Summary diagrams for a2

2. 2 Abiotic factors: the non-living/physical components of the environment (temperature, light, soil pH) Light intensity: affects plants only Carbon dioxide concentration: affects plant populations only Mineral ions: affects plants only Water availability: affects both plants and animals Temperature: affects both plants and animals Abundance: counting the number of organisms in the sample. Usually the abundance of each species is recorded. If we divide abundance by size of the sampling area we get the density (number/m2 ) Autotroph: an organism that can trap an inorganic carbon source using energy from light or chemicals Biomes: parts of the atmosphere that have very different environmental conditions to each other. Biosphere: the parts of the earth that support life. Then organisms of the biosphere depend on one another and the earth’s physical environment which consists of the…. Biotic Factors: A living factor that affects a population or a process (predation, competition, parasitism, disease) Carrying capacity: The highest population that can be maintained for an indefinite period of time by a particular environment Climax community: the final community in succession Community: all the populations of different species that live and interact together in the same area at the same time Competitive exclusion principle: when two species are competing for limited resources the one using the resources most effectively will eliminate the other. Two species can’t occupy same niche indefinitely when resources are limiting Consumers: an organism that obtains energy by eating other living things Decomposers: live in the soil (generally) and feed on detritus, dead, decaying organic matter. There are two groups, the detritivores and the saprobionts/saprophytes. Detritivores: organisms that feed on dead or decaying organic matter Ecosystems: an area within which the organisms interact with each other and their physical environment Detritus: dead or decaying matter Ecology: the study of interrelationships between organisms and their environment. The environment includes both abiotic and biotic factors Ecosystems: An ecosystem is a self-supporting system made up of all the interacting biotic and abiotic features in a specific area. Ecological niche: the position an organism fills in its environment, comprising its habitat, the resources it uses and the time at which it occurs there Environmental resistance: conditions that reduce the growth rate of a population Food webs: a diagram showing all the feeding relationships in a single ecosystem or community Gross primary production: the rate at which chemical energy is stored in plants Habitat: the place where an organism is found Inorganic fertiliser: a fertiliser containing inorganic ions such as, nitrate, ammonium, potassium and phosphate ions. Intraspecific competition: between members of the same species Interspecific competition: between members of different species Limiting factor: the one factor of many that affect a process, that is nearest its lowest value and hence is rate-limiting. Microhabitats: an area within a habitat that has specific conditions Net primary production: the energy that remains after the energy used in respiration has been subtracted from the gross primary production Organic fertiliser: a fertiliser containing organic substances such as, urea. Omnivores: animals that regularly feed at both primary and higher trophic level. Pioneers species: species which are first to colonise cleared or disturbed ground. Primary succession: succession that occurs on previously uninhabited ground Population: a group of organisms of the same species that live together in the same area at the same time Producers: an organism that uses solar energy in photosynthesis to produce carbohydrates Pyramid of numbers: A diagram that shows the number of organisms at each trophic level in an ecosystem/food chain at a given moment irrespective of size. Pyramid of biomass: A diagram that shows the total biomass at each trophic level in an ecosystem/food chain, at a given moment, irrespective of the numbers Pyramid of energy: A diagram that shows the energy transferred to each trophic level of an ecosystem/food chain in a period of time irrespective of the numbers and biomass. Richness: number of different species found in the sample Saprophytes/saprobionts: microorganisms (fungi and bacteria0 that feed through extracellular digestion, secreting enzymes onto organic matter and absorbing the soluble products into their body to use in respiration (releases carbon dioxide to the environment again for use in photosynthesis) or to use in assimilation building new cells (biomass) Secondary succession: succession that occurs on in a place where there was some vegetation already present and the area has been disturbed by natural disaster or by deforestation etc. Succession: the process by which a community changes over time, a directional process where organisms affect the environment making it less suitable for themselves and more suitable for the next dominating species. Food chains: A very simple diagram showing how energy flows through an ecosystem Trophic level: the position in a food chain at which an organism feeds

3. 3 Random sampling: to get a representative sample of the whole area. Area is divided into a grid using measuring tapes; random numbers are generated (from tables, calculator, computer) and used as co-ordinated to place quadrats. There should be a large number of samples to be representative, allow for anomalies, and improve reliability and to allow statistical analysis. One should aim to sample 2% of the total area. Systematic sampling: used when you wish to investigate an environmental gradient (change across a habitat). Commonly this uses a transect. In the line transect the organisms touching the string are recorded. In a belt transect quadrats are placed at along the transect (it can be continuous, or interrupted, where quadrats are placed at regular intervals). Measuring Abiotic factors: usually requires digital equipment, temperature probe, pH probe, light meter. These give quick, calibrated, quantitative accurate data and can be used to record data at regular intervals or continuously across a time period Abiotic factors: water/air temperature, pH, turbidity (suspended solids), oxygen levels (air and water), mineral levels in soil and water, soil depth, texture, wind speed and direction, humidity Quadrats vary in size 10cm, 50cm, 100cm sides are common, and they may be subdivided into 25 or 100 squares. To find the best size quadrat nesting is used. Different sized quadrats are used and the number of species counted. From the species area graph the most appropriate size quadrat can be identified that is likely to catch all species but not waste effort. Quadrats are used to get quantitative data like… Density: number of individuals of each species in quadrat divided by area of quadrat Species frequency: record the number of quadrats within which the species was found e.g. 12 out of 40 had a species so, frequency was 30% % cover: useful when difficult to identify individual plants. Estimate to nearest 5%, the % area of the quadrat covered by a particular species, easier when quadrat is subdivided, this is subjective though. Abundance scale: ACFOR, Abundant, Common, Frequent, Occasional, rare. Not quantitative, but can be made semi quantitative by making each point (ACFOR) correspond to a % cover range

4. 4 Sampling animals is made more difficult by the fact they move. So traps need to be used Sweep nets in long grass and crops to catch insects, standardise the sweeping time height to allow comparisons Beating trays: used to get invertebrates from trees. Tree is hit with a stick and invertebrates fall into a tray Pitfall traps: smooth sided cup buried in ground, a raised cover keeps out predators and rain. Used to catch invertebrates Longworth traps: To catch small mammals: prepared with dry bedding and food; placed randomly in the area. Animals enter and trigger the door to close, they are safe from predators Capture – Mark – Recapture: the problem with counting animals is getting a good estimate of the total number in the area; they move quickly, they cover larger area and they try to remain hidden. So the capture, release, recapture method is used 1 Capture a sample of animals using one of the trapping techniques described above. The larger the sample the better the estimate works. 2 Count all the animals in this sample (S1) and mark (using one of methods below) then so that they can be recognised later. Typical marks include: a spot of paint for invertebrates, leg-rings for birds, a shaved patch of hair for mammals, small metal disks for fish, etc. Larger animals can also be “marked” by collecting a small blood sample and making a DNA fingerprint. Ensure marking is not harmful to animals, or prevents reintegration to the population or that it will wash off, or that it makes them more susceptible to predators. 3 Release all the animals where they were caught and give them time to mix with the rest of the population (typically one day). 4 Capture a second sample of animals using the same trapping technique. 5 Count the animals in the second sample (S2), and the number of marked (i.e. recaptured) animals in the second sample (R). 6 Calculate the population estimate (N, the Lincoln-Petersen Index) using the formula: Assumptions Marking does not affect their survival Capture of marked and unmarked animals is random Marks are not lost Animals mix with population again randomly and completely There are no massive changes in population size between sampling s1 and s2 due to reproduction or migration/immigration, population thus remains stable between samples Animals are not trap happy or trap shy Limitations Animals must be captured which can harm them or alter behaviour steps taken to minimise this. Marks can be lost Marking could affect interaction with population after capture ‘Catchability’ of animals can vary with season, time of day, life stage, but assumes equal ‘catachability’. Immigration/emigration/migration/birth and death issues can be overcome by having a small delay between sampling N = population n1 = number first caught and marked n2 = number caught in second sample m = number in second sample that had markings Marking techniques: A spot of paint for invertebrates, leg-rings for birds, a shaved patch of hair for mammals, small metal disks for fish, etc. Larger animals can also be “marked” by collecting a small blood sample and making a DNA fingerprint. One new solution is to mark with an ultra-violet marking pen which can’t be seen undernormal sunlight, but can be seen under ultra-violet light.

5. 5 Succession: The change in a community over time due to changing environmental (abiotic) and biotic factors conditions. This change in plant life is often quite predictable until a stable climax community is reached. Primary succession: when succession begins on an area that has not been inhabited previously (a slow process) Secondary succession: occurs on previously inhabited areas (farm land left to re-grow, forest areas devastated by fires or floods). It is faster as the soil is already in place. The key idea is that each species of plant changes its environment to make it more suitable for new species to colonise. Consequently, these initial species are often out-competed as the new species are usually more sophisticated and bigger. As the succession proceeds the habitat becomes less harsh and abiotic factors less hostile. Daily temperature fluctuations decrease due to shade, water holding capacity of the soil improves due to an increase in organic matter, nitrates in the soil increase, roots help hold soil together minimising erosion, As the plant life becomes more diverse the animal community becomes more diverse as there are more food sources, more niches, habitats. The climax community supports a complex food web. Early colonisers, pioneer species are fast growing plants, with shallow roots and wind-dispersed seeds being replaced by taller, slower growing plants with deep roots and animal dispersed seeds. The change occurs in stages called seral stages. The initial habitat is very harsh…. Extreme pH High winds Lack of minerals Lack of water Temperature fluctuations High salinity Pioneers are organisms adapted to cope with these extremes Lichen, algae and mosses The action of pioneers and successive species alters, pH, builds a simple soil, add minerals to this soil by death and decomposition, improve water holding capacity Lichen: fungus and algae mutualistic relationship. They are excellent pioneers because Fungus: can make minerals available form rock (acidic secretions) and decomposition of organic matter. They prevent desiccation of algae and anchorage to the rock Algae are photosynthetic providing sugars for the fungus. Describe and explain how succession occurs: Colonisation of area by pioneer species; these organisms changes the environment; this enables new species to colonise; Repetition of this process results in the environment becoming less hostile, biodiversity increases, providing food, habitat, nesting sites and niches, Eventually a climax community is reached (Human activities: ploughing, harvesting, animal grazing, burning, may prevent the development of the climax community and result in an artificial or Plagioclimax community)

