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School biology notes: Carbon, nitrogen & water cycles, factors affecting decay rate

Carbon Cycle, Nitrogen Cycle, Water Cycle and Decomposition

their importance for ecosystems and a section on a rate of decay investigation, factors affecting rate of decay, biogas digester, making compost and preserving food

 Doc Brown's school biology revision notes: GCSE biology, IGCSE  biology, O level biology,  ~US grades 8, 9 and 10 school science courses or equivalent for ~14-16 year old students of biology

 This page will help you answer questions such as ...  Be able to describe and understand the steps in the carbon cycle?  Be able to describe and understand the steps in the nitrogen cycle?   Be able to describe the water cycle?  What factors affect the rate of decomposition of organic material?

Sub-index for this page

(a) Introduction to cycles

(b) The Carbon Cycle  *  (c) The Nitrogen Cycle  *  (d) The Water Cycle

(e) Decomposition - factors affecting the rate of decay of biological material

(f) A simple experiment to investigate effect of temperature on the rate of decay of milk

(g) Biogas from waste - the process, generator designs and rate factors

(h) Making compost - a natural organic fertiliser(i) Food preservation



(a) Introduction to cycles

An ecosystem is all the living organisms in a particular area including non-living conditions (abiotic factors) such as temperature, soil quality, water sources.

Within an ecosystem materials are continually recycled in many complex ways involving biotic (living) and abiotic (non-living) components in ecosystems.

For more on biotic/abiotic factors see Ecosystems and interactions between organisms   gcse biology notes

All living organisms are composed of the chemical elements they obtain from the environment in some way.

Plants will take in compounds of carbon (e.g. carbon dioxide from air), hydrogen (e.g. water through roots) and nitrogen (e.g. nitrates from soil) and the element oxygen from air.

Some plants can metabolise nitrogen from the air directly (e.g. legumes).

These elements and simple compounds are converted into all the complex biological molecules you find in plants such as carbohydrates, fats and proteins.

These are then consumed by plant eating animals, creating biomass that gets passed on up the food chain.

All of these elements and compounds must be recycled by some means back into the environment.

All the nutrients in our environment are being constantly recycled with many inputs balancing the many outputs.

The material might be recycled back into the soil or into the air.

This recycled material may come from animal waste products e.g. faeces or emitted gases!

When plants or animas die, their remains will slowly decay

Decomposer organisms like bacteria and fungi play are a very important part of ecosystems.

To decompose any dead plant or animal material, they secrete enzymes that break the dead organic material down into smaller soluble food molecules which can diffuse into the microorganisms i.e. absorption of nutrients.

Therefore decayed material in the soil is recycled by microorganisms and new plant growth and so re-enters the many complex food chains in an ecosystem.

All dead organisms decay because they are broken down by decomposers (often microorganisms) which digest the once living material replace lost nutrients like mineral ions back into the soil.

The decomposition by microorganisms is favoured by warm, moist and aerobic conditions.

A stable community

If the materials that plants take out of the soil and air to create biomass is balanced by recycled decayed material the community is described as stable - the natural cycle repeats itself continuously.

Poor land management and overuse of agrichemicals leads to an imbalance with a negative impact on the habitats of many plants and animals.


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(b) The Carbon Cycle

  • Know and understand that the constant cycling of carbon is called the carbon cycle.

    • Carbon is an important element in many of the compounds of living organisms and because there is only a fixed amount (ignoring fossil fuel burning) in the 'biosphere' it must be constantly recycled.

    • Know and understand that in the carbon cycle:

    • The natural ways in which carbon dioxide is captured from the atmosphere

      • (a) Most carbon dioxide is removed from the environment by photosynthesis in green plants on land and algae and phytoplankton in water.

        • Most carbon is 'captured' by photosynthesis in the leaves/stems of plants on land on land.

        • The carbon dioxide dissolves in water so photosynthesising green algae and other forms of plankton in lakes, seas and oceans make a major contribution to capturing and recycling carbon too.

        • Note that photosynthesis is relative rapid way in which carbon is absorbed from the atmosphere.

        • The carbon from the carbon dioxide is used to make carbohydrates, fats and proteins, which make up the body of plants and algae and ultimately the food of animals.

          • Its all about creating biomass for most food chains.

        • Photosynthesis uses sunlight energy to convert water and carbon dioxide into sugars like glucose, the 'waste product' being oxygen - though plants need oxygen for their respiration at night!

        • The simplest equation to illustrate photosynthesis is

        • water + carbon dioxide (+ sunlight) == chlorophyll ==> glucose + oxygen

        • When green plants and algae are eaten by animals and these animals are eaten by other animals, some of the carbon becomes part of the fats and proteins that make up their bodies, so carbon based materials and energy are moved up the food chain as biomass transfers.

        • The growth of photosynthesising organism in the seas and oceans is big contributor to the carbon sink (carbon stores) of the planet - all are removing carbon dioxide from the atmosphere..

          • Kelp, a large brown seaweed, grows profusely in shallow nutrient rich seawater.

          • Per unit area kelp stores more carbon than an equivalent growth of plants on land.

          • Trees are another good land-based carbon store.

        • For more see Photosynthesis - importance, rate factors explained  gcse biology revision notes.

        • The carbon store of the oceans is not only increased via photosynthesising organisms, carbon dioxide is slightly soluble in water adding to the carbon sink.

          • Unfortunately, this makes the water slightly more acidic (slightly lower pH) and, combined with warming oceans, this is having a disastrous effect on corals and their rich ecosystems.

        • The formation of limestone and fossil fuels also contribute to the 'carbon sink' and are described next.

      • (b) Some of the carbon dioxide dissolved in the sea becomes calcium carbonate and other calcium minerals and ends up as a sedimentary rock like limestone.

        • All the shells of marine organisms contain carbonates (mainly calcium carbonate CaCO3) e.g. corals and microscopic algae are covered with calcium carbonate. Over millions of years these shells fall to the ocean floor and the debris is compressed to form layers of the sedimentary rock limestone.

        • This mineralisation does store carbon, but this is a very slow geological process over thousands-millions of years.

        • However, carbon dioxide in rain forms 'carbonic acid' that weathers the limestone away releasing some of the carbon dioxide back into the atmosphere - polluted acid rain from burning fossil fuels, due to sulfur dioxide, accelerates the weathering of limestone - just look at medieval statues in ex highly industrial towns!

        (c) The remains of dead animals and plants can also store lots of carbon e.g. peat forms over thousands of years in bogs, and over millions of years some of these remains end up as coal and oil and gas hydrocarbons.

        • Not all the remains of plants and animals get broken down and the carbon oxidised to carbon dioxide.

        • BUT, although this process stores vast amounts of carbon, it is a very slow chemical-geological process over thousands-millions of years and incredibly slow compared to the rate we are burning fossil fuels.

        • In terms of the Earth's ecosystems, the decomposition of these carbon based organic materials from dead plants and animals ensures that habitats can be maintained to support the organisms that live in that particular ecosystem.

          • If this decomposition did not take place via microorganisms, all the waste would stack up and the nutrients needed to sustain new life would not be recycled - so we don't want all the carbon stored.

        • The case of peat bogs is of increasing concern to environmentalists.

          • In marshy areas, it takes thousands of years to create peat bogs form and they store large amounts of carbon (another part of our planet's carbon sink).

          • The low oxygen level and acidic marshy conditions prevent decomposer microorganisms from completely breaking down the plant material.

          • Peat is harvested as a fuel and a cheap compost for gardeners - it does improve soil quality making it more organic and increasing food production (at least on a small scale).

