objectives

Chemical waste in organisms

When chemical waste enters the habitat of living organisms, the chemicals can enter the organism and interfere with biological processes. Xenobiotics are foreign chemical compounds present in an organism that are not normally found. Xenobiotics can have negligible or severe effects on metabolic processes. Xenobiotics generally come from pollutants that are disposed of in waste water or landfills, either intentionally or accidentally, that find their way into organisms. These foreign compounds can include plastics, pesticides, pharmaceutical compounds or chemical solvents. When xenobiotics enter waste water from homes, factories, hospitals and agriculture, the compounds can sometimes be removed at the water treatment facility. Some xenobiotics can be metabolised (digested) and excreted by the organism, but some compounds are resistant to breaking down and remain within the organism, interfering with metabolic processes.

Antibiotic waste

One source of xenobiotics that has been steadily increasing is antibiotics. Antibiotics are drugs used to treat bacterial infections, such as ear infections, tonsillitis and strep throat. The disposal of expired or unused antibiotics poses a large threat to the environment, since these drugs are very commonly prescribed. People are advised to complete an entire course of antibiotics when prescribed, but often people will stop taking the medicine when they feel better, resulting in unused medicine that must be disposed of properly.

Pharmaceutical companies are also required to make drugs with an expiration date, after which the integrity and effectiveness of the drug cannot be guaranteed. The expired drugs would still have some medicinal effect, so they must also be disposed of properly to avoid releasing antibiotics into the environment.

Another source of antibiotic waste is from animals. Routinely, animals that are raised for food or food products are injected with antibiotics to prevent and control the infections that result from modern-day farming practices, which tend to crowd many animals into small spaces. Healthy animals, like cows, pigs and chickens, are often treated with antibiotics as a prevention, even if there is no evidence of active infection on the farm. The excreted animal waste would contain antibiotic-resistant bacteria and unmetabolised antibiotics, which then flow into the wastewater system. Animal manure applied to fields for growing crops then puts these harmful bacteria and antibiotics into the fruits and vegetables grown with contaminated soil.

When antibiotics are flushed down a toilet or thrown in the garbage, they can enter the water supply or leach into the soil. The risk is that the drugs will kill the bacteria that they come in contact with in nature. Bacteria often perform helpful functions in the ecosystem. Bacteria populations in nature can help to keep other, more harmful populations of bacteria, algae or fungi under control, so the presence of antibiotics in bodies of water or soil can kill the 'good' bacteria and allow for the growth of 'bad' bacteria or harmful overgrowths of algae or fungi.

Water treatment plants screen for and remove substances that cause immediate harmful effects to humans, such as heavy metals, pathogens and pesticides. However, substances that pose less harmful effects, such as antibiotics, may not be screened for or removed routinely. The effectiveness of the removal of antibiotics depends on the method of removal and the type of antibiotic.

Some antibiotics can be removed using the activated sludge process, where bacteria metabolise the compound, removing it from the water; however, there are some antibiotics that are resistant to metabolism. Other methods for removal involve treating the water with ozone or using carbon filters, both of which are more effective than the activated sludge process, but are very expensive measures. Some countries may not be able to afford these methods for antibiotic removal.

Biomagnification

Xenobiotics found in organisms can sometimes be digested and metabolised into smaller, less harmful compounds that can be excreted by the body. Other compounds cannot be metabolised and build up inside the organism. When xenobiotics build up and remain inside the body, they can interfere with metabolic processes. When one organism eats another organism that has stored xenobiotics, the concentration of the foreign substances increases. Biomagnification is the increase in concentration of a substance in a food chain. These substances generally refer to harmful compounds, such as pesticides or other toxins.

Compounds that are highly polar and water-soluble tend not to accumulate in organisms, since they can easily travel through the bloodstream, dissolve in sweat or urine and be excreted. Compounds that are nonpolar, however, do not dissolve easily in the bloodstream, sweat or urine and tend to accumulate in fatty tissues and organs, such as the liver. When one organism eats another, the fat-soluble substances are ingested and stored again in the next organism. The food chain, being a pyramid, requires animals at the top to consume more animals below them, so the accumulated toxins become more concentrated at each level of the food chain.

