Chemical process of decomposition

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Human body composition [1]

  Water (64%)
  Protein (20%)
  Fat (10%)
  Carbohydrate (1%)
  Minerals (5%)

Decomposition in animals 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. [2] Autolysis and putrefaction also play major roles in the disintegration of cells and tissues. [3]

Contents

The human body is composed of approximately: 64% water, 20% protein, 10% fat, 1% carbohydrate, 5% minerals. [1] 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. [4] 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 is the process that breaks down proteins. It is regulated by moisture, temperature, and bacteria. [5] 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:

During later stages of decomposition, more resistant tissue proteins are degraded by the effects of putrefaction. These include:

Keratin 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. [7] This is the reason that hair and nails are commonly found with skeletal remains. [8]

Proteolysis products

In general, proteolysis breaks down proteins into: [3] [4]

Continuing proteolysis leads to the production of phenolic substances. In addition, the following gases will also be produced: [4]

The sulfur-containing amino acids cysteine and methionine undergo bacterial decomposition to yield: [4]

Two common decarboxylation products of protein associated with decomposition are putrescine and cadaverine. These compounds are toxic at high levels and have distinctive, foul odours. [6] It is believed that they are components of the characteristic odours of decomposition commonly detected by cadaver dogs. [3]

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

Nitrogen release

Nitrogen is a component of amino acids and is released upon deamination. It is typically released in the form of ammonia, which may be used by plants or microbes in the surrounding environment, converted to nitrate, or can accumulate in soil (if the body is located on top of or within soil). [4] It has been suggested that the presence of nitrogen in soil may enhance nearby plant growth. [6]

In acidic soil conditions, ammonia will be converted to ammonium 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 and denitrification to yield nitrate and nitrite. In the absence of nitrifying bacteria, or organisms capable of oxidizing ammonia, ammonia will accumulate in the soil. [4]

Phosphorus release

Phosphorus 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, calcium, magnesium, and aluminum. Soil microorganisms can also transform insoluble organic complexes into soluble ones. [4]

Carbohydrate degradation

Early in decomposition, carbohydrates will be broken down by microorganisms. The process begins with the breakdown of glycogen into glucose monomers. [9] These sugar monomers can be completely decomposed to carbon dioxide and water or incompletely decomposed to various organic acids and alcohols, [3] or other oxygenated species, such as ketones, aldehydes, esters and ethers. [10]

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: [3]

Under anaerobic conditions, bacteria will decompose sugars into: [3]

which are collectively responsible for the acidic environment commonly associated with decomposing bodies. [3]

Other bacterial fermentation products include alcohols, such as butyl and ethyl alcohol, acetone, and gases, such as methane and hydrogen. [3]

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, which is made up of about 5-30% water, 2-3% protein, and 60-85% lipids, by weight, of which 90-99% are triglycerides. [3] 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. [11] The fatty acid content of the triglycerides varies from person to person, but contains oleic acid in the greatest amount, followed by linoleic, palmitoleic, and palmitic acids. [12]

Neutral lipid degradation

Neutral fat hydrolysis reaction Lipid hydrolysis.JPG
Neutral fat hydrolysis reaction

Neutral lipids are hydrolyzed by lipases shortly after death, to free the fatty acids from their glycerol backbone. This creates a mixture of saturated and unsaturated fatty acids. [13] 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. [12] 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. [4]

Fatty acid degradation

The fatty acids resulting from hydrolysis can undergo one of two routes of degradation, depending on the availability of oxygen. [3] 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. [3] 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. [13]

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 linkages. Eventually, the process will produce aldehydes and ketones. [4]

  • Initiation
  • Propagation
  • Termination

A summary of the lipid degradation products can be found in Table 1 [ where? ] below.

