AQA Unit 4 Biology

  • Created by: Ella
  • Created on: 26-01-14 13:11

Photosynthesis, Respiration & ATP

ATP (Adenine Triosephosphate) --> the immediate source of energy in a cell.

  • It's made from the nucleotide base adenine, a ribose sugar and 3 phosphate groups.
  • Its energy is stored as chemical energy in the phosphate bonds.
  • ATP diffuses to the part of the cell that requires energy.
  • Then it's broken down into ADP and Pi (inorganic phosphate) and chemical energy is released from the phosphate bond.
  • ATPase catalyses this reaction
  • ADP and Pi are recycled and the process starts again.

What properties make ATP a good source of energy?

  • It's a small and soluable molecule so can be easily transported around the cell.
  • Therefore, ATP also only stores and releases small, manageable amounts of energy at a time so no energy is wasted.
  • It can transfer energy to another molecule by transferring one of its phosphate groups.
  • ATP cannot pass out of the cell so the cell always has an immediate source of energy.
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Photosynthesis, Respiration & ATP

What is a coenzyme? - A molecule that aids the function of an enzyme.

  • They work by transferring a chemical group from one molecule to another.
  • In photosynthesis, the coenzyme used is NADP - which transfers hydrogen from one molecule to another (so can reduce or oxidise a molecule).
  • In respiration, coenzymes NAD, coenzyme A and FAD are used - NAD and FAD transfer hydrogen from one molecule to another. Coenzyme A transfers acetate between molecules.

When hydrogen is trasnferred between molecules, electrons are transferred too.

Photosynthesis takes place in the Chloroplasts of plant cells...

  • What are chloroplasts? - Small flattened organelles found in plant cells. They have a double membrane called the chloroplast envelope. 
  • Thylakoids are fluid filled sacs - these are stacked up within the chloroplast into structures called grana. Grana are linked together by bits of thylakoid membrane called lamellae.
  • Chloroplasts contain photosynthetic pigments - Chlorophyll a, Chlorophyll b and carotene --> these are coloured pigments that absorb the light energy needed for photosynthesis.
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Where are these pigments found? - In the thylakoid membranes, attached to proteins --> when the protein & pigment are attached, it's called a photosystem.

There are two photosystems used to capture light energy:

  • Photosystem I (PSI) --> which absorbs light best at 700nm
  • Photosystem II (PSII) --> which absorbs light best 680nm

How are chloroplasts adapted to carrying out Light Independent Reactions of photosynthesis?

  • * Stroma contains all the enzymes needed to carry out the Light Independent Reaction.
  • * Stroma fluid surrounds grana so products from Light Dependant Reaction can easily diffuse into stroma.
  • * It contains DNA & ribosomes so it can quickly and easily manufacture any proteins needed for the Light Independent Reaction.
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Photosynthesis is split into two stages...

The Light Dependant Reaction:

Takes place in the thylakoid membranes of the chloroplasts.

Requires light energy

Forms ATP, reduced NADP (ie. NADPH) and O2

The Light Independent Reaction:

Takes place in the stroma of the chloroplasts.

Doesn't use light energy (but instead relies on the products of the LD reaction).

Uses ATP and reduced NADP from the LDR to make Glucose from CO2.

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Photosynthesis - LDR step by step...

1. Light energy/a photon of light is absorbed by PSII in the thylakoid membrane.

2. This excites electrons in the chlorophyll so they leave PSII, moving to a higher energy level and move along the electron transport chain (ETC) to PSI.

3. Electrons from PSII then need to be replaced. Light energy splits H20 into 2H+, 2e- and 1/2O2 and the electrons are used to replace the e- in PSII.

3. As the excited electrons from the chlorophyll move down the ETC, they lose energy. This energy is used to transport H+ into the thylakoid from the stroma which creates a higher concentration of H+ inside the thylakoid than the stroma - i.e. a proton gradient across the membrane.

4. So H+ move down the their concentration gradient into the stroma via the enzyme, ATP synthase. --> This energy from this movement combines ADP and inorganic phosphate to form ATP.

