Module 5

photosynthesis

the process where energy from light is used to make organic compounds from water & carbon dioxide. light energy is converted into chemical energy

where does photosynthesis take place?

chloroplast
contains thylakoids which are stacked up to form grana which are linked by lamellae. within the thylakoids is the photosynthetic pigment chlorophyll - absorbs light energy. the stroma is a fluid-filled matrix.

photosynthetic pigments

absorb light energy. diff pigments absorb diff wavelengths of light.
types: chlorophylls (a&b), carotenoids (carotene), xanthophyll.
primary pigments: 2 types of chlorophyll a with slightly diff absorption peaks.
accessory pigments: includes other forms of chlorophyll a, chlorophyll b, carotenoids & xanthophyll

photosystems

light-harvesting clusters of pigments. each cluster is an antenna complex.
several hundred accessory pigment molecules surround a primary pigment & the light energy absorbed by diff pigments is passed on to the primary pigment.
the primary pigments act as reaction centres
photosystems I and II.

photosystem 1 (PS1)

arranged around a molecule of chlorophyll with a peak absorbance of 700nm = 'P700'

photosystem II (PSII)

arranged around a molecule of chlorophyll with a peak absorbance of 680nm = 'P680'

absorption spectrum

the absorbance of different wavelengths of light by a pigment can be measured using a spectrophotometer & the results can be plotted on a graph

action spectrum

the rate of photosynthesis can be measured under different wavelengths, & the results plotted on a graph

where does the light-dependent reaction take place?

in the thylakoids

what takes place in the light-dependent reaction?

light energy is used to split water (photolysis) into hydrogen ions, electrons & oxygen.
light energy is used to photoionise chlorophyll - the electrons lost are used to make ATP (chemiosmosis) and reduce NADP

chemiosmosis

the synthesis of ATP by means of a flow of protons (H+) across a membrane down a concentration gradient through the enzyme ATP synthase (stalked particle).

what are the two ways of synthesising ATP?

non-cyclic photophosphorylation and cyclic photophosphorylation.

non-cyclic photophosphorylation

light energy enters PSII & excites chlorophyll e- to a higher energy level; the chlorophyll is photoionised & the excited e- leaves PSII.
the enzyme that catalyses photolysis is associated with PSII & drives photolysis.
water is split into e-, H+ and oxygen
the e- from water replace the excited e- ejected from the chlorophyll (PSII).
the excited, high energy e- from PSII pass along an electron transport chain (through protein electron carriers) in the thylakoid membrane.
as the e- pass along the carriers they lose energy.
this energy is used to pump H+ ions from the stroma into the thylakoid lumen.
the e- are passed to PSI.
PSI absorbs light energy which gives the e- more energy. the chlorophyll is photoionised & the e- leave PSI, passing on to a protein complex where each e- is recombined with a proton (H+) to form a hydrogen atom which is taken up by the hydrogen carrier NADP to form reduced NADP.
the combination of water splitting & proton pumping causes protons to build up inside the thylakoid lumen.
this causes a proton gradient across the thylakoid membrane.
protons fall through the stalked particle (by FD) which is made of ATP synthase.
ATP is synthesised from ADP + Pi.

comparing cyclic & non-cyclic photophosphorylation

cyclic - photosystem I, needs light energy, ADP & Pi, and produces ATP

non-cyclic - photosystems I & II, needs light energy, water, NADP+, ADP & Pi, and produces ATP, NADPH, O₂

where does the light-independent reaction take place?

in the stroma

what takes place in the light-independent reaction?

CO₂ is reduced to carbohydrate.
requires ATP & reduced NADP from the light dependent reaction.
metabolic pathway is called the Calvin cycle

Calvin cycle

CO₂ diffuses into the stroma of the chloroplast.
it reacts with ribulose bisphosphate (5C), catalysed by the enzyme rubisco.
this produces 2 molecules of glycerate 3 phosphate (3C).
reduced NADP from the light-dependent reaction is used to reduce G3P to triose phosphate (3C) using energy supplied by ATP.
NADP is re-formed & returns to the light-dependent reaction.
some TP molecules are converted to organic substances, e.g. glucose & amino acids.
most TP molecules are used to regenerate RuBP using ATP from the light-dependent reaction.

how is the chloroplast adapted to maximise the rate of photosynthesis in the stroma?

