3.5

Question 1

What are the 4 key stages in aerobic respiration and where in the cell do they occur

Answer 1

1. Glycolysis (cytoplasm)
2. Link reaction (mitochondrial matrix)
3. Krebs Cycle (mitochondrial matrix)
4. Oxidative phosphorylation (cristae)

Question 2

What is photosynthesis?

Answer 2

-production of glucose using light energy
-occurs in plants and algae
-consists of a light dependent and light independent stage

Question 3

Adaptations of plants for photosynthesis?

Answer 3

-leaf located near top of plant = closer to light
-leaf is thin and wide = large surface area for light, short diffusion distance for CO2
-has many veins = connect to xylem to bring in water
-has stomata for gas-exchange (CO2/O2)
-has air spaces to support ease of gas-exchange

Palisade cells:
-located near top of leaf close to the light
-large surface area for light
-thin cell wall = short diffusion distance for CO2
-contains many chloroplasts (site of photosynthesis)
-large vacuole = pushes chloroplast to edge of cell closer to light

Question 4

Site and products of the two stages of photosynthesis?

Answer 4

Light dependent stage:
-thylakoid membrane
-ATP and reduced NADP

Light independent stage:
-stroma
-glucose (made by products of light dependent stage)

Question 5

Outline the light dependent stage

Answer 5

-light hits chlorophyll
-chlorophyll absorbs the light if correct wavelength
-electrons become excited and are lost from the chlorophyll (photoionisation)
-electrons enter an electron carrier system
-electrons move down the system releasing energy
-this pumps protons from stroma into thylakoid space
-protons accumulate in thylakoid space, then diffuse back into stroma
-they pass though ATP Synthase which joins ADP and Pi to make ATP (mechanism = chmeiosmosis, process = photophosphorylation)
-the electron ends up by joining with NADP to form reduced NADP
-light also hits water
-causes photolysis (breakdown of water due to light)
-forms: H+, e-, O2
-the H+ joins with the reduced NADP (now carries a hydrogen atom: H+ and e-)
-the e- replaces electrons lost from chlorophyll
-O2 given off as waste

Question 6

Outline the light independent stage

Answer 6

-involves the calvin cycle
-RuBP (5 carbon) joins with CO2 to make 2 lots of GP (3 carbon)
-the GP is reduced into TP (3 carbon)
-this uses energy from ATP and hydrogen atom from reduced NADP
-the TP can be used to reform RuBP (uses energy from ATP)
-the TP can also be used to form glucose (carbohydrate)
-GP can also be used to form amino acids (proteins) and fatty acids
-TP can also be used to form glycerol
-fatty acids and glycerol will form a lipid
-photosynthesis/calvin cycle = produces all the main biological molecules

Question 7

Effect of limiting factors on photosynthesis?

Answer 7

Light:
-RuBP decreases – being converted into GP but not being reformed from TP (no ATP)
-GP increases – not converted into TP (no ATP/reduced NADP) but is being formed from RUBP

CO2:
-RuBP increases – not converted into GP (no CO2) but is being reformed from TP
-GP decreases – not being formed from RuBP (no CO2) but being converted into TP

Question 8

Compensation point in plants

Answer 8

-the point in the day (light intensity) when the CO2 taken in by photosynthesis equals the amount given out by respiration = no net gas exchange
-at low light intensity: rate of respiration > rate of photosynthesis [CO2 released]
-at high light intensity: rate of photosynthesis > rate of respiration [CO2 absorbed]

Question 9

Measuring rate of photosynthesis

Answer 9

-measure amount of CO2 used or measure amount of O2 produced, in a certain time
-can be done using photosynthometer
-measures amount of O2 produced
-uses aquatic plants (e.g. elodea), as the O2 produced can be observed and collected
-the plant is surrounded in sodium hydrogencarbonate solution (CO2 source)
-the plant is kept in darkness before experiment runs (uses up all the O2 in the plant)
-as the experiment runs, O2 will be produced, this will be collected in a capillary tube
-the amount collected can be measured, this will be converted into a volume by multiplying length of oxygen bubble collected by πr2
-volume of O2 collected can then be divided by time to calculate rate of photosynthesis

Question 10

Light dependent and light independent stages of photosynthesis

Answer 10

Light dependent stage occurs in 3 reactions:
Photolysis:
-H2O —> 1/2 O2 + e- + H+
-light energy is absorbed by chlorophyll in photosystem II and splits water into oxygen, H+ and e-
-H+ is picked up by NADP to form NADPH and used in the LIR
-e- are passed along a chain of electron carrier proteins
-the oxygen is a waste product (either used for respiration or diffuses out of the leaf through the stomata)

