Unit 4 Processes

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Mark-release-recapture

Mark-release-recapture

  • A known number of organisms are caught and marked in a way that does not make them more liable to predation. 
  • The individuals are then released back into the community.
  • Sufficient time is left so that the marked organisms are fully reintegrated back in to the population.
  • Some time later, a given number of organisms is collected randomly and the number of marked individuals is recorded.
  • The size of the population is then calculated as follows:

total number of individuals in the first sample x total number of individuals in the second sample

number of marked individuals recaptured

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The light-dependent reaction

The light-dependent reaction

  • When a chlorophyll molecule absorbs light energy, it boosts the energy of a pair of electrons within this chlorophyll molecule, raising them to a higher energy level.
  • The electrons become so energetic that they leave they chlorophyll molecule. The electrons that leave the chlorophyll are taken up by an electron carrier.
  • The electrons are now passed along a number of electron carriers in a series of oxidation-reduction reactions. These electron carriers form a transfer chain that is located in the membranes of the thylakoids.
  • Each new carrier is at a slightly lower energy level than the previous one in the chain, and so electrons lose energy at each stage. This energy is used to combine an inorganic phosphate molecule with an ADP molecule in order to make ATP.
  • The replacement electrons in the chlorophyll molecule are provided from water molecules that are split using light energy. The equation for this process is:

2H2O ----> 4H+ + 4e- + O2
 water ----> protons + electrons + oxygen

  • These hydrogen ions are taken up by an electron carrier called NADP. On taking up the hydrogen ions the NADP becomes reduced. The reduced NADP then enters the light-independent reaction along with the electrons from the chlorophyll molecules.
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The light-independent reaction

The light-independent reaction

  • Carbon dioxide from the atmosphere diffuses into the leaf through stomata and dissolves in water around the walls of the mesophyll cells. It then diffuses through the plasma membrane, cytoplasm and chloroplast membranes into the stroma of the chloroplast.
  • In the stroma, the carbon dioxide combines with the 5-carbon compound ribulose bisphosphate (RuBP) using the enzyme rubisco.
  • The combination of carbon dioxide and RuBP produces two molecules of the 3-carbon glycerate-3-phosphate (GP).
  • ATP and reduced NADP from the light-dependent reaction are used to reduce the activated glycerate-3-phosphate to triose phosphate (TP).
  • The NADP is re-formed and goes back to the light-dependent reactoion to be reduced again by accepting more hydrogen.
  • Some triose phosphate molecules are converted to useful organic substances, such as glucose.
  • Most triose phosphate molecules are used to regenerate ribulose bisphosphate using ATP from the light-dependent reaction.
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Glycolysis

Glycolysis

  • Activation of glucose by phosphorylation. Before it can be split into two, glucose must first be made more reactive by the addition of two phosphate molecules (phosphorylation). The phosphate molecules come from the hydrolysis of two ATP molecules to ADP. This provides the energy to activate glucose (lowers the activation energy for the enzyme-controlled reactions that follow).
  • Splitting of the phosphorylated glucose.Each glucose molecule is split into two 3-carbon molecules known as triose phosphate.
  • Oxidation of triose phosphate. Hydrogen is removed from each of the two triose phosphate molecules and is transferred to a hydrogen-carrier molecule known as NAD to form reduced NAD.
  • The production of ATP. Enzyme-controlled reactions convert each triose phosphate molecule into another 3-carbon molecule called pyruvate. In the process, two molecules of ATP are regenerated from ADP.

Energy yields

  • two molecules of ATP (four are produced but two are used up in initial phosphorylation)
  • two molecules of reduced NAD 
  • two molecules of pyruvate 
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The Link Reaction

The Link Reaction

  •  The pyruvate (3C) is oxidised by removing hydrogen, this hydrogen is accepted by NAD to form reduced NAD, which is later used to produce ATP.
  • The 2-carbon molecule, called an acetyl group, that is thereby formed combines with a molecule called coenzyme A (CoA) to produce a compound called acetylcoenzyme A. 
  • A carbon dioxide molecule is formed from each pyruvate.

The overall equation can be summarised as:

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

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The Krebs Cycle

The Krebs Cycle

  • The 2-carbon acetylcoenzyme A from the link reaction combines with a 4 carbon molecule to produce a 6-carbon molecule.
  • This 6-carbon molecule loses carbon dioxide (CO2)and hydrogens to give a 4-carbon molecule and a single molecule of ATP produced as a result of substrate-level phosphorylation.
  • The 4-carbon molecule can now combine with a new molecule of acetylcoenzyme A to begin the cycle again.

