A2 Biology, topic 5

  • Created by: Abbie
  • Created on: 14-09-19 13:50

Photosynthesis overview

Photosynthesis stores energy in glucose, so can be defined as the process during which energy from light is used to make glucose from water and carbon dioxide (the light energy is converted to chemical energy in the from of glucose). The overall equation is:

6CO2 + 6H2O + energy -> C6H1206 + 6CO2

However, photosynthesis is a complex metabolic pathway that involves many intermediate reactions and can be described in 3 main stages:

  • Capturing the light- by choloplast pigments like chlorophyll
  • Light-dependent reaction- an electron flow is created due to light's effect on chrorophyllm causing photolysis, which splits wtare into protons, electrons and oxygen. The products are reduced NADP, ATP and O2
  • Light-independent reaction- Also called the Calvin cycle, it doesn't use light energy directly, but relies on the products of the light-dependent reaction

The energy produced in photosynthesis is stored in the glucose until plants release it during respiration. Animals then obtain glucose by eating plants/other animals, then respire using the glucose to release energy

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Adaptations of the leaf for photosynthesis

  • Large surface area- allows as much sunlight as possible
  • Leaves have minimal overlapping to avoid shadowing
  • Thin- short diffusion pathway
  • Stomata that open and close in response to changes in light intensity 
  • Has a network of xylem that brings water to leaf cells and phloem that carries away the sugars produced in photosynthesis
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ATP overview

Cells can't get energy directly from glucose, so ATP is produced during respiration to carry the energy to where it's needed. It's synthesised during a condensation reaction between ADP and Pi, using energy from the breakdown of glucoe. The energy is then stored as chemical energy within the phosphate bonds. When ATP diffuses to the part of the cell it's needed, it's hydrolysed back into ADP and Pi and the enrgy is released. The ADP and Pi are recyled, and the process repeats.

ATP has specific properties that make it a good energy source:

  • Only stores/releases small manageable amounts of energy, so none wasted as heat
  • Small and soluble, so easily transported around the cell
  • Easily broken down, so energy can be instantly released
  • Quickly re-made
  • Can make other molecules more reaction via phosphorylation
  • Can't pass out of cells, ensuring that the cell always has an immediate source of energy
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Technical terms for photosynthesis/respiration

  • Metabolic pathway- series of small reactions controlled by enzymes
  • Phosphorylation- adding a phosphate group to a molecule
  • Photophosphorylation- adding a phosphate to a molecule using light
  • Photolysis- the splitting of a molecule using light energy
  • Photoionisatopn- when light energy 'excites' electrons in an atom/molecule, giving them more energy and causing them to be released. This creates a positively-charged ion
  • Hydrolysis- splitting of a molecule using water
  • Decarboxylation- the removal of carbon dioxide from a molecule
  • Dehydrogenation- the removal of hydrogen from a molecule
  • Redox reactions- those that involve oxidation and reduction; the oxidation of one molecule always leads to the reduction of another. Oxidation also refers to a molecule losing hydrogen/gaining oxygen and reuction gaining hydrogen/losing oxygen
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Co-enzymes in Photosynthesis and respiration

Co-enzymes are molecules that aid the function of an enzyme by transferring a chemical group from one molecule to another:

  • The co-enzyme in photosynthesis is NADP, which transfers hydrogen from one molecule to another, meaning that it can reduce or oxidise a molecule
  • In respiration, co-enzymes include NAD, co-enzyme A and FAD. FAD is involves in the Krebs Cycle, co-enzyme A in the Link Reaction and NAD works throughout respiration to catalyse the removal of hydrogen from substances and transfer this onto other molecules involved in oxidative phosphorylation
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Photosynthesis and the chloroplasts

Photosynthesis occurs in the chloroplasts of plant cell. Chloroplasts are flattened organelles surrounded by a double membrane. Thylakoids are stacked up in the chloroplasts into grana, which are linked together by lamellae. Chloroplasts contain photosynthetic pigments (e.g. chlorophyll a and b) which absorb the light energy needed for photosynthesis. They're found in thylakoid membranes and are attached to proteins; together, the protein and pigment is called a photosystem.

Two photosystems are used by plants to capture light energy, these are photosystem I (PSI), which absorbs light best at a wavelength of 700nm and photosystem II (PSII), which best absorbs light at 680 nm.

