3.5.4 Nutrient cycles

There is a limited availability to nutrient ions (that are in a usable form, e.g. most living things cannot use nitrogen in it's gaseous state). The simple nutrient cycle is as follows:

• Nutrient taken up by producers as inorganic molecules
• Producer incorporates the nutrient into complex organic molecules
• The producer is eaten and the nutrient passes into the consumer
• It passes along the food chain when these animals, in turn, are eaten.
• When producers/consumers die their molecules are broken down by saprobionts that release the nutrient in it's original state.

We need to know the nitrogen cycle and the phosphorous cycle:

Nitrogen cycle
Organisms require nitrogen to manufacture nucleic acids/proteins/other nitrogen-contain compounds. Plants need nitrogen in the form  NO₃- which is actively transported from the soil into their roots.

• Ammonification: the production of ammonia from organic nitrogen-containing compounds. These include urea, proteins, nucleic acids, and vitamins. Saprobionts feed on faeces and dead organism. This releases ammonia which forms ammonium ions in the soil.
• Nitrification: Ammonium ions are converted to nitrate ions by means of an oxidation reaction(this releases energy which is where nitrifying bacteria get their energy from). There are two stages:
• oxidation of ammonium ions to nitrite ions (NO₂-)
• oxidation of nitrite ions to nitrate ions (NO₃-)
• Nitrogen fixation: Nitrogen gas is converted into nitrogen-containing compounds (this occurs naturally when lightening strikes). We need to know about two microorganisms that carry this out (there are other forms of nitrogen fixation but the ones by these microorganisms are the most important):
• Free-living nitrogen-fixing bacteria reduce gaseous nitrogen to ammonia which they can use to manufacture amino acids. Nitrogen-rich compounds are released from them when they decay upon death.
• Mutualistic nitrogen-fixing bacteria live in nodules on the roots of plants (such as peas/beans). The plant obtains amino acids from the bacteria and the bacteria obtain carbohydrates from the plants.
• Denitrification: When soil is waterlogged few aerobic nitrifying and nitrogen-fixing bacteria are found and more anaerobic denitrifying bacteria are found. These convert soil nitrates into gaseous nitrogen (this is BAD!!!). This is bad as it reduces the availability of nitrogen-containing compounds for plants.
  

NOTE: nitrifying bacteria require oxygen to oxidise ammonium ions to nitrate ions and consequently to raise productivity farmers plough their soil to aerate it. They also ensure a good drainage system as denitrifying bacteria can work anaerobically so thrive in waterlogged fields.

The phosphorous cycle

Phosphorous is a component of ATP, nucleic acids, and phospholipids.

• Phosphorous exists as phosphate ions (PO₄₃-) in sedimentary rock deposits. Geological uplifting of rocks brings these rocks to the surface (above sea level). Erosion and weathering dissolves the phosphate ions.
• Plants absorb the dissolved ions and incorporate them into their biomass
• Animals feed on the plants. The phosphate ions travel along the food chain.
• Excess phosphate ions are excreted - these are eroded and end up back in the sea forming new sedimentary rock deposits.
• Upon death, decomposers break down animals/plants releasing the phosphate ions back into the soil/water
• The phosphate ions are transported back into the sea where they form sedimentary rock again.

Mycorrhizae
Okay so we need to know a tinsey winsey bit about mycorrhizae. They are associations between certain types of fungi and the roots of some plants. Basically, they act like extensions which increases the surface area of the plant roots which aids the absorption of water and minerals. They hold water and minerals next to the roots which enables the plant to resist drought (to a certain extent). The fungus receives organic compounds (sugars/amino acids) in return so the relationship is mutualistic.


Fertilisers
Okay so we need to know about fertilisers and how they aid farmers etc. Basically, intensive farming means that mineral ions are continuously being taken up by crops but when the crops are harvested the minerals can not get back to the soil - this disrupts the nutrient cycles. This means that is it necessary to replenish these ions because their reduced concentrations will pose a limiting factor to plant growth meaning productivity will reduce.