          • The draining of bog lands and the removal of peat is decreasing the carbon sink.

          • Another worrying trend is the warming of arctic tundra lands and the melting of permafrost.

          • Permafrost a thick subsurface layer of soil that remains below the freezing point of water (<0oC) throughout the year, occurring chiefly in polar regions of the northern hemisphere.

          • This is releasing carbon into the atmosphere from oxidation of organic material AND methane gas (CH4) a powerful greenhouse gas.

          • This leads onto the section ....

    • The many ways in which carbon dioxide is returned to the atmosphere

      • (a) When green plants and algae respire, some of this carbon from the glucose from photosynthesis becomes carbon dioxide and is released back into the atmosphere.

        • the overall simplest equation for respiration is the opposite of photosynthesis

        • glucose + oxygen ==> water + carbon dioxide (+ energy)

      • (b) When animals respire some of their biomass carbon becomes carbon dioxide and is released into the atmosphere - summary equation for aerobic respiration as above.

      • (c) When plants, algae and animals die, microorganisms feed on their bodies and carbon dioxide is released into the atmosphere as carbon dioxide when these microorganisms respire - aerobic decomposition.

        • By the time the microorganisms and detritus feeders have broken down the waste products and dead bodies of organisms in ecosystems and recycled the materials as plant nutrients, all the energy originally absorbed by green plants and algae has been transferred, and much of the carbon returned to the atmosphere as carbon dioxide.

        • Animals produce waste (e.g. droppings) that is also broken down by the same microorganisms and detritus feeders.

        • Many carbon compounds are recycled in waste materials from plants and animals to maintain healthy ecosystems.  The decay processes ensure the constant recycling of nutrients for new growth in plants and ultimately providing for animals - the respiration of plants, animals and microorganisms returns carbon dioxide to the atmosphere.
      • (a) to (c) are natural processes that work in harmony, mainly with photosynthesising organisms.

        • What we see is a massive complex system of the continuous recycling of carbon and energy through soil, water and air - transferred by the many complex food chains (of food webs) of plants, algae, animals and the microorganisms and detritus feeders.

      • (d) to (f) are all due to human activity AND not in balance with photosynthesising organisms!

      • (d) Combustion of wood and fossil fuels releases carbon dioxide into the atmosphere.

        • It takes fossil fuels millions of years to form, but using biofuels is MUCH faster!

        • Ignoring fossil fuels, through the carbon cycle, carbon is recycled over and over again, through the atmosphere and food chains over a relatively short period of time.

        • The balance has been shifted in favour of atmospheric carbon dioxide (slowly rising) because of the rapidity with which we are burning fossil fuels which take so long to form.

        • Although described as renewable, even burning biofuels, still releases carbon dioxide back into the atmosphere.

      • (e) Large quantities of carbon dioxide are released in the manufacture of lime and cement - mainly from the latter due the enormous amount of building going on around the world.

        • In both production processes, calcium carbonate (limestone) decomposes giving of carbon dioxide.

        • CaCO3(s)  ==> CaO(s)  +  CO2(g)

      • (f) There are significant changes going on in the way that we manage land.

        • Deforestation of many of the world's greatest forests in South America and Asia is happening now and at an alarming rate.

        • Large areas of forest are being destroyed in favour of removing trees to clear the land to raise cattle and grow crops.

        • This is removing a major source of carbon storage via photosynthesis.

        • The trees are often burned or left to rot AND the soil erodes away exposing it to the weather and oxygen rich atmosphere, so even more organic material in the soil gets oxidised  to carbon dioxide - the microorganisms are decaying residual plant material like leaf litter and they will also release CO2 from aerobic respiration.

        • These processes considerably decrease biodiversity.

See also

FOSSIL FUELS, coal, oil & natural gas and the Carbon Cycle  gcse chemistry revision notes

and Limestone and lime - their chemistry and uses  gcse chemistry revision notes


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(c) The Nitrogen Cycle

  • Nitrogen is an extremely important element for all plant or animal life!
    • It is found in important molecules such as amino acids, which are combined to form proteins.
    • Protein is used everywhere in living organisms from muscle structure in animals to enzymes in plants/animals.
    • Therefore nitrogen containing molecules are passed along food chains.
    • Nitrogen in air cannot be absorbed by plants until it is converted into ions such as nitrite (NO2-) or nitrate (NO3-).
  • Nitrogen from the atmosphere - nitrogen fixation processes:
    • Air contains ~78% nitrogen gas.
    • N2 is a very stable molecule and the word fixation means to convert the nitrogen in air into some chemical form that is soluble in water and plants can use - this can be synthetically in the Haber process or by nitrogen-fixing bacteria.
    • Action of nitrifying bacteria, (nitrogen-fixing bacteria) e.g. they function in the root nodules of certain plants like peas/beans (the legumes), can directly convert atmospheric nitrogen into nitrogen compounds in plants.
      • e.g. nitrogen ==> ammonia ==> nitrates which plants can absorb.
      • This is a naturally occurring nitrogen fixation process.
      • Some nitrogen-fixing bacteria live in soil whilst others live in the swelled nodules in the roots of legumes.
      • When legume plants die and decompose the nitrogen is returned to the soil.
      • Nitrogen ions can leak out of the modules during plant growth.
      • The nitrogen-fixing bacteria have a mutualistic relationship with the plants - the bacteria get sugary food from the plant and the plant gets nitrogen ions from the bacteria (to make amino acids and proteins).
      • However, most plants cannot do this conversion from nitrogen => ammonia, though they can all absorb nitrates, so the 'conversion' or 'fixing' ability might be introduced into other plant species by genetic engineering.
    • The nitrogen from air, combining with hydrogen, is converted into ammonia (NH3) in the chemical industry, and from this artificial fertilisers are manufactured to add to nutrient deficient soils.
      • This done in the Haber process - a synthetic fixation process.
      • However, some of the fertiliser is washed out of the soil and can cause pollution - eutrophication.
    • The energy of lightning is so high it causes nitrogen and oxygen to combine and form nitrogen oxides which dissolve in rain that falls on the soil adding to its nitrogen content. This is also described as a natural nitrogen fixation process - atmospheric elemental nitrogen converted to a compound that enters the soil for plants to use.
      1. N2(g) + O2(g) ==> 2NO(g)
      2. 2NO(g) + O2(g) ==> 2NO2(g) 
      3. NO2(g) + water ==> NO2-(aq) or NO3-(aq) nitrates/nitrites in rain/soil
      4. Incidentally, reactions 1. and 2. can also happen in a car engine, and NO2 is acidic and adds to the polluting acidity of rain as well as providing nutrients for plants! See air pollution and acid rain
      5. Note that the Haber synthesis of ammonia is a synthetic method of nitrogen fixation.
  • Nitrogen recycling apart from the atmosphere:
    • Nitrogen compounds, e.g. protein formed in plants or animals, are consumed by animals higher up the food chain.
    • Then bacterial and fungal decomposers break down animal waste and dead plants/animals to release nitrogen nutrient compounds into the soil (e.g. in manure/compost) which can then be re-taken up by plants.
    • The bacteria and fungi break down proteins in rotting plants and animals and urea in animal waste and convert the nitrogen into ammonia, which is oxidised to nitrite or nitrate ions - so returning the nitrogen to the soil in a form that can be absorbed by plants.
  • Nitrogen returned to the atmosphere:
    • However, the action denitrifying bacteria will break down proteins completely and release nitrogen gas (N2) into the atmosphere.