5. In the mean time, the electrons have reached PSI. Light energy is then absorbed by PSI which excites the electrons to an even higher energy level. They are then transferred to NADP along with a proton from the stroma to form reduced NADP.

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Photosynthesis - Calvin Cycle step by step...

The Light Independent Reaction is also called the Calvin Cycle...

1. CO2 enters the leaf through the stomata and diffuses into the stroma of the chloroplast. Here it combines with 5 carbon Ribulose Biphosphate (RuBP) to form an unstable 6 carbon intermediate compound.

2. This compound quickly breaks down into two molecules of a 3 carbon compound called Glycerate 3-phosphate (GP) --> The Rubisco enzyme catalyses the reaction between CO2 and RuBP.

3. ATP and reduced NADP from the Light Dependent Reaction provides energy and H+ to reduce GP to Triose Phosphate (TP).

4. TP is then converted in to many useful organic compounds such as Glucose.

5.  Five out of every six molecules of TP produced in the cycle aren't used to make hexose sugars but to regenerate RuBP - which uses the last ATP produced by the LDR.

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Photosynthesis - TP and GP

Triose Phosphate (TP) and Glycerate 3-phosphate (GP) molecules are used to make carbohydrates, lipids and proteins...

Carbohydrates --> Hexose Sugars (e.g. Glucose) are made by joining two TP molecules together. Larger carbohydrates, such as starch, sucrose or cellulose, are made by joining hexose sugars together in different ways.

Lipids --> These are made from Glycerol, which is synthesised from TP, and fatty acids, which are synthesised from GP.

Proteins --> Some amino acids are made from GP, which are joined together via acetyl coenzyme A to make proteins.

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Photosynthesis - Calvin Cycle

The Calvin Cyle needs to turn 6 times to make one hexose sugar...

For every CO2 molecule that's put into the cycle, 2 TP molecules are made.

2 TP molecules makes one hexose sugar.

3 turns of the cycle produces 6 TP molecules BUT 5/6 of these TP molecules are used to regenerate RuBP

So actually, 3 turns of the cycle only make 1 TP that's used to make a hexose sugar.

This also means that 6 turns of the cycle need 18 ATP and 12 reduced NADP from the Light Dependent Reaction.

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Photosynthesis - Limiting Factors

Optimum conditions for (most) plant species in the UK:

  • High light intensity of a certain wavelength --> the higher the light intensity, the more energy it provides. Only certain wavelengths are used for photosynthesis (only red and blue light in sunlight - green is reflected which is why plants look green).
  • Temperature around 25*C --> Photosynthesis invloves enzymes (e.g. rubisco & ATP synthase). If the temperature is more than 45*C they may start to denature. Also, at high temperatures stomatas close to reduce water loss. This causes photosynthesis to slow down as less CO2 can enter the leaf when the stomata are closed.
  • Carbon Dioxide at 0.4% --> CO2 makes up 0.04% of gases in the atmosphere. Increasing it to 0.4% gives a higher rate of photosynthesis, but any higher and the stomata start to close.

Growers can create constant optimum conditions for plants in greenhouse to increase photosynthesis/growth and therefore yield in the following ways...

  • CO2 conc - Add CO2 to the air e.g. by burning a small amount of propane in a CO2 generator.
  • Heating and cooling systems can be used to keep a constant temperature.
  • Light can get throuhg the glass & lamps provide light at night.
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There are 4 stages to Respiration --> Glycolysis, the Link Reaction, the Krebs Cycle and Oxidative Phosphorylation.

Glycolysis takes place in the cytoplasm, whereas the other 3 stages take place inside the mitochondria.

Stage 1 --> Glycolysis - Making 2 Pyruvate molecules from 1 Glucose:

1. Phosphorylation - 2 phosphates are added to glucose (from 2 molecules of ATP) which forms 2 molecules of TP.

2. Oxidation - TP is oxidised (loses it hydrogen, which is collected by NAD forming 2 NADH) and forms 2 pyruvate molecules. From this, 4 ATP are produced which overall gives a net gain of 2 ATP.