6. 6 Bare rock Pioneer community Legumes and horse tails Grasses and ferns Small trees and shrubs Climax community Barren land develops: Fire, flood, deforestation, glaciers retreating, volcanic eruption, silt and mud deposition. Hostile (abiotic factors): pH, salinity, wind speed, nutrient levels, temperature fluctuations, water availability Chemical and physical weathering allows slow soil formation Pioneers must have adaptations to tolerate harsh abiotic factors: xerophytes, fast seed germination, low nutrient requirements, able to fix nitrogen, produce lots of seeds or spores (germinate fast and can tolerate acid soils, waterlogged soils) Lichen good pioneers mosses grow on top. They trap debris and increase organic matter through death and decay of themselves and detritivores forming a simple soil. Some free living nitrogen fixing bacteria may be present in soil. Nitrogen fixing bacteria (Rhizobium) found in root nodule of these plants and can fix atmospheric nitrogen allowing these plants to grow in a simple soil with lower nutrient levels. Their activity and death increases soil depth and nutrient quality. Increase in organic matter (humus) improves water holding capacity of soil and root growth aerates the soil and secretions change soil pH. Previous species (pioneers) have improved soil depth, quality (nutrients, pH, oxygen levels) and water holding capacity. Taller plants shelter soil reduce diurnal temperature variation and desiccation Pioneers can not compete and die out. Animal diversity and nesting increases Biodiversity increases rapidly due to hunting mating and nesting sites these birds bring in seeds. More niches are available, greater variety of habitats and food sources. Biodiversity may be greatest here before the dominant species of the climax community takes over and out competes many species. Nutrient cycling, light, temperature water availability of soil changes dramatically. Leaf litter may alter the soil pH significantly Interspecific competition leads to a reduction in biodiversity. Number of species and their populations will stabilise limited by…. Nutrient availability, light, number of producers, disease killing weak member sof species, predation, intra and inter specific competition. This is the most stable community with more complex food webs and a change in one species does affect others as greatly as other food sources exist. Succession: early pioneer species change the habitat making it more suitable for those that replace them in next stage. As it progresses biodiversity increases, as nesting sites, breeding sites, habitats, food sources are more varied and stable as abiotic factors are less harsh.

8. 8 So why conserve a forest ecosystem. Trees available as a sustainable resource; Maintain habitats / niches / shelter; Maintain diversity / avoid loss of species / protect endangered species. Maintain stability (of ecosystem); Maintain food chains / webs / supply of food; Reduced loss of soil / erosion; Reduced flooding; Act as carbon sink / maintainO2and C02 balance reduce greenhouse effect Reduce global warming; Source of medicines; Examples of sustainable management and reasons to preserve the indigenous species of a habitat…. 1. Protection of habitat: maintains food sources, nesting sites 2. Legal measures like e.g. quotas, hunting bans: prevents populations falling to dangerously low numbers 3. Capture/culling of non-native species: these can often replace/kill off indigenous species 4. Captive breeding: to boost numbers of populations and ensure members of species are together at most fertile time 5. Surrogacy / artificial insemination / genetic manipulation techniques; 6. There may be cultural and aesthetic reasons for conservation and a link to tourism and the economic benefits to economy. 7. Possible undiscovered benefits where some genes may provide medicinal products or characteristics for biotechnology. 8. Maintaining genetic diversity for future breeding programmes. 9. Avoid damage to food webs and it helps control local pests. 10. Ethical reasons, taking into consideration other organisms have occupied the earth longer than man and should be respected One key area of controversy is deforestation. This is essential for building material, paper, farmland, urbanisation, fuel. However, it leads to many problems 1. Soil erosion/ mud slides / flooding / leaching of minerals – trees no longer protect soil from rain / from wind / roots no longer hold soil; 2. Increased CO2 (in air) OR “greenhouse effect” – trees remove CO2 in photosynthesise, the large scale felling of trees and subsequent decay or burning releases CO2. 3. Less diversity– loss of food / loss of habitat / niches 4. Changed rainfall patterns / drought – less transpiration from trees; 5. Loss of pharmaceuticals / ‘medicines’ / timber / ‘wood’; Conservation: the concept of preservation/maintenance of biodiversity, through sustainable management of resources to maintain forests and the habitats/niches and food they supply that ultimately maintains biodiversity. Biodiveristy includes…genetic diversity (variety of alleles), species diversity (variety os species) and habitat diversity (variety of habitats) So the aims of conservationa are to: 1) maintain diversity 2) maintain organisms’ habitats Effective conservation does nto eman leaving the environment untouched, which would lead to a small range of climax communities, instead it requires active inetervaention to manage succession and maiantain a wide range of plagioclimaxes (false climax communities), some techniques for this intervaention Thinning of woodland to ensure light reaches the ground encouraging shrubs and wildflowers to grow. Hedgerows maintained in farmland, providing ecological corridors for animals to move between areas, nesting sites, food sources, habitats for insects that may be natural predators of crop pests Grazing by animals, maintains grassland but prevents growth of tress and shrubs Periodic burning to remove saplings and allow fire resistant heather to thrive Cutting back reeds that dominate and dry out fenland, pump water into the fenland to keep it waterlogged

9. 9 Decay/decomposition/rotting/putrefaction: is the breakdown of detritus by organisms collectively known as decomposers. There are two groups of decomposers 1) Saprobionts (previously called saprophytes): these are microbes (bacteria and fungi) 2) Detritivores: small invertebrates that eat detritus Saprotrophs/ saprobionts Use saprobiotic nutrition, extracellular digestion They secrete digestive enzymes Absorb the soluble products Use these in aerobic respiration Release carbon dioxide Some of the bacteria have cellulose to break down plant fibres. Herbivores depend on these in their guts. Other enzymes like deaminase help with the ammonification process in N cycle. In terrestrial environments the main saprobionts are fungi. Fungi are composed of long thin hyphae that grow throughout the soil giving a large SA:VOL . In aquatic environments the main saprobionts are bacteria Detritivores: Use holozoic nutrition Ingest food, digest it in a gut, absorb soluble products and egest waste. They speed up digestion by helping the activity of saprobionts by…… Increase surface area of detritus for saprobionts Tunnelling activity: aerate soil, provides oxygen for saprobionts to respire aerobically Excrete useful minerals (urea) which saprobionts can metabolise (iii) Explain the role of bacteria in making carbon in dead plant remains available to plants. (4) decomposers/ saprotrophs; release enzymes and digest detritus/extracellular digetsion absorb products of digestion/ suitable e.g. that relates to these are respired and CO2 released; CO2 diffuses in through the stomata used by plants in photosynthesis/ enters leaves; What is the importance of decomposers to the producers? (1) Supply of inorganic molecules / e.g. CO2 / nitrate / phosphate / minerals;

10. 10 Describe how the carbohydrates in the dead leaves in the beech wood would be recycled by the activity of detritivores and microorganisms and the carbon dioxide made available for plants. (7) Detritivores break leaves into small pieces / increase surface area; Deposit faeces; Increases rate of microbial action; Bacterial fungi decompose / break down leaves or organic matter; Secretion of enzymes for digestion; Absorption of sugars; Respiration by detritivores/ microorganisms; Release of carbon dioxide; Carbon dioxide used in photosynthesis; The level of carbon dioxide in the atmosphere (0.04%) remained constant for millions of years Most carbon dioxide removed in photosynthesis is balanced by respiration Some was diverted for longer periods of time in carbon sinks Fossilisation Biomass (trees and animals) Dissolved in oceans Incorporated in carbonate based rocks The balance has been skewed due to the industrial revolution and changes to meet human population increases as outlined below Combustion of fossil fuels for electricity and heating Deforestation for farm land, communication networks, housing, shops Increased acidity rain from combustion led to chemical weathering Rising global temperatures led to less carbon dioxide dissolved in the oceans Less trees means less carbon dioxide fixation in photosynthesis The levels of carbon dioxide in the atmosphere fluctuate as rates of respiration and photosynthesis vary. Daily variations: Lowest carbon dioxide in the day when photosynthesis is taking place Highest at night when only respiration is taking place in both animals and plants Seasonal variation: Lowest CO2 in summer when days are warmer (enzymes), brighter (light intensity), longer Highest CO2 in winter when days are cooler (enzymes), shorter, lower light intensity and tress lose their leaves less photosynthesis. Also increased combustion of fossil fuels to cope with cold winter The concentrations of carbon dioxide in the air at different heights above ground in a forest changes over a period of 24 hours. Use your knowledge of photosynthesis to describe these changes and explain why they occur. 1. High concentration of carbon dioxide linked with night/darkness; 2. No photosynthesis in dark/night / light required for photosynthesis/light-dependent reaction; 3. (In dark) plants (and other organisms) respire; 4. In light net uptake of carbon dioxide by plants/plants use more carbon dioxide than they produce/ rate of photosynthesis greater than rate of respiration; 5. Decrease in carbon dioxide concentration with height; 6. At ground level fewer leaves/less photosynthesising tissue/more animals/less light The carbon dioxide concentration was monitored at ground level in the centre of a small roundabout. The measurements were made on a summer day. Describe and explain how you would expect the concentration of carbon dioxide to fluctuate over the period of 24 hours. (5) 1Higher carbon dioxide concentration at night/during darkness; 2Photosynthesis only takes place during light; 3Photosynthesis removes carbon dioxide and respiration adds carbon dioxide; 4Respiration taking place throughout 24 hours; 5Quantitative consideration such as that in plants overall photosynthetic rate greater than respiration rate; 6Human effect such as additional carbon dioxide from heavy daytime traffic/street lighting could prolong photosynthesis; Carbon source: ecosystem releasing more CO2 than it accumulates as biomass. Carbon neutral ecosystems fix and release equal amounts of carbon over time Carbon sink is an ecosystem accumulating more carbon biomass than it releases, occurs when decay is prevented, peat bogs too acidic, ocean is cold and anaerobic, growing forests as trees grow and live long lives.