The stroma is within the inner membrane od the chloroplast; this is a gel-like substance that contains enzymes, sugars and organic acids. Carbohydrates that're produced by photosynthesis and not used straight away are stored as starch grains in the stroma. 

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Photosynthesis' two stages

Light-dependent reaction:

  • Needs light energy to occur, happens in the thylakoid membranes of chloroplasts. Here, light energy is absorbed by chlorophyll in the photosystems. This excites the chlorophyll's electrons , leading to their eventual release, causing chlorophyll to be photoionised
  • Some of the energy from the relaesed electrons is used to add a phosphate group to ADP to form ATP, and some is used to reduce NADP to from reduced NADP. The ATP transfers energy, and the reduced NADP transfers hydrogen to the light-independent reaction. During the process, water is oxidised to oxygen
  • During this reaction, the energy resulting from the photoionisation of chlorophyll is used for 3 things; to make ATP from ADP and Pi (photophosphorylation), mading reduced NADP from NADP and spliting water into protons, electrons and oxygen (photolysis)

Light-independent reaction:

  • Also called the Calvin Cycle, it doesn't use light energy directly, but does rely on the process of the LDR
  • Takes place in the stroma of the chloroplasts, here the ATP and reduced NADP from the LDR supply the energy and hydrogen to make simple sugars from oxygen
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Non-cyclic Photophosphorylation

Within the LDR, there are 2 types of photophosphorylation (PP)- cyclic and non-cyclic. Non-cyclic PP produces ATP, Reduced NADP and oxygen. Photosystems (in the thylakoid membrane) are linked by electron carrier, which are proteins that transfer electrons. Together, the photosystems and electron carriers from an electron transport chain; a chain of proteins that excited electrons flow through. The following processes all happen simulatenously:

1. Light energy is absorbed by PSII, exciting electrons in the chlorophyll, causing them to have more energy and be released from the chlorophyll down the electron transport chain to PSI 2. The excited electrons need to be replaced as they move down, so photolysis occurs, splitting water into protons, electrons and oxygen (this is where the oxygen in photosynthesis is made) 3. Excited electrons lose their energy as they move down the chain; this energy is used to transport protons into the thylakoid, so it has a higher concentration of protons than the stroma, forming a proton concentration gradient. As protons move down the gradient into the stroma (via the enzyme ATP sythase, which is embedded in the thylakoid membrane), the resulting energy combines ADP and Pi to form ATP. This process is called chemiosmosis 4. Light energy is abosorbed b PSI, which excites the electrons again to a higher energy level. These electrons are transferred to NADP, along with a proton strom the stroma, making reduced NADP.

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Cyclic Photophosphorylation

CPP only uses PSI, and is called 'cyclic' as the electrons from the chorophyll molecule aren't passed onto NADP, but are passed back to PSI via electron carriers. This means the electrons are recycled and can repeatedly flow through PSI. This doesn't produce any NADP or oxygen and only produces small amounts of ATP

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The Calvin cycle

This occurs in the stroma of the chloroplasts and makes triose phosphate (TP) from CO2 and ribulose bisphosphate (RuBP), a 5C compound. The TP can then be used to make glucose and other useful organic substances. The cycle requires ATP and H+ ions to keep it going. RuBP (starting compound) is regenerated, as it's a cycle:

1. CO2 diffuses into the stroma of the chloroplast and is combined with RuBP (ribulose bisphosphate), a 5C compound. This reaction is catalysed by the enzyme rubisco and produces an unstable 6C compound, which quickly breaks into 2 molecules of 3C glycertae 3-phosphate (GP)

2. The hydrolysis of  2 ATP (from LDR) provides energy from GP to turn into 2 3C triose phosphates (TP). This also requires H+ ions from reduced 2 NADP (LDR) which is converted into NADP. Some TP is converted into useful organic compunds, and some continues in the cycle to regenerate RuBP

3. 5/6 TP molecules in the cycle are used to regenerate RuBP, rather than making hexose sugars. This uses up the rest of the ATP (1) from the LDR

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Organic substances in photosynthesis

The Calvin cycle is the starting point for the production of all of the plant's organic substances, as TP and GP are converted into useful organic substances, including carbs, lipids and amino acids:

  • Carbs- hexose sugars (simple 6C sugars) like glucose are made by joining 2 TPs together. Larger carbs like starch are made by joining hexose sugars together in different ways
  • Lipids- made with glycerol, which is synthesised from TP. and fatty acids, which are synthesised from GP
  • Amino acids- some are made from GP
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Products of the Calvin Cycle

The cycle needs to turn 6 times to make 1 hexose sugar:

  • 3 turns of the Calvin Cycle produces 6 TP, as 2 are made from each carbon dioxide molecule
  • 5/6 of TP produced is used to regenerate RuBP, so that for every 3 turns, only 1 of the TPs produced is used to make a hexose sugar
  • TP is a 3C molecule and as hexose sugars have 6C, 2 TP molecules are needed to make 1 hexose sugar. This means the cycle has to turn 6 times to produce 1
  • These 6 turns require 18 ATPs and 12 reduced NADPs from the LDR (3 ATP and 2 NADP are used in each cycle)
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Optimal conditions for photosynthesis

  • High light intensity of a certain wavelength- light needed as energy for the LDR; higher intensity, more energy it provides. Only certain wavelengths of light are suited for photosynthesis, as the photosynthetic pigments chlorophyll a, b and carotene only absorb the red and blue light in sunlight, whilst reflecting the green light. 
  • Temperature around 25 degrees- photosynthesis uses various enzymes, so if the temperature is below 10 degrees, they'll become inactive, but will denature if it's much more than 45. Also, high temperatures cause the stomata to close to conserve water, so less carbon dioxide will enter the leaf, slowing photosynthesis down
  • Carbon dioxide at 0.4%- CO2 makes up 0.04% of gases in the atmosphere, increasing this to 0.4% gives a higher rate of photosynthesis, but any higher will cause the stomata to close

Plants also need a constant supply of water- too little and photosynthesis has to stop, but too much will cause the soil to become waterlogged and reduce the uptake of minerals like magnesium, which is needed to make chlorophyll a

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Limiting factors of photosynthesis

Light, temperature and CO2 can all limit photosynthesis; if any one factor is too high or low, then photosynthesis will be slowed down even if the other 2 are at the perfect levels. Any of the factors can become limiting, depending on the environmental conditions. This can be shown on a graph; once a set factor reaches a saturation point, this stops being the limiting factor (as something else is, and the graph will level off). 

Artificial growers use this information to create an environment increasing the growth/yield by having optimum conditions in a greenhouse/polytunnel:

  • CO2 concentration- CO2 is added to the air, e.g. in a CO2 generator
  • Light- light gets in through glass and lamps provode light at night
  • Temperature- greenhouses trap heat energy from sunlight, warming the air. Heaters/coolers can be used to maintain optimum temp and air circulation systems to evenly distribute air
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Respiration overview

Cells release energy from glucose during respiration to power their biological processes. There are 2 types of respiration:

  • Aerobic respiration- takes place using oxygen, and has 4 stages; glycolysis, the link reaction, the Krebs Cycle and Oxidative Phosphorylation:

C6H12O6 + 602 -> 6CO2 +6H20 + ATP

  • Anaerobic respiration- takes place without oxygen. In plants and fungi it produces ethanol and carbon dioxide and ATP, and in humans it produces lactate and ATP:

Animals: C6H12O6 -> 2C3H603 + 2ATP

Plants: C6H12O6 -> 2C2H5OH + 2CO2 + 2ATP

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Aerobic respiration

Respiration is the process by which plant and animals cells release energy from glucose to power cellular processes. Aerobic respiration requires oxygen, and can be split into 4 stages:

  • Glycloysis- gluocse is split into 2 3C pyruvate molecules. This is an anerobic process that begins both forms of respiration
  • Link reaction- 3C pyruvate undergoes several reactons, forming acetyl CoA
  • Krebs Cycle- Acetyl CoA undergoes a cycle of oxidation-reduction reactions, yeilding ATP, NADH and FADH
  • Oxidative Phosphorylation- electrons associated with NADH and FADH are released from Krebs, and move down an electron transport chain to synthesise ATP. Water is produced as a by-product
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  • Glucose needs to be more reactive before it's split into TP, so 2 ATPs undergo hydrolysis and the 2 phosphate molecules are added to the glucose. This creates a 6C phospharylated glucose. This splitting of ATP both provides the energy to activate the glucose and lowers the activation energy for the later enzyme-controlled reactions
  • The phosphorylated glucose is split into 2 3C molecules called triose phosphate
  • The TP is oxidated, removing hydrogens from each of the molecules. This is transferred to NAD to form NADH
  • Enzyme-controlled reactions convert the TP to pyruvate (3C). During this process, 2 molecules of ATP are regenerated from ADP (from each TP, so 4 in total)
  • The net gain is 2 ATP molecules (total yield is 4), 2 NADH and 2 pyruvate molecules

The enzymes for glycolytic pathway are found in the cytoplasm, so it doesn't reuire any organelles or a membrane to take place. As it doesn't require oxygen, in its absence, the pyruvate produced can be converted into lactate or ethanol in anaerobic respiration, which is needed to re-oxidise the NAD so glycolysis cam continue. But, anaerobic respiration can only yeild a small amount of the energy stored in pyruvate, so it produces less ATP as oxygen is needed to further break it down.

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The Link Reaction

  • Following glycolysis, the pyruvate is actively transported into the mitochondia's matrix, where it undergoes the link reaction
  • First, the pyruvate is oxidised to form acetate. During this, it loses 1C in the form of carbon dixoide, as well as losing one hydrogen
  • The hydrogen is taken up by an NAD to form NADH, which is later used to produce ATP during oxidative posphorylation
  • The 2C acetate is then combined with coenzyme A (CoA) to form acetylcoenzyme A
  • The link reaction occurs twice for every glucose molecule, as 2 pyruvates are made from each glucose during glycolysis
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The Krebs Cycle

  • Involves a series of oxidation-reduction reactions that occur in the mitochondria's matrix. This happens twice for each initial glucose molecule
  • The 2C acetyl CoA combines with a 4C molecule (oxalacetate) to form a 6C molecule (citrate), and the CoA goes back to the link reaction to be re-used
  • The 6C molecule loses 2C in a series of reactions, first becoming 5C, then 4C, undergoing 2x decarboxylation to achieve this. Each time, hydrogentation occurs, removing 2 hydrogens (in total) that're taken up by NAD to produce NADH
  • The 4C molecule (oxalacetate) then undergoes further dehydrogenation, producing FADH and NADH. During this time, 1 ATP is produced due to substrate level phosphorylation, in which a phosphate group is transferred to ADP. 
  • The oxalacetate can then combine with a new acetyl CoA to begin the cycle again

The Krebs Cycle is important in reducing the coenzymes (FAD and NAD) to allow them to carry hydrogen to be used in oxidative phosphorylation. This allows the majority of the ATP yeild from respiration to be produced

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Oxidative Phosphorylation

  • The 3 NADH and 1 FADH from Krebs are used here, as the energy from the electrons within the hydrogen can be used to make ATP. The process involves the electron transport chain and chemiosmosis
  • The mitochondria is the site of OP; the inner membrane (cristae), which contains the ATP synthase, is highly folded to allow a large SA to have as many enzymes and reactions happening as possible in a limited space
  • Hydrogen atoms are released from NADH and FADH, oxidising them. The H atoms are split into protons and electrons
  • The electrons move down the ETC in a series of oxidation-reduction reactions, with the energy lost during at each carrier being used by the electron carriers to actively transport protons from the matrix into the intermembrane space
  • This creates an electrochemical gradient as there's a higher concentration of protons outside the matrix, meaning they diffuse down the gradient and back into the matric via ATP synthase channels that're embedded in the inner mitochondrial membrane. This movement drives the synthesis of ATP from ADP and Pi
  • Chemiosmosis is responsible for ATP production, as it is driven by the movement of protons moving acriss a membrane due to the movement of the electrons creating an electrochemical
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Oxidative Phosphorylation (II)


  • Finally, at the end of the ETC in the matrix, oxygen (from the blood) becomes the final electron acceptor, as it picks up the extra electrons, combining them with the protons to form water as a by-product. The removal of the electrons is important to free up the end of the chain, as otherwise the process couldn't continue. 