Nucleic acid degradation

The breakdown of nucleic acids produces nitrogenous bases, phosphates, and sugars. [10] 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 is a composite tissue that is made up of three main fractions:

Partially skeletonized pig (sus Scrofa) Partially skeletonized pig (Sus scrofa).jpg
Partially skeletonized pig (sus Scrofa)
  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(the mineral that contains the calcium and phosphorus in a bone), 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. [4]

The process that degrades bone is referred to as diagenesis. The first step in the process involves the elimination of the organic collagen fraction by the action of bacterial collagenases. 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, are lost to the environment. [4] 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. [3]

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 (fauna and flora) agents. [3]

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 soils, retain water better than others, like sandy or silty soils. Further, acidic soils are better able to dissolve the inorganic matrix of hydroxyapatite than basic soils, thus accelerating the disintegration of bone. [3]

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. [14] Small and large mammals often disturb bones by removing them from grave sites or gnawing on them, which contributes to their destruction. [15] 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. [3]

Related Research Articles

Biopolymer Polymer produced by a living organism

Biopolymers are natural polymers produced by the cells of living organisms. Biopolymers consist of monomeric units that are covalently bonded to form larger molecules. There are three main classes of biopolymers, classified according to the monomers used and the structure of the biopolymer formed: polynucleotides, polypeptides, and polysaccharides. Polynucleotides, such as RNA and DNA, are long polymers composed of 13 or more nucleotide monomers. Polypeptides and proteins, are polymers of amino acids and some major examples include collagen, actin, and fibrin. Polysaccharides are linear or branched polymeric carbohydrates and examples include starch, cellulose and alginate. Other examples of biopolymers include natural rubbers, suberin and lignin, cutin and cutan and melanin.

Collagen is the main structural protein in the extracellular matrix found in the body's various connective tissues. As the main component of connective tissue, it is the most abundant protein in mammals, making up from 25% to 35% of the whole-body protein content. Collagen consists of amino acids bound together to form a triple helix of elongated fibril known as a collagen helix. It is mostly found in connective tissue such as cartilage, bones, tendons, ligaments, and skin.

Fatty acid Carboxylic acid

In chemistry, particularly in biochemistry, a fatty acid is a carboxylic acid with a long aliphatic chain, which is either saturated or unsaturated. Most naturally occurring fatty acids have an unbranched chain of an even number of carbon atoms, from 4 to 28. Fatty acids are usually not found in organisms in their standalone form, but instead exist as three main classes of esters: triglycerides, phospholipids, and cholesteryl esters. In any of these forms, fatty acids are both important dietary sources of fuel for animals and they are important structural components for cells.

Fat Esters of three fatty acid chains and the alcohol glycerol, one of the three main macronutrients, also known as triglycerides

In nutrition, biology, and chemistry, fat usually means any ester of fatty acids, or a mixture of such compounds; most commonly those that occur in living beings or in food.

Lipid A substance of biological origin that is soluble in nonpolar solvents

In biology and biochemistry, a lipid is a biomolecule that is soluble in nonpolar solvents. Non-polar solvents are typically hydrocarbons used to dissolve other naturally occurring hydrocarbon lipid molecules that do not dissolve in water, including fatty acids, waxes, sterols, fat-soluble vitamins, monoglycerides, diglycerides, triglycerides, and phospholipids.

Triglyceride

A triglyceride is an ester derived from glycerol and three fatty acids. Triglycerides are the main constituents of body fat in humans and other vertebrates, as well as vegetable fat. They are also present in the blood to enable the bidirectional transference of adipose fat and blood glucose from the liver, and are a major component of human skin oils.

Diagenesis Physico-chemical changes in sediments occurring after their deposition

Diagenesis is the process that describes physical and chemical changes in sediments first caused by water-rock interactions, microbial activity and compaction after their deposition. The increase of pressure and temperature only starts to play a role as sediments get buried much deeper in the Earth's crust. In the early stages, the transformation of poorly consolidated sediments into sedimentary rock (lithification) is simply accompanied by a reduction in porosity and water expulsion, while their main mineralogical assemblages remain unaltered. As the rock is carried deeper by further deposition above, its organic content is progressively transformed into kerogens and bitumens. The process of diagenesis excludes surface alteration (weathering) and deep metamorphism. There is no sharp boundary between diagenesis and metamorphism, but the latter occurs at higher temperatures and pressures. Hydrothermal solutions, meteoric groundwater, rock porosity, permeability, dissolution/precipitation reactions, and time are all influential factors.

Decomposition The process in which organic substances are broken down into simpler organic matter

Decomposition is the process by which dead organic substances are broken down into simpler organic or inorganic matter such as carbon dioxide, water, simple sugars and mineral salts. The process is a part of the nutrient cycle and is essential for recycling the finite matter that occupies physical space in the biosphere. Bodies of living organisms begin to decompose shortly after death. Animals, such as worms, also help decompose the organic materials. Organisms that do this are known as decomposers. Although no two organisms decompose in the same way, they all undergo the same sequential stages of decomposition. The science which studies decomposition is generally referred to as taphonomy from the Greek word taphos, meaning tomb. Decomposition can also be a gradual process for organisms that have extended periods of dormancy.