Pesticides

One pesticide that was extremely effective as an insecticide was dichlorodiphenyltrichloroethane, known as DDT. This pesticide was colourless, tasteless and nearly odourless, making it ideal for adding to crops, as the consumer would not be able to detect its presence. DDT was developed in 1874 and used for nearly 100 years as an insecticide in agriculture and to control the populations of disease-carrying mosquitoes before concerns about its safety emerged. Insects began to develop a resistance to DDT, decreasing the effectiveness of the compound. It was later learned that DDT was accumulating in insects and moving up the food chain, becoming toxic even to larger animals, such as birds and aquatic organisms. The use of DDT was banned in 2004 worldwide with only restricted use for the control of disease-carrying mosquitoes.

Heavy metals

Heavy metals can also accumulate in organisms, resulting in biomagnification. Since heavy metals are elements, they cannot be broken down by metabolic processes the way that some compounds can. Certain heavy metals have a high affinity for tissues and become stored, rather than excreted by the body through sweat, urine or faeces.

Mercury is an example, especially in the form of methylmercury, which is an organometallic ion with the formula [CH3Hg]+. Methylmercury is formed by aquatic microbes, which are then eaten by fish. The presence of the methyl group makes this compound nonpolar with poor solubility in water. As a result, methylmercury can easily cross the blood-brain barrier (a layer of fat), causing toxic neural effects, and across the placenta and into unborn babies. Methylmercury also binds very well to proteins, causing interference with the function of proteins.

Waste in the environment

The problem with plastic

One major source of waste in the environment comes from the use of plastics. Over the last 50 years, the production and use of plastic has been on the rise. It is lightweight, durable, flexible and inexpensive, making it an ideal alternative to wood, metal, fabric or glass materials for many consumer products. The use of pre-sterilised disposable plastic containers and syringes also reduces the risk of disease-spreading pathogens in hospitals, making plastic a safer alternative to the glass or metal which requires sterilisation between patients.

Plastics are traditionally made from addition polymers formed from alkenes. When alkenes are added together, they form long chains of hydrocarbons with functional groups attached that give rise to plastics with various properties, such as rigidity or flexibility, higher or lower density, durability or any other property that is desirable for use in a product. The alkenes used are generally obtained from fossil fuels, making traditional plastics known as petroleum-based plastics.

Although many plastic substances can be recycled, many end up in landfills. The stable hydrocarbon chains that give rise to the durable nature of plastic makes it desirable for storing last night's leftover dinner, but also makes it very difficult to break down over time, resulting in high levels of plastic waste. Plastics must be exposed to high temperatures or sunlight in order to break down. Even when plastics are capable of breaking down, they often produce compounds that are harmful to the organisms in the ecosystem. Since the plastic waste is buried in landfills, there are few opportunities for it to be exposed to high temperature or light to accelerate its decomposition.

This plastic waste is sometimes contained within a landfill site, but can also find its way to the natural habitats of many organisms. Aquatic ecosystems are especially at risk, as plastic products often float, which blocks sunlight for aquatic plants. Sea birds and fish also ingest plastic or become entangled, causing death. The floating plastic does, however, get exposed to high levels of sunlight, which can result in some degradation, releasing potentially harmful compounds into the water.

The sunlight causes the covalent bonds in the plastic to break in a process known as photodegradation. The polymer simply breaks into shorter sections, but still contains harmful products, which could be eaten by aquatic animals. Some countries have restricted the use of plastic in efforts to reduce the waste, but when it ends up in the ocean, it becomes the world's problem.

Solutions to the problem with plastic

Use of bacteria

Natural sources of waste, such as plant or animal material, break down over time with the help of bacteria, whether in landfills or the environment, in a process known as biodegradation. The bacteria slowly digest and absorb the nutrients in the plant and animal remains, recycling nutrients to the soil over time. Bacteria, however, typically cannot digest plastic materials the same way they can with plant or animal material. Recent research, however, has shown that some bacteria are capable of digesting some plastics, raising hope for the backlog of plastic in landfills.

One strain of bacteria, Ideonella sakaiensis, has been observed to secrete an enzyme that is capable of breaking down polyethylene terephthalate, a plastic commonly known as PET, that is commonly used in beverage bottles. The enzyme, named PETase, can digest the polymer into individual monomers, which the bacteria can then metabolise for energy and growth.