1) the fluid of the stroma contains all the enzymes needed to carry out the light-independent reaction.
2) stroma fluid surrounds the grana so the products of the light-dependent reaction in the grana can readily diffuse into the stroma.
3) it contains both DNA & ribosomes so it can quickly & easily manufacture some of the proteins involved in the light-independent reaction.

what is a limiting factor?

a factor which when in short supply will reduce the rate of reaction.

what are the main external factors that affect the rate of photosynthesis?

light intensity, temperature & carbon dioxide concentration.

how light intensity affects photosynthesis

increases the rate of light-dependent reactions - photoionisation, photolysis, ATP production & reduction of NADP for the light-independent stage.
light causes stomata to open so carbon dioxide can enter leaf (increases rate)

how temperature affects photosynthesis

increases the rate of enzyme controlled reactions up to 25°c. above 25°c, the rate falls due to enzymes working less efficiently (may denature ATP synthase/rubisco).
increasing the temp increases the rate of transpiration - could lead to closure of stomata so reduced uptake of carbon dioxide (decreases rate)

how carbon dioxide affects photosynthesis

increases the rate of light-independent reactions, providing no other factor is limiting, up to 0.4%

compensation point

the light intensity at which carbon dioxide produced by respiration is used in photosynthesis

how can the rate of photosynthesis be measured?

by measuring the rate of substrate being used & product being formed.
oxygen can be collected & the volume is recorded to measure the rate.

agricultural practices to overcome limiting factors

farmers can use the knowledge of the limiting factors of photosynthesis to maximise the yield of their crops.
they can provide crops with very high light intensity, high carbon dioxide levels & optimum temp 24 hours a day, all year long.
there is a need to balance increase in yield & income with the cost of providing each of these conditions, & this will vary throughout the year.
(will cost more in winter - darker and colder).

aerobic respiration

requires oxygen & produces carbon dioxide, water & much ATP.

metabolic pathway with 4 key stages:
glycolysis (cytoplasm), link reaction (matrix), krebs cycle (matrix), oxidative phosphorylation (cristae).

glycolysis

the splitting of the 6-carbon glucose molecule into two 3-carbon pyruvate molecules. in cytoplasm.

glucose is phosphorylated by the addition of 2 phosphate molecules from 2 ATP molecules.
each molecule of phosphorylated glucose is split into two 3-carbon triose phosphate molecules which are oxidised (loses H) to form 2 molecules of pyruvate.
NAD collects the remaining hydrogen ions, forming 2 reduced NAD (used in OP).
2 molecules of ATP are regenerated from ADP (used by cell).

in aerobic respiration, pyruvate goes to the LR. in anaerobic, it is converted into lactate in animals, or ethanol and carbon dioxide in plants.

link reaction

the 3-carbon pyruvate molecules enter into a series of reactions which lead to the formation of acetylcoenzyme A (2C). in mitochondrial matrix.

pyruvate is actively transported into the mitochondrial matrix & is oxidised to acetate.
pyruvate is decarboxylated to release CO₂.
1 molecule of NAD is reduced (by H) to form reduced NAD.
the 2-carbon acetate combines with coenzyme A (CoA) to form acetylcoenzyme A (acetyl CoA).

krebs cycle

the introduction of acetyl CoA into a cycle of oxidation-reduction reactions that yield some ATP & a large quantity of reduced NAD & FAD. in mitochondrial matrix.

Acetyl CoA combines with a 4-carbon molecule (oxaloacetate) to form a 6-carbon molecule (citrate). CoA returns to LR.
the 6C citrate molecule is decarboxylated & oxidised to a 5C molecule.
the hydrogen is used to produce reduced NAD from NAD.
the 5C molecule is then decarboxylated & oxidised to regenerate the 4C molecule oxaloacetate.
the hydrogen is used to produce 1 reduced FAD & 2 reduced NAD.
ADP is converted to ATP by substrate-level phosphorylation (phosphate directly transferred from 1 molecule to another).

oxidative phosphorylation

the synthesis of ATP as a result of energy released by the ETC.

hydrogen (carried by reduced NAD & FAD) is split into protons & electrons.
the e- are passed along the ETC, losing energy at each e- carrier.
this energy is used to pump H+ ions by active transport across the mitochondrion inner membrane into the intermembrane space.
creates a conc gradient of H+. they passively diffuse across the membrane through stalked particles made of ATP synthase.
releases energy used to drive the synthesis of ATP from ADP + Pi.
at the end of the ETC, e- combine with H+ and oxygen to form water.
oxygen is the final e- acceptor.

anaerobic respiration

takes place in the absence of oxygen. produces lactate (animals) or ethanol & CO₂ (plants and fungi).
only glycolysis occurs - pyruvate must be removed so glycolysis can continue (only source of ATP).
LR & KC cannot take place as there is no NAD/FAD available to be reduced.
2 molecules of ATP produced in glycolysis.
oxidising the reduced NAD allows glycolysis to continue (& so ATP can be produced).