  • More 'biological detail' of the NITROGEN CYCLE with reference to the above diagram so you can show an understanding of how nitrogen is recycled.
    • Nitrogen gas in the air (78%, ~4/5th) cannot be used directly by most plants and all animals.
      • No animals and only a few specialised plants can directly use the very unreactive nitrogen from air, but all plants nitrogen in some form to synthesise amino acids and proteins for growth and maintenance and for DNA in cell reproduction.
      • However, nitrogen can be changed into nitrogen compounds like nitrates which the plants can use.
      • Animals rely on plants or other animals in the food chain for their source of nitrogen compounds e.g. protein in grass, crops or other animals.
    • The action of lightning can convert nitrogen gas into nitrates.
      • The very high electrical energy discharges from lightning activates nitrogen and oxygen molecules to react and form nitrogen oxides. These dissolve in rain to form nitrates which end up in the soil when rainwater trickles into the soil.
    • There are four types of bacteria involved in the nitrogen cycle
      • (1) Action of Nitrogen-fixing bacteria (nitrifying bacteria) living in root nodules of plants or in the soil, their function is to fix nitrogen gas directly from the atmosphere into a chemical form the plant can metabolise.
        • Members of the leguminous family contain symbiotic bacteria called rhizobia within the root nodules, producing nitrogen compounds that help the plant to grow and compete with other plants. When the plant dies, the fixed nitrogen is released, making it available to other plants and this helps to fertilize the soil.
        • So, leguminous plants like peas, lentils, clover and beans can absorb nitrogen from the air via their root nodules (swellings on the root surface) which contain bacterial enzymes capable of converting ('fixing') atmospheric nitrogen into soluble ammonia/ammonium ions, these are oxidised to the nitrate ion - a nutrient essential for synthesising amino acids, proteins for plant growth.
          • Legumes and their root nodule bacteria are an example of mutualism, because the plant root supplies the bacteria with carbohydrate food (sugars) and minerals and the bacteria supplies the plant with nitrogen in the form of the nitrite  or nitrate ion - different species of nitrifying bacteria produce different ions.
          • This mutual relationship benefits both the plant and its associated bacteria.
          • The process of converting nitrogen in air into nitrogen compounds is sometimes called 'nitrogen fixation'.
        • When these leguminous plants decompose the nitrogen compounds in the tissues and root nodules is returned to the soil - a good composting action.
          • Ions containing nitrogen can diffuse out of the nodules during plant growth.
          • Leguminous plants have a mutualistic relationship with bacteria.
          • The bacteria get food like sugars from the plant and the plants get nitrogen ions from the bacteria to use in making proteins.
      • (2) Action of decomposers - soil bacteria:
        • The function of decomposers, bacteria, fungi and worms in the soil, is to break down the remains of dead animals and plants converting proteins and urea (from animal waste) into soluble ammonia or ammonium ions - so can be absorbed by the roots of plants.
        • This decomposition (decay) returns nitrogen to the soil.
        • This process is sometimes called putrefaction by putrefying bacteria.
        • The ammonium ions are oxidised to nitrate ions (see below), which plants can absorb through their roots to complete the recycling process.
      • (3) Action of nitrifying bacteria:
        • Nitrifying bacteria oxidise ammonia/ammonium ions from the decayed material to form nitrites, which are further oxidised to nitrate ions that be absorbed by plants through their root systems.
      • (4) Action of denitrifying bacteria:
        • Denitrifying bacteria convert nitrates back into nitrogen gas which is returned to the atmosphere.
        • Therefore they are of no benefit to any living organism.
        • These particular bacterial organisms can remove the oxygen from nitrate compounds to form the element nitrogen gas.
        • The action of denitrifying bacteria is of no use to any living organism!
        • The function of denitrifying bacteria is the opposite of the nitrogen-fixing bacteria (1).
        • Denitrifying bacteria are most often found in waterlogged soils, conditions unsuitable for most plant or animal life.
        • These denitrifying bacteria live in anaerobic conditions like waterlogged soils and use the nitrate ion to respire.
        • These denitrifying bacteria use the oxygen rich nitrate ion (NO3-) as an oxidant instead of oxygen gas.
    • Plants absorb nitrates from the soil.
      • Plants get their nitrogen from soil.
      • Plants absorb nitrates (soluble in water) in the moisture that the roots absorb from the surrounding soil.
      • Plants can use the nitrate ion in forming amino acids from which the plant can make its proteins.
      • Nitrogen compounds are then passed along the food chains e.g. animals eat plants (herbivores) and animals eat animals (carnivores).
    • Nitrates are needed by plants to make proteins for growth.
      • Nitrates are an essential nutrient for plants to synthesis amino acids and hence proteins.
    • Nitrogen compounds pass along a food chain or web of food chains.
      • All food chains involve the passing of carbon compounds e.g. sugars, carbohydrates, fats and proteins up to the next trophic level i.e. the consecutive eating along a food chain (and waste produced on the way).
        • e.g. grass ==> cow ==> human
        • Plants make their own protein from nitrates, but animals must obtain it from plants or other animals. In fact the protein is broken down in digestion to amino acids and each animal makes its own proteins from these amino acid residues.
  • Ways in which farmers can increase the nitrate content of soil
    • As plants grow they will use up the available nitrates in soil, which can become deficient in essential nutrients.
    • When the crops are harvested, the nitrate content of the soil is now reduced - its ended up as protein in the grain.
    • Unless the nitrate is replaced, the nitrate content in the soil will decrease with each crop grown.
    • To avoid the soil becoming infertile leading to poor plant growth and deficiency disease, the nitrate must be replaced.
    • There are three ways of doing this.
      1. Spreading an organic fertilisers like animal manure or some composted plant material which is decomposed by bacteria/fungi to release nitrogen compounds into the soil. This is a good method because it is essentially recycling organic substances from animal waste or plant material, both returning nitrogen compounds to the soil on decomposition.
      2. Spreading synthetic fertilisers (e.g. NPK products) made from ammonium and nitrate compounds. Can you name them? However, the use of artificial fertilisers can create pollution problems like eutrophication if overused. See the notes on ...

        Biodiversity, land management, waste management, maintaining ecosystems - conservation

      3. Crop rotation avoids growing the same crop in the same field over and over again. Several different crops are grown each year in a seasonal cycle. The cycle should include a leguminous plant (nitrogen-fixing crop) like beans or peas that will naturally return nitrates to the soil for another crop the following year - the plant itself can also be ploughed into the field.

 


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(d) The Water Cycle and its importance to life

What happens to water on the Earth's Surface?

The water on the Earth's surface is continually being re-cycled.

Water is the most abundant substance on the surface of our planet and is essential for all life.

Water in rivers, lakes and the oceans is evaporated by the heat energy of the Sun's radiation (liquid ==> gas/vapour, an endothermic process).

Water also evaporates directly from leaves of plants in the process called transpiration.

The water vapour formed rises high in warm air convection currents into the atmosphere, cools and forms clouds of condensed water (gas/vapour ==> liquid/solid, an exothermic process).

Eventually the water falls as rain, hail or snow, collectively called 'precipitation'.

If the precipitation falls on land, and any excess rain/melt water runs off into rivers, lakes, seas and oceans and eventually re-evaporates by the sun's energy to repeat the cycle.

Some water will percolate into soil or porous rocks, most becoming ground water, but this will eventually flow into lakes and rivers. Some water will accumulate in artesian wells.

This is known as the water cycle and is essential for all life based on land.

Water is essential to maintain all habitats.

All organisms need water for cellular fluids, and require it for transport systems.

Water is needed for some chemical reactions in all organisms, including photosynthesis in plants.

When the precipitation of water falls on land it (usually) provides clean fresh water for plants and animals.