For each molecule of pyruvate, the link reaction and the Krebs cycle produce:

  • reduced coenzymes such as NAD and FAD which have the potential to produce ATP molecules
  • one molecule of ATP
  • three molecules of carbon dioxide.

As two pyruvate molecules are produced for eahc original glucose molecule, the yield for a single molecule of glucose is double the quantities above.

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The Electron Transport Chain

The Electron Transport Chain

  • The hydrogen atoms produced during glycolysis and the Krebs cycle combine with the coenzymes NAD and FAD that are attached to the cristae of the mitochondria.
  • The reduced NAD and FAD donate the electrons of the hydrogen atoms that they are carrying to the first molecule in the electron transport chain.
  • This releases the protons from the hydrogen atoms and these protons are actively transported across the inner mitochondrial membrane.
  • The electrons meanwhile, pass along a chain of electron transport carrier molecules in a series of oxidation-reduction reactions. The electrons lose energy as they pass down the chain and some of this is used to combine ADP and inorganic phosphate to make ATP. The remaining energy is released in the form of heat.
  • The protons accumulate in the space between the two mitochondrial membranes before they diffuse back into the mitochondrial matrix through special protein channels.
  • At the end of the chain the electrons combine with these protons and oxygen to form water. Oxygen is therefore the final acceptor of electrons in the electron transport chain.

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Anaerobic Respiration

Anaerobic Respiration

In the absence of oxygen, neither the Krebs cycle nor the electron transport chain can take place, leaving only the anaerobic process of glycolysis as a potential source of ATP. For glycolysis to continue, its products of pyruvate and hydrogen must be constantly removed. In particular, the hydrogen must be released form the reduce NAD in order to regenerate NAD. Without this, the already tiny supply of NAD in cells will be entirely converted to reduced NAD, leaving no NAD to take up the hydrogen newly produced from glycolysis. Glycolysis will then grind to a halt. The replenishment of NAD is achieved by the pyruvate molecule form glycolysis accepting they hydrogen from reduced NAD.

In eukaryotic cells (nucleus), only two types of anaerobic respiration occur within regularity:

  • In plants, and in microorganisms such as yeast, the pyruvate is converted to ethanol and carbon dioxide.

pyruvate + reduced NAD ----> ethanol + carbon dioxide + NAD

  • In animals, the pyruvate is converted to lactate.

pyruvate + reduced NAD ----> lactate + NAD

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Energy losses in food chains

Energy losses in food chains

Plants normally convert between one per cent and three per cent of the Sun’s energy available to them into organic matter. Most of the Sun’s energy is not converted to organic matter by photosynthesis because:

  • Over 90 per cent of the Sun’s energy is reflected back into space by clouds and dust or absorbed by the atmosphere.
  • Not all wavelengths of light can be absorbed and used for photosynthesis.
  • Light may not fall on a chlorophyll molecule.
  • A factor, such as low carbon dioxide levels, may limit the rate of photosynthesis.

The total quantity of energy that the plants in a community convert to organic matter is called the gross production. The rate at which they store energy is called the net production.

net production = gross production – respiratory losses

A low percentage of energy transferred at each stage is the result of the following:

  • Some of the organism is not eaten.
  • Some parts are eaten but cannot be cannot be digested and are therefore lost in faeces.
  • Some of the energy is lost in excretory materials, such as urine. 

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Intensive rearing and energy conversion

Intensive rearing and energy conversion

Enery conversion can be made more efficient by ensuring that as much energy from respiration as possible goes into growth rather than other activities or other organisms. this is achieved by keeping animals in confined spaces, such as small enclosures, called 'factory farming'. This increases the energy-conversion rate because:

  • movement is restricted and so less energy is used in muscle contraction
  • the envrionment can be kept warm in order to reduce heat loss from the body
  • feeding can be controlled so that the animals receive the optimum amount and type of food for maximum growth with no wastage
  • predators are excluded so that there is no loss to other organisms in the food web.

Other means of imporving the energy-conversion rate include:

  • selective breeding of animals to produce varieties that are more efficient at converting the food they eat into body mass
  • using hormones in increase growth rates.
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The Nitrogen Cycle

The Nitrogen Cycle

  • Ammonification - Saprobiotic microorganisms, mainly fungi and bacteria, feed on organic ammonium-containing compounds in the soil which include urea and proteins, nucleic acids and vitamins .This releases ammonia, which then forms ammonium ions in the soil.
  • Nitrification - Nitrification is the conversion of ammonium ions to nitrate ions. It is an oxidation reaction and so releases energy. It is carried out by free-living soil microorganisms called nitrifying bacteria that respire aerobically. The conversion occurs in two stages:

1. oxidation of ammonium ions to nitrite ions NO2-

2. oxidation of nitrite ions to nitrate ions NO3-

  • Nitrogen fixation - The process by which nitrogen gas is converted into nitrogen-containing compounds. It is carried out my microorganisms, of which there are two types:

1. free-living nitrogen-fixing bacteria. They reduce gaseous nitrogen to ammonia, which they use to manufacture amino acids. Nitrogen-rich compounds are released from then when they die

2. mutualistic nitrogen-fixing bacteria. They live in nodules on the roots of plants. They obtain carbohydrates from the plants and the plant gets amino acids from the bacteria.

