-COOH. Salts and esters of butyric acid are known as butyrates or butanoates...

  • acetic acid
    Acetic acid
    Acetic acid is an organic compound with the chemical formula CH3CO2H . It is a colourless liquid that when undiluted is also called glacial acetic acid. Acetic acid is the main component of vinegar , and has a distinctive sour taste and pungent smell...


which are collectively responsible for the acidic environment commonly associated with decomposing bodies.

Other bacterial fermentation products include alcohols, such as butyl and ethyl alcohol, acetone, and gases, such as methane and hydrogen.

A summary of the carbohydrate degradation products can be found in Table 1 below.

Lipid degradation

Lipids in the body are mainly contained in adipose tissue
Adipose tissue
In histology, adipose tissue or body fat or fat depot or just fat is loose connective tissue composed of adipocytes. It is technically composed of roughly only 80% fat; fat in its solitary state exists in the liver and muscles. Adipose tissue is derived from lipoblasts...

, which is made up of about 5-30% water, 2-3% protein, and 60-85% lipids, by weight, of which 90-99% are triglycerides. Adipose tissue is largely composed of neutral lipids, which collectively refers to triglycerides, diglyercides, phospholipids, and cholesterol esters, of which triglycerides are the most common. The fatty acid
Fatty acid
In chemistry, especially biochemistry, a fatty acid is a carboxylic acid with a long unbranched aliphatic tail , which is either saturated or unsaturated. Most naturally occurring fatty acids have a chain of an even number of carbon atoms, from 4 to 28. Fatty acids are usually derived from...

 content of the triglycerides varies from person to person, but contains oleic acid in the greatest amount, followed by linoleic, palmitoleic, and palmitic acids.

Neutral lipid degradation

Neutral lipids are hydrolyzed
Hydrolysis
Hydrolysis is a chemical reaction during which molecules of water are split into hydrogen cations and hydroxide anions in the process of a chemical mechanism. It is the type of reaction that is used to break down certain polymers, especially those made by condensation polymerization...

 by lipases shortly after death, to free the fatty acids from their glycerol
Glycerol
Glycerol is a simple polyol compound. It is a colorless, odorless, viscous liquid that is widely used in pharmaceutical formulations. Glycerol has three hydroxyl groups that are responsible for its solubility in water and its hygroscopic nature. The glycerol backbone is central to all lipids...

 backbone. This creates a mixture of saturated and unsaturated fatty acids. Under the right conditions (when sufficient water and bacterial enzymes are present), neutral lipids will be completely degraded until they are reduced to fatty acids. Under suitable conditions, the fatty acids can be transformed into adipocere
Adipocere
Adipocere , also known as corpse, grave or mortuary wax, is a wax-like organic substance formed by the anaerobic bacterial hydrolysis of fat in tissue, such as body fat in corpses...

. In contrast, fatty acids may react with sodium and potassium ions present in tissue, to produce salts of fatty acids. When the body is located near soil, the sodium and potassium ions can be replaced by calcium and magnesium ions to form soaps of saturated fatty acids, which can also contribute to the formation of adipocere.

Fatty acid degradation

The fatty acids resulting from hydrolysis can undergo one of two routes of degradation, depending on the availability of oxygen. It is possible, however, for both routes to take place at the same time in different areas of the body.

Anaerobic degradation

Anaerobic bacteria dominate within a body following death, which promote the anaerobic degradation of fatty acids by hydrogenation
Hydrogenation
Hydrogenation, to treat with hydrogen, also a form of chemical reduction, is a chemical reaction between molecular hydrogen and another compound or element, usually in the presence of a catalyst. The process is commonly employed to reduce or saturate organic compounds. Hydrogenation typically...

. The process of hydrogenation transforms unsaturated bonds (double and triple bonds) into single bonds. This essentially increases the amounts of saturated fatty acids, while decreasing the proportion of unsaturated fatty acids. Therefore, hydrogenation of oleic and palmitoleic acids, for example, will yield stearic, and palmitic acids, respectively.

Aerobic degradation

In the presence of oxygen, the fatty acids will undergo oxidation. Lipid oxidation is a chain reaction process in which oxygen attacks the double bond in a fatty acid, to yield peroxide
Peroxide
A peroxide is a compound containing an oxygen–oxygen single bond or the peroxide anion .The O−O group is called the peroxide group or peroxo group. In contrast to oxide ions, the oxygen atoms in the peroxide ion have an oxidation state of −1.The simplest stable peroxide is hydrogen peroxide...

 linkages. Eventually, the process will produce aldehydes and ketones.

A summary of the lipid degradation products can be found in Table 1 below.

Nucleic acid degradation

The breakdown of nucleic acids produces nitrogenous bases, phosphates, and sugars. These three products are further broken down by degradation pathways of other macromolecules. The nitrogen from the nitrogenous bases will be transformed in the same way that it is in proteins. Similarly, phosphates will be released from the body and undergo the same changes as those released from proteins and phospholipids. Finally, sugars, also known as carbohydrates, will be degraded based on the availability of oxygen.