This flow of fresh water via the water cycle transports nutrients from location to another i.e. from one ecosystem to another.

Water is an important raw material and has many uses See GCSE Chemistry Notes on Water

 

The importance of water to life

If it wasn't for the water cycle raining down freshwater, life as we know it would not exist.

Soil absorbs fresh water and plants take it in through their roots for photosynthesis and transporting dissolved substances like sugars around the plant.

This means some of the water is incorporated into food chains.

Water in animals is returned to the soil and atmosphere by excretion, respiration and sweating.

Most land or aquatic plants and animals need freshwater, apart from organisms adapted to live in salty water.

Salty water is potentially toxic to many organisms if ingested.

All living things on our planet need water to survive and perform all their biological functions - in fact most biochemical reactions need water as a reaction medium.

Therefore a lack of water makes it difficult for many organisms to exist.

 

Estimating the percentage mass transfer of a plant

A large volume of water can pass through a large tree in just one day.

The water is absorbed through the roots, but most is lost from the leaves by transpiration.

If you know the mass of water absorbed by the roots and the mass evaporated from the leaves, you can calculate the % mass transfer of water e.g.

Suppose an oak tree absorbs 3000 kg of water through its roots and loses 2500 kg through transpiration.

Calculate the % mass transfer of water.

% mass transfer = (2700/3000) x 100 = 90%

 

We need good sources of fresh water

We, and most land based animals, need freshwater from precipitation in the water cycle.

In times of drought e.g. in parts of Africa, animals suffer and die from lack of water - uncertainties in weather patterns, maybe worse due to global warming, make the situation worse.

In 'cooler' developed countries, reservoirs provide a constant supply of potable water - fit for domestic use.

In 'hot' dry countries that can afford it, desalination is an option.

Desalination is the process of obtaining pure water from salty water e.g. removing all the mineral salt ions from sea water.

simple distillation diagram All desalination processes are costly - they use lots of energy.

Method 1. Desalination by distillation

The simplest method is distillation in which you boil off pure water in a large heated flask/tank. The thermometer monitors the boiling temperature of the liquid.

From the flask/tank the steam is cooled in the condenser so the water vapour condenses and the water runs into a clean tank/flask. All the much higher boiling mineral salts are left behind as a solid residue.

This process is sometimes called thermal desalination.

A simple laboratory demonstration is illustrated in the left diagram (from GCSE chemistry revision notes).

Method 2. Desalination using reverse osmosis

The other principal method used is reverse osmosis which forces water to go in the opposite direction to concentration gradient rule.

Normally, water will pass through a semi-permeable membrane (right diagram of a partially permeable membrane) from a less concentrated solution to a more concentrated solution i.e. from a higher concentration of water to a lower concentration of water.

Think of the purple circles as the salt ion particles.

In reverse osmosis, the water molecules are forced to go in the opposite direction (left diagram).

(i) Salt water is first treated by filtration to remove any insoluble solid debris like sand or twigs. The soluble salts are obviously left in solution.

(ii) The water is then pumped under very high pressure into a vessel partitioned by a semi-permeable membrane.

(iii) The high pressure forces the water to go in the opposite direction to 'normal' osmosis i.e. from a higher salt concentration to lower salt concentration (from a lower concentration of water to a higher concentration).

(iv) Therefore the salt particles concentrate on the input side of the partially-permeable membrane and pure water on the output side - so the salts are removed to give potable water.

The more concentrated salt water produced is steadily replaced by 'fresh' salt water and the purified water drained off to a clean storage tank.

Research is going on to find more effective membranes to increase efficiency and reduce costs e.g. fabricated graphene sheets are being tested for making semi-permeable membranes.

 For more see Water Treatment, pollution and producing potable water (gcse chemistry revision notes)


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(e) Decomposition - factors affecting the rate of decay of biological material

As already described, waste materials from plants and animals must be recycled to maintain healthy ecosystems and avoid a build-up of too much waste, including dead plants and animals.

The decay processes ensure the constant recycling of the 'elements of life' to provide nutrients for new growth in plants and ultimately providing the minerals, protein and carbohydrate food for animals.

The waste products and dead animals or plants are broken down by decomposers.

Decomposers break down the smaller bits of dead material, in doing so they release waste carbon dioxide, water and energy (from their respiration), and, most importantly, nutrients that plants can use.

The three main types of decomposers are bacteria and fungi microorganisms and detritus feeders.

The latter include millipedes, springtails, woodlice, dung flies and other insects, maggots, slugs and worms - they obtain nutrients by digesting the dead plant and animal material - they are all well equipped with enzymes which they secrete to break the molecules down!

The smaller the pieces of dead material are, the greater the surface area exposed to enzyme action, so helping the decay chemistry to be optimised.

Decomposers decay waste in compost heaps (e.g. in garden) and in sewage works (as part of the purification process to make potable water).

Just as in GCSE chemistry, where you study the factors that control the rates of chemical reactions, we can look at what factors control the rate of decomposition of this organic material.

The rate of decomposition of organic material from dead organisms or their waste if living, is affected by various environmental factors.

Many of the factors you will come across in your chemistry "Factors affecting the rates of chemical reactions"

A note on mouldy food!

The following discussion of the four factors affecting the rate of decay also apply to the rotting of food.

Generally speaking the quantity of mould (microscopic fungi) growing on a portion of food increases exponentially (curve upwards!), but the decay takes days, weeks or even months!

From the graph the average rate of mould growth over the 10 days:

= 17 / 10 = 1.7 arbitrary units of mould per day

For the initial 4 days the average rate is:

2.5 / 4 = 0.63 arbitrary units of mould per day.

See section on Methods of preserving food

 

(1) The availability of oxygen

Many decomposers require oxygen for aerobic respiration.

Therefore the rate of decomposition increases with increase in the ambient oxygen concentration.

This will produce more carbon dioxide, rather than methane gas (biogas - which you may wish to make).

This is the situation with a garden compost heap, where the decay is mainly via aerobic bacteria.

DO NOT confuse this situation with the production of biogas using anaerobic bacteria, where oxygen levels need to be minimised.

If the oxygen levels are low the rate of decomposition is reduced - you get this in the anaerobic conditions in water-logged soils and biogas digesters to make methane fuel.

However, some decomposer microorganisms can respire anaerobically (not needing oxygen) but this is transfers less energy (less exothermic) and these decomposers work more slowly.

Anaerobic decomposition-digestion produces more methane (biogas), rather than carbon dioxide.

See Respiration - aerobic and anaerobic in plants and animals.  gcse biology revision notes

and biogas production (on this page)

 

(2) The temperature conditions

Most decomposers work most efficiently in warm conditions, but not at too high a temperature.

(Remember that enzymes are denatured at high temperatures and these enzymes control the digestion breakdown of organic material at the molecular level.)

(c) doc bAll chemical reactions speed up with increase in temperature, but enzymes work best (fastest) within an optimum temperature range, often around 40oC. The diagram on the right is for an enzyme with an optimum temperature around 35oC.

At higher temperatures, reactant molecules have a greater average kinetic energy to overcome the activation energy barrier and so reactions can proceed faster.

The enzymes secreted the decomposer organisms that digest the dead or waste material, can therefore work faster, more efficiently, as the temperature is increased - but only so far!

However, at temperatures above ~50oC, the protein structure of the enzymes begins to breakdown (denatured) and the decomposition rapidly decreases with further increase in temperature.

The disrupted structure of the protein enzymes means the substrate molecules can't 'dock in' to the active site where the chemical transformation takes place.