lactic acid fermentation

anaerobic respiration in animals.
reduced NAD is oxidised so glycolysis can continue.

ethanol fermentation

anaerobic respiration in plants & fungi.
reduced NAD is oxidised so glycolysis can continue.

aerobic vs anaerobic respiration

aerobic - oxygen required, glycolysis, LR, KC, OP, 38 ATP, pyruvate made by glycolysis, cytoplasm, matrix and cristae.

anaerobic - no oxygen required, glycolysis only, 2 ATP, lactate or ethanol & CO₂ produced, cytoplasm.

producer

photosynthetic organisms that manufacture organic substances using light energy, water, carbon dioxide & mineral ions.

consumer

organisms that obtain their energy by feeding on other organisms.
grouped into primary, secondary & tertiary consumers.

trophic level

the level at which an organism feeds in a food chain.

food chain

describes a feeding relationship between organisms
arrows represent direction of energy flow.

food web

many food chains linked together showing a more complex feeding relationship.

what is the ultimate source of energy?

sun

how is energy transferred through an ecosystem?

sunlight is converted into chemical energy by photosynthesising organisms & passed as food between other organisms in a food chain.
plants synthesise organic compounds from CO₂.
most of the sugars synthesised by plants are used by the plant as respiratory substrates.
the rest are used to make other groups of biological molecules which form the biomass of the plant.
energy is transferred through the ecosystem through biomass, most of it being lost at each trophic level of the food chain.

how is energy lost at each tropic level?

some of the organism is inedible.
some is indigestible (egested).
respiration.
excretion
the loss of energy at each trophic level limits the length of the food chain.

what happens to the energy lost through excretion/death?

as animals excrete & organisms die, chemical energy is locked up in the biomass.
detritivores (e.g. worms & woodlice) break this down & feed on the remains.
decomposers (e.g. bacteria & fungi) complete the process by breaking down the biomass completely.

how do plants utilise the sugars from photosynthesis?

respiration - energy to drive other reactions in plants
polymerisation - starch as an energy store
polymerisation - cellulose for support in cell walls as the plant grows
synthesis - amino acids & proteins

food chains & webs

summarise the feeding relationships in a community.
show how energy is transferred through an ecosystem.
each stage represents a tropic level.
webs are more realistic than chains as they show the complexity of feeding relationships.
saprobionts have a significant role in feeding relationships.
no new energy can enter a food chain so all the consumers depend on the amount of energy incorporated into the producers.
not all the energy at a particular trophic level is transferred to the next; released as heat during respiration, movement, egested etc. so not all energy is converted to biomass which is then eaten by a consumer.

biomass

the total mass of living material in a specific area at a given time.
(chemical energy stored in the plant).

measuring biomass

it is easy to measure fresh mass, but differing amounts of water make this unreliable.
water content can fluctuate during the day/year & water has no significant energy content.
measuring the mass of carbon or dry mass overcomes this.
dry mass = mass of organism with water removed.
to measure mass of carbon or dry mass, the organisms must be killed so this can only usually be made on a small sample, however this won't be representative.
biomass is measured using dry mass per given area.

how could you estimate the chemical energy store in dry mass (biomass)?

use a bomb calorimeter

a sample of dry material is weighed and burnt in pure oxygen within a sealed container called a bomb.
the bomb is surrounded by a water bath with a known volume with its start temp recorded.
the energy released heats the water.
the change in temp of the water is used to calculate the chemical energy of the dry biomass.

energy released from mass of burnt biomass = kJkgˉ¹

what measurements need to be taken in bomb calorimetry?

mass of sample
mass of water (same as vol)
start and end temp.

what problems are there which would influence accuracy in bomb calorimetry?

we are assuming that all of the thermal energy released when burning the sample is passed to the water.
however, the water isn't the only thing that absorbs the energy. the bomb cell also absorbs energy & so does the wire. some energy is lost to the air too.
this means you will underestimate the energy content of the biomass.

primary productivity

the rate at which energy is stored in producers (as biomass) in the community.

what does primary productivity depend on?

amount of sunlight
ability to use energy to synthesis organic compounds
other growth factors, e.g. mineral ions

why doesn't all the solar energy that reaches the earth end up reaching producers?

it is absorbed by rock/water
it doesn't reach a producer (might be shade)

why isn't all of the solar energy that falls on to leaves converted into organic matter?

it is reflected
it passes through (transmitted)
wavelength could be incorrect (plant may not be able to absorb all wavelengths, e.g. they reflect green)
heat (infrared energy not light energy).