The series of electron carriers prevents the energy from the electrons being released in one big step and wasted as heat. Each carrier has a slightly lower energy level. ensuring the electrons can move down an energy gradient and the energy be released slowly and usefully.

The overall ATP yield from respiration is 32, with the majority of this being made during OP.

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Alternative respiratory substrates

  • Respiration of lipids- first the lipids are hydrolysed into glycerol and fatty acids. The glycerol is then phosphorylated and converted into TP, which enters the glycolysis pathway and then Krebs. The fatty acid is broken into 2C fragments, which are converted into acetyl CoA and can then enter Krebs
  • Respiration of proteins- they're first hydrolysed into amino acids, the amino group is removed and they enter at several points depending on the number of carbons. 3C compounds are converted to pyruvate and 4/5 C compounds to intermediates in Krebs
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Anaerobic respiration

Without oxygen, Krebs and OP can't occur, as all the FAD and NAD will quickly become reduced and not be able to function as co-enzymes. So, glycolysis is the only source of ATP. For it to continue, the products of pyruvate and hydrogen (NADH) must constantly be removed. So, the pyruvate needs to oxidise the NADH (allowing it to continue to oxidise TP), which produces either lactate or ethanol. This is catalysed by specific enzymes.  Anaerobic respiration can occur in both plants and animals:

  • In animals, the pyruvate is converted into lactate: pyruvate + reduced NAD = lactate + oxidated NAD. In animals, anaerobic respiration occurs as a means of overcoming a temporary shortage of oxygen, which has survival value, as often although oxygen debt occurs, the muscles need to continue working. The combination of pyruvate and hydrogen is catalysed by the enzyme lactate dehydrogenase, and us used to create lactate. This allows the pyruvate to be removed and the NADH to be oxidised. A total profit is 2ATP is produced. Lactate is carried from muscles to the liver, where it's converted back to pyruvate when more oxygen is available
  • In plants, the pyruvate is converted into carbon dioxide and ethanol. Initially, the pyruvate is converted into ethenal (ethenal hydrogenase) and Co2 is lost. It's then converted into ethanol using ethanol dehydrogenase.
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Ecosystems key terms

  • Producers- photosynthetic organisms that can synthesise energy from sunlight to make their own food
  • Consumers- organisms that obtain their energy by consuming other organisms. Those that directly eat plants are primary consumers, then secondary, tertiary etc
  • Saprobionts (decomposers)- organisms that break down materials, using enzymes, in dead organisms into valuable minerals and elements in a form that can be absorbed by plants. This is mostly done by fungi and bacteria
  • Biomass- the total mass of a living material in a specific area/volume at a given time
  • Food chain- describes the feeding relationship between producers and consumers. This follows the energy transfer in terms of where energy is passed on and lost
  • Food web- describes the way in which many food chains are linked together
  • Apex predator- the consumer at the top of the food chain; they're not eaten by anymore
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Plants produce biomass

Ecosystems have producers, like plants, which produce their own food through photosynthesis. They're able to synthesise organic compounds (e.g. glucose) from atmospheric and aquatic carbon dioxide to be used during respiration; glucose is used as a respiratory substrate. The rest of this glucose is used to make biological molecules such as the cell walls of cellulose, making up plant's biomass.

However, less than 3% of sunlight is generally converted into energy by plants:

  • over 90% of sun's energy is reflected into space by clouds and dust, or absorbed by the atmosphere
  • Low levels of carbon dioxide may limit the rate of photosynthesis 
  • Not all wavelengths of light can be absorbed and used for photosynthesis
  • Light may not all fall on the chlorophyll- so can't be absorbed for photosynthesis
  • Some sunlight misses leaves entirely or is reflected off leaf surfaces
  • Energy losses as energy absorbed by chlorophyll is transferred to carbohydrates during reactions of photosynthesis
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Measuring biomass

Biomass can be measured in terms of the mass of carbon the organism contains, or the dry mass of its tissue per unit area:

  • Dry mass is the mass of an organism in a given area at a given time with the water removed- this is done due to the water content of living tissue varying. The value is given in gm-2/-3
  • To measure dry mass, a sample of the orgaism is dried and weighed at regular intervals; once the mass is constant, you know all the water is gone
  • Measuring mass of carbon means organisms must be killed, so is usually only made on a small sample- may be unrepresentative. The mass of carbon present is generally taken to be 50% of the dry mass
  • You can estimate how much energy is stored in biomass by burning the biomass in a calorimeter- the amount of heat given off tells you how much energy is in it. 
  • When dry biomass is burnt, the energy is used to heat a known volume of water- the change in temp of the water is used to calculate the chemical energy of the dry biomass. You can measure biomass in joules or calories
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  • Gross Primary Production- the total amount of chemical energy (converted from chemical energy) in a given area or volume of a lant. However, plants use 20-50% of this energy for respiration so the remaining chemical energy is called the net primary production: NPP= GPP-R 
  • NPP is available to the plant for growth and reproducrion, so is stored in its biomass. It's therefore available to consumers and decompers within the ecosystem too
  • Primary production is often expressed as a rate, so would be called primary productivity in these cases
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Consumer net production

Around 90% of the total energy that consumers take is lost in various ways:

  • not all food is able to be eaten
  • some is consumed but can't be digested- lost as faeces
  • some energy is lost to the environment through respiration or excretion of urine. 

The remaining energy is stored in the consumer's biomass; this is the net production of the consumers and can be calculated using N+ I-(F + R) where 'I' is the chemical energy injested in food. 

The net production of consumers can also be called secondary production/secondary productivity when expressed as a rate. 

The net production of consumers can be used to calculate how efficient energy transfer is between trophic levels.

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Increasing efficiency of energy transfer

Farmers aim to increase the amount of energy available to humans by reducing the energy lost to other organisms and during respiration:

  • Simplifying food webs reduces loses by getting rid of pests using insecticides and herbicides to kill insects that eat and damage crops as well as weeds to remove competition with crops for the sun's energy/nutrients in the soil. Biological agents like pathogenic bacteria and viruses that kill pests can also be effective; farmers can use intergrated systems combining chemical and biological methods for the greatest NPP increase
  • Reducing respiratory loses- movement increases the rate of respiration, so animals may be kept in pens to restrict movement. These are generally indoors and kept warm so that less energy is used up generating body heat. This results in more biomass being produxed and a higher NPP,  however, it does raise ethical issues as it can be highly distressing to the animals and severly restrict their quality of life. 
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In natural ecosystems, nutrients are recycled through food webs, however human activity often disrupts this. Many fungi and bacteria are saprobionts, allowing important chemical elements in the remains of dead plants and animals to be recycled.Sabprobionts engage in extracellular digestion by secreting enzymes to digest food externally, and then absorbing nutrients. This process is called saprobiotic nutrition, and during this process, organic molecules are broken down into inorganic ions. Some fungi from symbiotic relationships (interactions between different species) with plant roots; these interactions are called mycorrhizae:

  • fungi have long, thin 'hyphae' (strands), which connect to the plant's roots
  • hyphae greatly increase the SA of the plant's root system, helping it absorb ions from the soil (that're usually scare, e.g. phosphorus), as well as more water. The fungi then obtain organic compounds (e.g. glucose) from the plant
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The Nitrogen Cycle

  • Plants and animals need nitrogen to make proteins and nucleic acids (DNA and RNA). The atmosphere is made up od around 78% of nitrogen, but plants and animals can't use it in this form. This is because nitrogen gas (N2) is made of 2 nitrogen atoms held together by a triple covalent bond, which are very hard for the plants to break apart. They need bacteria to convert it into nitrogen-containing compounds (inorganic ammonium or nitrate ions), which are released when bacteria and fungi break down organic matter
  • The nitrogen cycle demonstrates how nitrogen is converted into a usable form and then passed on between living organisms and the environment
  • The cycle includes food chains (as nitrogen is passed on when organisms are eaten), as four different processes that involve bacteria: nitrogen fixation, ammonification, nitrification and denitrification
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Nitrogen fixation/Ammonification

Nitrogen Fixation:

  • Nitrogen gas in the atomsphere is converted into nitrogen-containing compounds by nitrogen-fixing bacteria
  • The bacteria convert atmospheric nitrogen into ammonia, which then becomes ammonium when mixed with water (i.e. in solution); at which point, plants can use it. They do this through an enzyme called nitrogenase, which is strong enough to break the tripple covalent bond holding the nitrogen gas together.
  • The bacteria responsible form a mutualistic relationship with the plants, providing them with nitrogen compounds and gaining carbohydrates