There are two types of fertiliser a farmer could add:

• natural/organic fertilisers consist of dead/decaying matter as well as animal wastes
• artificial/inorganic fertilisers are mined from rock deposits and converted into different forms and blended together to give the appropriate balance of minerals for a particular crop.

So, how do fertilisers actually increase productivity I hear you ask. Well, when there is a good concentration of nitrogen (for example) in the soil, plants develop earlier, grow taller, and have greater leaf area (which means an increased rate of photosynthesis).

However. fertilisers are not all fun and games. There are some not so good effects including:

• reducing species diversity as nitrogen-rich soils favour the growth of grasses/rapidly growing species such as nettles. These species out-compete some slower growing ones
• leaching which has the potential to pollute watercourses. This is the process by which rainwater dissolved any soluble nutrients (e.g nitrate ions) deep into the soil and eventually into water courses. These can even affect humans as a high nitrate ion concentration in drinking water can prevent efficient O2 transport in babies (there is also a potential link to stomach cancer). Leaching can also cause eutrophication.
• eutrophication (caused by leaching) is the process by which nutrient concentrations increase in bodies of water...
• nitrate ions are a limiting factor for plant/algal growth
• nitrate ion concentration increases due to leaching and nitrate ion concentration ceases to be a limiting factor - plants and algae grow more
• Algae mostly grow at the surface (algal bloom) and this layer absorbs light preventing it from penetrating the lower depths
• Light becomes a limiting factor for plants and lower level growing algae and they die
• saprobionts use this decaying matter as food and their populations grow rapidly increasing the demand for O2
• The O2 concentration in the water is reduced  and nitrates are released from decaying matter
• O2 becomes a limiting factor for aerobic organisms and fish etc eventually die
• without aerobic organisms there is less competition for anaerobic organisms whose populations rise
• anaerobic organisms further decompose dead matter which releases more nitrates and some toxic wastes such as hydrogen sulphide making the water putrid.

3.5.3 Energy and ecosystems

The ultimate source of all energy within an ecosystem is the sun. We have seen in 3.5.1 how plants absorb light energy and CO2 and turn it into biomass (well, they turn it into glucose which they then turn into biomass). The rest of the sugars synthesised are used by the plant as respiratory substrates (glucose is a substrate of respiration).

Biomass
Biomass is the total mass of living material in a specific area at a given time. The presence of varying amounts of water male fresh biomass unreliable - when comparing biomass, dry biomass should be used. However, because obtaining dry biomass requires killing the organism only  small sample is used and this is hardly representative. Biomass is measured using dry mass per given area in a given time. The unit is g m^-2 where an area is being measured and gm^-3 where a volume is being measured. You can measure the chemical energy store of dry mass using calorimetry:

1. A dry sample is weighed and burnt in pure oxygen in a sealed chamber known as a bomb
2. The bomb is surrounded by a water bath
3. The heat of combustion causes a small temperature rise in this water
4. We know how much energy is required to raise the temperature of 1g of water by 1°, we can calculate the energy released from the mass of burnt biomass (in kJ kg^-1)

Productivity
Plants actually only convert between 1%-3% of the light energy available to them from the sun. The other 97%-99% is not absorbed because...

• Over 90% of the Sun's energy is reflected back into space by clouds/dust or it is absorbed by the atmosphere
• not all wavelengths of light can be absorbed/used for photosynthesis (the best are 640-700nm wavelengths of light)
• light simply may not fall on a chlorophyll molecule
• there may be a limiting factor on the rate of photosynthesis.