Photoionisation of chlorophyll:
-light energy is absorbed by the chlorophyll
-the energy results in electrons becoming excited and raising up an energy level to leave chlorophyll
-hence, the chlorophyll has been ionised by light

Chemiosmosis:
-electrons that gained energy and left the chlorophyll move along a series of proteins embedded within the thylakoid membrane
-as they move along the electron transfer chain, they release energy
-some of the energy from electrons is used to pump the protons from photolysis across thylakoid membranes
into thylakoid lumen from stroma by active transport
-hence electrochemical gradient produced as high concentration of protons (ions) on one side of the membrane
-facilitated diffusion occurs through ATP synthase
-the protons pass through the enzyme ATP synthase, which results in the production of ATP
-the protons combine with the co-enzyme NADP to become NADPH
-as the protons move from a high to low concentration gradient, this is known as chemiosmosis

Light independent stage: (Calvin cycle)
-uses carbon dioxide, reduced NADP, and ATP to form a hexose sugar
-the ATP is hydrolysed to provide energy for this reaction
-the NADPH donates the hydrogen to reduce molecules GP in the cycle
-Calvin cycle occurs in the stroma, which contains the enzyme RuBisco, which catalyses this reaction
-this stage is temperature-sensitive due to the fact it involves an enzyme

-carbon dioxide reacts with ribulose bisphosphate (RuBP) to form two molecules of glycerate 3-phosphate (GP), a 3-carbon compound
-this is catalysed by the enzyme rubisco
-to reduce this GP into triose phosphate (TP), ATP and NADPH from the light-dependent reaction are used
-some of the carbon from TP leaves the cycle each turn to be converted into useful organic substances
-rest of the molecule is used to regenerate RuBP, with energy from ATP
-the glucose product can join to form disaccharides (e.g. sucrose), and polysaccharides (e.g. cellulose/starch)
-it can also be converted into glycerol and combine with fatty acids to make lipids for the plant

Calvin’s experiment:
-examined the products in the LIR using radioactive carbon
-CO2 that is radioactively labeled is inserted, allowing the carbon molecules to be labeled and traced
-he would then measure the amount of radioactive GP and RuBP under different conditions, mainly in the light and dark, as a way to prove which factors impact the LIR

Question 11

Role of pigments in plants:

Answer 11

-chlorophyll is located in the photosystems on the thylakoid membrane
-mix of colored proteins that can absorb light
-There are 5 key closely related pigments, but chlorophyll a is the most abundant

Chlorophyll a = blue/green (found in all plants)
Chlorophyll b = yellow/green
Carotene = orange
Xanthophyll = yellow
Phaeophytin = grey

-there are different proportions of each pigment in leaves, which gives leaves slightly different colors
-each pigment absorbs a different wavelength of visible light
-this maximizes the spectrum of visible light that the plant can absorb, hence increases the amount of light energy absorbed

-pigments in chlorophyll can be isolated using chromatography
-pigments are added to chromatography paper, which is placed in a solvent
-solvent dissolves the pigments
-the more soluble the pigment, the further up the chromatography paper it will move
-can be converted into an Rf value, a way to then compare and identify pigments in chromatography

Question 12

Define oxidation and reduction in the light dependent reaction

Answer 12

Oxidation:
-substance gains oxygen or loses hydrogen
-loses electrons
-energy is given out

Reduction:
-substance loses oxygen or gains hydrogen
-gains electrons
-energy is taken in

Question 13

Outline how ATP is made in light-dependent reaction

Answer 13

-chlorophyll molecule absorbs light energy, it boosts the energy of a pair of e- within this chlorophyll molecule
-raises the pair of e- to a higher energy level
-hence they are in an excited state
-causes them to leave the chlorophyll molecule, hence chlorophyll becomes ionised by photoionisation
-electrons that leave the chlorophyll are taken up by an electron carrier
-chlorophyll has been oxidised as lost a pair of e-
-electron carrier has been reduced as it gained a pair of e-

-the electrons are now passed along several electron carriers in a series of oxidation-reductions reactions
-hence electron transfer chain is formed in the thylakoid membrane
-each new carrier is at a slightly lower energy level than the previous one
-so electrons lose energy at each stage
-some of this energy is used to combine an inorganic phosphate with an ADP molecule
-forms ATP (known as the chemiosmotic theory)

Question 14

Outline photolysis of water in light-dependent reaction, including the importance of its products

Answer 14

-water molecules are produced by the splitting of water
2H2O —> 4H+ + 4e- + O2
-the electrons replace the electrons lost from the chlorophyll molecule by photoionisation
-H+ pass out of the thylakoid space through ATP synthase channels
-NADP becomes reduced NADP by use of the H+
-oxygen is either used in respiration or diffuses out as a waste product

