On the Wild Side

Thylakoid membrenes - a system of interconnected flatterned, fluid filled sacs. Proteins, including photosynthetic pigments and electron carriers, are imbedded in the membrane and are involved in the light dependant reaction.

Starch grain - stores the products of photosynthesis

A smooth outer membrane - which is freely permeable to molecules such as CO2 and H2O

A smooth inner membrane - which contains many transport molecules. These are membrane proteins which regulate the passage of substance in and out of the chloroplast. These substances include sugars and proteins synthesised in the cytompasm of the cell but used within the chloroplast.

Granum - a stack of thylakoids joined to one another. Grana (plural) resemble a stack of coins.

Thylakoid space - fluid within the thylakoid sacs contains enzymes for photosynthesis.

Stroma - the fluid surrounding the thylakoid membranes. Contains all the enzymes needed to carry out the light-independant reactions to photosynthesis

DNA loop - chloroplasts contain genes for some of their proteins

6CO2 + 6H2O -------> (in the presence of light and chlorophyll) C6H12O6 + 6O2 
The energy needed (from light) to break CO2 and H2O is greater than the energy released from the formation of C6H12O6 and O2 therefore products of reaction = higher energy level than reactants resulting in a 'store of energy'.

Releasing Hydrogen form water

• To split H2O into its elements (oxygen + hydrogen) requires energy.
• Photolysis is the process in which photosynthesis splits water using energy from sunlight

Storing Hydrogen in carbohydrates

• H2 reacts with CO2 to store H2
• CO2 reduced forming C6H12O6 which can be stored or converted to other organic molecules

Use of glucose

• Potential to release large amounts of energy
• H2 stored in carbohydrates reacts with O2 releasing energy
• Aerobic respiration = H2 (in glucose) reacts with O2 --> H2O, energy + CO2

• Photosystem II absorbs light energy
• Excites chlorophyll a (p680)
• Chlorophyll premotes 2e- to higher energy level
• e- picked up by electron carriers
• e- pass along the chain releasing enough energy to produce ATP from ADP + Pi
• Chlorophyll p680 and p200 are unstable because of lost electrons
• e- promoted from photosystem II replace the ones lost (chlorophyll p200) in photosystem I
• Photosystem II gets a replacement e- from photolysis of water
• Photolysis of H2O also produces O2 which is released as a waste gas and 2H+ one of which is used to reduce the NADP+ and NADPH
• Electrons held by electron carrier also get passed to NADP+

Products are:
O2 released as waste gas
NADPH (passed into light independent reaction) 
ATP (passed into light independent reaction) 

No NADPH or O2 just ATP

• Only involves photosystem I
• Light absorbed by chlorophyll a
• Chlorophyll a exited and promotes electron to higher energy level
• e- picked up by electron carrier
• Enough energy released to photophosphorylate

During the light dependant stage;

• ATP is formed form ADP + Pi
  • Adding Pi to another molecule =  phosphorylation
  • Light provides energy for this = photophosphorylation
• Water is split into H ions, e- + O2
  • to split = lysis
  • light provides energy for this = photolysis
• Electron carrier NADP+ picks up H+ and becomes reduced
  • NADP+ ----> NADPH + H+

• ATP is created from the phosphorylation (addition of inorganic phosphate) of ADP

• Phosphate must be separated from water molecules (this requires energy)

• ATP in water has a higher energy than ADP and Pi in water. Therefore, ATP in water is a way of storing chemical potential energy.

• During the formation of ATP phosphate and water are separated.

• Pi and water can then be brought together in energy giving reactions each time the cell requires energy.

• In this way ATP transfers energy around the cell

• RuBP combines with CO2 to form an unstable 6C compound.

• The 6C compound breaks down into a 3 molecules of glycerate-3-phosphate (GP) both of which are 3C compounds

• ATP is broken down and the energy released is used to phosphorylate phosphate 2 molecules of glycerate biophosphate (3C)

• NADPH is then used to reduce glycerate biophosphate in order to produce 2x glyceraldehyde-3-phosphate (GALP) (3C)

• For every 6 molecules of GALP produced, 5 continue in the cycle and combine with CO2 to produce more RuBP using energy from ATP.