The gross primary production (GPP) is the total quantity of chemical energy store in plant biomass, in a given area/volume, in a given time. Some plants use as much as 20-50% of this energy for respiration - the remaining chemical energy store is the net primary productivity (NPP)...

net primary productivity (NPP) = gross primary productivity (GPP) - respiratory losses (R)

This net primary production is then available for plant growth, but also to other trophic levels if they eat the plant. Usually, around 10% of the available energy is used in growth by primary consumers, secondary and tertiary consumers use around 20% of the available energy. This is because:

• Some parts of the organism is not consumed (e.g roots)
• Some parts cannot be digested so are lost in faeces (e.g we can't digest sweetcorn)
• Some energy is lost in excretory materials (e.g urine)
• Some energy lost as heat from respiration --> lost to the environment

The net production of consumers can be calculated using the equation...

N = I - (F + R)

N = net production

I = chemical energy store of ingested food

F = energy lost in waste materials (faeces/urine)

R = energy lost in respiration

This explains why the total amount of energy available is less at each level as you move up the food chain, and why most food chains only have four or five trophic levels.

Farming practices
As we can see from above, energy transfer along the food chain is pretty dismal. Farming practices are designed to increase yields (the amount of harvest) by increasing the efficiency of energy transfer along the food chains which produce our food. 

Any practice that reduces the respiratory loses (energy lost as heat when respiring) will increase the yield in a human food chain. One practice that achieves that is the intensive rearing of domestic livestock. Energy conversion can be made efficient by ensuring that as much energy as possible from respiration goes into growth rather than other activities. This can be achieved by:

• restricting movement --> less energy is used in muscle contraction
• keeping environment warm (most intensively reared species are homeothermic) --> reducing heat loss from the body
• Controlling feeding --> animals receive the optimum amount and type of food for maximum growth
• no predators --> no loss to other organisms in the food web

Another practice that increases the efficiency of energy transfer is to reduce losses to non=human food chains - this can be done by simplifying food webs by reducing/eliminating organisms which compete with the plant/animal that is being farmed. E.g. pest control removed weeds/pests. The cost of pest control must be balanced with the benefits it brings.

3.5.2 Respiration

There are four stages to aerobic respiration and two stages to anaerobic respiration. Respiration produces energy in the form of ATP

Aerobic respiration

Glycolysis
Glycolysis occurs in the cytoplasm of cells and is an anaerobic process (it does not require oxygen). It occurs in four stages:

1. Phosphorylation of glucose to glucose phosphate: Glucose is made more reactive by the addition of two phosphate molecules (phosphorylation). The phosphate comes from the hydrolysis of two ATP molecules. This provides the energy to activate glucose and lower the activation energy for the following enzyme controlled reactions.
2. Splitting of the phosphorylated glucose: Each glucose molecule is split into two triose phosphate molecules (3 carbon molecules)
3. Oxidation of triose phosphate: Hydrogen is removed from each of the triose phosphate molecules and transferred to NAD (NAD reduces to NADH/reduced NAD).
4. The production of ATP: Enzyme controlled reactions convert triose phosphate into pyruvate, two molecules of ATP are formed from ADP+Pi in the process. In total, 4 ATP molecules are produced as there are two triose phosphate molecules each producing two ATP molecules.

In total, glycolysis produces net two molecules of ATP (4 in total but 2 are used to phosphorylate the glucose), two molecules of NADH, and 2 molecules of pyruvate.


Link reaction
The pyruvate molecules are actively transported into the mitochondrial matrix. Here, they are oxydised in the link reaction so that potential energy can be released in the krebs cycle. A series of reactions known as the link reaction follows:

1. The pyruvate is oxidised to acetate: The 3C pyruvate molecule loses a carbon and two hydrogens. The hydrogens are accepted by NAD forming NADH/reduced NAD.
2. The 2C molecule combines with coenzyme A producing acetylcoenzyme A.