11. 11 High frequency/shortwave solar radiation pass easily through the earth’s atmosphere Some solar radiation is reflected by clouds Greenhouse gases: CO2 (69.6%), CH4 (12.4%), N2 O (15.8%) Earth surface absorbs the solar radiation and heats up emitting long wave/low frequency infrared radiation Infrared radiation does not pass easily through the greenhouse gases and is absorbed and re-emitted. This was how earth stayed at ambient temperature Crops Higher/lower rainfall or higher/lower temperature may result in failing crops/plant life causing a change in the distribution of plant life and hence animals dependent on them. There may be changes in the type of crop that can be grown, no longer possible, now possible. Higher night temperature will affect the ability of some crops to set fruit or seed giving lower yields and less seeds for next planting. Warmer/shorter winters and warmer longer summers may allow pests to survive longer or appear in greater numbers than before, causing extensive crop damage, thus increase expenditure on pesticides. Melting polar ice caps cause loss of fertile low lying land (Nile delta). May lead to destruction of forests to provide farm land and as consequence this only adds to the issues. Rising sea levels due to melting of ice shelves and glaciers and thermal expansion of the ocean means salt water is extending further up rivers making soil salinity increase affect water availability for crops and irrigation difficult. Selects for xerophytes and changes biodiversity of the animals feeding. Animal Migratory birds are not travelling as far south as they would normally and are migrating north earlier. This means that food sources may mot be ready yet, plants with day length dependent flowering are not yet in bloom and as a consequence seeds, fruit and insects may not yet be abundant. As air temperature rises the Alpine snow line is rising. Animals that live on or above the snow line are forced to move with it and are forced in to smaller areas. This increases competition. Those that can not move up (higher altitudes less oxygen) also face extinction. Disruption of niches available within a community. Each organism is adapted to a particular niche and, as these change so does the species distribution. A niche is the place or function of an organism in an ecosystem. Organisms compete for a niche. If there is a niche for a flying organism that can feed on nectar, and carry pollen this can be filled by a bird, insect or mammal. Global warming forces migration and thus they compete for the niche and may displace indigenous species. Loss of glaciers and ice melting earlier affects hunting of Arctic animals; they must take longer riskier swims. Water As ocean temperatures increase less carbon dioxide can dissolve in them so this furthers the problem Increased evaporation leads to increased cloud cover, more solar energy reflected and the temperature could decrease. Others Ice albedo effect reduced. (albedo is a measure of how strongly an object reflects light). Ice reflects almost all the suns energy that hits it (important in maintaining global climate). As polar ice melts more energy is absorbed by the earth. Positive feedback loop. Increased extreme weather events Alteration to the timing of seasons Advantages Growing in regions that had previously been too dry of cold Growing seasons are prolonged so greater yields Higher carbon dioxide and temperature faster photosynthesis (limiting factors) Causes of greenhouse effect: combustion of fossil fuel, deforestation (reducing photosynthesis, decay/burning of trees releases carbon dioxide), agriculture (methanogenic bacteria in rice fields and ruminant intetsines) has led to mass increase in cattle rearing and rice fields to meet food demands, landfill sites have these bacteria too.

12. 12

13. 13 Dead/waste (urine) organic matter Ammonia NH3 Ammonium Compounds NH4 + Nitrites NO2 - Nitrates NO3 - Ammonification by Decomposers: saprobionts with extracellular digestion secreting proteases to form amino acids and then deaminase enzymes (removes amino group) ultimately leading to ammonium ions Water Nitrosomonas Nitrobacter Nitrogen Fixation: reduction of atmospheric nitrogen by free living soil bacteria (azobacter/clostridium) to ammonium ions, this is then passed through nitrification. Symbiotic organisms (Rhizobium) found in leguminous plants using an enzyme system Nitrogenase. This provides the plant directly with ammonium compounds, so nitrification does not follow, plant can assimilate ammonium compounds more easily than nitrates, but cannot absorb them in the soil, hence need for nitrate formation Bacteria get carbohydrates from the plant Bacteria that fix nitrogen are called Diazotrophs N2 + 6H  2NH3 (requires nitrogenase enzyme and 15 ATP molecules) Active uptake and assimilation Denitrification: occurs where there is a lack of oxygen in the soil leading to more anaerobic denitrifying bacteria, pseudomonas and thiobacillus Nitrification: Oxidation of ammonium compounds by these two different strains of nitrifying bacteria. These bacteria are chemoautotrophs: they gain their energy by the chemical oxidation (chemo) of ammonium compounds and use carbon dioxide to synthesise organic compounds. Autotroph means they do not depend on preformed organic material. This oxidation reaction is exothermic, releasing energy which bacteria use to make ATP instead of respiration. Mineralised nitrogen: Nitrogen as inorganic ions/nitrate/ammonia / nitrite Excretory nitrogen: Nitrogen in waste products of metabolism/urea/uric acid /ammonia Organic compounds containing nitrogen: Protein/amino acid/nucleic acid/ATP / urea;

14. 14 Substances found in fallen leaves contain the elements carbon and nitrogen. Explain how the activities of decomposers and nitrifying bacteria recycle the substances in fallen leaves for re- use by the trees. (7) A question asking about making carbon available and N available again for the trees, so answer both parts…. Carbon available because…… (Decomposers/saprobionts): Secrete enzymes (extracellular digestion) These enzymes hydrolyse organic matter; the soluble products are absorbed by named process e.g. diffusion/active transport; these products are used in respiration Releases carbon dioxide; Carbon dioxide used in photosynthesis; N available again because saprobionts release ammonia from organic material; Through action of proteases and deaminase enzymes (Nitrifying bacteria):convert Ammonia nitrate; Via nitrite An oxidation reaction Nitrates absorbed and used in synthesis of amino acids/protein/nucleic acids/other correct organic –N; Sources of ammonium compounds: 1) Decomposers (mainly saprobionts) convert (nitrogen in organic compounds) into ammonia/ammonium; 2) Nitrogen fixing bacteria: Convert nitrogen (gas) into ammonium; adding usable nitrogen to an ecosystem. This is a reduction process. This can be done by free living soil bacteria, the ammonium compounds must undergo nitrification then as plants cannot absorb the ammonium but can absorb nitrates. In N fixing bacteria associated with root nodules the plant uses the ammonium compounds directly. Nitrification: (Ammonium)  nitrite; then Nitrite  nitrate; by nitrifying bacteria (Nitrosomonas / Nitrobacter respectively) this is an oxidation reaction

15. 15 The law of diminishing returns: the increased application of fertiliser does not increase yield and so becomes uneconomic Eutrophication: the main cause is leaching of fertiliser from farms and sewage form houses and factories. Nitrate and phosphate concentration are the biggest limiting factors to grow of aquatic plants. Algae grow fastest, and this results in the algal bloom. Farming practices disrupt natural mineral cycles. Minerals taken from the soil by plants directly and animals indirectly are not returned. So the soil depletes of minerals. Plant growth is limited by mineral levels, particularly, NPK. So the problem can be tackled by… N fixing crops: crop rotation that includes leguminous crops one year of 4. The clover is then ploughed back into the soil. Clover will add humus to soil, nitrates (needed for protein synthesis), it is cheap, releases it minerals slowly causing less run-off and pollution. Inorganic fertilisers: soluble artificial fertilisers containing NPK. Organic fertilisers: natural fertilisers, animal manure, composted veg, sewage sludge. The also contain NPK, but in organic matter, urea, proteins, lipids and organic acids. These minerals must be released by decomposition. A combination of both the types of fertiliser maximises productivity. Considerations needed as beyond a certain point addition of fertilisers will have no further increase on growth so is an unnecessary expense. A Balance between increase in yield and profit against cost of buying and applying fertiliser. Fertilisers often contain Nitrogen/ Phosphates/ Potassium: 1) N = protein synthesis 2) Phosphates = help production of DNA, RNA, NADP and ATP 3) Potassium = Proteins synthesis, chlorophyll production (magnesium important here too) Explaining eutrophication Increased phosphate/nitrates causes algal bloom; algae (cover surface and) block out light; Plants (under surface) unable to photosynthesise; They die, and algae die (due to minerals now depleting) Algae are too numerous to be eaten by their consumers they accumulate Sudden increase in detritus (plant & alage) Increase in (aerobic) bacteria (decomposers); Bacteria use up oxygen in water; (high BOD) In respiration; Other aerobic organisms die, Anaerobes thrive releasing H2 S, CH4 , NH4

16. 16 Agricultural ecosystem Agricultural ecosystems are comprised largely of domesticated animals and plants used to produce food for man. There are considerable energy losses at each trophic level of a food chain. Humans are often third or even fourth in the chain. This means the energy we receive from our food is only a small proportion of the total energy available from the sun. Agriculture tries to ensure as much of this energy as possible is transferred to humans (effectively it channels energy away from other food chains and into the human food chain) this increase the productivity of the human food chain. Productivity Productivity is the rate at which something is produced. Plants are producers as they produce chemical energy from light energy in photosynthesis. The rate at which the plants assimilate this chemical energy is called gross productivity (measured for a given year and expressed as KJm-2 year-1 . Some of this chemical energy is used by the plant in respiration, so the remaining chemical energy is the net productivity and this is available to the next organism in the food chain (not all of this energy passes to the organism due to, indigestible and inedible parts) Net productivity = gross productivity – respiratory losses Net productivity is affected by two main factors 1) The efficiency of the crop carrying out photosynthesis, maximised by reducing the effects of limiting factors, carbon dioxide, light, temperature, water, minerals. 2) Area of the ground covered by leaves (photosynthetic organs) The two major differences in this system are 1) Energy input: naturally the sun is the only source of energy input. The additional energy input in the agricultural ecosystem is required for preventing the development of the climax community and also maximising the growth, Energy is required in ploughing, sowing crops, removing weeds, suppressing pests and disease, housing and feeding animals and transport etc. 2) Productivity: Natural ecosystems have a low productivity. The additional energy input to agricultural systems is used to reduce the impact of limiting factors. Energy used to exclude other species reduces competition and the ground is almost completely covered by the crop. The application of fertilisers and pesticides and disease prevention help increase productivity.

