topic 5 - photosynthesis & respiration

What is the overall photosynthesis reaction?

Where does photosynthesis occur within the chloroplasts?

In the thylakoid membrane and the area it encloses - mainly in the grana.

What is the structure of the grana?

Thylakoid membrane surrounding the outside - contains photosystems

Thylakoid lumen in the inside - contains other molecules and ions

Stroma surrounding it - contains other molecules & ions and is where the LIR occurs

What stages is photosynthesis composed of?

2 stages (which both occur in the chloroplasts)-

Light dependent reaction - LDR

Light independent reaction - LIR

What are the photosystems and their role in photosynthesis?

The photosystems (PS1 & PS2) are funnel like structures in the thylakoid membrane and contains pigments like chlorophyll a & b that absorb light energy etc.

The photosystems are where many of the reactions in the LDR occur.

How do the thylakoid membrane and the photosynthetic pigments in it result in a higher rate of photosynthesis?

The membranes create a large surface area so many LDRs can happen.

There are many pigments including chlorophyll a & b which absorb different wavelengths of light so that as much energy can be gained as possible.

What are the biology definitions of reduction and oxidation?

Reduction - gain of hydrogen

Oxidation - loss of hydrogen

What metal does chlorophyll contain in its structure and how is this useful in photosynthesis?

Chlorophyll contains a Mg atom in its structure which can lose 2 electrons if the right wavelengths of light hit chlorophyll.

These 2 electrons can be used to generate energy, protons & in reactions in the LDR (duh).

What happens in the light dependent reaction overall?

Phosphorylation of ADP to form ATP

Production of NADPH/reduced NADP

• Both of these products are moved between the LDR to the LIR - all others are considered waste products

What is NADP and its forms?

NADP is a molecule formed by and used in photosynthesis that can be oxidised NADP+ or reduced NADPH₂

These forms are often written as NADP & NADPH.

What is the structure and function of ATP synthase?

ATP synthase is both an enzyme and an ion channel for protons found in the thylakoid membrane.

It is a large multiunit protein/ quaternary protein which has a rotating top - the tree looking thing.

On the rotating top molecules of ADP & Pi can bind on, on opposite sections which can move closer together.

What are the two types of phosphorylation that occurs in the LDR and why are they different?

Non-cyclic phosphorylation

• NADPH & ATP is produced

• both PS2 & PS1 are involved

• occurs in a linear way with movement of electrons from PS2 to PS1

Cyclic phosphorylation

• only ATP is produced

• only PS1 is involved

• occurs in cycle with movement of electrons contained in PS1

Why there two different types of phosphorylation?

The LIR/Calvin Cycle needs more ATP than NADPH which is why both types produce ATP but only non-cyclic produces NADPH.

What are the general steps of the LDR - non-cyclic phosphorylation?

• Photoionisation

• Movement down the Electron Transport Chain (ETC)

• Photolysis

• Synthesis of NADPH

• Synthesis of ATP

What are the general steps of the LDR - cyclic phosphorylation?

• Photoionisation

• Movement down the Electron Transport Chain (ETC)

  • this is contained in PS1

• Synthesis of ATP

  • as no NADPH is produced photolysis doesn’t occur

Where does photoionisation occur?

Can occur in both photosystems but if its noncyclic then it’ll be in PS2, if its cyclic it’ll be in PS1.

What happens in photoionisation - noncyclic phosphorylation?

• Light photons of the right wavelength hit the chlorophyll causing 2 Mg electrons to become excited/highly energised

  • Mg —> Mg²⁺ + 2e^-

• The electrons leave chlorophyll and then PS2

• They travel down a set of proteins called the ETC - idea of a pinball machine

What happens in photoionisation & movement down the ETC - cyclic phosphorylation?

• Light photons of the right wavelength hit the chlorophyll causing 2 Mg electrons to become excited/highly energised

  • Mg —> Mg²⁺ + 2e^-

• The electrons leave chlorophyll but remain in PS1

• They travel down the ETC contained in PS1 and end up back at chlorophyll - same image of pinball machine

• This pumps protons from the stroma across the thylakoid membrane into the thylakoid lumen

• This causes a build up of protons

What happens in the synthesis of ATP - cyclic phosphorylation?