The overall equation:

pyruvate + NAD + coA --> acetyl coA + reduced NAD + CO2

Krebs cycle
This involves a series of oxidation and reduction reactions:

1. The 2C acetylcoA combines with a 4C molecule producing a 6C molecule
2. The 6C molecule loses CO2 and hydrogen in a series of oxidation-reduction to give a 4C molecule and a single ATP molecule (substrate level phosphorylation)
• NAD is reduced to NADH
• 2xCO2 is removed
• FAD os redced to FADH
• ATP produced
3. The 4C molecule can now combine with a new acetlycoA

For each pyruvate molecule the link reaction and krebs cycle produces:

• Reduced coenzymes (NADH, FADH) which have the potential to provide energy to produce ATP molecules by oxidative phosphorylation (the electron transport chain).
• One ATP molecule
• 3 CO2 molecules

The krebs cycle is important for many reasons including the following:

• Breaks down macromolecules into smaller ones (e.g pyruvate into co2)
• Produces hydrogen ions that are carried by NAD and FAD to the etc for oxidative phosphorylation
• Regenerates the 4C molecule so acetylcoA does not accumulate
• It is a source of intermediate compounds that cells can use to manufacture important substances such as chlorophyll/amino acids/fatty acids.

Oxidative phosphorylation (ATP synthesis)
Within the inner folded mitochondrial membrane sits enzymes and proteins involved in oxidative phosphorylation - it follows that cells that need to respire lots have a lot of mitochondria present.This is the last stage in aerobic respiration and is the mechanism by which some of the energy of electrons within hydrogen atoms is conserved in the formation of ATP. That was a bit of a mouthful. We think it works by chemiosmotic theory - here is the process:

1. Hydrogen atoms produced during glycolysis and the krebs cycle are currently being transported by NADH and FADH.
2. The electrons of the hydrogen atoms are donated to the first molecule in the etc
3. The electrons pass along the etc in a series of oxidation-reduction reactions
4. The energy released by this flow is used to actively transport protons across the inner mitochondrial membrane into the inter-membranal space
5. The protons accumulate in the inter-membranal space and a diffusion gradient is established
6. They diffuse back into the mitochindrial matrix through ATP synthase channels embeded in the inner mitochondrial membrane
7. Electrons at the end of the etc combine with these protons and oxygen forming water - oxygen is the final electron acceptor.

Anaerobic respiration

Glycolysis
As above.


Fermentation
In the absence of O2, krebs and the etc cannot take place as soon all the FAD anf NAD will be reduced and none will be available to tae up the hydrogen atoms produced during the krebs cycle so enzymes will stop working. For glycolysis to continue pyruvate and hydrogen must constantly be removed.

The NAD is replenished because pyruvate accept the hydrogen from NADH. The NAD can then be used in glycolysis again. In plants (and microorganisms such as yeast) the pyruvate is converted into ethanol and lactic acid, in animals it is converted into lactate.

Ethanol production:
The pyruvate molecule loses a carbon dioxide and accepts a hydrogen from NADH which produces ethanol.

pyruvate + NADH --> ethanol + CO2 + NAD

Lactate production:

Each pyruvate molecule takes up two hydrogen atoms from NADH.

pyruvate + NADH --> lactate + NAD

The only ATP produced from anaerobic respiration is formed by glycolysis (net 2 ATP molecules).

Alternative respiratory substrates

Sugars (glucose) are not the only substances that can be oxidised to release energy.

Respiration of lipids
Lipids are hydrolysed to glycerol and fatty acids. Glycerol is phosphorylated and converted to triose phosphate which enters the glycolysis pathway and so on. The fatty acid is broken down into 2C fragments which are converted to acetylcoenzymeA which enters the krebs cycle. The oxidation of lipids produces 2C fragments and lots of hydrogen atoms which can be used to produce ATP during oxidative phosphorylation. This is why lipids release more than double the energy of the same mass of carbohydrate.

Respiration of protein
Protein is hydrolysed to amino acids. They have their amino group removed (deamination) and enter the respiratory pathway at different points depending on the number of C atoms they contain. 3C convert to pyruvate, 4C and 5C convert to intermediates in the Krebs cycle.

3.5.1 Photosynthesis

Photosynthesis is important as it converts light energy into metabolic energy (in the form of ATP) which can be passed along the food chain. Photosynthesis can be split into three 'sections': capturing of the light energy (by chloroplast pigments such as chlorophyll), the light-dependant reaction, and the light-independant reaction.