17. 17 Explain how farming practices increase the productivity of agricultural crops. 1. use of Fertilisers contain minerals NPK (added to soil); 2. Nitrate for proteins and phosphate/phosphorus for ATP/DNA; 3. Pesticides/biological control prevents damage/consumption of crop; 4. Weed killers/herbicides remove competition; 5. Selective breeding / genetic modification (of crops); 6. Glass/greenhouses enhance temp/CO2/ light limiting factors 7. Ploughing aerates soil to improves drainage; 8. Ploughing aeration of soil allows nitrification/decreases denitrification; 9. Benefit of crop rotation in terms of soil nutrients/fertility/pest reduction; 10. Irrigation/watering to remove limiting factor; 11. Protection of crops from birds/pests/frost by covers/netting etc.; Describe and explain the effects of monoculture on the environment. Removal off hedgerows; since small fields impracticable for large machines; so soil more exposed to wind; resultant increase in soil erosion (once); so reduction in diversity; since smaller variety of niches/habitats; since smaller variety of producers/plants also, deeper rooted plants removed; resultant increased soil erosion (once); increased risk of large-scale crop failure/increased disease/increased number of pest; since large numbers of same crop species grown close to each other; increased use of fertilisers result in eutrophication/damage to soil structure; reduction of gene pool increases susceptibility to disease Pests spread more rapidly Productivity: the amount of biomass produced by that ecosystem in a year measured either as Biomass: Kgm-2 y-1 Energy: MJm-2 y-1 Gross Primary Productivity (GPP) = amount of energy fixed by producers in photosynthesis and stored as chemical energy in glucose Gross Secondary Productivity (GSP) = amount of energy absorbed by secondary consumers But energy losses as heat from respiration, indigestible parts of food, uneaten parts of food etc. means not all energy is available to the next level in the food chain, so…… Net Primary productivity (NPP) and Net Secondary Productivity (NSP) is the amount of energy accumulated in producer or consumer biomass and available to the next trophic level Net productivity = Gross Productivity – losses due to respiration and heat. NPP gives us an indication of how good the ecosystem is at fixing solar energy Productivity is of interest to farmers who wish to maximise the NPP (arable farms) NSP (pastoral farms). So intensive methods are employed to improve productivity, such as….. Genetic engineering Selective breeding Fertilisers Pest control Factory farming herbicides Large fields Monoculture Mechanisation Some increase gross productivity (fertilisers) while some decrease respiratory loses (factory farming) The cost of sheds, heating, machinery, producing fertilisers demand energy and are costly, so the gains must outweigh the cost Factory farming/intensive rearing of livestock: increasing NSP Animals are kept indoors for part or all of the year, usually at very high density. The barn is kept warm by the collective body heat of so many animals in close proximity, and in very cold conditions buildings can be heated (though this costs the farmer). Less energy is lost as respiratory heat, so increasing NPP. In addition, animals can’t move much, so they don’t expend energy in muscle contraction. More of the food they eat is converted to useful biomass rather than being lost in respiration. Animals are given specialised, high-energy food, high nutritive value so animals grow quickly and can be sold sooner. The food is low in plant fibres (cellulose), so it is easy to digest and less energy is wasted in egested faeces. The food also contains mineral and vitamin supplements that the animals would normally obtain from fresh food and exposure to sunlight. The dense packing of animals makes it easy for pathogens to spread from host to host so animals are given antibiotics to mitigate the effect of infectious disease. Antibiotics also increase growth rate by killing intestinal bacteria. Animals are selectively bred to be fast-growing (see unit 2), and they are slaughtered before growth stops in adulthood, so more energy is transferred to biomass thus, the farmer doesn’t waste any food, and earns profit early. These methods are costly. Intensive farming depends on high levels of inputs to achieve high productivity. But the gains in productivity should exceed the. Factory farms produce large amounts of animal waste, which often pollute surrounding water ways. Factory farming also raises many ethical questions about the welfare of the animals.

18. 18 Explain how the use of pesticides can result in resistant strains of insect pests. 1. Variation/variety in pest population; 2. Due to mutation; 3. Allele for resistance; 4. Reference to selection; 5. Pests with resistance (survive and) breed / differential reproductive success; 6. Increase in frequency of allele; The same idea could lead to herbicide resistant weeds Pests are any organisms that damages farmers crops Pests: they reduce the yield in a variety of ways They include: weeds, fungi, animals Weeds: compete for, light, minerals, water carbon dioxide. They are usually fast growing compared to the crops establishing roots and shoots quickly and out- competing the crop. Insects reduce yields by….. Feeding on the organ of the plant that forms the crop Feeding on the leaves and reducing surface area for photosynthesis Feed on the roots and affect mineral uptake Feed on sugars in the phloem Spread disease Control can be cultural, chemical or biological. Modern practices try to combine all three in integrated pest management Pesticides: These include herbicides, insecticides, fungicides and bactericides. Characteristics of pesticide: selective toxicity, kill specific target, thus they need to be narrow spectrum (more expensive). Broad spectrum pesticides may kill pollinating insects and useful predators of the pest. Biodegradable: broken down by decomposers. Persistent pesticides may accumulate in the food chain (bioaccumulation). Particularly if fat soluble, not excreted form the body like water soluble chemicals. Chemically stable to have shelf life. Insecticides: can be contact, remaining on the surface of the crop and only killing insects that come in contact with it. Systemic insecticides are absorbed and transported through the crop and kill any insects that feed on the crop Easy to apply, and applied in a way to minimise damage to surrounding environment Cultural control Practices that reduce pest problems without using chemicals or biological agents. Provide suitable habitats close to crop for natural predators of the pest Weeding: removal of weeds and diseased crops Crop rotation: breaks the life cycle of host specific pests Intercropping: planting two crops in the same field rye grass and wheat encourages ladybirds to feed on aphids on wheat. Tilling: ploughing to turn soil burying weeds and expose insects to predatory birds Insect barriers: sticky bands on fruit trees to catch crawling insects Beetle banks: strips of uncultivated land around and within fields. This allows invertebrates to thrive that may predate a pest. Regularly monitor the crops for early signs of pest problems Principles of Biological control: controlling pests using other living organisms (predators, pathogen or parasites). Examples: The scale insect destroyed citrus trees, controlled by the ladybird beetle, ladybirds controlling aphids on wheat The control organism can be a predator/parasite or pathogen Specific to the pest The population of the control organism varies with that of the pest, both should eventually become low The control reduces the size of the pest population below the economic threshold, to a point where it no longer causes significant economic loss However, it does not eradicate (kill all) the pest The control species must be carefully selected/screened to……. Target only the pest species To ensure it too does not become a pest Survive in its new habitat to establish and maintain its population Can reproduce It is active during the growing season and when pest is a problem Ensure it does not carry disease Ensure that a new pest will not take over that niche Trials should be carried out in quarantine before being brought to farm Herbicides Weeds are plants growing where they are not wanted; they compete for resources and can harbour pests and disease that affect the crop. Crop seeds are treated with fungicides before sowing Advantages of biological control If well screened it will only target pest Self-perpetuating population (one application needed) No chemical residue left on the crop Pest won’t become resistant to control agent Cheaper (saves cost of repeated chemical use) Continuous control Disadvantages of biological control Doesn’t eradicate the pests Expense or setting up due to research May becomes a pest itself if no natural predators (must be well screened) Slow acting compared to chemicals Subject to environmental factors Possible effects on non-target species Can’t be used in stored grain or dead bodies will accumulate in produce Another Sterile males of the pest could be introduced to reduce success of reproduction Pheromones could be used attracting the pest to devices that destroy them

19. 19 Integrated Pest Management (IPM) Brings together all forms of pest management, aim to reduce effect of pesticides on the environment without compromising the maximisation of crop yields. There are 4 stages Identify pests and population density at which they cause economic harm (economic threshold) only act when population exceeds threshold Use suitable cultural methods to avoid population reaching threshold If population exceeds threshold use biological control to reduce it If biological control fails to reduce population use chemical control at low and controlled levels and at times of year to minimise impact on the environment Evaluate the effectiveness of each stage before proceeding to next Benefits If one method fails others are still partially effective Reduced amount of pesticide needed Increase yield Reduced chances of resistant species developing Less impact on food webs Fewer chemicals used Long term effect rather than the initial improvement seen by chemical methods alone, but loss in effectiveness over time and the need to reapply chemicals Biological control Farming aims to maximise yield and minimise expenditure and impact on environment. Essential to meet the growing needs of the human population. It uses many practices Selective breeding (pg27): for fast growing animals, high yielding crops, reduce allele frequency, genetic diversity Factory farming (pg52): restricted movement and warm holding sheds (more biomass less energy waste), specialised diets high in protein and fat and carbohydrates, low in cellulose so high digestibility. Antibiotics in food, reduce spread of disease, kills gut bacteria increasing growth rate. Monoculture (pg52): growing one crop that grows most effectively in the area. Reduce labour, more than one crop per year, but demands a lot of fertiliser. Requires, hedgerow removal to make more space for growing and to operate machinery. This reduces diversity due to loss of habitat and food sources, possibly lead to increased pest issues as predators of pest may have lived in hedgerows Pesticides (pg53): weeds and animal pests are controlled using chemicals, but these may affect the environment. Resistance may develop. Look to use IPM, takes the best of cultural, biological and chemical control to maximise yield minimise environmental damage Genetic engineering: inserting genes into crops making them herbicide resistance (this may encourage excess use of herbicides), genes into crops to make toxins to insects, may mutate and harm humans, may lead to resistant insects developing. Transfer of gene to non-crop species producing resistant weeds or disrupting food chains Fertilisers (pg51): organic, inorganic or a combination. Good and bad points discussed on page 51. Steps to selecting the Biological agent The search for agent in pests country of origin, in areas with a similar climate to the planned area of release: more likely to find suitable control agent, and it will be more likely to survive. Study the effect of the parasite on other organisms in the lab: see how it affects native species, as it may compete for food/habitat or prey on them. Release of large numbers of agent: Increase the chances of successful introduction to increase chances of reducing pest numbers below economic threshold The stable coexistence of pest and parasite at: means one application should be enough, means pest population should stay below threshold, if pest dies out so will agent, reapplication would be needed