• A concentration gradient of protons has formed between the thylakoid lumen and the stroma

  • theres a higher conc in the lumen because of the pumping of protons

• The protons (by facilitated diffusion)/chemiosmosis move out of the thylakoid lumen through ATP synthase

• An ADP & Pi bound to the rotating top of ATP synthase will move closer together as protons move through the ion channel

• Eventually with enough protons ADP & Pi are close enough to react together.

What happens in the Movement down the Electron Transport Chain (ETC) - noncyclic phosphorylation?

• The electrons move down the ETC to PS1 and lose energy while doing so

• This energy is used to pump protons from the stroma across the thylakoid membrane into the thylakoid lumen

• Protons build up in the thylakoid lumen

What happens in photolysis - noncyclic phosphorylation?

• Energy from photons is used to split water

• H₂O —→ 2H⁺ + 2e^- + ½ O₂

  • the oxygen produced is a waste product that diffuses out of the cells into air spaces etc

• This occurs in the thylakoid lumen

• At the same time the 2 electrons produced are used to reduce Mg²⁺ to form Mg in the PS2 chlorophyll

What happens the synthesis of NADPH?

• At PS1 the electrons arrive but have lost the majority of their energy through movement in the ETC

• They are then re-energised by light energy

• The electrons move through a series of proteins so chemiosmosis happens as the electrons lose energy

• In the stroma - outside the thylakoid - the 2 electrons pass to NADP reducing it to become NADPH

  • the gaining of 2 electrons means it can pick up 2 hydrogens

  • 2H⁺ + 2e^- + NADP -→ NADPH₂

What happens in the synthesis of ATP - noncyclic phosphorylation?

• A concentration gradient of protons has formed between the thylakoid lumen and the stroma

  • theres a higher conc in the lumen because of the pumping of protons

• The protons (by facilitated diffusion) move out of the thylakoid lumen through ATP synthase

• An ADP & Pi bound to the rotating top of ATP synthase will move closer together as protons move through the ion channel

• Eventually with enough protons ADP & Pi are close enough to react together.

What does the light dependent reaction look like overall?

Overall what happens in the LIR/Calvin Cycle?

Carbon dioxide and the products of the LDR - ATP & NADPH are used to produce two molecules of triose phosphate which can be used to make glucose and other organic substances.

Where does the LIR/Calvin Cycle take place?

The stroma of the chloroplast.

What can the Calvin Cycle be split up into?

Three steps- the Calvin Cycle is a cycle so it isn’t actually a series of steps as we can start the cycle at any point.

• Carboxylation

• Redox reaction

• Regeneration

What happens in carboxylation of the Calvin Cycle?

Ribulose Triphosphate/RuBP - a compound made up of 5 carbons - has CO₂ added onto it by Rubisco - an enzyme.

This forms an unstable 6 carbon intermediate that immediately splits into 2 three-carbon molecules each with a phosphate bonded to one of its ends - two glycerate phosphate/GP.

Overall - 1RuBP + 1CO₂ —> 2GP

What happens in the redox reaction step of the Calvin Cycle?

The two GP molecules formed each go on to react with NADPH in a redox reaction where each GP is reduced gaining 2 electrons and one proton. This forms 2 triose phosphate molecules.

NADPH is oxidised to NADP⁺ that can then return to the LDR.

ATP is also required to provide more energy to convert GP to triose phosphate so it’s converted into ADP + Pi which are also returned to the LDR.

Overall 2GP —> 2Triose Phosphate which requires 2NADPH + 2ATP.

What happens in regeneration in the Calvin Cycle?

At the “end” of the Calvin Cycle RuBP needs to be regenerated so the cycle continues.