Question 15

Outline the light-independent reaction

Answer 15

-CO2 diffuses in through the stomata and dissolves in the water surrounding mesophyll cells
-it diffuses through the cell surface membrane and then the chloroplast envelope to the stroma
-CO2 reacts with ribulose bisphosphate (RuBP) which is catalysed by rubisco
-2 molecules of glycerate 3-phosphate (GP) are produced
-GP is converted to triose phosphate (TP) using reduced NADP and energy supplied by ATP
-reduced NADP becomes NADP and can be recycled in the light dependent reaction
-some TP is converted to organic substances, e.g. starch, cellulose, lipids, glucose, amino acids, nucleotides, etc
-most TP is used to regenerate RuBP using ATP, allowing the Calvin Cycle to continue

Question 16

What is glycolysis?

Answer 16

sugar splitting
-oxygen not required
-occurs in cytoplasm in both anaerobic/aerobic respiration
-provides indirect evidence for evolution as it occurs in every living organism

-2 phosphate groups from 2 ATP molecules are added to glucose by substrate-level phosphorylation
-splits into 2 triose-phosphate molecules
-both TP molecules are oxidised to form 2 pyruvate molecules by removing a H from each
-H is picked up by 2 NAD molecules to become reduced NAD
-net gain of ATP = 2

Question 17

What is the Link Reaction?

Answer 17

-pyruvate is actively transported from cytoplasm to mitochondrial matrix
-pyruvate is oxidised to acetate, so a CO2 and 2 hydrogens are lost
-2 molecules of NAD accept a hydrogen each to become 2 molecules reduced NAD
-acetate combines with coenzyme A to form acetyl CoA

Question 18

What is the Krebs Cycle?

Answer 18

-once CoA has transported acetate from the link reaction to the Krebs cycle, acetate is unloaded from CoA
-acetate (2C) joins with oxaloacetate (4C) to form citrate (6C)
-citrate loses a CO2 molecule (decarboxylated) and 2 hydrogens (dehydrogenated)
-hydrogens are accepted by 2 NAD to form 2 reduced NAD
-the 5C molecule is decarboxylated and dehydrogenated, forming a 4C molecule
-another reduced NAD is formed from NAD
-the 4C molecule is converted into another 4C molecule, where substrate-level phosphorylation occurs (1 ATP produced from ADP)
-the second 4C molecule is converted to another 4C molecule
-FAD accepts two hydrogens to make reduced FAD
-third 4C molecule is dehydrogenated to form oxaloacetate, which makes reduced NAD

Question 19

What is Oxidative Phosphorylation?

Answer 19

-reduced co-enzymes donate electrons to first electron carrier
-electrons pass through electron transport chain
-energy released is used to actively transport H+ into inter-membrane space
-H+ accumulate in inter-membrane space, and diffuse back to mitochondrial matrix through ATP synthase (mechanism: chemiosmosis)
-oxygen i the final electron acceptr, and electrons and protons combine with it to form water

Question 20

Gain of ATP
Advantage of this

Answer 20

-glycolysis: 2 ATP (net gain)
-link Reaction: 0
-Krebs Cycle: 2 ATP
-oxidative phosphorylation: 28
-total: around 32 ATP per glucose molecule

Question 21

Lipids as respiratory substrate

Answer 21

Triglycerides are broken down into glycerol/fatty acids

Glycerol:
-glycerol is converted into TP, which enters glycolysis
-TP is further broken down to produce pyruvate, which enters the mitochondria for aerobic respiration

Fatty acids:
-beta-oxidation in mitochondria
-fatty acid combines with acetyl CoA
-each fatty acid breaks down into acetyl-CoA molecules
-acetyl-CoA enters Krebs cycle, where it is fully oxidised

Question 22

Proteins as respiratory substrate

Answer 22

-broken down into amino acids
-deamination forms ammonia which is excreted
-product can be pyruvate or oxaloacetate, depending on amino acid
-pyruvate enters glycolysis
-oxaloacetate enters Krebs

Question 23

Outline anaerobic respiration in mammals

Answer 23

Glycolysis:
-glucose is broken down into 2 molecules of pyruvate (3C)
-net gain = 2 ATP molecules and 2 NADH molecules

Lactate Formation:
-pyruvate is converted to lactate (lactic acid)
-by lactate dehydrogenase
-NADH donates electrons, regenerating NAD
-allows glycolysis to continue

Question 24

Outline anaerobic respiration in plants

Answer 24

Fermentation after glycolysis:
-pyruvate is converted to ethanol and carbon dioxide.
-pyruvate is decarboxylated (CO₂ removed)
-forms ethanal
-ethanal is reduced by NADH to form ethanol
-NAD is regenerated, allowing glycolysis to continue.