Bone degradation

Bone
Bone
Bones are rigid organs that constitute part of the endoskeleton of vertebrates. They support, and protect the various organs of the body, produce red and white blood cells and store minerals. Bone tissue is a type of dense connective tissue...

 is a composite tissue that is made up of three main fractions:
  1. a protein fraction that mainly consists of collagen (a hard tissue protein that is more resistant to degradation than other tissue proteins), which serves as support
  2. a mineral fraction that consists of hydroxyapatite, which stiffens the protein structure
  3. a ground substance made of other organic compounds

The collagen and hydroxyapatite are held together by a strong protein-mineral bond that provides bone with its strength and its ability to remain long after the soft tissue of a body has been degraded.

The process that degrades bone is referred to as diagenesis
Diagenesis
In geology and oceanography, diagenesis is any chemical, physical, or biological change undergone by a sediment after its initial deposition and during and after its lithification, exclusive of surface alteration and metamorphism. These changes happen at relatively low temperatures and pressures...

. The first step in the process involves the elimination of the organic collagen fraction by the action of bacterial collagenases
Collagenases
Collagenases are enzymes that break the peptide bonds in collagen.They assist in destroying extracellular structures in pathogenesis of bacteria such as Clostridium. They are an exotoxin and help to facilitate the spread of gas gangrene...

. These collagenases break down protein into peptides. The peptides are subsequently reduced to their constituent amino acids, which can be leached away by groundwater. Once the collagen has been removed from bone, the hydroxyapatite content is degraded by inorganic mineral weathering, meaning that important ions, such as calcium
Calcium in biology
Calcium plays a pivotal role in the physiology and biochemistry of organisms and the cell. It plays an important role in signal transduction pathways, where it acts as a second messenger, in neurotransmitter release from neurons, contraction of all muscle cell types, and fertilization...

, are lost to the environment. The strong protein-mineral bond that provided bone with its strength will become compromised by this degradation, leading to an overall weakened structure, which will continue to weaken until full disintegration of bone occurs.

Factors affecting bone degradation

Bone is quite resistant to degradation but will eventually be broken down by physical breaking, decalcification, and dissolution. The rate at which bone is degraded, however, is highly dependent on its surrounding environment. When soil is present, its destruction is influenced by both abiotic (water, temperature, soil type, and pH) and biotic
Biotic component
Biotic components are the living things that shape an ecosystem. A biotic factor is any living component that affects another organism, including animals that consume the organism in question, and the living food that the organism consumes. Each biotic factor needs energy to do work and food for...

 (fauna
Fauna
Fauna or faunæ is all of the animal life of any particular region or time. The corresponding term for plants is flora.Zoologists and paleontologists use fauna to refer to a typical collection of animals found in a specific time or place, e.g. the "Sonoran Desert fauna" or the "Burgess shale fauna"...

 and flora
Flora
Flora is the plant life occurring in a particular region or time, generally the naturally occurring or indigenous—native plant life. The corresponding term for animals is fauna.-Etymology:...

) agents.

Abiotic factors

Water accelerates the process by leaching essential organic minerals from bone. As such, soil type plays a role, because it will affect the water content of the environment. For example, some soils, like clay
Clay
Clay is a general term including many combinations of one or more clay minerals with traces of metal oxides and organic matter. Geologic clay deposits are mostly composed of phyllosilicate minerals containing variable amounts of water trapped in the mineral structure.- Formation :Clay minerals...

 soils, retain water better than others, like sand
Sand
Sand is a naturally occurring granular material composed of finely divided rock and mineral particles.The composition of sand is highly variable, depending on the local rock sources and conditions, but the most common constituent of sand in inland continental settings and non-tropical coastal...

y or silty soils. Further, acidic soils are better able to dissolve the inorganic matrix of hydroxyapatite than basic soils
Alkali soils
Alkali, or alkaline, soils are clay soils with high pH , a poor soil structure and a low infiltration capacity. Often they have a hard calcareous layer at 0.5 to 1 metre depth. Alkali soils owe their unfavorable physico-chemical properties mainly to the dominating presence of sodium carbonate...

, thus accelerating the disintegration of bone.

Biotic factors

Microorganisms, mainly bacteria and fungi, play a role in bone degradation. They are capable of invading bone tissue and causing minerals to leach into the surrounding environment, leading to disturbances in its structure. Small and large mammals often disturb bones by removing them from grave sites or gnawing on them, which contributes to their destruction. Finally, plant roots located above burial sites can be extremely destructive to bone. Fine roots can travel through the tissue and split long bones, while larger roots can produce openings in bones that may be mistaken for fractures.

Summary of macromolecule degradation products

Table 1. Degradation products of proteins, carbohydrates, and lipids
Proteins Carbohydrates Lipids
Proteoses, peptones, polypeptides, and amino acids Glucose Free fatty acids (saturated and unsaturated)
Phenolic substances and gases Organic acids and alcohols Salts of fatty acids
Organic acids and decarboxylation products Water, carbon dioxide Aldehydes and ketones
Nitrogen and phosphorus Gases Adipocere
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