RuBP is a 5 carbon molecule which needs to be regenerated from 3 carbin triose phosphate molecules. This means 5 triose molecules are needed to form 3 RuBP molecules - 15 carbon atoms.

The Calvin Cycle happens all though out the stroma producing other triose phosphate molecules or we can “wait” for multiple turns of one Calvin Cycle.

This regeneration requires more ATP - from the LDR - and the triose phosphate molecules not used in regeneration form organic molecules e.g. glucose.

Overall : 5Triose Phosphate —> 3RuBP

In summary, what happens in the Calvin Cycle?

• CO₂ combines with RuBP - this is catalysed by the Rubisco enzyme

• Two molecules of GP are produced

• 2 GP molecules are reduced to 2 Triose Phosphates using 2ATP and 2NADPH

• Triose Phosphate is converted into glucose and other useful organic compounds

• RuBP is regenerated when 5 Triose Phosphates have been produced - this uses ATP

What are the products of the Calvin Cyle/LIR?

In one turn of the cycle :

• 2NADPH

• 2x ADP + Pi

  • these pass back into the LDR

• 2Triose Phosphate

In multiple turns of the cycle : 

• 3RuBP from 5Triose Phosphate so at least 3 turns 

• Glucose from 2 Triose Phosphate molecules but due to the need to regenerate RuBP 3 turns only produces 1Triose Phosphate glucose so overall 6 turns are needed for 1Glucose

• This also means that for every 3 turns of the cycle only 1Triose Phosphate is produced

What are the limiting factors of photosynthesis?

• Light intensity 

• Temperature

• CO₂ concentration

How does light intensity affect photosynthesis?

Low light intensity

• Less photoionsiation can occur in the LDR leading to less ATP & NADPH made and used in the LIR. Less triose phosphate is produced so less glucose & RuBP are produced also due to the effect of less ATP so there’s less RuBP for the LIR.

High light intensity

• Rate of photosynthesis increases to a point due to higher light intensity where the rate will then plateau as something else becomes limiting. This could be the rate of enzyme activity in photolysis if the electrons from photoionisation etc cannot be re-energised fast enough.

How does temperature affect photosynthesis?

Changes in temperature will effect the rate of enzyme activity such as Rubisco & ATP Synthase and the rate of diffusion will be affected - in the LDR in chemiosmosis and in the LIR in diffusion of CO₂ from the atmosphere into the stroma of the plant cells in the leaf.

Increasing temp will increase the rate of both of these to an extent as once temp gets too high membranes start to melt and enzymes start to denature. Decreasing temp however means that enzyme activity is reduced and membranes become more rigid up to a point.

How does CO₂ concentration affect photosynthesis?

Increasing CO₂ concentration means more RuBP can be converted to GP so the quantity or conc of RuBP is low while GP is high - the opposite occurs when CO₂ concentration is low.

As CO2 conc affects the production of GP then the amount of NADPH that is oxidised to NADP+ in the conversion of GP to triose phosphate is affected. If the CO2 conc is too low not enough NADP+ is formed and returned to the LDR so the LDR & LIR are both slowed down.

What are the different stages of respiration?

• Glycolysis

• Link Reaction

• Krebs Cycle

• Electron Transport Chain

Where does respiration occur within the cell?

• Glycolysis - cytoplasm

• Link Reaction - in the mitochondrial matrix

• Krebs Cycle - in the mitochondrial matrix

• Electron Transport Chain - found in the membrane of the cristae/inner membrane

What happens in each stage of respiration (very basic summary)?

• Glycolysis - glucose is converted to 2 pyruvate molecules

• Link Reaction - pyruvate is converted into acetylCo-Enzyme A

• Krebs Cycle - acetylCoA is used to produce NADH & FADH

• Electron Transport Chain - NADH & FADH transfer electrons & protons to the ETC, pumping protons etc to produce ATP

What happens in substrate level phosphorylation vs oxidative phosphorylation?

Substrate level - the Pi is added to the ADP is from a molecule, the substrate of an enzyme is passing the Pi

Oxidative - the Pi is not from a molecule - its bonded to ATP synthase and the energy etc is from chemiosmosis

What are the steps of glycolysis?