Stage 2 --> The Link Reaction - Converting Pyruvate to Acetyl Coenzyme A:

1. One carbon is removed from pyruvate in the form of CO2.

2. NAD is reduced by collecting hydrogen from the pyruvate which changes it into acetate.

3. Acetate is combined with coenzyme A to form acetyl coenzyme A.

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Respiration continued...

REMEMBER: the Link reaction occurs twice for every Glucose molecule!

Stage 3 --> The Krebs Cycle - Produces ATP and reduced coenzymes:

1. Acetyl Coenzyme A from the Link Reaction, combines with Oxaloacetate (4C) to form Citrate (6C). Coenzyme A is recycled back into the Link Reaction.

2. A molecule of CO2 is then removed (Decarboxylation) and hydrogen is removed (Dehydrogenation) which is used to produce reduced NAD from NAD.

3. This converts the 6C Citrate molecule into a 5 carbon molecule.

4. The 5C molecule is then converted into a 4C molecule, during which 1 molecule of reduced FAD and 2 reduced NAD.

5. ATP is also produced by the direct transfer of a phosphate group from an intermediate compound to ADP (Substrate - level Phosphorylation)

6. Citrate has now been converted into Oxaloacetate.

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Respiration: Oxidative Phosphorylation...

1. Reduced NAD and reduced FAD are oxidised to NAD and FAD which releases hydrogen atoms which then split into protons and electrons.

2. The electrons move along the electron transport chain (of 3 electron carriers) losing energy at each carrier.

3. This energy is used by each of the electron carriers to pump protons from the mitochondrial matrix into the intermembranal space.

4. The concentration of protons is now higher in the intermembranal space than in the mitochondrial matrix - this forms an electrochemical gradient (a concentration gradient of ions).

5. Protons move down the electrochemicl gradient back into the mitochondrial matrix via ATP synthase --> This movement drives the synthesis of ATP from ADP and Pi (also called Chemiosmosis).

6. In the mitochondrial matrix, at the end of the ETC, the protons, electrons and O2 (from the blood) combine to form water --> Oxygen is said to be the electron acceptor.

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Populations and Ecosystems

Habitat - The place where an organism lives.

Population - All the organisms of one species in a habitat.

Community - Populations of different species in a habitat.

Ecosystem - All the organisms living in a particular area and all the non-living conditions.

Niche - The role of a species within its habitat.

The niche a species occupies within its habitat includes:

  • Biotic interactions --> e.g. the organisms it eats and those it's eaten by.
  • Abiotic interactions --> e.g. the O2 the organism breathes in, & CO2 it breathes out.
  • Every species has its own unique niche --> a niche can only be occupied by one species.
  • If two species try to occupy the same niche, they will compete with eachother.

The population of the species that has the competative advantage over the other, will gradually increase until the other diminishes - know as the competative exclusion principle.

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Investigating Populations

Abundance - The number of individuals of one species in a particular area.

Measures of Abundance:

  • Frequency - The number of samples a species is recorded in.
  • Percentage Cover - How much of an area you're investigating is covered by a species

Distribution - This is where a particular species is within the area you're investigating.


  • Capture a sample of a species using an appropriate technique and count them.
  • Mark them in a harmless way and then release them back into the habitat.
  • After a week or so, take a second sample from the same population and count how many of the second sample were marked.

Total pop.size = (n.o. caught 1st sample x n.o. caught 2nd sample) / n.o. marked 2nd sample.

The accuracy of this method depends on a few assumptions --> Whether the marked sample had enough time/opportunity to mix back in with the population. That the marking hasn't affected the individuals chances of survival and is still visible. Changes in population size are small during the period of the study.

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Variation in Population Sizes

Interspecific Competition - Competition between species:

  • Different species compete with eachother for the same resources.
  • This means that the resources available to both populations are reduced.
  • These limitations mean that they may have less energy for growth, or less space to live which lowers their reproduction and survival chances so the population sizes are lower for both species. If one species happens to be slightly better adapted to its surroundings than the other at a particular time, it will out compete the other species.