  • Nitrogen compounds from dead organisms are turned into ammonia by saprobionts, which goes on to foem ammonium ions. This includes the conversion urine and faeces, as they also contain nitrogen compounds.
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  • Nitrifying bacteria convert the ammonium oins in the soil into nitrates, i.e. nitrogen compounds that can be used by plants. Initial nitrifying bacteria converts the ions into nitries, then further bacteria converts this into nitrates. These are even easier than ammonium for plants to take up


  • Nitrogen compounds are returned to the soil by excretion from animals, or when organisms die/decay. Nitrates in the soil are converted into nitrogen gas by denitrifying bacteria using the enzyme nitrate reductase. These use nitrates in the soil to carry out respiration and produce nitrogen gas. This happen in anaerobic conditions, e.g. in waterlogged soil. 

Nitrogen can also get into an ecosystem by lightening (which has enough energy to cause nitrogen fixtion) or by artificial fertilisers, which are produced from atmospheric nitrogen on an industrial scale in the Haber Process, and are used to prodce ammonium and nitrate ions in fertiliser.

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The Phosphorus Cycle

Plants and animals need phosphorus to make bio molecules like phospholipids, DNA and ATP. It's found in rocks and dissolved in the oceans in the form of phosphate ions. Phosphate ions dissolved in water in the soil can be assimilated (absorbed and then used to make more complex molecules) by plants and other producers. The phosphorus cycle shows the passing of phosphorus through an ecosystem:

  • Phosphate ions in rocks are released into the soil via weathering. The ions are then taken up by plants using their roots. Mycorrhizae greatly increase the rate at which phosphorus can be assimilated
  • Phosphate ions are transferred through the food chain as plants are eaten and then so on. The ions are lost from animals in waste producrs.
  • When plants/animals die (and from their urine/faeces), saprobionts break down organic compounds, releasing phosphate ions into soil for assimilation by plants.
  • Weathering of rocs also releases phosphate ions into seas, lakes and rivers and it's taken up by aqauatic producers and passed along the food chain to birds. Waste produced by sea birds is called 'guano' and contains a high proportion of phosphate ions, returning a significant amount of ions to the soil. It's often used as a natural fertiliser.
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  • Crops take in minerals fro the soil as the grow, but are removed from the field when they're harvested, rather than decompsing there, so the mineral ions that they contain (phosphates and nitrates) aren't returned to the soil by decompers in the nitrogen/phosphorus cycles. These ions are also lost when animals, or animal products, are removed from the land- animals contain nutrients from the grass they've eaten. If they're moved elsewhere, these nutrients aren't replaced through their remains or waste products. 
  • Therefore, fertilisers are used to replace the lost minerals, meaning more energy from the ecosystem can be used for growth. These can be artificial or natural.
  • Artificial fertilisers are inorganic- contain pure chemicals (e.g. ammonium nitrate) as powders or pellets
  • Natural fertilisers are organic matter- include manure, composted vegetables and crop residue.
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Environmental issues of fertilisers

  • An excess of fertiliser is sometimes used, meaning that fertilisers could leach into waterways. Leaching is when water-soluble compounds in soil are washed away, often into nearby ponds and rivers. This can lead to eutrophication, and is more likely to occur if fertiliser is applied just before heavy rainfall. 
  • Inorganic ions in chemical fertilisers are relatively soluble, so excess minerals are more likley to leach into waterways if not used immediately. As the nitrogen and phosphorus in natural fertilisers are still contained within molecules that need to be decomposed before use by plants, their release into soil for uptake is more controlled; makes leaching less likely. Leaching of phosphates is less likely than that of nitrates as phosphates are less soluble in water
  • Using fertiliers changes the balance of nutrients in the soil; too much of a nutrient can cause plants to die.
  • Eutrophication- mineral ions from fertiliser stimulate rapid growth of algae in ponds/rivers. Lots of algae blocks light from below plants, causing then to die as they can't photosynthesise enough. Bacteria feed on dead plants, further decreasing oxygen concentration by carrying out aerobic respiration. Aquatic organisms die as there isn't enough dissolved oxygen.
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