• Phosphorylation - glucose is phosphorylated to triose phosphate

• Oxidation - triose phosphate is oxidised to pyruvate

What happens in glycolysis - phosphorylation?

• Glucose is phosphorylated twice using ATP

• This produces hexose biphosphate making it more reactive and able to split

• The hexose biphosphate splits symmetrically & vertically producing 2 triose phosphate molecules

• This means that 6C glucose is converted into 3C triose phosphate

• Another phosphate - not from ATP - is added to each triose phosphate

• This means that each triose phosphate has 2 phosphate ions bonded to it

What happens in glycolysis - oxidation?

• Each of the 2 triose “biphosphates” are oxidised

• 2 phosphates are passed to ADP making 2ATP per 1Triose phosphate

• Each triose phosphate also loses one H⁺ which is gained by NAD

• Overall 2Triose Phosphate → 2Pyruvate meanwhile 4ADP + 4Pi → 4ATP & 2NAD + H+ → 2NADH

Overall what happens in glycolysis?

• One glucose is phosphorylated by 2ATP to produce 1Hexose biphosphate

• Hexose biphosphate splits into 2Triose phosphate molecules

• Each of the 2Triose phosphate molecules have one phosphate added to it forming 2Triose “biphosphate”

• The 2Triose “biphosphate” are oxidised to form 2Pyruvate 

• This reaction reduces 2NAD and phosphorylates 4ADP producing 2NADH and 2ATP

• Overall: 2Pyruvate + 2ATP + 2NADH

Why are only 2 ATP molecules produced at the end of glycolysis?

2ATP molecules are used at the start to phosphorylate Glucose and 4ATP molecules are produced from 2Triose phosphate → 2Pyruvate so the net gain of ATP is 2 molecules.

What happens to each of the products formed in glycolysis?

2Pyruvate - diffused or actively transported into the mitochondria for the Link Reaction

2NADH - goes to the ETC in aerobic respiration

2ATP - used in the cells activities

What happens in the Link Reaction?

• 2Pyruvate is diffused into the mitochondrial matrix via facilitated diffusion (it can’t diffuse simply as there is a slight charge on it)

• In the mitochondrial matrix each Pyruvate is converted into acetylcoenzymeA in a reaction between Pyruvate and Co-Enzyme A

• This requires the loss of CO₂ as Pyruvate is a 3C molecule and acetylCoA is a 2C molecule

• This reaction also reduces NAD to NADH as on Pyruvate a COOH is lost to lose CO₂ so a H⁺ is also lost

Why does pyruvate have to react with Coenzyme A in the Link Reaction?

So that it is more reactive and can be used in the Krebs Cycle - the Coenzyme basically carries pyruvate to the Krebs Cycle.

Overall what are the products of the Link Reaction?

From one glucose molecule fed into glycolysis meaning that the Link Reaction happens twice : 

• 2CO₂ - one per pyruvate 

• 2NADH  - one per pyruvate 

• 2AcetylCoA - one per pyruvate

What happens to the products of the Link Reaction?

• 2CO₂ - released as waste

• 2NADH  - goes to the ETC 

• 2AcetylCoA - goes to the Krebs Cycle

What are the 3 molecules featured in the Krebs/Citric Acid Cycle?

Oxaloaceate, Citrate, 5C intermediate 

The cycle “starts” with Oxaloacetate so this is what needs to be reformed at the “end” and the cycle overall is the interconversion between these molecules.

What happens in the Krebs Cycle?

• “Starts” with 2C AcetylCoA reacting with 4C Oxaloacetate to form 6C citrate 

• Coenzyme A returns to the Link Reaction 

• Citrate is decarboxylated and oxidised to form a 5C intermediate

• This releases 1CO₂ and reduces 1NAD to 1NADH

• The 5C goes through this process again to produce a 4C molecule + 1CO₂ & 1NADH

• The 4C molecule is oxidised again which reduces FAD+ to FADH

• ATP is also formed via substrate level phosphorylation

• More oxidation occurs to turn this 4C molecule into Oxaloacetate so another NAD+ is reduced to NADH 

What are the products of the Krebs Cycle(not including the reformed Oxaloacetate)?