The chemical equation is 6CO2 + 6H2O (+ light energy) = C6H12O6 + 6O2.

The light dependant reaction
In the light dependant reaction some of the light energy is converted into chemical bonds. In short, an electron flow is created causing water to split (photolysis) into protons, electrons, and oxygen. NADPH, ATP, and oxygen are produced. It occurs in thylakoids as they contain the photosynthetic pigment chlorophyll.

There are two purposes to the light dependant reaction. It captures light to... add an inorganic phosphate to ADP (making ATP), and to split water into protons and hydrogen and oxygen (photolysis). Here is the process of the light dependant reaction:

• A photon is absorbed by a chlorophyll molecule on thylakoid membrane. This chlorophyll molecule is part of photosystem 2 (Plastoquinone Oxidoreductase)
• An pair of electrons absorb this energy which raises them to a higher energy level. The electrons are now said to be excited (photoexcitation)
• The pair of electrons are so excited they leave photosystem two onto an electron carrier (the beginning of the electron transport chain). The electron carrier becomes reduced. 
• The chlorophyll molecule becomes ionised (this is known as photoionisation) and also oxidised.
• The electrons pass along a number of electron carriers (an electron transport chain) in a series of oxidation-reduction reactions located in the thylakoid membranes.
• The electrons lose energy at each stage as each carrier has a slightly lower energy level than the previous - this produces the energy needed to move them along.
• Having lost electrons, the chlorophyll molecule in photosystem wants to replace them. It splits water using light energy (photolysis) producing hydrogen ions (protons), oxygen, and electrons.
• The cytochrome complex uses a bit of the energy from the electron transport chain to pump protons into the thylakoid
• The thylakoid begins to fill up with protons from photolysis and proton pumping. A concentration gradient is established between the thylakoid and stroma (across the thylakoid membrane).
• Protons travel down this concentration gradient and diffuse across the thylakoid membrane through ATP synthase - this energy is used to form ATP from ADP + Pi.
• Since the electrons keep losing energy as they travel to each electron carrier they're now a little tired. The electrons get reenergised as they now enter photosystem 1
• The reexcited electrons move to another electron carrier
• All of the energy produced is used to form NADPH by reducing NADP (adding a proton/hydrogen ion)
• products: ATP, NADPH, and oxygen

The light independent reaction
The protons from the photolysis in the light dependant reaction are used to produce sugars (e.g glucose) and other organic molecules (e.g starch). This is known as the Calvin cycle and does not require light energy (hence light independent):

• In the stroma, CO2 is combined with RuBP (ribulose bisphosphate) with the help of a rubisco enzyme
• This new six carbon molecule is very unstable so it breaks in two producing two lots of 3-phosphoglycerate (glycerate-3-phosphate/GP) which are pretty stable
• ATP adds a Pi onto each 3GP
• NADHP adds an electron to each
• Now we have two molecules of Glyceraldehyde 3 phosphate (G3P) - also known as triose phosphate.
• Triose phosphate can be converted into useful organic substances such as glucose (for short term energy storage), cellulose (structure), or starch (or long term storage)
• Some of the G3Ps form the above (glucose/starch/cellulose) - the others go into reforming RuBP which required ATP

So that's photosynthesis. All we need to know now is a little bit about what might limit the rate of photosynthesis.

Photosynthesis is limited by a limiting factor - not by many things at once. Many things can affect the rate of photosynthesis but it is only limited by the one whose level is at a least favourable value (the one in short supply). This means that changing the levels of the other factors will not change the rate of photosynthesis if the level of the limiting factor is still low. Limiting factors of photosynthesis can include:

• Light (as light intensity increases the volume of o2 produced and co2 absorbed increases to a point where it is balanced by the volume of o2 absorbed and co2 released by respiration. At this point there will be no net exchange of gases - this is known as the compensation point)
• Carbon dioxide concentration (affects enzyme activity - particularly rubisco)
• Temperature
• Water