on the wild side

- Adenosine triposphate, the immediate source of energy in a cell

• ATP is made from the nucleotide base adenine, combined with a ribose sugar and three phosphate groups
• When needed, the third phosphate bond can be broken by a hydrolysis reaction
• This is catalysed by ATPase and the result is ADP, inorganic phopshate and energy
• ATP is synthesised in catabolic reduction/oxidation (redox) reactions which requires energy and ATPase and so the reaction is reverisble 
• But ATP mainly synthesised by removal of hydrogen atoms in a metabolic pathway
• When two hydrogen atoms are removed from a compund, they are picked up by a hydrogen carrier which then becomes reduced
• Electrons are passed along an electon transport chain and components in chain are reduced when they receive the electons, and oxidised when they pass on
• These redox reactions release energy which is used to drive synthesis of ATP

Carbon Dioxide + Water --> Oxygen + Glucose

6CO2 + 6H2O --> 602 + C6H12O6

- Happens in the thylakoid membrane
- Electron transport chain
- ADP + Phosphate --> ATP
- NADP = Coenzyme

1. Light energy provided by the sun.
2. Light absorbed by chlorophyll (pigment in chloroplasts).
3. Light energy excites electrons in the cholorphyll.
4. The electrons pass along protein carriers in an electron transport chain.
5. During this electron transport chain, the enrgy released form the oxidation and reduction of carriers enables ATP to form from ADP and a phosphate. (Photophosphorylation).
6. Electrons and hydrogen ions from the water move along a series of carriers and are accepted by the coenzyme NADP. The NADP becomes reduced NADP (NADPH).
7. As well as two hydrogen ions being taken from the water (H2O), two electrons are also taken to replace those originally from the chlorophyll. The point of the electron transport chain is to split water (photolysis).
8. The oxygen from the water is released through the leaf (waste product).

- Happens in the stroma
- Carbon Dioxide is "fixed" into glucose
- ATP --> ADP + Phosphate
- RuBISCO = Coenzyme

• RuBP combines with carbon dioxide from the air to form an unstable 6C compound
• The enzyme RUBISCO catalyses this reaction
• The unstable 6C compound breaks down into two molecules of a 3C compund, glycerate-3-phosphate (GP) 
• GP is then reduced to form glyceraldehyde-3-phosphate (GALP), a 3C sugar. The hydrogen comes from the reduced NADP and the energy required from ATP
• For every 6 molecules of GALP produced, 5 continue in the cycle and combine with carbon dioxide to produce more RuBP using energy from ATP
• The remaining molecule of GALP is converted to glucose, for respiration in a plant. 
• This is converted into sucrose for transport round the plant and polysacharides such as starch for energy storage and cellulose for structural support
• Glucose is also needed as a building block for amino acids, nucleic acids and lipids

Habitat- the place where an organism lives

Population- group of organisms of the same species, living and breeding together 

Community- all the populations of different species of organisms living in a habitat 

Niche- the role of an organism in the community; its way of life

Abiotic factors- non-living elements of the habitat of an organism

Biotic factors- living elements of a habitat which affect the ability to survive there

Producer- an organism that can make its own organic compounds from inorganic compounds by photosynthesis or by using the energy released from chemical reactions

Primary Consumer- an organism that consumes plant material for its food; herbivore

Secondary Consumer- an organism that feeds on primary consumers; carnivore

Trophic level- the position an organism occupies in a food chain 

- The major ecosystems

• The biosphere could be considered as the largest ecosystem on Earth
• But too large to study, so dived into into smaller parts called biomes
• Example of a biome- tropical rainforest- high humidity, plenty of sunlight- very high biodiversity

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

• Starts in newly formed habitats where there has never been a community before
• The first organisms to colonise are known as pioneer species; bought to habitat by wind or animals. Only those plant species that can cope with the extreme conditions in the new habitat will grow and survive
• Organic material accumulates, changing the conditions of the habitat
• The inorganic rock grains and organic humus are the start of the formation of soil
• The development of a soil enables the seeds of small shallow-rooted plants to establish
• As conditions improve, seeds from plants well suited to the conditions can give rise to adult plants. These compete with other plants and win and replace the existing plants
• As the plant changes, so does the associated animal community
• Eventually a stable climax community develops, dominated by trees. This remains unchanged unless conditions in the habitat change