Per 1Glucose = 2 turns of the Krebs Cycle as 1AcetylCoA is needed for the cycle to “start” and 2 are produced from 1Glucose:

• 4CO₂ - 2 per AcetylCoA

• 6NADH - 3 per AcetylCoA

• 2FADH - 1 per AcetylCoA

• 2ATP - 1 per AcetylCoA

What happens to each of the products of the Krebs Cycle(not including the reformed Oxaloacetate)?

• 4CO₂ - waste product diffused out of the cell etc

• 6NADH - goes to the ETC

• 2FADH - goes to the ETC

• 2ATP - used by the cell

Where does the Electron Transport Chain occur?

Proteins in the ETC & ATP synthase are embedded in the cristae/inner mitochondrial membrane. It also involves the intermembrane space between the outer membrane and inner membrane.

What happens in The Electron Transport Chain?

• Oxidation of NADH & FADH occurs at the ETC releasing protons and electrons

• The electrons pass along the ETC from protein to protein through a series of redox reactions releasing energy

• At the end the electrons are passed onto the final electron acceptor - Oxygen producing water

• This energy is used to pump the protons into the intermembrane space across the inner membrane

• Over time the concentration of protons builds up causing facilitated diffusion to occur via ATP synthase producing ATP molecules

What are the products of the Electron Transport Chain?

• NAD+

• FAD+

• Many molecules of ATP

• H₂O

What happens to the products of the Electron Transport Chain?

• NAD+ - returns to Gycolysis mainly but also Link Reaction, Krebs Cycle

• FAD+ - returns to the Krebs Cycle

• ATP - used by the cell

• H₂O - waste product

What is the total number of ATP molecules produced at the end of areobic respiration?

32 - most of these are from oxidative phosphorylation in the ETC

Why is the theoretical ATP yield of 32 molecules rarely achieved in practice?

• Some ATP is used moving hydrogen from NADH made in glycolysis into the mitochondria

• Some ATP is used moving pyruvate into the mitochondria via active transport

• Some is used to generate heat to maintain a suitable body temperature for enzyme-controlled reactions.

What is the role of Oxygen in respiration?

It is the final electron acceptor of electrons in the ETC.

What does a lack of Oxygen in areobic respiration lead to?

• There is less Oxygen able to recieve electrons at the end of the ETC

• Electrons cannot be passed along the ETC because there's nowhere for them to go at the end.

• Electron carriers remain reduced (full of electrons) — NADH and FADH₂ cannot unload their electrons.

• This means less protons can be pumped etc leading less ATP being produced as the ETC can’t function

• FADH & NADH also can’t be oxidised to FAD+ & NAD+

• This effects the Link Reaction (NAD+) and the Krebs Cycle (both) causing both stages to stop as there isn’t anywhere to put the electrons & protons produced in them

• This means pyruvate builds up as it less can be converted to AcetylCoA in the Link Reaction

• As there is a lack of NAD+ glycolysis can’t continue so are all of areobic respiration is at least slowed

What is the role of anaerobic respiration?

To maintain glycolysis and so continue some ATP production.

What are the two different anaerobic respiration pathways?

• Ethanol fermentation - e.g. in yeast cells

• Lactate fermentation - e.g. in animal cells

What happens in ethanol fermentation?

• Glycolysis occurs as normal to produce pyruvate & ATP

• 3C Pyruvate is converted to 2C Ethanal by decarboxylation

• Ethanal is reduced to Ethanol in a redox reaction with NADH

• This produces the NAD+ required for Glycolysis allowing anerobic respiration to continue

What is the issue with ethanol fermentation?

Ethanol is toxic at high concentrations and can kill the yeast/other cells with are carrying out anaerobic respiration.