Intraspecific Competition - Competition within a species:

  • The population of a species increases when the resources are plentiful. As the population increases, there'll be more organisms competing for the same amount of food and space.
  • Eventually, resources such as food and space become limiting so the population will start to decline.
  • A smaller population then means that there's less competition for space and food, which is better for reproduction so the population will start to grow again.

Predation is where an organism kills and eats another organism. The population sizes for predators and prey are interlinked --> as the population of one changes, it causes the other population to change.

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Th Carbon Cycle

1. CO2 from the air diffuses into the leaves of plants through the stomata, and is used by the plant for photosynthesis - it becomes carbon compounds in plant tissues.

2. Carbon is then passed on to primary consumers when they eat the plants, and so on.

3. The living organism dies.

4. Saprobionts secrete digestive enzymes onto the dead tissues of the organism (extracellular digestion).

5. The products of the digestion (including the carbon compounds from the dead organism) are absorbed by the saprobionts.

6. The saprobionts respire aerobically which produces CO2, that returns to the air.

If dead organic matter ends up where there is no saprobionts, then their carbon compounds can become part of fossil fuels which are then released when burnt (combustion).

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Global Warming

...Caused by Greenhouse Gases such as CO2 and Methane...

CO2 concentration is increasing:

* More fossil fuels are being burnt which releases CO2

* Destruction of natural sinks (things that keep CO2 out of the atmosphere by storing carbon) e.g. deforestation.

Methane concentration is also increasing:

* More fossil fuels being extracted.

* More decaying waste.

* More cattle.

* More methane being released from natural stores e.g. frozen ground (permafrost)

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The Nitrogen Cycle

Plants and animals need nitrogen to make proteins and nucleic acids (DNA and RNA). The atmosphere is made up of 78% nitrogen, however the plants and animals are unable to use it in this form. So it needs to be converted...

1.  Nitrogen Fixation - Bacteria, such as Rhizobium found in root nodules, convert N2 from the air into ammonia which can be used by plants.

2. Ammonification - When organisms die, saprobionts convert their nitrogen compounds into ammonium compounds.

3. Nitrification - The ammonium compounds are then converted into nitrogen compounds by nitrifying bacteria, that can then be used by plants. First they're converted into Nitrites (by Nitrosomonas) and then Nitrates (by Nitrobacter).

4. Denitrification - Nitrates in the soil can also be then converted into nitrogen gas by denitrifying bacteria (they use nitrates in the soil for respiration and produce N2 gas).

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Farming Practices

Intensive farming practices increases productivity: For animals/livestock...

  • Livestock can be fed high energy/concentrated foods for a higher intake/absorbed nutrients for growth and so livestock grow more/bigger/have larger biomass.
  • Can restrict movement of livestock so less (kinetic) energy is used/wasted moving around and more energy used towards growing/increasing biomass.
  • Livestock kept indoors/controlled conditions --> e.g. can regulate heating so livestoc use less energy keeping warm/less heat energy lost.
  • Can select which animals to breed --> control breeding to maximise offspring &/or desired characteriti for higher productivity and also to reduce deaths.
  • Slaughtered whilst young/still growing so more energy is converted to biomass.

For plants/crops...

  • Fertilisers can be added to the soil which provide nutrients (e.g. nitrates) that the plants can use to make proteins/DNA/to grow/increase yield and Pesticides decrease/remove competition and/or prevents damage to crop.
  • Greenhouses can be used to  control conditions e.g. enhance light, temperature, CO2 etc..
  • Selective breeding/genetic modification of crops to increase yield/productivity.
  • Ploughing aerates soli which increases/allows nitrification.
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Controlling Pests

Biological agents:

  • Only needs one application.
  • Specific to particular pest, although may sometimes affect (kill/damage) other non-pest species.
  • Pests don't develop resistance.
  • Keeps pest population low but pests are never fully removed.
  • Biological agent may become a pest themselves.