The evolution of an ecosystem from exisitng soil that is clear of vegetation

• Starts on bare soil where an exisiting community has been cleared
• The first organisms to colonise are known as pioneer species. Seeds of many plant species will already be lying dormant in the soil and others will be brought by wind or animals. The species best adapted to cope with the conditions will grow and survive. (They are unlikely to be the same species as would colonise in primary succession)
• Conditions in the habitat change with the growth of the poineer species
• As conditions improve, seeds from plants well suited to the conditions can give rise to adult plants. These compete with other plants and win and replace the existing plants
• As the plant changes, so does the associated animal community
• Eventually a stable climax community develops, dominated by trees. This remains unchanged unless conditions in the habitat change

Interspecific competition (between species)

• This occurs when different species within a community compete for the same resources
• Can lead to reduction in the resources available to both species
• This means that both populations will be limited by the lower amount of food, meaning less energy for growth and reproduction, so population sizes will be smaller
• If two species are competing the better adapted species will out-compete the other

Intraspecific competition (within a species)

• This is for a limited resource between members of the same population or species
• When resources are plentiful, the population increases and the number of organisms competing for the same resources also increases
• Eventually resources become limiting and 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

Predation

• 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

Parasitism

• Diseased animals will be weakened and do not reproduce successfully 
• Sick predators cannot hunt well and diseased prey animals are mor elikely to be caught
• Parasites can wipe out whole populations
• Parasites and infectious diseases spread more rapidly when there is a high popuation density , as individuals are in close proximity
• In a community with greater biodiversity, the effect on the whole population will be less 

• E.g light, temperature, wind and water currents, water availibility, oxygen availibility
• The population size varies because of abiotic factors 
• 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.

• 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

- The rate at which energy is incorporated into the plants

Net primary productivity is the energy stored in body tissues 

NPP= GPP- plant respiration

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

• 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) 

• Fuels produced from biomass- material that is or was recently living
• Burnt to relsease energy, which produces CO2
• No net increase in CO2 concentration- same amount produced as taken in
• Alternative to fossil fuels- stops increase in CO2 concentration by burning fossil fuels

Arguements for

• Can reduce the use of limited fossil fuels
• Provide a renewable energy resource that is carbon neutral
• Waste biomass e.g. farm or food industry waste can be recycled to make biofuels

Arguments against

• Biofuel production causes loss of habitats and reduces biodiversity
• Food shortage can occur locally where biofuels are replacing food crops. Loss of land for food crops can increase the price of foods
• Production of biofuels requires energy such as farming, transport and processing so only limited net savings in energy and greenhouse gas emission

• Planting of new trees in exisiting 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 the trees
• This means more carbon is kept out of the atmosphere, so there's less CO2 contributing to global warming

• 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

 Carbon dioxide

• The concentration is increasing as more fossil fuels are burnt 
• Changes in Earth's orbit, solar radiation and volcanic eruptions contribute to the levels
• High correlation between temperature and carbon dioxide levels
• Mass of scientific evidence to support rise in temperatures is due to massive increase in greenhouse gasses

Methane

• Produced by decay of domestic waste and the incomplete combustion of fossil fuels
• Atmospheric concentrations have increased rapidly since the mid 19th century
• As temperature increases, methane 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

Temperature Records

Temperature records can be looked at to see if the climate has changed. The general trend is increasing temperature= evidence for global warming. However, the accuracy of thermometers has changed over time.

Tree-Ring Analysis - Dendrochronology

Method for determining how old a tree is using its rings. Most trees produce one ring every year. The thickness of the ring depends on the climate when the ring was formed. When it's warmers the rings are thicker (growth conditions better).

Scientists can take cores through tree trunks and date each ring by couinting them back from when the core was taken. Looking at the thickness determines the climate of that year.

Pollen in peat bogs

Can be used to show how temperature has chnaged over thousands of years. Pollen is often preserved in peat bogs (acidic wetland areas). They accumulate in layers so the age of the pollen increases witrh depth.