The resulting graph shows the result of the two competing effects - showing the optimum temperature and at high temperatures the enzyme controlled digestion reactions stop.

 

(3) The water content of the soil and rotting material

All decomposers (like all of life) require water to survive, no matter where their location.

The vast majority of chemical reactions in living organisms require the medium of water.

Decomposition increases in moist conditions compared to dry conditions.

The vast majority of chemical processes in living organisms need the medium of water.

Waste material to make biogas methane is mixed with water - all organisms need water to carry out their biological processes e.g. enzymes work better mixed with water - better contact with the organic waste being digested-decomposed.

However, there are situations where there is little oxygen and too much water!

A good example is water-logged soil, where it is difficult for air to permeate into the 'mud'.

As a consequence, the water contains little dissolved oxygen, but decomposers do need it to respire - but can do so anaerobically producing some methane - but this is a slower rate of respiration.

Consequently, in water-logged soils, the rate of decomposition is considerably slowed down.

 

(4) The concentration of the 'decay' organisms

The more digesting organisms (microorganisms/detritus feeders) in contact with a given amount of waste plant/animal material, the faster the rate of decomposition-digestion.

The bacteria and fungi that live on dead material secrete their digestive enzymes onto the food to digest it into soluble substances (smaller molecules) that can be absorbed.

This is called extracellular digestion because it happens outside the cells of the microorganisms.

The more microbes the better, because there are more enzymes in greater concentration!


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(f) Simple experiment to investigate effect of temperature on the rate of decay of milk

Introduction

Milk naturally contains an enzyme called lipase and this breaks down fats into glycerol and fatty acids.

In the experiment you add extra lipase to speed up the decay process in milk.

You make the milk alkaline (pH >7) so that the fatty acids formed are neutralised raising the pH to >7 and this changes the colour of an indicator - this colour change is a visual marker for the reaction time.

In other words, as the milk breaks down (decays-decomposes) the pH of the milk decreases.

The experiment measures the relative rate of decay of fats in milk at different temperatures but you could adapt the experiment to keep the temperature constant and vary the concentration of lipase.

I'm not giving precise details of concentrations, and volumes quoted are just typical values.

What I do describe are the principles of the experiment and how to do it.

For an exam you need to appreciate all aspects of the experiment - design, what is needed (apparatus and chemicals), how to do it and how to process the results and draw conclusions.

 

Apparatus and chemicals needed

Thermostated water bath, test tubes, thermometer, 10 cm3 measuring cylinder

Milk,  lipase solution,  sodium carbonate solution,  phenolphthalein indicator solution

 

Investigation method (with added explanation)

For the experiment mixtures:

choose a constant volume and constant concentration of the lipase, sodium carbonate and phenolphthalein solutions,

so, for a fair test, the total volume in each experiment is the same and the only thing that varies is the temperature of the thermostated bath (see diagram).

Procedure:

Set the required temperature for the water bath and check it is constant with a thermometer.

Measure a volume of the lipase solution into a test tube, enough for several experiments.

Measure out a volume of milk in another 2nd test tube and add a few drops of phenolphthalein indicator to the milk - then add a measure of the sodium carbonate solution to this mixture.

NOTE: The solution should turn pink because the solution is alkaline and phenolphthalein turns pink above pH 10, but becomes colourless below pH 8.

Both test tubes are placed in the water bath and left to reach the ambient set temperature of the water bath.

When ready, using a calibrated dropping pipette, you measure 1 cm3 of the lipase into the milk mixture, shake gently to mix thoroughly (or stir with clean glass rod) and start the stopwatch.

The enzyme will immediately start to decompose the milk producing an acidic product (a fatty acid).

Stop the watch and measure the time taken for the pink colour of the indicator to become colourless as the alkaline sodium carbonate is neutralised by the fatty acid formed.

Repeat the experiment several times for each temperature and repeat the whole experiment at different temperatures e.g. 10, 15, 20, 25, 30, 35, 40, 45, 50oC recording everything in a neat clear table - all the values should be recorded and the average time for each temperature too.

You can use ice cubes to cool the water bath to temperatures below room temperature, but its tricky to keep the temperature constant.

 

(c) doc bResults

The reciprocal of the time gives you a measure of the rate of the decay reaction.

e.g. if the reaction time was 40 seconds, the rate is 1/40 = 0.025 s-1.

Using the average times and rates for each temperature, plot a graph of the rate versus temperature.

The rate of reaction is basically a measure of a fixed quantity of decay (unit of fatty acid formed) per unit time.

 

Conclusion

You should find the rate:

(i) increases at first (normal rate of reaction rule from chemistry),

(ii) goes through a maximum at the optimum temperature (typical of an enzyme)

(iii) and the rate falls away at higher temperatures as enzyme lipase protein becomes denatured.

For more details of enzyme theory see Enzymes - structure, functions, optimum conditions, investigation experiments, digestion  gcse biology revision notes

 

Extension to investigation

You can adapt the experiment to keep the temperature constant and vary the concentration of lipase.

You can choose a constant temperature close to the optimum e.g. 30oC for the thermostated bath.

For the experiment mixtures:

choose a constant volume of lipase solution, BUT using different concentrations,

choose a constant concentration AND volume of sodium carbonate and phenolphthalein solution,

so, for a fair test, the total volume in each experiment is the same and the only thing that varies is the lipase concentration.

All the apparatus, chemicals and method are the same for the temperature varying experiment previously described.

Your results should look something like the graph above-right.

Initially the rate of milk decay should be proportional to the enzyme concentration - as long as everything else is kept constant.

 

The background chemistry to this investigation

lipases

Lipids, like many organic molecules, only contain the elements carbon, hydrogen and oxygen.

Lipase enzymes break down lipids like natural fats and oils (triglyceride esters) into glycerol and long chain fatty acids. Lipids are NOT polymers because they are not very long chain molecules.

Enzyme reaction word equation: lipid == lipase enzymes ==> glycerol + long chain fatty acids

The sort of molecular change that takes place - details you do not need to know for GCSE level biology.

However in GCSE chemistry you would be expected to recognise the acidic carboxylic acid group -COOH, an important 'molecular feature' in understanding this decay experiment.

See also

Enzymes - structure, functions, optimum conditions, investigation experiments, digestion  gcse biology revision

See also Enzymes and Biotechnology (gcse chemistry revision notes)


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(g) Biogas from waste - the process and generator/digester/fermenter designs

See also Biofuels & alternative fuels, hydrogen, biogas, biodiesel GCSE chemistry revision notes

Introduction to biogas

Biogas (mainly methane CH4) is produced naturally in marshes, septic tanks and sewers - oxygen deficient places anywhere anaerobic bacteria thrive!

Compost consists of decomposed organic material including plant waste from the garden or food waste from the kitchen.

When enclosed in a compost bin it gradually decomposes into a rich organic material that is a really good natural fertiliser - a good example of partially recycling the biomass from photosynthesis.

Air is admitted to the compost 'heap' and little methane gas is made, in fact aerobic bacteria decomposers are producing carbon dioxide.

Its no use for producing useful quantities of biogas.

As an alternative, using specific microorganisms, by enclosing the organic waste in a tank, you can produce biogas.

Sludge waste from a sewage works (animal waste!) or a sugar factory (plant waste) can be used to make gas on a larger scale.

So, microorganisms (anaerobic bacteria) can be used to break down organic waste under anaerobic conditions to produce biogas, which is mainly the hydrocarbon methane gas, CH4.

Biogas can be produced from variety of waste raw 'organic' materials such as agricultural waste, manure, municipal waste, plant material, sewage, green waste or food waste.