• The remaining molecule of GALP is converted into lipids, amino acids & glucose (hexose sugar) that are then used in the respiration and synthesis of other organisms.

• Main route of energy into an ecosystem is through photosynthesis
• Photosynthesis convert energy from sunlight into a form that can be used by other organisms
• Energy is then transferred through other organisms of the ecosystem by the consumption of other organisms
• Each stage of the food chain is called a tropic level.
• Energy locked up in things that can't be eaten gets recycled back into the ecosystem via decomposers.

However, not all energy is transferred to the next tropic level.

• Around 90% of the total available energy is lost.
• Around 60% of available energy is never taken in.
  • Some sunlight can't be used because it hits part of the plant that can't photosynthesise.
  • Some parts of organisms aren't eaten and so energy is not consumed
  • Some parts are indigestible and so pass through the organism as waste. 

• Net producers are called net primary producers (NPP) and gross productivity is called gross primary productivity (GPP)

• The relationship between both NPP and GPP can be calculated using the following equation;

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  • NPP = GPP - plant respiration

• Net productivity of a tropic level can be calculated when you know the gross productivity and respiratory losses in each tropic level using the following equation;

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  • Net Productivity = Gross Productivity - Respiratory Loss  

• The energy efficiency of the energy transfer from one tropic level to another is calculated using the following equation;

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  • % efficiency of energy transfer between tropic levels = (net productivity of a level / net productivity of previous level) x 100

Increasing atmospheric CO2 concentration is one cause of global warming. If it is known how carbon compounds are recycled between organisms and the atmosphere it may be possible to reduce the atmospheric CO2 concentration.

• Carbon is absorbed by plants during photosynthesis becoming carbon compounds in their tissues.
• Carbon is passed on to animals when they eat the plants and to decomposers when they decompose dead organic matter.
• Carbon is returned to the atmosphere as all living organisms carry out respiration producing CO2.
• If dead organic matter ends up in places where there aren't any decomposers, the fossil fuels over millions of years.
• The carbon in fossil fuels is released as CO2 when they are burnt (combustion) 

• Bio-fuels are fuels produced from bio-mass - materials that is or once was living.

• Bio-fuels are burnt to release energy, producing CO2

• There is no net increase in atmospheric CO2 concentration when biofuels are burnt (the amount of CO2 produced is the same as the amount taken in when the material is growing).

• Using biofuels as a alternative to fossil fuels as it stops the increase in atmospheric CO2 concentration caused by burning fossil fuels.

• Reforestation is the planting of new trees in existing forests that have been depleted

• More trees means more CO2 is removed from the atmosphere by photosynthesis.

• CO2 is converted into carbon compounds and stored as plant tissues in trees. This means more carbon is kept out of the atmosphere, so there's less CO2 contributing to global warming.

• Non-living features of an ecosystem e.g. solar energy input, climate, topography, O2 availability, pollution and catastrophes)

• The population size varies because of abiotic factors e.g. the amount of light or space available, the temperature or chemical composition of their surroundings.

• When abiotic conditions are ideal for a species, organisms can grow fast and reproduce successfully.

• When abiotic conditions aren't ideal for a species, organisms can't grow as fast or reproduce as successfully.

• Organisms can only exist where the abiotic factors they can survive in exist e.g. some plants can only grow on south facing slopes in the Northern hemisphere because that's where the solar input is greatest.

Interspecific competition (between species)

• Interspecific competition can lead to the  reduction in the resources available to both species is reduced. This means that both populations will be limited by the lower amount of food = less energy for growth and reproduction. This means population sizes will be smaller
• If 2 species are competing the better adapted species will out-compete the other.

Intraspecific competition (within a species)

• The population (of a species) increases  when resources are plentiful. As the population increases the number of organisms competing for the same resources increases.
• Eventually resources become limiting. The population begins to decline.
• A smaller population results in less competition so the population can increase again.
• The maximum, stable population of a species that an ecosystem can support is called the carrying capacity.

• As the prey population increases, more food becomes available to predators,so the predator population grows.

• As the predator population increases, more prey are eaten, so the prey population begins to fall.

• This means there is less food for the predators, so their population decreases and so on.