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The Nitrogen Cycle

The Nitrogen Cycle

  • Denitrification - Fewer aerobic nitrifying and nitrogen-fixing bacteria are found and there is an increase in anaerobic denitrifying bacteria. These convert soil nitrates into gaseous nitrogen. Land must be kept well aerated to prevent the build up of denitrifying bacteria.
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Eutrophication

Eutrophication

  • In most lakes and rivers there is naturally very little nitrate and so nitrate is a limiting factor for plant and algal growth.
  • As the nitrate concentration increases as a result of leaching, it ceases to be a limiting factor for the growth of plants and algae amd both grow exponentially.
  • As algae mostly grow at the surface, the upper layers of water become densely populated with algae. This is called 'algal bloom'.
  • This dense surface layer of algae absorbs light and prevents it from penetrating to lower depths.
  • Light then becomes the limiting factor for the growth of plants and algae at lower depths so they eventually die.
  • The lack of dead plants and algae is no longer a limting factor for the growth of saprobiotic algae and so these too grow exponentially, using dead organisms as food.
  • The saprobiotic bacteria require oxygen for their respiration, creating an increased demand for oxygen.
  • The concentration of oxygen in the water is reduced and nitrates are released from the decaying organisms.
  • Oxygen then becomes the limiting factor for the population of aerobic organisms, such as fish. These organisms ultimately die as the oxygen is used up altogether.
  • Without the aerobic organisms, there is less competition for the anaerobic organisms, whose populations now rise exponentially.
  • The anaerobic organisms further decompose dead material, releasing more nitrates and some toxic wastes.
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Selection

Selection

  • All organisms produce more offspring than can be supported by the supply of food, light, space, etc.
  • This means there is competition between members of a species to be the ones that survive.
  • Within any population of a species there will be a gene pool containing a wide variety of alleles.
  • Some individuals will possess combinations of alleles that make them better able to survive in their competition with others or variation may be caused by a mutation, again making the individual better able to survive.
  • These individuals are more likely to obtain the available resources and so grow more rapidly and live longer. As a result, they will have a better chance of successfully breeding and producing more offspring.
  • Only those individuals that successfully reproduce will pass on their alleles to the next generation.
  • Therefore, it is the alleles that give the parents an advantage in the competition for survival that are most likely to be passed on to the next generation.
  • As these new individuals have ‘advantageous’ alleles, they in turn are more likely to survive, and so reproduce successfully.
  • Over many generations, the number of individuals with the ‘advantageous’ alleles will increase at the expense of the individuals with the ‘less advantageous’ alleles.
  • Over time, the frequency of the ‘advantageous’ alleles in the population increases while that of the ‘non-advantageous’ ones’ decreases.
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Geographical Isolation

Geographical Isolation

  • The individuals of species X form a single gene pool and freely interbreed.
  • Climate changes over the centuries lead to drier conditions which reduce the area of forest and separate it into two regions that are many hundreds of kilometres apart.
  • Further climate changes cause one forest region (A) to become much colder and wetter and the other forest region (B) to become warmer and drier.
  • Variation within the two populations arises as a result of mutation.
  • In region A, phenotypes are selected that are better able to survive in colder, wetter conditions.
  • In region B, different phenotypes are selected – ones that are better able to survive in warmer, drier conditions.
  • The type and frequency of the alleles in the gene pools of each group of species X become increasingly different.
  • In time, the differences between the two gene pools become so great that they are, in effect, separate species.
  • Further climate change and regrowth of the forest may lead to the two species being reunited. However, they will not be able to interbreed as they are now different species.
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Succession

Succession

  • The area of land is colonised by a pioneer species
  • This causes a change in the abiotc environment because when the pioneer species die and decompose they release sufficient nutrients into the soil to support a small community of plants.
  • The continued erosion of rock and the increasing amount of organic matter available from the death of these plants over time causes a thicker layer of soil to be built up.
  • The stability of the environment increases and the area becomes less hostile.
  • This therefore enables other species to colonise and survive so there is a change in the biodiversity of the environment. Eventually a dominant species out-competes the pioneer species leading to their emlimination from the community.
  • This results in a climax community that consists of animals as well as plants.
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