Putrefaction is the fifth stage of death, following pallor mortis, algor mortis, rigor mortis, and livor mortis. This process references the breaking down of a body of an animal such as a human post-mortem. In broad terms, it can be viewed as the decomposition of proteins, and the eventual breakdown of the cohesiveness between tissues, and the liquefaction of most organs. This is caused by the decomposition of organic matter by bacterial or fungal digestion, which causes the release of gases that infiltrate the body's tissues, and leads to the deterioration of the tissues and organs. The approximate time it takes putrefaction to occur is dependent on various factors. Internal factors that affect the rate of putrefaction include the age at which death has occurred, the overall structure and condition of the body, the cause of death, and external injuries arising before or after death. External factors include environmental temperature, moisture and air exposure, clothing, burial factors, and light exposure.

Osteoblast

Osteoblasts are cells with a single nucleus that synthesize bone. However, in the process of bone formation, osteoblasts function in groups of connected cells. Individual cells cannot make bone. A group of organized osteoblasts together with the bone made by a unit of cells is usually called the osteon.

Hydroxyapatite Naturally occurring mineral form of calcium apatite

Hydroxyapatite, also called hydroxylapatite (HA), is a naturally occurring mineral form of calcium apatite with the formula Ca5(PO4)3(OH), but it is usually written Ca10(PO4)6(OH)2 to denote that the crystal unit cell comprises two entities. Hydroxyapatite is the hydroxyl endmember of the complex apatite group. The OH ion can be replaced by fluoride, chloride or carbonate, producing fluorapatite or chlorapatite. It crystallizes in the hexagonal crystal system. Pure hydroxyapatite powder is white. Naturally occurring apatites can, however, also have brown, yellow, or green colorations, comparable to the discolorations of dental fluorosis.

Maceration (bone)

Maceration is a bone preparation technique whereby a clean skeleton is obtained from a vertebrate carcass by leaving it to decompose inside a closed container at near-constant temperature. This may be done as part of a forensic investigation, as a recovered body is too badly decomposed for a meaningful autopsy, but with enough flesh or skin remaining as to obscure macroscopically visible evidence, such as cut-marks. In most cases, maceration is done on the carcass of an animal for educational purposes.

Bioglass 45S5

Bioglass 45S5 or calcium sodium phosphosilicate, commonly referred to by its commercial name Bioglass and NovaMin, is a glass specifically composed of 45 wt% SiO2, 24.5 wt% CaO, 24.5 wt% Na2O, and 6.0 wt% P2O5. Glasses are non-crystalline amorphous solids that are commonly composed of silica-based materials with other minor additives. Compared to soda-lime glass (commonly used, as in windows or bottles), Bioglass 45S5 contains less silica and higher amounts of calcium and phosphorus. The 45S5 name signifies glass with 45 weight % of SiO2 and 5:1 molar ratio of calcium to phosphorus. This high ratio of calcium to phosphorus promotes formation of apatite crystals; calcium and silica ions can act as crystallization nuclei. Lower Ca:P ratios do not bond to bone. Bioglass 45S5's specific composition is optimal in biomedical applications because of its similar composition to that of hydroxyapatite, the mineral component of bone. This similarity provides Bioglass' ability to be integrated with living bone.

Autoxidation refers to oxidations brought about by oxygen at normal temperatures, without the intervention of flame or electric spark. The term is usually used to describe the degradation of organic compounds in air. Many common phenomena can be attributed to autoxidation, such as food going rancid, the 'drying' of varnishes and paints and the perishing of rubber. It is also an important concept in both industrial chemistry and biology. Autoxidation is therefore a fairly broad term and can encompass examples of photooxygenation and catalytic oxidation.