Biogas is produced by anaerobic digestion with methanogen or anaerobic microorganisms, which digest biodegradable materials.

Specially grown crops of maize are used in some large-scale biogas digesters.

The residue from the digestion process can be used as rich source of fertiliser.

 

Advantages of using biogas-methane

(a) The biogas can be burned like any other fuel to produce heat.

Biogas is a relatively cheap fuel for cooking, heating, vehicle fuels and small scale production of electricity.

The heat can be used to generate steam to drive a turbine and electrical generator.

This is quite handy for small scale electricity production in remote areas far from a national grid supply. It could also power road vehicles too.

(b) Theoretically it is eco-friendly, its a renewable resource and carbon neutral.

The decomposed plants are replaced by new crops, and, with the animal waste from eating plant material, the carbon is recycled by carbon dioxide formation on burning.

The growth of new crops removes and balances the same carbon dioxide by the process of photosynthesis in plant leaves.

(c) The raw materials for biogas are relatively cheap and readily available, mainly from agricultural sources.

(d) Burning biogas is also eco-friendly because it is a relatively clean fuel, although it produces carbon dioxide and water on combustion it does not produce much pollutant gases such as sulfur dioxide, oxides of nitrogen or carbon or hydrocarbon particulates.

(e) The leftover waste after digestion can be used as a fertiliser.

(f) In developing countries biogas generation advantages include (i) reduces soil and water pollution, (ii) its a simple and low-cost technology that encourages a green recycling economy and (iii) a healthier and less polluting cooking alternative.

Animal dung makes a great source of biogas on a small scale for cooking.
 

Disadvantages of using biogas-methane

(a) At the moment biogas cannot be produced on a huge scale.

(b) An unfortunate disadvantage is that the systems used in the production of biogas are not efficient.

The biogas contains Impurities and even after refinement and compression, it still contains impurities.

(c) There have been few recent technological advancements.

(d) Biogas is less suitable for dense Metropolitan Areas.

(e) Unfortunately, by its nature, biogas cannot be readily stored as a liquid - you need a very high pressure and a very low temperature to liquefy it (boiling point of methane is -161oC at normal atmospheric pressure!).

Therefore the biogas from the digester must be used immediately for cooking, heating, lighting or using the heat from combustion to make steam to drive a turbine-generator to make electricity.

 

The composition of biogas

Typical values are quoted below, but a wide variation depending on the source of the organic material.

Component of biogas % in biogas Comments
methane, CH4 50 to 80% the fuel gas
carbon dioxide, CO2 15 to 50%  
water vapour, H2O variable  
traces of other gases < 5% small amounts of H2S, N2, H2, CO

 

The design of a biogas generator - also called a digester or fermenter

All biogas generators have the same basic design and are based on a tank of varying size.

The tank has to hold sufficient amount of rotting organic matter to ensure a steady production of biogas.

The starting organic waste material can be animal dung, farm waste like slurry or garden waste.

The waste material is digested in a tank to which the microorganisms are be added.

You need an input pipe to inject the waste organic material into the tank.

You also need an output pipe to extract the residue (waste slurry), which can be used as a fertiliser.

Batch biogas generators

You manually fill the biogas generator with a relatively small amount of waste material, the batch to be digested.

The batch is left to digest and when no more gas is produced you have to extract the residue (by-product for fertiliser).

Then the biogas generator is then completely cleaned out and fresh lot of organic waste put in and the process repeated to make the next batch of biogas.

This means you cannot have a continuous stream of biogas.

Continuous biogas generators (the diagram above is more like a continuous process)

With a continuous biogas generator, the organic waste is continually fed in through the inlet pipe and, at the same time, the residue of digested waste is continually removed to be used as fertiliser.

This system allows for a continuous supply of biogas, a big advantage over the batch process system and a better design for larger scale production.

The best optimum reaction conditions for producing methane

The factors affecting the rate of decay were discussed in detail in section (f), so just a brief summary is repeated here.

To keep the microorganisms continuously anaerobically respiring away as efficiently as possible!

1. Warm conditions e.g. a constant temperature of around 35oC to 45oC - an optimum temperature for many enzymes, which actually carry out the biochemical processes of digestion.

biogas generator optimum temperature graph for enzymes in anaerobic bacteria gcse biology igcse exam revision

A typical enzyme graph of rate of reaction versus temperature.

(i) Initially rate increases with increase in temperature, molecules have more kinetic energy, more forceful fruitful collisions to break bonds and form new products e.g. CH4.

(ii) However, above ~50oC, the enzyme starts to be become denatured, the protein structure of the active site is altered and cannot function properly, and the rate dramatically falls with further increase in temperature.

2. Exclusion of oxygen, so anaerobic decomposition takes place via anaerobic respiration.

3. Mix the waste with water to make a sort of slurry to give a better reaction medium.

4. A high concentration of decomposer microorganisms - some will be already present in the animal/plant waste, but you can add more to increase their concentration.

biogas generator graph of rate versus enzyme concentration gcse biology igcse exam revision

Initially the rate of decay to produce biogas is proportional to the enzyme concentration, which in turns depends on the concentration of anaerobic bacteria.

See also Biofuels & alternative fuels, hydrogen, biogas, biodiesel GCSE chemistry revision notes

and factors affecting the rates of chemical reactions GCSE chemistry revision notes


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(h) Making compost - a natural organic fertiliser

Compost is all about recycling organic kitchen or garden waste to make a natural organic fertiliser and return useful nutrients to the soil for crops or garden plants - we are usually talking about a relatively small scale operation.

The 'ideal conditions' for decomposers like bacteria and fungi to do their 'stuff'!

Some rates of reaction ideas from chemistry come in handy as well as the decay factors described above.

1. Its best if the compost material is shredded to increase the surface area for the decomposers to 'attack'.

2. The compost bin sides should have holes/mesh to allow air in (provides oxygen) and circulate - many microorganisms need oxygen for aerobic respiration.

Some microorganisms do not need oxygen for respiration (anaerobic), but they work more slowly.

For more details see Aerobic and anaerobic respiration

3. Warm conditions favour faster decay, hopefully the bulk of the composting material warms up from the heat released by the decomposition reactions to further speed up the decay.

Every 10o rise in temperature roughly doubles the rate of decay - but not too high or the microbial enzymes are denatured above 50oC and the organisms die.

Some compost bins are thermally insulated to keep heat in, but they must still be able to allow air to enter and circulate e.g. a mesh intake or some regular holes in the side of the compost bin.

4. The compost should contain some moisture, but not to dry or too damp - water is produced by the aerobic respiration of the decomposer microorganisms, but more is needed for the decomposer organisms to carry out their chemistry - water is both a reactant and a solvent for many biochemical processes.

5. You can add compost makers (decay accelerators) to speed up the process,


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(i) Food preservation methods

Food preservation techniques are important to

Increase the shelf life of food products and ensure we don't suffer from food poisoning due to contamination from pathogens.

Shelf life is the length of time that a commodity may be stored without becoming unfit for use, consumption, or sale. It might refer to whether a commodity should no longer be on a pantry shelf and unfit for use, or just no longer on a supermarket shelf (unfit for sale, but not yet unfit for use).
 

Here, to make the food product as safe as you can, you want to

minimise the risk of contamination, and slow down the rate of decay as much as possible.

Therefore we need to apply our knowledge of the 'rate of decay' factors described in a previous section and the technicalities of food packaging e.g.

you can slow down the decomposition of food by reducing the temperature, minimising water content and keeping out air (oxygen) and potential pathogens.