• However, predator-prey relationships are also affected by other factors, such as availability of food for prey.

• A niche is the role of a species within a habitat

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  • Its biotic interactions (what an organisms eats/is eaten by)
  • its abiotic interactions (e.g. the oxygen it breaths in/the CO2 it breaths out)

• Every species has its own unique niche that can only be occupied by one species

• It may look as though two species are sharing the same niche but there will be slight variations.

• The abundance of different species can be explained by the niche concept (two species occupying similar niches will compete, so fewer individuals will be able to survive in that area).

• The distribution of different species can be explained by the niche concept (organisms can only exist in habitats where all the conditions that make up their role exist).

The process by which an ecosystem changes over time. The biotic conditions change as the abiotic conditions change.

• Primary succession; happens on land or rocks that are newly exposed
• Secondary succession; happens where land that has been cleared of plants but where soil remains.

Primary succession starts when a species colonises a new land surface. Seeds and spores are blown in by the wind and begin to grow. The first species to colonise are called pioneer species (at first serial stage).

• Abiotic conditions are hostile. Pioneer species only grow because they are specialised tocope with harsh conditions.
• The pioneer species change the abiotic conditions (they die, microorganisms decompose the dead organic material, forming a basic soil).
• This make conditions less hostile allowing new species to grow, out-competing the pioneer species. 

• Secondary succession happens in the same way, but because there's already a soil layer, succession starts at a later serial stage (Pioneer species are larger plants e.g. shrubs).

• At each stage, different plants and animals that are better adapted for the improved conditions move in, out-compete the plants and animals already there, and become the dominant species in that ecosystem.

• As succession goes on, the ecosystem becomes more complex. New species move alongside existing species resulting in increased species diversity.

• The final serial stage is called a climax community (The ecosystem is supporting the largest and most complex community of plants and animals it can - it is stable)

Differences in climax communities

• Which species make up the climax community depends on what the climates like in an ecosystem. The climax community for a particular climate is called a climatic climax.

• The sun radiates energy, largely as visible light, some of which the earth absorbs causing the earth to warm up.

• The earth's surface then radiates this energy as infrared.

• Some of this energy is prevented from escaping by the gasses in the atmosphere.

• These gasses are called greenhouse gasses which create the greenhouse effect, keeping the earth warm enough for life to survive.

CO2

• CO2 concentration is increasing as more fossil fuels are burnt (burning fossil fuels releases CO2)
• CO2 released by the destruction of natural by the destruction of natural carbon sinks.
• Changes in the Earth's orbit, solar radiation and volcanic eruptions all contribute to CO2 levels.
• High correlation between temperature and carbon dioxide levels.
• Mass of scientific evidence to support rise in global temperatures is due to massive increase in greenhouse gasses.

CH4

• Produced by anaerobic decay of organic materials in waterlogged conditions, decay of domestic waste, decomposition of animal waste, in the digestive systems of animal and the incomplete combustion of fossil fuels.
• Atmospheric concentrations have increased rapidly since the mid 19th century
• As temperature increases, CH4 will be released from natural stores.
• Increased levels of methane add to the atmospheric greenhouse gasses preventing more infrared radiation escaping and further warming the Earth

• An increase in temperature will affect the metabolisms of all organisms.

• Therefore, increased temperatures will mean the rate of metabolism in some organisms will speed up so their growth rate will increase. They will also progress through their life cycles faster.

• But the temperature will become too high for some organisms. Their metabolic reactions will slow down so their rate of growth will decrease. This means they'll process through their life cycle slower.

• Global warming will also affect the distribution of some species - all species exist where their ideal conditions for survival are. When these conditions change, they have to move to a new area where conditions are better. If they can't move they die out in that area. Also, the range of a species may expand if the conditions in previously uninhabitable areas change.

• This may also cause alien species to move into areas, out-competing existing species.

Changing rainfall patterns

• Global warming will change rainfall patterns; some areas will get more rain, others will get less.

• Changing rainfall will affect the life cycle of some plants e.g. some desert plants.

• Changing rainfall patterns will affect the distribution of some organisms.

Seasonal changes

• Global warming is thought to be changing the timings of the seasons.

• Organisms are adapted to the timings of the seasons and the changes that happen.