20. 20 Biomass is measured in Kg/m2 or g/m2 of in marine ecosystems Kg/m3 The dry biomass is measured as water content varies and water contains no energy. But this requires killing the organisms, thus only a sample is used and this may not be representative of the population. Sample is randomly selected, dried in oven at 800 C evaporates water, does not burn organic matter until the mass is constant. Weigh a few individuals and get an average, then multiply the number of them by this value. Only measures the number organisms present at that time, so seasonal variation is not accounted for and this means that inverted pyramids may exist in marine ecosystems, when the mass of phytoplankton is less than that of zooplankton feeding on it. Across the year the mass of phytoplankton must be greater than the mass of the zooplankton Inverted pyramids are possible when the producer’s reproduction rate is faster than the rate of consumption (quickly eaten and so don’t reach a high biomass, but reproduce quickly to sustain the consumer) and has a short life unlike the consumers. If we compared the biomass of the phytoplankton against the increase in biomass of the zooplankton, the biomass of the phytoplankton would be greater Limitations of pyramids of biomass Does not show biomass can vary at each trophic level over time Variability in abiotic factors in an area may make comparisons between ecosystems difficult Samples required and must be large enough and random to represent the population Biomass may not be equivalent to energy, as 1g of fat has twice the energy as 1g of carbohydrate. Seasonal variations may not be accounted for Food Chains/webs: illustrate the relationship between members of a community in an ecosystem. Eacvh stage int eh food chain is called a trophic level, the arrows represent the flow of energy and matter. Food chains start with producers (plants, algae, plankton and photosynthetic bacteria) Pyramids of numbers: shows the number of organisms at each trophic level. The width of the bars can represent numbers using a linear or logarithmic scale. Usually numbers decrease as we move up the chain and the size of the organisms increase But…........... There is no account of the size of the organisms: 1 large tree is treated the same as tiny aphids. The numbers of 1 species may be too large to represent on the same scale as another species The transfer of matter and energy in an ecosystem can be displayed using ecological pyramids. There are three kinds. Pyramids of energy: represent the flow of energy into each trophi c level over a period of time. The units are usually KJm-2 yr-1 . They are never inverted. Allows comparison of productivity in an area No inverted pyramids

21. 21 Energy enters the food chain in the form of light energy. The light can either be absorbed, reflected of transmitted. Only that which is absorbed by the chlorophyll can be converted into chemical energy (glucose and its derivatives). As little as 1% of the solar energy reaching the earth is fixed into biomass of the producer Very little light energy is used by the plant because….. Wrong wavelength Misses chloroplasts and is transmitted Reflected Energy losses due to inefficiency of photosynthesis Some is used to evaporate water Other factors can limit the effectiveness of photosynthesis (temp/CO2) Only a small percentage of the light energy absorbed by the chlorophyll is stored as biomass because………… Energy is lost as heat in respiration and other metabolic processes Photosynthesis is inefficient (energy lost as electrons are passed on) CO2 and Temperature are limiting factors The total quantity of energy that plants in a community convert into organic matter is called the gross production. Plants use 20-25% of this energy in respiration leaving little to be stored. So, the stored energy is called the net production Net production = gross production – respiratory losses

22. 22 Consumers take in concentrated chemical energy in the form of organic molecules that constitutes the biomass of producers or consumers they eat. A lot of biomass is not absorbed by the consumer (bones, hair, cellulose, teeth, roots of plants etc.) and the energy in this biomass is passed onto the decomposers. Much of the energy that is absorbed is lost as heat in various metabolic reactions, particularly respiration and friction in movement. The heat losses are bigger in warm blooded animals and very active animals. Not all the chemical energy in the biomass of the organisms being consumed is passed to the next trophic level because….. Not all of the organisms are eaten by those at the next stage Not the entire organism is eaten (roots, woody material, teeth, bones, claws etc) Energy is lost in excretory products (urine) Not all of the food is digested: plant material is much more difficult to digest than meat, due to the cellulose and lignin, consequently the efficiency of the energy transfer from producer to primary consumer is 10% whereas from primary consumer to secondary consumer it may be as high as 15-20%. Energy lost in respiration (heat and movement): this uses biological molecules as a fuel source to release energy and produce ATP. The process releases some energy as heat which escapes to the surroundings. The ATP is used in many processes, active transport, anabolic processes, cell division, muscle contraction, when use energy is eventually lost as heat. Energy lost in maintaining body temperature: this is higher in mammals and birds (homeothemrs, warm blooded, endotherms) than cold blooded animals, it is higher again in smaller organisms as they have a larger surface area to volume ratio. Consequently food chains are rarely more than 4 trophic levels because…… Energy losses occur at each stage, as excreted products, egested indigestible parts, parts that are uneaten, heat from respiration and movement. There is not enough energy left to sustain a large enough breeding population at a higher trophic level. It may be possible to find 6 and 7 trophic levels; this may be a result of…. Aquatic food chains, where the organisms are cold blooded and so energy losses at each stage are slightly lower with regards maintaining body temp Animals may feed at lower trophic levels in different food chains There is a very large density of producers (larger producer biomass) and so the collective % of light energy absorbed may be greater thus allowing more trophic levels C = P + R + U + F The energy used in the production of new tissue. P = C – R – U - F

23. 23 Energy losses……. Sun  producer: energy lost that is reflected, the wrong wavelength, does not fall on chlorophyll, factors like temperature and carbon dioxide limit the rate of photosynthesis Trophic level  trophic level Parts of the organism are not eaten (roots, bones, teeth, fur), Parts of the organism are indigestible (particularly plant material cellulose, lignin) energy lost in faeces Some energy is lost in excretory materials (urine) Energy is used in respiration to drive, active transport, synthesis, cell division, muscle contraction and none of these processes are 100% efficient, so all respiratory energy is eventually lost as heat. Energy transfer from producer to primary consumer is about 5-10% of the net primary productivity. This is lower than primary consumer to secondary consumer (10-20%) because…. Much plant material is indigestible lignin and cellulose) A lot of the plant biomass may not be consumed by an individual herbivore Animal material is more digestible and has a higher energy value. Carnivores may be highly specialised for feeding on their prey. But still much less than 100% efficient because….. Animal tissue is not eaten or digested (bones, teeth fur) The energy is the waste (faeces and urine) and uneaten parts and dead organisms is absorbed by decomposers, used in the growth of these organisms and in respiration and the energy is eventually lost as heat In some cases it may become fossilised and the energy is released in combustion The efficiency of energy transfer differs at different stages as the energy is transferred through the ecosystem….. Some light energy is reflected, the wrong wavelength of does not fall on chlorophyll. Photosynthesis has a low efficiency (2%), there are losses in excretion and uneaten biomass, energy loss as heat, there is a lower efficiency of energy transfer between producer and herbivore than primary consumer and secondary consumer, meat is more digestible, they efficiency of transfer is lower in warm blooded animals and older animals that are no longer growing

24. 24 Productivity: the amount of biomass produced by that ecosystem in a year measured either as Biomass: Kgm-2 y-1 or Energy: KJm-2 y-1 Gross Primary Productivity (GPP) = amount of energy fixed by producers in photosynthesis and stored as chemical energy in glucose Gross Secondary Productivity (GSP) = amount of energy absorbed by secondary consumers But energy losses as heat from respiration, indigestible parts of food, uneaten parts of food etc. means not all energy is available to the next level in the food chain, so…… Net Primary productivity (NPP) and Net Secondary Productivity (NSP) is the amount of energy accumulated in producer or consumer biomass and available to the next trophic level Net productivity = Gross Productivity – losses due to respiration and heat. Only a small percentage of light energy is converted into chemical energy (GPP). It is low because… Some light is the wrong wavelength Some light is reflected Some light does not fall on the chlorophyll Inefficiency of photosynthesis CO2, temperature, nutrients can be limiting factors Of the GPP only a small percentage is available for transfer along the food chain (NPP) due to energy lost as heat in respiration Agricultural systems aim to increase GPP… Irrigation Fertilisers (add minerals NPK to soil) Pest control: cultural, biological, chemical or integrated Herbicides (reduce competition) Selective breeding for high yielding crops/ GM crops Monoculutre: growing one crop, the best crop for area year on year (environmental consequences to consider) Glass/greenhouses enhance temp/CO2/ light limiting factors Ploughing aerates soil to improve drainage and aeration of soil allows nitrification/decreases denitrification; Protection of crops from birds/pests/frost by covers/netting Energy losses occur at each stage of the food chain Producer  consumer  consumer………. because………. Energy lost in parts of the organism not consumed (roots, bones, fur, teeth) Energy lost in parts of the organism not digested (particularly cellulose/lignin) Energy is lost in excretory products like urine Energy lost as heat form respiration Active and warm blooded animals these losses are greater, small mammals the losses can be greater due to the large surface area to volume ratio and extent of heat loss Agricultural practices, intensive rearing of animals (factory farming), looks to minimise these losses and increase NSP…….. Slaughtered when still growing so more energy transferred to biomass Fed on controlled diet so higher proportion of (digested) food absorbed (high protein low plant diet) Movement restricted so less energy used Kept inside heated shed so less heat loss Genetically selected for high productivity/rapid growth In most communities the biomass at each trophic level is less than that above because………not all the organisms are eaten by those Loss of energy at each stage in the food chain by respiration and/or movement and/or excretion, uneaten material Less energy to be passed on Explain why a food chain rarely contains more than four trophic levels. Energy losses (at each trophic level) In……. excretion / egestion / movement /respiration /as heat So (too) little left to sustain a large enough breeding population at higher trophic levels Food chains can be 6-7 trophic levels when…. It’s an aquatic food chain, cold blooded animals Animals are feeding at a number of trophic levels There is a large density of producers, so GPP and hence NPP increases