Some bacteria can breakdown ethanol into acetic acid - vinegar - which kills any surrounding cells instead of it.

What happens in lactate fermentation?

• Glycolysis occurs as normal producing pyruvate & ATP

• 3C Pyruvate is reduced to 3C lactic acid 

• This requires the oxidation of NADH → NAD+ and so produced the NAD+ needed for Glycolysis

What is the issue with lactate fermentation?

• Lactic acid is toxic as it lowers the pH resulting in the denaturing of the proteins 

• In animals lactic acid will also enter the blood lowering the blood pH and then be transported to the liver 

• There the lactic acid is detoxified by converting it back to glucose 

• However this requires ATP & Oxygen, creating an oxygen debt after anaerobic respiration

What are the differences between the two types of anaerobic respiration?

Ethanol Fermenation

• Doesn’t happen in animal cells - instead in yeast cells

• Requires both decarboxylation & reduction of pyruvate

• Produces ethanol as the final product

• Doesn’t create an oxygen debt

Lactate Fermentation

• Happens in animal cells

• Requires only reduction of pyruvate

• Produces lactic acid as the final product

• Creates an oxygen debt 

What is an autotroph?

Organisms that produce their own food using sunlight, water, and carbon dioxide (photosynthesis) or inorganic chemical reactions (chemosynthesis).

What is the role of plants in any ecosystem?

As plants are autotrophs they will always act as primary producers as they’re able to produce their own carbohydrates.

They will always be the first/bottom trophic level.

What is a food web?

Shows the connections between organisms in an ecosystem.

Split into trophic levels which are the different stages in a food web or chain. Biomass is transferred up each trophic level.

What happens to the organic materials synthesised by plants in photosynthesis?

Most of the sugars synthesised by plants are used as respiratory substrates. The rest are used to make other groups of biological molecules which form the biomass of the plants.

What is biomass?

• The mass of living material present in an organism or tissue sample

• This is the amount of biological molecules that make up living tissue

Why is biomass energy transfer between trophic levels inefficient?

Only around 10% of chemical food energy is passed between organisms in the food chain. The majority of biomass is lost due to uneaten parts of the organism (e.g. bones), decay of dead material, excretion, and exothermic reactions in the body (like heat lost in respiration).

How can biomass be measured?

• Mass of carbon (carbon atoms in organic molecules)

• Dry mass of tissue after all water has been removed

Per given area for both.

How can the chemical energy in dry biomass be measured?

Using calorimetry:

1. Sample of biomass burned in calorimeter in pure oxygen

2. Heat released is measured (measure change in temperature of the water)

3. From the heat released, the chemical energy stored is calculated

Why is water excluded in dry mass?

Water does not store any chemical energy.

How can you measure how productive an ecosystem is?

How productive an ecosystem is depends on biotic and abiotic factors, if these maximise the rate of photosynthesis (high light intensity etc) then more carbohydrates can be produced and transferred between trophic level. This can be quantified using GPP & NPP.

What is Gross Primary Production (GPP)?

The total amount of chemical energy converted from light energy by photosynthesis in a given area and time.

What is Net Primary Production (NPP)?

The chemical energy store in plant biomass after respiratory losses to the environment have been taken into account.

NPP = GPP - R

What can NPP be used for?

As its the chemical energy avaliable to be used outside of respiration its used by plants for growth and reproduction. It is also available to other trophic levels in the ecosystem which is first the primary consumers - herbivores and decomposers (which consume plant material).

What is the net production of consumers (N)?

The energy stored in a consumer’s biomass after losses from ingestion, excretion and respiration are taken into account.

How can you calculate the net production of consumers?

N = I - (F+R)

• Where I is the chemical energy store in ingested food

• F is the chemical energy lost due to the environment in faeces/urine

• R is the respiratory losses to the environment

What is primary productivity?

• The rate at which plants (producers) convert solar energy into chemical energy (biomass) in a given area per unit time = the rate of primary production

• Measured as biomass produced per area per time, e.g., kJ ha⁻¹ year⁻¹

• Can be split into gross primary productivity and net primary productivity

What is secondary production?