• Therefore seasonal cycles will affect the life cycles of some animals.

• Changing seasonal cycles will also affect species distribution of some species.

• Temperature has a direct effect on the rate of enzyme-catalysed reactions.

• At low temperatures reactions between enzymes and reactants are very slow. This is because at low temperatures the enzymes and substrate molecules move very slowly and so less collisions.

• At increased temperatures there are more collisions due to the increased energy of the substrates and enzymes.

• Increased collisions means that the substrate will bind to the active site more frequently and therefore will increase the rate of reaction.

• The rate of reaction approximately doubles for each 10C rise in temperature. This produces a curved graph.

• However, after the optimum temperature for the rate of reaction is reached,enzymes start to become denatured and so the rate of reaction falls dramatically as there are no enzymes to catalyse the substrate molecules.

Temperature records

• Since the 1850's temperature has been measured around the word using thermometers.
• This gives a reliable, but short term, record for global temperature change.
• Methods for recording temperature have improved since the 1850's and is no longer done with a thermometer. This increases the accuracy of the data. The 'old' data is still important in helping scientists analyse the global temperature increases. 

Pollen in Peat bogs

• Pollen is often preserved in peat bogs which accumulate in layers so the age of the pollen increases with depth.
• Cores can be taken, pollen grains extracted and identified from each layer
• Only full grown plant species produce pollen, so the samples only show the plants that were successful at the time.
• The climate for the preserved plants can be calculated using knowledge of known, similar plant species.
• Because plant species vary with the climate, the preserved pollen will vary as the climate changes over time 

Dendrochronology (tree rings)

• Used as a method of working out how old a tree is using tree rings
• Most trees produce 1 ring a year which is created by the formation of Xylem vessels.
• The thickness of the ring depends on the climate when using the ring formed - when it's warmer, the rings are thicker (because conditions for growth are better).
• Cores through tree trunks can be taken, each ring can be dated by counting back from when the core was taken. By looking at the ring thickness, it is possible to see the climate conditions of each year.

Carbon dioxide levels

• High correlation between temperature and CO2 levels
• A rise in temperature is followed by an increase in CO2 releases from oceans
• Measured using ice core samples, bubbles trapped in the ice contain CO2 and so levels can be measured dating back 100s of 1000s of years.
• This gives a large amount of data on CO2 levels.

It is possible to make predictions about global warming in the future (extrapolations) by using data that has already been collected.

These predictions can then be used to model the amount of global warming that might happen in the future.

However, these models have limitations;

• Only limited data
• Limited knowledge of how the climate system works
• Failure to include all factors including climate
• Changing trends in factors included

To extrapolate data it must be assumed that;

• There is enough data to extend the trend accurately
• Present trends continue. 

Why is it controversial?

Global warming is considered, by some to be a controversial issue because;

• Science cannot prove theories, only disprove them. Because an idea is proposed to explain an explanation and it is then tested, the results can only disprove the hypothesis. The results can then only support the idea rather than proving it, this could leave room for other explanations.

• Incomplete knowledge of how the climate system of the planet works and the data sets used for making predictions have limitations.

• When preserving or interpreting data almost everyone is influenced by their view point biasing the evidence.

• Ethical arguments when considering global warming.

• It is agreed that to some degree humans are causing global warming

• It is agreed that global warming is happening

• It is also agreed that human activity is increasing the atmospheric CO2 concentration

• The scientific consensus is that the increase in global temperature is caused by the increase in atmospheric CO2 levels.

• BUT some scientists have drawn different conclusions from the data, concluding that the increase in atmospheric CO2 is not the main cause of increased global temperatures.

• Any conclusions reached are affected by the reliability of their data, the quantity of evidence and bias.

• Biased conclusions aren't objective.

Like the issue itself, people disagree on the best way of dealing with global warming. 

• Increasing the use of Bio-fuels
  • Some farmers support this - some governments fund the farming of bio-fuels.
  • Drivers might support this - the price of bio-fuels is usually lower than that of oil based fuels.
  • Consumers might oppose this - using farmland to grow crops for bio-fuels could cause food shortages.
  • Conservationists might oppose this - forests have to be cleared to grow crops for bio-fuels.
• Increasing the numbers of wind turbines
  • Companies that make wind turbines support this - their sales would increase
  • Environmentalists support this - wind turbines provide electricity without increasing the atmospheric CO2 concentrations.
  • Local communities might oppose this - some think turbines ruin the landscape.
  • Bird conservationists might oppose this - many birds are killed flying into turbines.