25. 25 Eutrophication: Nitrates and Phosphates leached from farm land Algal Bloom blocks light penetrating the water Death of aquatic plants below surface death of algae as nutrients deplete Increase in the numbers of saprobionts Respiration of decomposers uses up oxygen in water Aerobic organisms die Biochemical Oxygen Demand (BOD): a high BOD indicates a high level of organic matter in waterways. The more bacteria, the more O2 they will use and so a high BOD results Fertilisers: used to replace minerals in the soil. IN agricultural practices nutrient cycles are disrupted, minerals are removed from the soil, but not replaced by decay. Two types: organic and Inorganic Combination of both is most effective, using the slow release of organic minerals in early stages and applying faster acting more readily available organic minerals at key stages in growth Law of diminishing returns: the increased application of fertiliser does not increase yield and so is uneconomic. Nitrogen needed for: Protein/amino acid/nucleic acid/ATP / urea; Potassium needed for: Protein synthesis, chlorophyll production Phosphates needed for: production of DNA, RNA, NADP and ATP Nitrogen cycle: Ammonification: release of inorganic nitrogen form organic nitrogen (proteins/amino acids). Saprobiotic organisms; secrete enzymes which hydrolyse organic compounds; releasing ammonia; Nitrification: oxidation of ammonium ions into nitrite and then nitrate by nitrifying bacteria Nitrogen fixing: reduction of nitrogen to ammonia by nitrogen fixing bacteria in soil (nitrification follows) or in mutualistic relationship with plants (legumes) (plants use ammonia directly) Denitrification: Conversion of nitrate to nitrogen; bacteria use nitrate for respiration; occurs in waterlogged (anaerobic conditions), by denitrifying bacteria Nitrates are absorbed by the plant roots used in amino acid/protein synthesis. Farmers growing legumes because: Clover contain N fixing bacteria; when clover decays it adds nitrogen compounds to soil; less fertiliser needed; Carbon Cycle How organic carbon is made available as CO2 by detritivores and saprobionts: Detritivores break leaves into small pieces increase surface area; increase rate of microbial activity. Add useful products of excretion (increase nitrogen); tunnelling aerates soil increases oxygen. Saprobionts decompose organic matter; Secreting enzymes for digestion (extracellular digestion); Absorption of products (sugars); Respiration by detritivores and saprobionts; Release of carbon dioxide; Carbon dioxide used in photosynthesis; Differences in how detritivores and saprobionts obtain nutrients: Decomposers secrete enzymes onto organic matter extracellular breakdown; Detritivores ingest organic matter and digest it in a gut

26. 26 Why??????? Higher productivity in agriculture: Remove issues of limiting factors: greenhouses can control tmepertaure, light internisty, carbon dioxide levels, irrigation ensures water is readily avilible, use of fertilisers means that minerals are readily avilible, management of pests reduces competition for resources form ‘weeds’ and minimises crop damage form animal pests. Selecetive breeding for high yielding crops or fast growing animals and genetic engineering of crops for tolerance or pest resistance. Factory farming of animals, reduces energy losses by restricting movement, warm holding sheds, high energy and highly digestible foods, growth hormones, antibiotics Lower species diversity in agriculture: Removal of hedgerwos removes habitats for animals and food sources, growing one type or limited types of crops reduces biodiversity Lower genetic diversity: Selective breeding for certain charcateristics reduces the gene pool (risk associated with this, susceptibility, variation maximises chances of survival) Limited natural recycling and high input of fertilisers: Minerals are removed form the soil by crops and are not returned (decomposed) in that area. Soild depletes of minerals. Fertilisers used to replace lost minerals and to maximise yield. Organic inorganic, or combination of both, consider problems of eutrophication. Competition controlled naturally and artificially Pest control, cultural, biological, chemical and integrated management.

27. 27

28. 28 The predator prey relationship The population sizes of the predator and prey are interdependent. An increase in the prey population means more food and delayed increase in the predator population follows. The increased number of predators kills more prey, so prey numbers fall Lack of food means predators numbers fall Key notes Predator population changes always lags behind the prey Predator number is always lower than the prey (due to energy loss in a food chain). Although the predator prey relationships are a significant contributor to the fluctuations they are not the only reasons as disease, arrival of new predators and climatic factors may also act. The changes in population are not always as severe as shown in many illustrations; this is because organisms usually have a number of food sources. The experiment shows that both food and predation affect hare population. Food availability has more of an effect. The combined effect is more effective than either separately. This graph is drawn from data on the fur trading for both species. However, this assumes that the numbers of fur traded is representative of the relative size of the populations. The population of the snowshoe hare fluctuated in a series of peaks and troughs. Each peak and trough is repeated roughly every ten years. The population of the lynx cycles in ten yearly peaks and troughs similar to that of the hare. The peaks in the lynx population typically occur after that of the hare The hare increases when lynx population is low as more survive. This increases food availability for the lynx so fewer starve and subsequently their population increases (rear more young), this increases predation on the hares so their population declines reducing food for the lynx so they decline in numbers.

29. 29 A population = the number of organisms of a particular species living in a habitat. This number is determined by a variety of interacting factors, abiotic (environmental, physical, non-living) and biotic (living factors) Lag phase: small numbers initially and the time needed to breed and for young to reach breeding age Exponential phase = rapidly increasing numbers in the population Stationary phase: carrying capacity is reached and the population remains relatively constant. Slight fluctuations in the population now affected by, food, predation, competition A 4th phase (decline phase) of the population curve may exist (usually not in a natural environment) in certain circumstances and here there is a decline in the population due to depleting resources for numerous possible reasons Human influence (hunting, deforestation, urbanisation) Or in bacterial growth when nutrients run out No population will grow indefinitely as the availability of resources and competition for these will limit growth. The factors that limit growth….Are called Environmental resistance and can be density-dependent or density-independent Temperature: Plant growth, Cold blood animals and Warm blooded animals are affected, when it is cold they expend more energy keeping warm, this will slow growth and slow reproduction Light: Light affects photosynthesis. pH: enzyme activity is affected by this Water/humidity: low water availability limits diversity, only xerophytes growing, limits the food sources and habitat and thus animals that can flourish. Abiotic factors Climatic: temperature, light, humidity, wind speed, rainfall Edaphic (soil): pH, mineral and moisture content Topographic: altitude Human factors: pollution Catastrophes: floods, fires, and earthquake These factors can vary within a habitat creating microclimates and microhabitats. These factors tend to be density-independent factors: the size of their impact is independent/is not related to the size of the population. Low light will limit plant growth regardless of the size of the plant population. A drop in temperature could kill many organisms whether the population is large or small These factors can often be seasonal Interspecific competition: competition for resources between members of different species usually having evolved slightly different ecological niches. When species which occupy a similar niche are brought in close contact one will usually out-compete the other (competitive exclusion principle), this will be the best adapted. Animals may find this situation arising due to deforestation and climate change forcing animals to migrate. Having a more varied diet helps maximise chances of survival Competitive exclusion principle: when two species are competing for limited resources the one using the resources most effectively will eliminate the other. Thus two species cannot occupy the same niche indefinitely when the resources are limiting Intraspecific competition: competition for resources between members of the same species, this is most intense as members have the same niche competing for exactly the same resources. This has a stabilising effect on a population, if population gets too big intraspecific competition increases and the population falls again. This is the driving force behind natural selection, as variants that are best competitors will survive and pass on their genes Biotic factors Food Competitors Predators Parasites Pathogens Biotic factors are usually density-dependent factors: the size of the effect depends upon the size of the population. Competition is greater if the population is greater. Higher population would mean transmission of disease is more rapid and more likely. If a population is high animals are more easily targeted by predators.

30. 30 An example of interspecific competition P. Caudatum grows slowly at first then accelerating exponentially from around day 4 to day 8. The growth rate then slows reaching a maximum around 12 days; this max population is sustained until day 20. When P. Caudatum is grown with P. Aurelia the population grows faster initially, reaching its maximum much earlier. The maximum population is much reduced (<half) and is not maintained for the 20 days, it reaches zero. This suggests that the P. Caudatum is unable to compete effectively and thus the population starves. P. aurelia‘s growth is slowed when P. Caudatum is present as availability of food is reduced due to competition. On both occasions P. aurelia reaches the maximum, as it out-competes the P. caudatum, which dies out making food available for growth A second example of interspecific competition The graph for Scotland shows evidence that changes in the red squirrel population are due to competition from the grey squirrel because, the fall in the red is mirrored by the increase in grey after 1985 In Wales between 1970 and 75 both populations fall, this could be a result of, lack of food, adverse weather, increase in squirrel predators, disease One suggestion for the competitive advantage of grey over red is that grey squirrels will forage in the trees like the red, but are more willing to forage on the forest floor increasing chance of finding food.

31. 31 A niche is the role the organism has within the habitat. The niche includes abiotic and biotic factors that the organism needs. Organisms are well adapted to their niche. Species with a narrow niche are called specialists. Many specialists can co-exist in a habitat as they are not competing for the same resources, this can give a high biodiversity Species with abroad niches are called generalists, and generalists in the same habitat will compete meaning that only a few will exist, giving a low biodiversity. Only species X would be found in section 1 Temperature and pH conditions where it is suitable for both X and Y to co-exist are found in section 3 The section where it would be too high a temperature for X and too low a pH for Y is section 2 Competition between X and Y would be found in section 3 No population of either X or Y would be found in section 4 because, the pH is too high for X and the temperature is too low for Y The abiotic factors that comprise an organism’s niche can be shown on a graph. For example, if a particular plant can only grow in a temperature range of 10–17°C and a soil pH of 6–7.5, then these ranges can be plotted on two axes of a graph, and where they intersect (the shaded box in the graph on the left) shows those aspects of the plant’s niche. We can add further axes to show the suitable ranges of other factors like humidity, light intensity and altitude, and so get a more detailed description of the niche (graph on right).

32. 32 The population of most animals has been kept in check by the availability of food, disease, climate, predators to name some of the limiting factors of the environment Modification of the human environment has led to a population explosion. The development of agricultural practice The industrial revolution Recycling Medical advances Understanding diets Waste management Improved quality of food So the typical sigmoid population growth is not followed by human populations but rather the exponential phase continues and no stationary stage is reached to stabilise the population. The increase in population, or growth rate, depends on four factors: Growth rate = (birth rate – death rate) + (immigration rate – emigration rate) The equation shows that growth rate can increase by increasing the birth rate or decreasing the death rate (ignoring migration). The staggering human population growth over the last two centuries is entirely due to a massively decreased death rate caused by the improvements in farming described earlier, and in medicine. The increased growth rate has therefore happened at different times for different countries. Factors affecting birth rates Economic conditions – usually lower income = higher birth Religion – some religions encourage big families and are against birth control Social pressure/conditions – a large family can improve social standing Birth control – pills and abortion can affect Political factors – governments influence by taxation and education Factors affecting death rates Age profile – greater proportion of elderly the higher the death rate Life expectancy – longer in MEDNs Food supply – adequate and balanced diet reduce death rate Water supply and sanitation Medical care Natural disasters War