gross primary productivity

the chemical energy store in plant biomass in a given area at a given time

calculating net primary productivity

NPP = GPP - R

GPP = gross primary productivity (energy stored in biomass)
R = respiratory losses

net primary productivity

the chemical energy available for plant growth & reproduction.
it's also available to other trophic levels in the ecosystem such as herbivores and decomposers.

calculating net production of consumers

N = I - (F + R)

N: net production (energy stored in consumers' biomass & available to next trophic level after some has been lost).
I: chemical energy in ingested food
F: chemical energy lost in faeces & urine
R: energy lost through respiration

how do farmers increase net productivity?

by increasing the efficiency of energy transfer; more energy is used for growth & less is lost through respiration.

restrict movement of livestock to reduce the rate of respiration & supply high energy content food.
warm pens to reduce energy loss by generating body heat.
Broiler chickens; selectively bred for rapid growth.
treating livestock with antibiotics - reduce energy loss to pathogens.

more biomass is produced & more chemical energy can be stored, increasing net production & the efficiency of energy transfer to humans.

benefits: more food produced quickly at a lower cost
weaknesses: ethical issues. conditions cause animals pain & distress & restricts their natural behaviour.

what is the importance of nutrient cycles?

they provide elements for metabolic processes & constructing organic molecules.

general nutrient cycle

the nutrient is taken up by producers as simple, inorganic molecules.
the producer incorporates the nutrient into complex organic molecules.
when the producer is eaten, the nutrient passes into consumers.
it then passes along the food chain when these animals are eaten by other consumers.
when the producers & consumers die, their complex molecules are broken down by saprobiontic microorganisms (decomposers) that release the nutrient in its original simple form back to the environment.

saprobionts

organisms that break down complex materials in dead organisms into simple ones, releasing valuable minerals & elements in a form that can be absorbed by plants (bacteria and fungi).
detritivores act first, feeding on detritus to give it a bigger SA for saprobionts to work on.

the role of saprobionts in nutrient cycles

they are responsible for converting substances needed by plants into inorganic molecules that can be absorbed by plants via nutrient cycles.

describe the phosphorus cycle

phosphorous exists mostly as phosphate ions, PO₄³ˉ, in sedimentary rock deposits.
these rocks can be eroded resulting in ions dissolved in water. equally, those dissolved ions can settle as sediment & be turned back into rocks.
additionally, when fertilisers are applied to land, they can dissolve & run off into bodies of water.
the dissolved ions can also be absorbed through the roots of plants in/near these bodies of water.
once these ions are incorporated into molecules within the plants, they can then be consumed by animals & so the ions pass into the animals.
the animals can then excrete some of the phosphorous-containing molecules they consume (guano) which may then end up back dissolved in water.
alternatively, they can excrete these molecules, or can themselves die & decompose - the phosphate ions are in these remains (shells).
the remains can then be eroded, returning the ions to bodies of water in the dissolved form.
or the remains may become deposited & become incorporated into rocks.

why is the phosphorus cycle important?

phosphorus is an important biological element as it is a component of ATP, phospholipids & nucleotides.

how is the phosphorus cycle different to the carbon and nitrogen cycles?

in the carbon & nitrogen cycles, the main reservoir of each element is in the atmosphere.
in the phosphorus cycle however the main reservoir is in mineral form rather than in the atmosphere.

mycorrhizae

they are mutualistic associations between certain types of fungi & the roots of plants.
the fungi act like extensions of the plants root system, increasing total SA for absorption of water & minerals.
as the mycorrhizae holds water & minerals, plants with mycorrhizae are more resistant to drought.
mycorrhizae also improve uptake of relatively scarce ions like phosphate ions.
the fungus receives organic compounds such as sugars & amino acids from the plant.

nitrogen cycle

the main reservoir of nitrogen is as gas in the atmosphere, N₂, which comprises 78% of the air.
it is held by a triple covalent bond & so is not available for use by plants or animals.
nitrogen fixation takes place - nitrogen is converted to nitrogen-containing compounds.
nitrification takes place - converts ammonium ions to nitrates
denitrification takes place - returns nitrogen to environment AND nitrate ions are absorbed & used by plants.
once the nitrogen is locked up in molecules of the biomass of plants, it becomes available to the next trophic level - consumers feed on the plants & take up the nitrogen.
the producers & consumers can produce waste & die - this matter can then be broken down by saprobionts.
ammonification takes place, returning the ammonium ions to the soil.