Development of bioplastics

Petroleum-based plastics are widely criticised for their inability to break down over time, causing waste in the environment, and also requiring alkene compounds that are not renewable. Newer biodegradable plastics are being developed that can more easily be digested by bacteria into harmless carbon dioxide and water. These bioplastics are made up of starches, cellulose or biopolymers, obtained from renewable sources, such as food waste.

Starch plays a large role in about half of all bioplastics that are in use in the market today. These bioplastics are completely biodegradable, durable and perform like traditional petroleum-based plastics. Starch-based bioplastics are made from renewable plant-based sources, such as corn and grasses, and can be used to make a variety of products that are suitable for storing foods, without the risk of unwanted chemicals leaching into the food. When disposed of in the landfill, ordinary bacteria can digest the starch during biodegradation.

Enzymes in environmental remediation

Recall that enzymes produced by bacteria can play a role in the degradation of plastic waste. Other types of waste in the environment can also be treated with the use of enzymes, allowing for the degradation of harmful compounds that would otherwise be difficult to remove mechanically. Bioremediation is the process of using microorganisms, such as bacteria, to clean up waste by metabolising the harmful or toxic compounds into smaller, more harmless products.

Host-guest chemistry

One domain of chemistry, called supramolecular chemistry, involves the study of complexes (supramolecules) formed from several molecules that make a chemical system. One aspect of supramolecular chemistry is host-guest chemistry, the formation of a supramolecular complex formed between two or more molecules or ions that are held together by non-covalent bonds, such as intermolecular forces. The interaction of multiple species is the basis behind using enzymes to attract particular compounds, such as heavy metals, in the environment.

A host-guest complex is generally formed between a larger, synthetic compound, the 'host', and a smaller compound, the 'guest'. Hosts are typically enzymes, while the guests are the toxins or pollutants. The interaction between the host and the guest can be London dispersion forces, hydrogen bonding, dipole-dipole interactions or even an ionic bond. The binding between the host and the guest is specific, similar to the lock-and-key model of enzymes and substrates, allowing for the specific targeting and removal of toxins or other pollutants.

Since the host molecules are synthetic compounds, they can be designed to remove specific toxins or pollutants from wastewater. For example, caesium-137 is a radioisotope that must be removed from nuclear waste in an efficient manner. The host molecule, p-tert-butylcalix[4]arene, binds efficiently to Cs-137 ions, removing them from nuclear waste. The size and specificity of the binding site between the host and guest allows only for the specific interaction between host and guest.

Enzymes used to clean up waste

The host-guest model of supramolecular chemistry can also be applied to the use of enzymes (the host) to clean up other types of waste (the guest) from chemical spills. Oil spills are particularly notorious for being difficult to clean up, especially when spilled in bodies of water. The oil, being nonpolar, forms a separate layer on the surface of the water, a polar substance. Oil also sticks to plants and wildlife, forming a coating that can be very difficult to remove. In the past, oil spills could be trapped and collected by skimming a layer off the water or by adding compounds to break the oil up into smaller droplets, reducing the harm to wildlife, but not completely removing the oil from the ecosystem.

New enzymes have been developed to metabolise the oil, converting it to carbon dioxide and water through a biodegradation process. With this method, more of the oil can be targeted and rather than trying to remove it by physical methods, the oil is converted chemically into harmless products. The enzyme targets the oil droplets, surrounds them and undergoes a reaction, breaking the oil compounds into carbon dioxide and water. Since enzymes are catalysts, the same enzyme molecule can then perform the reaction over and over again. There are no hazardous substances used in the spill or harmful products left for additional clean up.

Enzymes are also used to clean up other types of waste, such as sewage and waste water at water treatment facilities. Even the waste generated industrially at factories can be treated with enzymes to metabolise harmful compounds into smaller, safer molecules.

Enzymes used in biological detergents

Detergents are water-soluble compounds that are used to dissolve impurities, making them effective cleansing agents. Detergents are different from soaps as they are more water-soluble, even in hard water. Detergents are amphiphilic, meaning they have both polar and nonpolar groups, allowing them to attract both polar and nonpolar impurities. The detergent surrounds the impurity, forming a micelle, allowing it to become more soluble in water to wash it away.