33. 33 Demographic Transition Model: A model to show population changes in a country over time resulting from changes in social and economic situation of the country. Stage 1 High birth and death rates: Limited food causes starvation. Disease causes high but fluctuating death rate. Young are very susceptible to disease and starvation so high infant mortality rate. Short life expectancy means populations remain low and stable Stage 2 More reliable food supply, improving nutrition, and improved living conditions and reduced disease reduces death rates. Birth rates are high so population growth is rapid. Stage 3 Significant fall in birth rate is linked to social change. The increase in industrialisation and urbanisation means that families are less dependent on having children to contribute to the household. Birth control is practised. Stage 4 Stable population with low birth and death rates. Typically death rate is low and stable, birth rate is more variable. Proportion of elderly increases. In some countries death rate now exceeds birth rate a population declines (a possible 5th stage to this model) Most LEDNs are still in stages 2 and 3. Most MEDNs are in stage 4, and some have entered into the possible 5 stage, where the total population is declining. The problem here is that how do they support an increasingly older population that are dependent on a declining number who work. To help tackle these problems immigrants are being encouraged from countries where the population is growing. In the second and third stages the death rates fall before birth rate so the population still grows. In final stage birth rate and death rate are low so the population is stable. Developed countries in stage 4 Developing in stages 2 or 3 so pop growth is mainly here. Social Conditions affecting population structure. The growth of a population rarely follows the demographic transition model exactly; there are many factors that interact and are in turn affected by environmental factors. Three important factors affecting growth are Food supply Individual growth and health are food dependent. Lack of food increases infant mortality due to malnourishment, and malnourished have less chance of surviving infectious diseases. This also affects birth rate as fertility drops in malnourished women. Food shortage can be affected by, drought, crop diseases; other environmental factors (flood etc) there may also be difficulties with distribution. Sewage disposal This is tied into the supply of safe drinking water and the spread of water borne disease (cholera). Drinking water In UK it is taken from deep underground or from rivers or stored reservoirs. Social Conditions and life expectancy Human population growth in the past was limited by food supply, but agriculture offered humans a degree of control over their food production. As populations grew and settled in towns water borne disease had a significant effect due to poor sewage. Many other diseases were controlled until the invention of the vaccination. In modern developed countries fertility can be controlled.

34. 34 The demographic transition model leads to a change in the age structure of a population. These changes can be illustrated in population pyramids or survival curves. Pyramids it helps to group the bars as pre-reproductive (<15), reproductive (15-44), post reproductive (>45) The shape tells about the future growth of the population… The wider the base the faster the population growth. A narrow base suggests a falling population Steep pyramid suggests a longer life expectancy A pyramid with a wide base and with a narrow tip suggests high infant mortality and short life expectancy Survivor curves are created by tracking a group of individuals from birth until the last one dies. The age each one dies at is recorded. The percentage of the group surviving at each stage is plotted. The life expectancy (mean life span) can be calculated by reading of the age at which 50% survive. Type I: long life expectancy, low infant mortality expected in affluent countries Type II: intermediate life expectancy and roughly constant death rate. Type III: short life expectancy, most die young (shown in animals with low parental care and produce large number of off-spring to compensate) in human populations this is evident in countries with poor health care, sanitation and nutrition. A bowing curve to the right demonstrates an improved ability to survive suggesting improved living conditions, medical care, and technology. Although people talk about quality of life in preference to length, the fact remains that length of life is the most objective way to measure quality

35. 35

36. 36 The light-dependent reactions use light energy to split water and make ATP, oxygen and energetic hydrogen atoms. This stage takes place within the thylakoid membranes of chloroplasts, and is very much like the respiratory chain, only in reverse. • The light-independent reactions don’t need light, but do need the products of the light- dependent stage (ATP and H), so they stop in the absence of light. This stage takes place in the stroma of the chloroplasts and involves the fixation of carbon dioxide and the synthesis of glucose. • Plants do not turn carbon dioxide into oxygen; they turn carbon dioxide into glucose, and water into oxygen. The chloroplast is adapted for its function. Contains chlorophyll for light absorption; Range of different pigments to absorb different wavelengths; Stacking / arrangement of grana/thylakoids maximises light catchment; layering of membrane allows a lot of pigment; Stroma contains enzymes for photosynthesis; (Calvin cycle) Outer membrane keeps enzymes in chloroplast; Starch grains / lipid droplets store products of photosynthesis; Ribosomes and DNA for enzyme/protein synthesis; Shape of chloroplast gives large surface area for CO2, absorption. Disc shape provides large surface for light absorption; Permeable membrane allows diffusion of gases / carbon dioxide; Membranes provide surface for attachment of electron / hydrogen acceptors; The absorption spectrum is the graph of absorbance of different wavelengths of light by a pigment The action spectrum shows the rate of photosynthesis at different wavelengths. Note the peaks of absorption occur at 650-700nm (red light) and 400-450nm (blue light). These absorption peaks correspond to the peaks in photosynthetic rate shown in the action spectrum Chlorophyll is a fairly small molecule (not a protein) Chlorophyll and the other pigments are arranged in complexes with proteins, called photosystems. Each photosystem contains some 200 chlorophyll molecules and 50 molecules of accessory pigments, together with several protein molecules (including enzymes) and lipids. These photosystems are located in the thylakoid membranes and they hold the light- absorbing pigments in the best position to maximise the absorbance of photons of light. The chloroplasts of green plants have two kinds of photosystem called photosystem I (PSI) and photosystem II (PSII). These absorb light at different wavelengths and have slightly different jobs in the light dependent reactions of photosynthesis. How the leaf is adapted for photosynthesis Large surface area to collect solar energy; transparent nature of cuticle to allow light penetration; position of chlorophyll to trap light; stomata to allow exchange of gases; thin / max. surface area to volume ratio for diffusion of gases; spongy mesophyll / air spaces for carbon dioxide store; xylem for input of water; phloem for removal of end products;

37. 37 The light-dependent stage of photosynthesis. Light absorbed by chlorophyll in photosystem (PSI/PSII) electrons excited to a higher energy level Electrons are emitted form chlorophyll (oxidised) picked up by electron acceptor Electrons pass down chain of carriers energy released as electrons pass down the electron transport chain energy used in producing ATP from ADP and phosphate; (ADP + Pi+ energy (ATP) A process called photophosphorylation Photolysis of water Provides electrons to replace those lost from PS II (stabilising the chlorophyll/reducing it) Provides the protons/H+ i ons to reduce NADP Reduced NADP formed by accepting electrons and H+; The way in which ATP and reduced NADP are produced in the light-dependent reaction In context of ATP formation light raises energy level of (excites) electrons These pass through electron carriers; energy is released as electrons pass down the transport chain energy is used to form ATP from ADP + P; Reduced NADP is made by accepting protons / H + ions; And electrons; From photolysis / water; The role of electron transport chains in the light dependent reactions 1. Electron transport chain accepts excited electrons; 2. From chlorophyll / photosystem; 3. Electrons lose energy along chain; 4. ATP produced; 5. From ADP and Pi; 6. Reduced NADP formed; 7. When electrons (from transport chain) and H + combine with NADP; 8. H + from photolysis; PSII absorbs light, excites electrons to a higher energy level. This drives photolysis of water (2H2 O  O2 + 4H+ + 4e- ), the protons build up in the thylakoid lumen and the electrons replace those in the chlorophyll. Excited electrons pass along electron carriers releasing energy as they go which pumps protons form stroma to lumen of thylakoid Electrons are finally picked up by NADP The protons are used to make ATP using the ATP synthase enzyme (photophosphorylation) The H+ ions are then picked up by NADP forming reduced NAPD

38. 38 Plants produce ATP in their chloroplasts during photosynthesis. They also produce ATP during respiration. Explain why it is important for plants to produce ATP during respiration in addition to during photosynthesis. 1. In the dark no ATP production in photosynthesis; 2. Some tissues unable to photosynthesise/produce ATP; 3. ATP cannot be moved from cell to cell/stored; 4. Plant uses more ATP than produced in photosynthesis; 5. ATP for active transport; 6. ATP for synthesis (of named substance); In light independent reaction/Calvin cycle; 1. Carbon dioxide combines with ribulose bisphosphate/RuBP CO2 acceptor; 2. This reaction is catalysed by ribulose bisphosphate carboxylase (RuBISCo) 3. Produces two molecules of glycerate (3-)phosphate/GP; 4. GP is reduced to triose phosphate/TP; 5. Using reduced NADP; 6. Using energy from ATP; 7. Some TP is converted to hexose compounds/other organic substances 8. Some TP is used to regenerate ribulose bisphosphate; 9. This regeneration of RuBP requires ATP 10. 10 molecules of 3C/TP/GP form 6 molecules of 5C/RuBP; Explain how ATP and reduced NADP are used in the light-independent reactions. GP converted to triose phosphate (GALP) this involves a reduction; reduced NADP provides the reducing power ATP supplies energy for this reaction; ATP is also used to provide the phosphate for production of RuBP;

39. 39

40. 40 The ‘Lollipop’ experiment was used by Melvin Calvin to work out the details of the light independent reactions. Single celled algae are grown in a solution of radioactive hydrogencarbonate (14 C) which supplies radioactive Carbon dioxide and will be incorporated into the compounds. At 5 second intervals samples of the algae are dropped in to hot methanol (stops chemical reactions instantly, through enzyme denaturation), the compounds are separated (two way chromatography) out and those that are radioactive are identified and the pathway established by the time at which the substances appear. The rapid action tap is essential because the reactions occur quickly and the samples can be removed after a precise time period. Photosynthometer (Audus apparatus). Set up to avoid air bubbles within and ensure it is air tight (air entering/leaving will alter volume of gas making results unreliable. Water bath keeps temperature constant, so change sin rate are only due to light. Temperature can be adjusted to investigate temp effect. Potassium hydrogencarbonate is used to produce excess CO2 for plant so it does not limit Light source with adjustable intensity is used The rate of photosynthesis by a plant or alga can be measured by recording the amount of oxygen produced, or carbon dioxide used, in a given period of time. But these measurements are also affected by respiration, which plants do all the time, so the respiration rate must be measured separately. The conditions at which the rates of photosynthesis and respiration are equal, so there is no net change in oxygen or carbon dioxide concentration, is called the compensation point. Many of the environmental factors that affect photosynthesis also affect respiration. Temperature influences enzyme. Photosynthesis is more sensitive to temperature with an optimum of about 30- 35°C, whereas respiration often has an optimum nearer to 45°C. There is a temperature compensation point around 40°C (A), above this temperature plants lose mass as the rate of respiration is greater than the rate of photosynthesis. Carbon dioxide is the substrate for the enzyme rubisco in the light-independent stages of photosynthesis, so the higher the carbon dioxide concentration the faster the rate of the Calvin cycle. The rate of respiration is not affected by carbon dioxide concentration, and the carbon dioxide compensation point is usually very low, at about 50ppm (A). Normal carbon dioxide concentration in the air is about 400ppm (B), whereas the optimum concentration for most plants is nearer to 1000ppm, so carbon dioxide is often the limiting factor. Light is the source of energy for the production of ATP and NADPH in the light-dependent stages of photosynthesis, so the higher the light intensity the faster the rate of photosynthesis. The rate of respiration is not affected by light intensity, and the light compensation point is usually low. Shade plants are adapted to growing in low light conditions (such as a forest floor), so have a very low light compensation point (A) and a low optimum intensity. Shade plants make good house plants, since they are adapted to the low light intensities indoors. Sun plants have a higher compensation point (B), and have a very high optimum near the light intensity of a bright summer’s day (C). Both photosynthesis and respiration are affected by time of day: photosynthesis by changes in light and respiration by changes in temperature. At night respiration exceeds photosynthesis, while during the day photosynthesis exceeds respiration, so there are two compensation points each day (A and B). Over a 24-hour period the amount of photosynthesis is greater than the amount of respiration, so plants gain mass and have a net uptake of carbon dioxide.

