biology unit 4

1. 1

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.

7. 7

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