Detergents are often mixtures of compounds to improve the performance of the detergent. Newer detergents contain enzymes that are capable of digesting the impurity into smaller compounds, making them even more soluble and easier to wash away. Some detergents can contain a combination of different enzymes to break down different types of stains. For example, lipases break down fat/oil-based stains, proteases break down protein-based stains and amylases break down carbohydrate-based stains (see Table 1). This is particularly beneficial for laundry detergents, which could contain various types of stains in the same wash load including stains from food, grease, grass and body fluids.

The use of enzymes in detergent allows for:

• washing at colder temperatures, reducing energy requirements
• requiring the use of less detergent
• more effective stain removal for a variety of stains
• less pre-treating of stains required with separate products

Green chemistry

What is 'green' chemistry?

Green, or sustainable, chemistry aims to reduce waste and energy to produce safer compounds and to limit the use and production of dangerous or harmful compounds in the process. The principles of green chemistry vary from country to country, but the basic concepts are still the same. Table 1 provides some examples of green chemistry principles.

Applying green chemistry to biochemistry

Use of enzymes

The use of enzymes as catalysts in chemical reactions allows for the specific targeting of substrates in a chemical reaction, which provides for a more efficient reaction. Since enzymes are regenerated following a reaction, less material waste is generated, as a single enzyme molecule can perform several cycles of the same reaction over and over again. Enzymes secreted by microorganisms can also be used to treat the waste, making it safer for disposal.

Choice of solvent

Since many biochemical reactions involve biomolecules, the choice of solvent is often an aqueous medium, rather than a nonpolar solvent which is more of a challenge to dispose of. Often, aqueous solvents for biochemical reaction must be buffered (HL only) to maintain a limited pH range for the molecules involved. The choice of buffer agents can be selected carefully to ensure that the chemical waste produced following the reaction is safe for disposal.

Microscaled experiments

Since cells are extremely small, many biochemical experiments can be performed with small volumes and low concentrations, requiring less materials and generating less waste.

Energy efficiency

To simulate biological conditions, biochemical experiments must be performed at the same temperature that the organism would operate, which often happens to be at temperatures that are energy efficient. For example, the human body operates at 37°C, which is close to room temperature conditions, so only low heat is required. Many traditional chemistry experiments are performed at higher temperatures in order to increase the rate of the reaction, but in biochemistry, high temperatures often results in the denaturing of biomolecules, so high temperatures are not an option.

Safer waste production

Although aqueous solvents are generally used, the waste generated by biochemical reactions could contain compounds that could be infectious or contain microorganisms that should not be released into the local water supply. For this reason, biochemical waste must be treated and handled carefully. Treating live cultures of yeast or bacteria with bleach or a similar disinfecting agent is a common practise in many biochemical laboratories. The bleach kills the cells, so that they are no longer a risk and the culture can often be flushed down the sink with lots of water. The equipment that has come in contact with live cultures can also be treated with bleach to avoid contaminating future experiments. For more robust pathogens, such as viruses, sterilisation with chemical agents is often not enough to ensure that they have been killed. The process of autoclaving uses heat and steam to sterilise waste and equipment.

Challenges and criteria for 'greenness'

When a particular substance to be used in biotechnology is assessed for its 'greenness', there are challenges. There are several different factors that must be examined before a substance can be accepted and classified as being 'green'. Green chemistry metrics are systems used to measure the 'greenness' of a substance, but there are different systems that place value on various principles of green chemistry as well as cost and time.

Yield

Assessing the yield of a reaction is considered by some to be important in assessing the greenness of a process. For reactions with a percentage yield approaching 100%, there would be very little waste from leftover reactants, making the process efficient in terms of waste production, but it may be at the cost of other green chemistry principles. For example, increasing the yield of a reaction may require more energy, reducing the overall greenness of the process, or it may also produce large quantities of an undesirable byproduct, which requires disposal.

Atom economy

Atom economy encourages using all materials involved in the reaction to make the final product, and restricting the production of leftover compounds or byproducts. Atom economy takes into consideration the mass of the reactants, including catalysts, but not the solvent medium that the reaction takes place in, since the solvent is not incorporated into the final product. This measurement encourages the reduction of waste, as a high atom economy (near 100%) is valued as a green principle.