Gene mutations

• The gene pool is the complete range of alleles present in a population.
• New alleles are usually generated through mutations of the gene during DNA replication.
• How often an allele occurs in a population is called the allele frequency - it's usually given as a percentage.
• The frequency of an allele changes over time - this is evolution.

Natural selection

• Individuals within a population vary because they have different alleles.
• This means that some individuals are better adapted for their environment than others.
• Individuals with this allele are more likely to survive to reproduce, passing on their genes than individuals without the mutation.
• This means that a greater proportion of the population will have the beneficial allele. The next generation is more likely survive thus increasing the allele frequ.
• This is the process of natural selection. 

Genomics

• Organisms that have moved away from each other more recently have similar DNA.

• This can be shown by DNA hybridisation, DNA profiling, DNA sequencing and DNA molecular clocks.

Protenomics (the study of proteins)

• Organisms that have divided away from each other more recently should have more similar proteins as less time has passed for changes to occur.

• Shown by protein sequencing.

• Parent population can move freely around the area which allows free gene movement between individuals (can interbreed).

• Geographical isolation (e.g. mountain range/ocean) split populations. These isolated groups prevented from interbreeding with parent population.

• If the populations are subject to different selection pressures (e.g. climate) certain random mutations are favored which leads to natural selection and eventually the formation of a new species.

• If the barrier remains, sub species continue to evolve differently due to the selection pressures eventually becoming a new species.

• If the barrier disappears, and the two species have been separated for a long time, the two species mix freely but cannot interbreed to produce fertile offspring.

• Behavior;
  • Sexual selection (e.g. peacocks tails) - a female animal selects a mate with particular plumage/mating routine etc. individuals without this don't mate and therefore become reproductively isolated.

• Structure (of reproductive organs)
  • Changes in genitalia prevent mating causing reproductive isolation.

• Hybrid individability (Hybrid - breeding of two species)
  • When zygote is produced but fails to divide
• Hybrid sterility
  • Offspring are produced but are infertile

• Gamete mortality
  • How long the gametes last for (human semen can last up to 4 days)
• Polypoidy
  • When chromosomes duplicate themselves to give triplets instead of pairs. This could cause offspring to become infertile.

In order to test theories and ideas, data needs to be collected to prove or disprove it (e.g. DNA and proteomic data has been collected that provides evidence for the theory of evolution. Scientists within the scientific community accept the theory of evolution because they've shared and discussed the evidence of evolution to make sure its reliable and valid. Scientists validate data in three ways;

• Scientific Journals - academic magazines where scientists can publish articles describing their work.
  • Used to share new ideas, theories, experiments, evidence and conclusions
  • Allows other scientists to replicate experiments and see if they can get the same results using the same method.
  • If the results are replicated repeatedly, the scientific community can be relatively confident that the evidence collected is reliable.
• Peer review - Before scientists can get work published, it must go through the process of peer review.
  • This is the process by which other scientists specialised in that field anonymously assess and review the work. 
  • Peer review is used by the scientific community in attempt to validate published research.
• Conferences - meeting that scientists attend to discuss each others work.
  • Valuable because an easy way to share and discuss ideas.  

Investigating populations of organisms - Involves looking at the abundance & distribution of a species in a particular area.

• Abundance - the number of individuals of one species in a particular area. The abundance of mobile organisms and plants can be estimated by counting the number of individuals in samples taken. Percentage cover can also be used.
• Distribution - this is where a particular species is within the area being investigated.

Random sampling

• Choose an area to sample -a small area within the area of investigation
• Samples should be random to avoid bias.
• Use an appropriate technique to sample the population
• repeat the process, taking as many samples as possible to give a more reliable estimate for the whole area.
• The number of individuals for the whole are can then be calculated by taking an average of the data collected in each sample x the size of the whole area. The % cover can be estimated by taking an average of all the samples.