nitrogen fixation (NC step 1)

can be done 3 ways (all require energy)
1) lightning: nitrogen + oxygen → oxides of nitrogen
2) industrial processes: haber process - combine hydrogen & nitrogen to form ammonia.
3) fixation by micro-organisms - by free-living bacteria & mutualistic bacteria.

fixation by free-living bacteria
bacteria reduce nitrogen to ammonia, NH₃ (ammonium ions, NH₄⁺, form when dissolved in water).

fixation by mutualistic bacteria
live in root nodules of leguminous plants.
nitrogenase converts N₂ to NH₄⁺ using H⁺ & ATP.
requires anaerobic conditions because oxygen inhibits nitrogenase.
plant uses ammonium ions to make amino acids.

how is the relationship between the bacteria & the plant mutualistic? (NC fixation)

nitrogen gas diffuses into nodule
sugars pass from phloem (in plant) into bacterial cells.
enables them to respire & manufacture amino acids.
amino acids pass from bacterial cells into phloem.

nitrification (NC step 2)

1) oxidation of ammonium ions to nitrites
(NH₄⁺ → NO₂ˉ)
2) oxidation of nitrites to nitrates (NO₂ˉ→NO₃ˉ)
carried out by nitrifying bacteria
after this denitrification takes place to some nitrate ions and the others are absorbed by plants.

denitrification (NC step 3)

anaerobic denitrifying bacteria reduce soil nitrates into nitrogen gas which returns to the environment

ammonification (NC step 4)

saprobionts feed on faeces & dead organisms releasing ammonia which then forms ammonium ions in the soil.

the ammonia comes from the organic nitrogen-containing compounds of the dead organism/ its waste, e.g. urea, protein, nucleic acids & vitamins.

mineral elements required by plants

nitrogen as NO₃ˉ in proteins, nucleic acids etc.
phosphorus as H₂PO₄ˉ in nucleic acids, ATP & phospholipids.
magnesium as Mg²⁺ in chlorophyll, required by enzymes
iron as Fe²⁺ & Fe³⁺ in chlorophyll synthesis

how is the rate of plant growth limited?

usually limited by the availability of mineral ions in the soil, which are lost by harvesting crops & remove g livestock, adding more of these ions as fertilisers improves yield.

artificial fertilisers

the most commonly used fertilisers are the soluble, artificial (inorganic) fertilisers containing nitrate, phosphate & potassium ions (NPK)
made from rocks

disadvantages of artificial fertilisers

as nitrate & ammonium ions are very soluble, they do not remain in the soil for long & are quickly leached out, ending up in local rivers & lakes & causing eutrophication.
they are also expensive.

eutrophication

highly soluble nitrate enters the water.
causes an algal bloom - the algae living at the surface take up the nitrate & rapidly reproduce, causing the upper layers of water to become densely populated with algae.
this blocks out light to submerged plants meaning they cannot photosynthesis & therefore can't provide oxygen to the water.
the algae & other plants die due to a lack of photosynthesis & are decomposed by respiring aerobic saprobionts.
the little oxygen left in the water is used by the saprobionts so the oxygen concentration in the water decreases more.
due to a lack of oxygen, fish & other aerobic species die & are decomposed by anaerobic species.
water becomes turbid with detritus particles.
finally anaerobic bacteria may reduce nitrite & nitrate levels.

natural fertilisers

organic - e.g. animal manure (farmyard manure or FYM), composted vegetable matter, crop residues, blood & bones, seaweed, sewage sludge.
these contain the main elements found in artificial fertilisers (NPK), but in organic compounds such as urea, cellulose, lipids & organic acids.

how do plants absorb the ions from organic fertilisers?

plants cannot make use of these organic materials in the soil; their roots can only take up inorganic mineral ions such as nitrate, phosphate & potassium.
the organic compounds are digested by soil organisms, such as worms & saprobionts, who then release inorganic ions that the plants can use (ammonification then nitrification).

strict fertiliser regulations for farmers

restrict the amount of fertiliser applied to the soil.
only apply fertiliser when the crops are actively growing.
leave a 10 metre wide strip next to a water course.
do not spread fertiliser when heavy rain is forecast.

advantages of natural fertilisers

less soluble than artificial fertilisers, so the minerals are released more slowly as they are decomposed. this prevents leaching & means they last longer.

cheap as organic wastes need to be disposed of.

improves soil structure by binding soil particles together & provides food for soil organisms such as earthworms. this improves drainage & aeration.

disadvantages of natural fertilisers

they are bulky & less concentrated in minerals than artificial fertilisers, so more needs to be spread on a field to have a similar effect.

may contain unwanted substances, e.g. weed seeds, fungal spores, heavy metals.

very smelly.