41. 41

42. 42

43. 43 The different stages of respiration take place in different parts of the cell. This compartmentalisation allows the cell to keep the various metabolites separate, and to control the stages more easily. The energy released by respiration is in the form of ATP. Stage 1 (glycolysis) is anaerobic respiration, this occurs in the cytoplasm Stages 2 (link reaction occurs in the matrix) and 3 (oxidative phosphorylation, chemiosmosis, electron transport, occurs on the cristae) are the aerobic stages and occur in the mitochondria 1. Glucose enters cells from the tissue fluid by facilitated diffusion using a specific glucose carrier. This carrier can be controlled (gated) by hormones such as insulin, so that uptake of glucose can be regulated. 2. Glucose is phosphorylated using 2 ATPs. keeps glucose in the cell by effectively removing “pure” glucose, so glucose will always diffuse down its concentration gradient from the tissue fluid into the cell (glucose phosphate no longer fits the membrane carrier). It “activates” glucose for biosynthesis reactions. 3. The Hexose Bisphosphate splits into two triose phosphate (3 carbon) sugars. 4. The triose sugar is changed over several steps to form pyruvate, a 3-carbon compound. In these steps some energy is released to form ATP (the only ATP formed in glycolysis), and a hydrogen atom is also released. This hydrogen is later used by the respiratory chain to make more ATP. The hydrogen atom is taken up and carried to the respiratory chain by the coenzyme NAD, which becomes reduced NAD in the process. Pyruvate can also be turned back into glucose by reversing glycolysis, and this is called gluconeogenesis. 5. In the absence of oxygen pyruvate is converted into lactate or ethanol in anaerobic respiration 6. In the presence of oxygen pyruvate enters the mitochondrial matrix. It is converted to a compound called acetyl coA. Since this step links glycolysis and the Krebs cycle, (link reaction). In this reaction pyruvate loses a CO2 and a hydrogen to form a 2-carbon acetyl compound, which is temporarily attached to coenzyme A (or just coA), so the product is called acetyl coA. The hydrogen is taken up by NAD again. 7. The acetyl CoA then enters the Krebs Cycle. The 2-carbon acetyl is transferred from acetyl coA to the 4-carbon oxaloacetate to form the 6-carbon citrate. Citrate is then gradually broken down in several steps to re-form oxaloacetate, producing carbon dioxide and hydrogen in the process. Some ATP is also made directly in the Krebs cycle. As before, the CO2 diffuses out the cell and the hydrogen is taken up by NAD, or by an alternative hydrogen carrier called FAD. These hydrogen atoms are carried to the inner mitochondrial membrane for the final part of respiration. The removal of hydrogen/dehydrogenation is done by enzymes/dehydrogenases. The resulting H is accepted by NAD/which forms reduced NAD. This occurs in glycolysis and Krebs cycle, (FAD is used as well in Krebs);

44. 44 1. Reduced NAD releases its H and is oxidised to NAD, which returns to the Krebs cycle. Reduced FAD attaches to a protein further along the respiratory chain. The H split into H ions and electron. 2. The electrons are passed along the chain of proteins in the inner mitochondrial membrane, releasing its energy as it goes. 3. This energy is used to pump H ions into the intermemberane space, creating a proton gradient between the inner membrane space and the matrix. 4. The H ions can only move down their electrochemical gradient through a special channel in the ATP synthase enzyme, as they move down this gradient, they release energy that can be used to phosphorylate ADP. 4 protons = 1 ATP This is why reduced FAD yields less ATP, as it does not provide as much energy to pump H ions into the intermeembrane space as reduced NAD does 3. Oxygen (terminal electron acceptor) combines with hydrogen and electrons to form water (O2 + H+ + e- _ H2O). In absence of oxygen electron transport chain stops. Aerobic respiration yields more ATP per molecule of glucose than anaerobic. Explain. Oxygen as terminal hydrogen/electron acceptor; Operation of electron transport chain/ oxidative phosphorylation; Thus pyruvate can enter the Krebs cycle; Significance of ATP formed in glycolysis; Explain why oxygen is needed for the production of ATP on the cristae of the mitochondrion. ATP formed as electrons pass along transport chain; oxygen is terminal electron acceptor accepting electrons from electron transport chain; It also accepts H + forming H2O Electrons cannot be passed along electron transport chain if no O2 to accept them; Describe how ATP is made in mitochondria 1. Substrate level phosphorylation in Krebs 2. Krebs cycle/link reaction produces reduced NAD and FAD; 3. Electrons released from reduced NAD/FAD 4. (Electrons) pass along carriers/through electron transport chain (redox reactions) 5. Energy released; phosphorylates 6. ADP/ADP + Pi; 7. Protons move into intermembrane space; 8. ATP synthase; Describe the roles of the coenzymes and carrier proteins in the synthesis of ATP. hydrogen attaches to NAD/FAD (reduction) Electrons transferred from coenzyme to coenzyme on transport chain series of redox reactions; this releases energy to pump protons H + /protons pumped into intermembrane space; H + / protons flow back through /enzyme; ATPase; Energy used to synthesise ATP from ADP and Pi

45. 45 If there is no oxygen (anaerobic conditions) then water cannot be made, electrons can‘t leave the respiratory chain, so NADH cannot unload any hydrogen to the respiratory chain. This means that there is no NAD in the cell; it’s all in the form of NADH. Without NAD as a coenzyme, some of the enzymes of the Krebs cycle and glycolysis cannot work, so the whole of respiration stops. Anaerobic respiration circumvents this problem by adding an extra step to the end of glycolysis that regenerates NAD, so allowing glycolysis to continue and some ATP to be made. Anaerobic respiration only makes 2 ATPs per glucose, but it’s better than nothing! There are two different kinds of anaerobic respiration: In animals and bacteria the extra step converts pyruvate to lactate (or lactic acid). This is a reduction, so reduced NAD is used and NAD is regenerated, to be used in glycolysis. The reaction is reversible, so the energy remaining in the lactate molecule can be retrieved when oxygen becomes available and the lactate is oxidised via the rest of aerobic respiration. Unfortunately the lactate is poisonous, causing acidosis in muscles cells, which stops enzymes working, possible affects the binding of calcium to troponin in the muscle and causes muscle fatigue and cramp. Anaerobic respiration in muscles cannot be continued for very long. In plants and fungi the extra steps converts pyruvate to ethanol. This is also a reduction, so NADH is used and NAD is regenerated, to be used in glycolysis. Ethanol is a two-carbon compound and carbon dioxide is also formed. This means the reaction is irreversible, so the energy in the ethanol cannot be retrieved by the cells. Ethanolic anaerobic respiration is also known as fermentation, and we make use of fermentation in yeast to make ethanol in beer and wine. Describe what happens to pyruvate in anaerobic conditions and explain why anaerobic respiration is advantageous to human skeletal muscle. Forms lactate Use of reduced NAD / NADH; Regenerates NAD; NAD can be re-used to oxidise more respiratory substrate allows glycolysis to continue; Can still release energy/form ATP when oxygen in short supply/when no oxygen; Give two ways in which anaerobic respiration of glucose in yeast is Similar to anaerobic respiration of glucose in muscle cells ATP formed/used; pyruvate formed/reduced; NAD/reduced NAD; glycolysis involved/two stage process; Different from anaerobic respiration of glucose in a muscle cells Ethanol/alcohol formed by yeast, lactate (allow lactic acid) by muscle cell; CO2 released by yeast but not by muscle cell;

46. 46 Counting ATP How much ATP do we get per molecule of glucose? • Some ATP molecules are made directly by the enzymes in glycolysis or the Krebs cycle. This is called substrate level phosphorylation (since ADP is being phosphorylated to form ATP). • Most of the ATP molecules are made by the ATP synthase enzyme in the respiratory chain. Since this requires oxygen it is called oxidative phosphorylation. Scientists don’t yet know exactly how many protons are pumped in the respiratory chain, but the current estimates are: 10 protons pumped by NADH; 6 by FADH; and 4 protons needed by ATP synthase to make one ATP molecule. This means that each NADH can make 2.5 ATPs (10/4) and each FADH can make 1.5 ATPs (6/4). Previous estimates were 3 ATPs for NADH and 2 ATPs for FADH, and these numbers still appear in most textbooks, although they are now probably wrong. Remember two ATP molecules were used in the activation of glucose at the start of glycolysis, so this must be subtracted from the total We had: (per glucose molecule) 10 reduced NAD’s (2 from glycolysis 2 from link 6 from kerbs) 2 reduced FAD’s (from Krebs) 2 ATP made by substrate level phosphorylation in the Krebs cycle 2 ATP made by substrate level phosphorylation in glycolysis (4 were made but we invested 2 so it’s a net 2 ATP here) Reduced NAD makes either, (depending on the books you read) 3 ATP per reduced NAD or 2.5 Reduced FAD makes either, (depending on the books you read) 2 ATP per reduced FAD or 1.5 So…………… 10 × 3 = 30 10 × 2.5 = 25 2 × 2 = 4 2 × 1.5 = 3 2 ATP 2 ATP 2 ATP 2 ATP Total = 38 Total = 32

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