Scientists can take cores from peat bogs and extract pollen grains from the different aged layers. The plant species is identified- only mature plants produce pollen, so samples show species were successful at that time. The climates that different plant species live in now are known by scientists are when they find preserved pollen form similar plants, it indicates a similar climate. A gradual increase in pollen from a plant species that's more successful in warmer climates would show a rise in temperature. A decrease in pollen that needs cold conditions would also show the same thing.

Rising temperatures- An increase in temperature will mean meatoblic reactions in some organisms will speed up, so they'll progress through their life cycle faster, but if too high, they'll progress slower

Changes to distribution- All species exist where their ideal conditions for survival are, but when they change, they'll have to move where conditions are better. If they can't move, they may die out. The range of some species mat also expand if conditions in previously uninhabitable areas change

Changing rainfall patterns- Some areas will get more rain, some less, affecting life cycles of some organisms e.g. ocotillo plants will have to remain dormant for longer periods if there is less rainfall. Distribution also affected e.g. deserts could increase- species will have to move or die out

Season cycles- Chaninging seasonal cycles affects life cycles of some organisms, e.g. red squirrels giving birth earlier due to availability of food

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

• At low temperatures reactions between enzymes and reactants are very slow, as 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 and the activation energy required for reaction is lowered

• 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.

Species - a group of organisms with similar morphology, physiology and behaviour, which can interbreed and are reproductively isolated from other species

Speciation - development of a new species. Occurs when populations same species become reproductively isolated- changes in allele frequencies cause changes in phenotype>can't breed to produce fertile offspring.

Reproductive isolation occurs via:

• Prezygotic reproductive barriers
  • Habitat isolation- different habitats selection- reduces contact in reproductive season
  • Temporal isolation- if two populations get out of sync, they cannt mate 
  • Mechanical isolation- changes in genitalia (mutation) prevent successful mating
  • Behavioural isolation- won't recognise others from same species as mating partners
• Postzygotic reproductive barriers
  • Low hybrid zygote vigour- zygote doesn't develop properly- offspring can't reproduce- abnormalities
  • Low hybrid adult viability- offspring fail to thrive and grow properly
  • Hybrid infertility- offspring healthy but infertile e.g. mule- infertile offspring of horse and donkey

Geographical isolation and natural selection lead to reproductive isolation

• Geographical isolation- when a physical barrier divides the population of a species e.g. floods, earthquakes
• Conditions on either side will be slightly different e.g. different climate
• Duifferent characteristics (phenotypes) will become advantageous on each side, so allele frequencies will change in each population
• Mutations will take place independently in each population, also changing allele frequencies
• These changes will lead to changes in phenotype frequencies e.g. become more common on that side so phenotypes more common due to natural selection
• Individuals will have changed so they won't be able to breed with one another to produce fertile offspring- reproductively isolated
• The two groups become separate species

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.
• There is competition for survival between members of a species
• Organisms best adapted to the conditions are more likely to survive and reproduce
• Organisms with adaptive features that give a selective advantage to survive and reproduce
• The offspring are more likely to have any alleles that contribute to adaptive features, so the alleles become more common in the population
• Organisms not well adpated are more likely to die before maturity and so do not produce offspring
• Over time, the compositions of the species will change to the more adapted form

• DNA evidence
  • Suggests all organisms have evolved from shared common ancestors
  • Closely related species diverged (evolved into different species) more recently
  • Evoultion caused by gradual changes in base sequences of DNA
  • So organisms that diverged away from each other more recently should have similar DNA as less time has passed for changes to occur
  • E.g. humas, chimps and mice all evolved from a common ancestor- DNA base sequence of humas and chimps is 94% the same, human and mouse 85%
• Proteomics
  • Study of proteins e.g. shape, size, amino acid sequence of proteins
  • The sequence of amino acids in a protein is coded for by the DNA sequence in a gene
  • Related organisms have similar DNA sequences so similar amino acid sequences
  • So organisms that diverged away form each other more recently should have similar proteins, as less time has passed for changes to occur