• The production of biomass by primary consumers/heteroraphs.

• The process by which heterotrophs, such as animals, consume organic matter produced by autotrophs or other heterotrophs and convert it into their own biomass.

• Secondary productivity is the rate of secondary production

• Still measured in kJ ha⁻¹ year⁻¹/similar units e.g. m^-2 not ha⁻¹

Why do we measure rates of productivity in kJ ha⁻¹ year⁻¹?

• kJ for energy

• ha⁻¹ to standardise the results allowing different environments to be compared - its takes into account that different environments will be different sizes and that conditions can differ slightly in the same environment

• year⁻¹ to taken into account the impact of different seasons will have on abiotic conditions - it provides an annual average to allow for fair comparisons between environments

How is the efficiency of energy transfer increased in farming?

• Humans are fed directly from primary producers (plants), or fed from one type of animal. this reduces energy lost from non-human food chains

• Livestock are kept in pens/cages/restricted areas. this reduces respiratory losses, so more energy is converted into biomass

What is the nitrogen cycle?

The process by which nitrogen and its compounds are converted between different forms in the environment and living organisms.

It allows nitrogen from the air to be converted into compounds that can be absorbed & used by plants.

What are the steps in the nitrogen cycle?

• Nitrogen fixation – nitrogen gas → ammonia/nitrates

• Nitrification – ammonia → nitrites → nitrates

• Assimilation – plants absorb nitrates to make proteins

• Ammonification – saprobionts release ammonia from dead matter and waste

• Denitrification – bacteria convert unused nitrates in the soil to nitrogen gas

What are saprobionts?

Decomposer organisms that obtain their energy from the external digestion of dead decaying matter.

They do this by secreting digestive enzymes such as carbohydrases, proteases etc producing glycerol, fatty acids etc and the nitrogen containing amino acids. The amino acids can then be broken down to release ammonium in ammonification.

What happens in nitrogen fixation?

• Conversion of atmospheric nitrogen (N₂) into ammonia (NH₃) or ammonium ions (NH₄⁺)/ ammonium compounds

• Done by: nitrogen-fixing bacteria in root nodules (e.g. Rhizobium) & free-living nitrogen-fixing bacteria in soil.

What types of plant have root nodules and why is this useful?

Legumes/ leguminous plants have root nodules.

The nitrogen fixating bacteria in the root nodules & plant have a mutualistic relationship - the bacteria fixate nitrogen into ammonium containing compounds for the plant, in exchange for carbohydrates made by the plant

This means the plants are more likely to survive in soil with a low nitrate ion concentration

What happens in nitrification?

For plants which don’t have nitrogen fixating bacteria/ root nodules the ammonium in the soil has to be converted into nitrate.

• Ammonium ions in the soil are converted into nitrites by nitriting bacteria

• The nitrites are converted into nitrates by different nitrating bacteria

Both of these are oxidation reactions so can only happen in aerobic conditions.

What happens in assimilation?

The nitrogen can now be taken up by plants as it’s in an absorbable form - nitrates.

Why is the nitrogen cycle important to plants (and all organisms)?

There are many important nitrogen containing compounds : ATP, nucleotides (of all nucleic acids), amino acids → proteins, co-enzymes e.g. NADH & NADPH etc.

What happens in ammonification?

Dead organic material (plant or animal) is decomposed by saprobionts in the soil which break down nitrogen containing compounds e.g. urea into ammonium ions.

What happens in denitrification?

Nitrate ions are converted back into nitrogen gas.

This is done by denitrifying bacteria which work in anaerobic conditions e.g. waterlogged soils where the concentration of oxygen is low.

As denitrification removes nitrates from soil it reduces the amount of nitrogen avaliable for plant growth.

What does the nitrogen cycle look like?

What is the phosphorous cycle?

The process by which phosphorous is absorbed from the evironment and then returned to the environment in multiple different forms.