Methods involved

1. Keeping the food at a low temperature to slow down the rate of decay e.g. storing food products appropriately in a refrigerator (~2-4oC ideally, NOT 0oC or food freezes!)) or a freezer - the latter is so low in temperature (e.g. -18oC) it stops decay all together!

The lower the temperature the lower the rate the microorganisms can degrade the food and therefore reproduce - less organisms - less decay- slower rate of decomposition.

This is all about slowing the rate of the enzyme decay chemical reactions.

2. If it is possible, and appropriate, to reduce the water content in food, this removes the medium the microorganisms need to survive and reproduce.

You can also add salt and/or sugar to food causes microorganisms to lose water by osmosis, denaturing the microbial cells and killing them - but note that modern dietary views advise us to minimise our intake of salt and sugar!

3. Storing the food in airtight conditions ensures neither oxygen or pathogens from air can get in and contaminate the food.

Food cans can be filled and sterilised at high temperatures to kill pathogens and the cans sealed under high pressure.

4. Many products are airtight sealed in plastic packages from which all the air (including oxygen) is removed - this is vacuum sealing and completely inhibits any microorganism from respiring aerobically.


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Some learning objectives based on the above notes

  • Be able to demonstrate an understanding of how recycling can reduce the demand for resources and the problem of waste disposal, including ....
    • Paper from wood - recycling paper reduces the number of trees to be cut down (e.g. deforestation) and both transport and energy costs are reduced. Recycled paper has become quite acceptable for many paper based products.
    • Plastics from limited oil reserves - oil is becoming increasingly expensive and the reserves will not last forever, so recycling plastics makes the oil go a bit further and reduces waste that is often not biodegradable or take a very long time to degrade and decompose.
    • Metals from limited mineral ore deposits - high grade ores are being used up and less economic lower grade ores are increasingly exploited using even more energy, often from burning fossil fuels.
      • We are using up lots of non-renewable resources e.g. like fossil fuels and metal ores.
      • However, in the case of metal ores, we can recycle metals to reduce costs, including energy bills, and make the original ore source go further.
      • BUT note that recycling isn't without its costs and inconveniences. Recycling involves collection of waste, sorting into different material categories, purifying each material and then dealing with the residual waste.
        • Sorting can take time and some materials are difficult to separate efficiently e.g. plastics, whereas iron objects can be readily separated with a magnet.
        • Sorting equipment can be expensive and some sorting is done by hand.
        • Recycled material is often not as good as the original material and cannot be recycled forever. Its easy to recycle metals like iron, steel, aluminium and copper many times, though each time useful metal is lost, but plastics and paper can only be recycled a few times.
    • All living things are made of elements like carbon, nitrogen, hydrogen and oxygen which are all obtained from the environment they live in e.g. from the air, soil or water.
    • By one means or other these elements are returned to the environment as e.g. carbon dioxide in air, water or nitrogen in air or nitrogen compounds in soil.
    • If this did not happen, new life could not be formed from the living feeding on pre-existing food (alive or dead).
    • Food chains and decomposers play important roles in this recycling as exemplified by the carbon cycle and nitrogen cycle, both of which are illustrated and described below.
    • The function of bacteria, decomposers, food chains etc. is all explained.
  • Be able to show an understanding of how carbon is recycled (CARBON CYCLE diagram above):
    • a) during photosynthesis plants remove carbon dioxide from the atmosphere
      • carbon dioxide + water == light energy/chlorophyll  ==> glucose + oxygen

      • This is the process by which plants make food, for themselves, and for most animal life, including us too!

      • Note that the only way carbon dioxide is removed from the air is photosynthesis in green land based plants or marine organisms like phytoplankton (this point ignores long term formation of carbonate rocks like limestone).

    • b) carbon compounds pass along a food chain
      • All food chains involve the passing of carbon compounds e.g. sugars, carbohydrates, fats and proteins up to the next trophic level i.e. the consecutive eating along a food chain (and waste produced on the way).
        • e.g. grass ==> cow ==> human
    • c) during plant or animal aerobic respiration organisms release carbon dioxide into the atmosphere
      • sugars e.g. glucose + oxygen ==> carbon dioxide + water (+ energy)
      • this is the main aerobic energy releasing process in most living organisms.
    • d) decomposers release carbon dioxide into the atmosphere - slow aerobic respiration
      • Microorganisms like bacteria and fungi in the soil feed off decaying plant material and animal droppings or remains.
      • Most dead plant matter consists of cellulose which most animals can't digest, but bacteria and fungi, do have the enzymes to break it down and without their help there would be no carbon cycle.
      • Most of these bacteria and fungi respire aerobically so they need a good supply of oxygen to produce the carbon dioxide essential to keeping the carbon cycle going.
    • e) combustion of fossil fuels releases carbon dioxide into the atmosphere
      • Coal, formed millions of years from the remains of tropical plant material, mainly consists of carbon,  Burning coal produces a lot of pollution as the greenhouse gas carbon dioxide.

        • The main reaction on burning is ...

        • carbon + oxygen ==> carbon dioxide

        • C(s) + O2(g) ==> CO2(g)

      • Natural gas (mainly methane) and petrol molecules like octane (and lots of other molecules) from oil and gas reserves.

        • methane + oxygen ===> water + carbon dioxide

        • octane + oxygen ===> water + carbon dioxide
  • HT only: Be able to show an understanding of how nitrogen is recycled (NITROGEN CYCLE diagram above):
    • a) Nitrogen gas in the air (78%, ~4/5th) cannot be used directly by most plants and all animals.
      • No animals and only a few specialised plants can directly use the very unreactive nitrogen from air, but all plants nitrogen in some form to synthesise amino acids and proteins for growth and maintenance and for DNA in cell reproduction.
      • However, nitrogen can be changed into nitrogen compounds like nitrates which the plants can use.
      • Animals rely on plants or other animals in the food chain for their source of nitrogen compounds e.g. protein in grass, crops or other animals.
    • b) Nitrogen-fixing bacteria living in root nodules of plants or in the soil can fix nitrogen gas.
      • Leguminous plants like peas, lentils, clover and beans can absorb nitrogen from the air via their root nodules (swellings on the root surface) which contain enzymes capable of converting ('fixing') atmospheric nitrogen into soluble nitrate - a nutrient essential for amino acids, proteins and therefore plant growth.
        • Legumes and their root nodule bacteria are an example of mutualism (see section 3.19 b) because the plant root supplies the bacteria with carbohydrate food and minerals and the bacteria supplies the plant in the form of the nitrate ion.
        • The process of converting nitrogen in air into nitrogen compounds is sometimes called 'nitrogen fixation'.
    • c) The action of lightning can convert nitrogen gas into nitrates.
      • The very high electrical energy discharges from lightning activates nitrogen and oxygen molecules to react and form nitrogen oxides. These dissolve in rain to form nitrates which end up in the soil when rainwater trickles into the soil.
    • d) Decomposers break down dead animals and plants
      • Decomposers, e.g. various organisms like bacteria, fungi or worms can break down dead animals or plants. They break down proteins to amino acids.
    • e) Soil bacteria convert proteins and urea into ammonia or ammonium ions.
      • Decomposer bacteria in the soil can change proteins from dead plants/animals and urea in animal urine/droppings into ammonia/ammonium ion compounds.
      • d) plus e) is sometimes called putrefaction by putrefying bacteria.
    • f) Nitrifying bacteria convert this ammonia to nitrates - the process of nitrification
      • Nitrifying bacteria oxidise ammonia/ammonium ions from the decayed material to form nitrates, the nitrate ion can be absorbed by plants through their root systems.
    • g) Plants absorb nitrates from the soil.
      • Plants absorb nitrates (soluble in water) in the moisture that the roots absorb from the surrounding soil.
      • Plants can use the nitrate ion in forming amino acids from which the plant can make its proteins.
    • h) Nitrates are needed by plants to make proteins for growth.
      • Nitrates are an essential nutrient for plants to synthesis amino acids and hence proteins.
    • i) Nitrogen compounds pass along a food chain or web of food chains.
      • All food chains involve the passing of carbon compounds e.g. sugars, carbohydrates, fats and proteins up to the next trophic level i.e. the consecutive eating along a food chain (and waste produced on the way).
        • e.g. grass ==> cow ==> human
        • Plants make their own protein from nitrates, but animals must obtain it from plants or other animals. In fact the protein is broken down in digestion to amino acids and each animal makes its own proteins from these amino acid residues.
    • j) Denitrifying bacteria convert nitrates to nitrogen gas.
      • Particular bacterial organisms can remove the oxygen from nitrate compounds to form the element nitrogen gas.
      • These denitrifying bacteria live in anaerobic conditions like waterlogged soils and use the nitrate ion to respire.
      • This is the opposite function of the nitrogen-fixing bacteria (b).
  • Know that many trees shed their leaves each year and most animals produce droppings at least once a day.