Lipid metabolism is the synthesis and degradation of lipids in cells, involving the breakdown or storage of fats for energy and the synthesis of structural and functional lipids, such as those involved in the construction of cell membranes. In animals, these fats are obtained from food or are synthesized by the liver. Lipogenesis is the process of synthesizing these fats. The majority of lipids found in the human body from ingesting food are triglycerides and cholesterol. Other types of lipids found in the body are fatty acids and membrane lipids. Lipid metabolism is often considered as the digestion and absorption process of dietary fat; however, there are two sources of fats that organisms can use to obtain energy: from consumed dietary fats and from stored fat. Vertebrates use both sources of fat to produce energy for organs such as the heart to function. Since lipids are hydrophobic molecules, they need to be solubilized before their metabolism can begin. Lipid metabolism often begins with hydrolysis, which occurs with the help of various enzymes in the digestive system. Lipid metabolism also occurs in plants, though the processes differ in some ways when compared to animals. The second step after the hydrolysis is the absorption of the fatty acids into the epithelial cells of the intestinal wall. In the epithelial cells, fatty acids are packaged and transported to the rest of the body.

Fatty acid synthesis is the creation of fatty acids from acetyl-CoA and NADPH through the action of enzymes called fatty acid synthases. This process takes place in the cytoplasm of the cell. Most of the acetyl-CoA which is converted into fatty acids is derived from carbohydrates via the glycolytic pathway. The glycolytic pathway also provides the glycerol with which three fatty acids can combine to form triglycerides, the final product of the lipogenic process. When only two fatty acids combine with glycerol and the third alcohol group is phosphorylated with a group such as phosphatidylcholine, a phospholipid is formed. Phospholipids form the bulk of the lipid bilayers that make up cell membranes and surround the organelles within the cells

Phospholipid-derived fatty acids

Phospholipid-derived fatty acids (PLFAs) are widely used in microbial ecology as chemotaxonomic markers of bacteria and other organisms. Phospholipids are the primary lipids composing cellular membranes. Phospholipids can be saponified, which releases the fatty acids contained in their diglyceride tail. Once the phospholipids of an unknown sample are saponified, the composition of the resulting PLFA can be compared to the PLFA of known organisms to determine the identity of the sample organism. PLFA analysis may be combined with other techniques, such as stable isotope probing to determine which microbes are metabolically active in a sample. PLFA analysis was pioneered by D.C. White at the University of Tennessee, in the early to mid 1980s.

Mineralized tissues

Mineralized tissues are biological tissues that incorporate minerals into soft matrices. Typically these tissues form a protective shield or structural support. Bone, mollusc shells, deep sea sponge Euplectella species, radiolarians, diatoms, antler bone, tendon, cartilage, tooth enamel and dentin are some examples of mineralized tissues.

Lipid droplets, also referred to as lipid bodies, oil bodies or adiposomes, are lipid-rich cellular organelles that regulate the storage and hydrolysis of neutral lipids and are found largely in the adipose tissue. They also serve as a reservoir for cholesterol and acyl-glycerols for membrane formation and maintenance. Lipid droplets are found in all eukaryotic organisms and store a large portion of lipids in mammalian adipocytes. Initially, these lipid droplets were considered to merely serve as fat depots, but since the discovery in the 1990s of proteins in the lipid droplet coat that regulate lipid droplet dynamics and lipid metabolism, lipid droplets are seen as highly dynamic organelles that play a very important role in the regulation of intracellular lipid storage and lipid metabolism. The role of lipid droplets outside of lipid and cholesterol storage has recently begun to be elucidated and includes a close association to inflammatory responses through the synthesis and metabolism of eicosanoids and to metabolic disorders such as obesity, cancer, and atherosclerosis. In non-adipocytes, lipid droplets are known to play a role in protection from lipotoxicity by storage of fatty acids in the form of neutral triacylglycerol, which consists of three fatty acids bound to glycerol. Alternatively, fatty acids can be converted to lipid intermediates like diacylglycerol (DAG), ceramides and fatty acyl-CoAs. These lipid intermediates can impair insulin signaling, which is referred to as lipid-induced insulin resistance and lipotoxicity. Lipid droplets also serve as platforms for protein binding and degradation. Finally, lipid droplets are known to be exploited by pathogens such as the hepatitis C virus, the dengue virus and chlamydia trachomatis among others.

SN2 Palmitate is a structured triglyceride where palmitic acid is bonded to the middle position (sn-2) of the glycerol backbone. Structured triglycerides are achieved through an enzymatic process using vegetable oils. Current usage of structured triglycerides is mainly for infant formula providing a human milk fat substitute.

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