Chemical pesticides:

  • Quick acting.
  • Can be applied to specific area.
  • Kills a greater variety of pests.
  • Pests may be able to develop resistance to them.
  • May directly kill/damage other non-pests.
  • May indirectly affect other non-pest species --> a secondary consumer may eat many primary consumers that contain a small amount of chemical pesticide, which is enough to poison the secondary consumer.
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...The process by which an ecosystem changes over time...

There are two types of succesion:

  • Primary --> This happens of newly formed or exposed land - there's o soil or organic matter to start with e.g. sea level dropping, volcano eruption to form a new rock surface.
  • Secondary --> Land that's been cleared of all the plants but the soil remains e.g. forest fires, deforestation.

Stages of Succession (The Seral Stages):

  • Primary succession starts when species colonise a new land surface --> The first species to colonise are called the pioneer species.
  • Abiotic conditions are hostile & only the pioneer species can live/survive there because they're specialised/adapted.
  • Pioneer species change abiotic conditions/make conditions less hostile (form organic matter) so new organisms can live there.
  • Secondary Succession happens (in the same way) - there is already a soil layer.
  • New/different plants that are better adapted for the improved conditions move in --> they out compete species already there.
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Succession/Climax Community

...Over time, the ecosystem becomes more complex --> species diversity increases...

And eventually it reaches Climax Community:

When an ecosystem is supporting thet largest and most complex community of plants and animals it can.

  • The organisms that make up the final stage of ecological succession.
  • It's a balanced equilibrium - it won't change much more/i in a steady state.
  • In the UK, this is deciduous woodland.
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Conservation is the protection and management of species and habitats (ecosystems). It involves active intervention by humans to maintain these ecosystems and biodiversity.

Why conservation is important:

Species are resources for lots of things that humans need e.g. rainforests contain species that provide things like drugs, clothes and food --> resources that may be useful for the future could be lost.

Ethics - Other species have occupied the earth longer than we have. A lot of people think that organisms have the right to exist and shouldn't become extinct due to human activity.

Conserving species and habitats can help to prevent climate change e.g. when trees are burnt, CO2 is released into the atmosphere, which contributes to global warming. If they're conserved, this wont happen.

Conservation also helps to prevent the disruption of food chains which would lead to loss of resources.

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Ways to conserve...

Seedbanks - Stores lots of seeds from different plant species. Lots of seeds can be stored and for a long time. But need to be regularly tested to see if they're still viable which can be expensive and time consuming.

Fishing Quotas - Limits the amounts of certain fish species that fishermen are allowed to catch. They reduce the numbers that are caught/killed so their populations aren't reduced too much and the species aren't at risk from becoming extinct. Many fishermen don't agree and continue to do it anyway. They think quotas just cause job losses.

Captive Breeding Programmes - Breeding animals in controlled environments. This increases their numbers and some can be put back into the wild. However, some animals have problems breeding outside their natural setting and reintroducing animals back into the wild could bring new diseases to habitats, harming other species living their.

Relocation - Species then be more likely to survive and their numbers increase. But native species in the new area could be outcompeted.

Protected areas - Habitats are conserved and managed. Can become tourist destinations which causes conflict between the need to conserve and allow people to visit/use them.

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Monohybrid Inheritance - the inheritance of a single characteristic (gene) controlled by different alleles.

Codominance - Where both alleles are equally dominant so that both alleles of the gene are expressed in the phenotype. e.g. sickle cell anaemia.

Sex linkage - Any gene that is carried on either the X or Y chromosome is said to be sex linked. e.g. Colour blindness and haemophillia.

--> Genetic Pedigree diagrams show how traits run in families which is one useful way to trace the inheritance of sex linked characteristics.

All the alleles of all the genes of all the individuals in a poplation at any one time is known as a gene pool --> the number of times an allele occurs within the gene pool is referred to as the allele frequency.

The Hardy- Weinberg principle provides a mathmatical equation that is used to calculate the frequencies of the alleles of a particular gene in a population: p2 + 2pq + q2 = 1

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