  • All plants and animals eventually die and know that microorganisms play an important part in decomposing this material so that it can be used again by plants.

  • Appreciate that the same material is recycled over and over again and can lead to stable communities.

    • You are expected to use your skills, knowledge and understanding to evaluate the necessity and effectiveness of schemes for recycling organic kitchen or garden waste.

    • Like using a compost bin!, to which you can add garden waste and kitchen waste. Its best if the compost material is shredded and the compost bin sides have holes/mesh to allow air in and circulate. You can add compost makers (decay accelerators) to speed up the process, but hopefully the bulk of the composting material warms up by heat released by the decomposition reactions to further speed up the decay.

  • a) Appreciate that living things remove materials from the environment for growth and other processes.

    • Plants need carbon as carbon dioxide from air, hydrogen as water, oxygen from air/water and nitrogen from air/soil or as nitrates from the soil, plus other minerals via water through the roots.

    • From these elements and compounds, plants can make carbohydrates, fats and proteins as well as a source of absorbed minerals.

    • Therefore, when animals eat plants they digest the carbohydrates, fats, proteins and minerals, and then convert these materials into their own fats and proteins.

    • Know that these materials are returned to the environment either in waste materials or when living things die and decay.

      • These means all the essential elements of life are recycled through the soil and can re-enter the food chain again.

  • b) Know and understand materials decay because they are broken down (digested) by microorganisms.

    • Know that microorganisms are more active and digest materials faster in (i) warm, (ii) moist and (iii) aerobic conditions.

      • (i) Warm conditions help speed up the chemical reactions of decay.

      • (ii) Water is an important medium for the reactions of living organisms.

      • (iii) Aerobic conditions require well oxygenated soil ie air able to circulate into the soil and litter.

  • c) The decay process releases substances that plants need to grow.

  • d) Know and understand that in a stable community, the processes that remove materials (plant/animal growth) are balanced by processes that return materials (microorganism decay) and the materials are constantly cycled (in a way 'recycled').

  • Revise and practical work-investigations that helped develop skills and understanding which may have included the following (which should also be revised, helps in understanding 'how science works' and context examination questions):

    • designing and carrying out an investigation to measure the rate of decay of bread by, for example, exposing cubes of bread to air before placing them in sealed Petri dishes at different temperatures and/or different moisture levels,

    • investigating the rates of decay using containers (eg thermos flasks) full of grass clippings, one with disinfectant, one with dry grass, one with wet grass and one with a composting agent.

      • If the container is sealed, a thermometer or temperature probe can be placed through a cotton wool plug to monitor the temperature

    • potato decay competition, using fresh potatoes - you decide on the environmental conditions and the rate of decay is measured over a 2 week period,

    • using a sensor and data logger to investigate carbon dioxide levels during the decay process.

  • Biogas (mostly methane CH4 and some carbon dioxide), is formed by the anaerobic decomposition-fermentation of organic waste by microorganisms (bacteria with right enzymes to decompose organic compounds).

    • Organic waste eg plant or animal from domestic refuse (waste food), farm waste (usually from animals), sewage sludge waste, factory waste (from sugar factories) sources etc. is broken down by microorganism to the simplest organic compound, namely methane.

    • It can be carried in quite simple biogas fermenters, sometimes called biogas digesters or biogas generators.

    • The anaerobic fermentation should carried out in the absence of air with the right bacteria and at a constant temperature appropriate to the optimum rate of catalysis of the enzymes in the bacteria e.g. 30-40oC.

    • The biogas is easily stored because it isn't easily liquified and is an explosive flammable gas.

    • The gas can be used directly for heating, lighting and cooking.

    • The gas can also be burned to provide heat to make steam to drive a turbine and electrical generator.

    • Biogas generation can be done on a small domestic scale or large scale and the residue (what's left after tapping off the biogas) can be used as fertiliser.

    • All this waste will rot naturally, often under aerobic conditions, so its worth noting, that, disposing of organic waste in a biogas generator in this way, is better than letting the methane diffuse into the atmosphere where its acts as a powerful greenhouse gas.

    • All biogas generators will have features in common ...

      • an inlet for the waste organic material to be fermented,

      • a valve controlled outlet for the biogas formed,

      • an outlet for the waste material left over after the digestion has finished.

    • Biogas generators (biogas digesters or biogas fermenters) are designed to operate in one of two ways ...

      • In a batch process, the biogas is made in small amounts or batches i.e. the biogas generator is filled up and left to ferment, the biogas is continually tapped off once the anaerobic fermentation starts and then when gas production falls significantly the residue is cleaned out. The generator is then re-filled new organic waste material and the whole process repeated.

        • Cheaper batch process technology than continuous process because of simpler digester design.

        • Batch processes are not as efficient because after each batch has fermented the process must be stopped and the generator stopped, cleaned and re-filled to restart.

      • In a continuous process, the waste organic material is continually fed/pumped into the generator, the gas continually drawn off and the residue continually removed/pumped out.

        • The continuous process generator employs more costly technology because of the extra pumps needed.

        • A continuous process is more efficient and economic than a batch process, no stopping, cleaning out and re-filling required.

      • Either production method requires good temperature control of 30-40oC, so biogas generators may need insulation if too cold or a heating source if too cold.

      • Ideally the biogas generator should be sited near the source of organic waste e.g. a small scale batch process on a farm or a large scale continuous process at a sewage farm.

  • The use of biofuels has both environmental and economic benefits.

    • Biofuels should be 'carbon neutral', that is the carbon dioxide they release on burning is re-absorbed by the plants the carbon originally came from.

    • On burning they do not release sulfur oxides that cause acid rain.

    • Biogas digesters are a good way of using potentially harmful and polluting organic waste (contain pathogens), rather than just dumping it in the ground, where, it will still break down and release methane - a powerful greenhouse gas contributing to global warming.

    • In poor rural areas biogas from animal dung is a convenient way of providing heat for cooking, especially if wood is scarce and in general the raw waste organic material is cheap and readily available.

Practical work you may have done

  • building a simple biogas generator to collect methane and demonstrating how the methane can be burned as a fuel

  • investigating and designing a way of measuring the gas output of a biogas generator and compare the amount of gas produced by different materials.


See also

Ecosystems - biotic & abiotic factors - interactions between organisms - interdependency  gcse biology notes

Food chains, food webs and biomass   gcse biology revision notes


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