Question 25

explain how ATP is synthesised during oxidative phosphorylation

Answer 25

-electrons and H+ ions are donated to the electron transport chain (located in the inner mitochondrial membrane) from NADH and FADH2 (generated during glycolysis, the Krebbs cycle and the Link reaction)

-energy is relesed as these electrons and protons flow along electron transport chain, which can be used to pump H+ ions from the mitochondrial matrix into the intermembrane space.

-creates a concentration gradient and a pH gradient.so H+ ions flow through ATP synthase enzymes embedded in the inner mitochondrial membrane

-allows ADP and Pi to react to from ATP.

Question 26

explain the role of oxygen in aerobic respiration

Answer 26

final terminal acceptor
without it, the electron transport chain will stop running, and ATP will no longer be produced by chemiosmosis.

Question 27

explain how energy is released by respiration in the absence of oxygen (plants)

Answer 27

-reduced NAD transfers its hydrogens to ethanal to form ethanol

-pyruvate is decarboxylated to ethanal

-produces CO2

-ethanal is reduced to ethanol by the enzyme alcohol dehydrogenase

Ethanal is the hydrogen acceptor

Ethanol cannot be further metabolised; it is a waste product

Question 28

explain how energy is released by respiration in the absence of oxygen (animals)

Answer 28

-reduced NAD transfers its hydrogens to pyruvate to form lactate

-pyruvate is reduced to lactate by enzyme lactate dehydrogenase

-lactate can be further metabolised
-it can be oxidised back to pyruvate which is then channelled into the Krebs cycle for ATP production (requires extra oxygen / oxygen debt, which explains why animals breathe deeper/faster after exercise)
-it can be converted into glycogen for storage in the liver

Question 29

Explain how energy enters an ecosystem

Answer 29

-originates from the Sun
-absorbed by plants during photosynthesis and converted into chemical energy
-becomes biomass

Question 30

Explain how energy is transferred between organisms in the ecosystem

Answer 30

-in food webs from producers to consumers
-flows in one way

Question 31

Define the following terms:
tropic level
food chain
food web
producer
consumer
saprobiont

Answer 31

tropic level
-each stage of the food chain

food chain
-describes a feeding relationship between organisms at different trophic levels
-shows direction of energy transfer

food web
-many food chains linked together
-organisms typically do not rely on a single food

producer
-photosynthetic organisms
-use light energy, water, CO2 and mineral ions to produce organic substances

consumer
-organisms that obtain their energy by feeding on other organisms
-primary: consumers that eat producers
-secondary: consumers that eat primary consumers
-tertiary: consumers that eat secondary consumers
-secondary/tertiary consumers tend to be predators

saprobiont (decomposer)
-organisms that break down decaying or dead material into simple materials
-e.g. fungi/bacteria
-includes valuable minerals/elements
-can be absorbed by plants

Question 32

Define biomass
Explain how it is measured

Answer 32

-total mass of living material in a specific area at a given time
The mass of living material of the organism or tissue
The chemical energy that is stored within the organism or tissue

-measured using dry mass per given area, in a given time
-units: grains per square metre (g m^-2) if an area is sampled
-grams per square metre (g m^-3 )if volume is sampled
The dry mass of an organism or tissue (in a given area)
The mass of carbon that an organism or tissue contains
The mass of carbon that a sample (i.e. an organism or tissue) contains is generally taken to be 50% of the dry mass of the sample

-chemical energy store in dry mass can be measured by calorimetry

Question 33

Explain how energy is lost along a food chain

Question 34

Explain what is meant by gross primary productivity and net primary productivity

Answer 34

Gross primary production (GPP) = rate at which plants are able to store chemical energy via photosynthesis
-only about 1% of the light falling on a plant is used in photosynthesis to produce glucose
-99% of the light either passes through the leaf without hitting chloroplasts, is reflected off of the leaf, or is transferred to heat energy
-after that 1% is successfully absorbed and used to form glucose, the quantity of energy now stored in glucose is the gross primary production
Units: J m^-2 or kJ km^-2
-if there are no primary producers present in this area of land, there will be no gross primary production)
Aquatic environments: kg m-3 or kJ m-3

NPP = chemical energy that is leftover in a plant after respiratory loss is known as the net primary production

NPP = GPP - R

-NPP represents the energy that is available to organisms at higher trophic levels in the ecosystem
-e.g. as primary consumers (herbivores and omnivores) and decomposers

Question 35

general sequence of nutrient cycles

Question 36

why do living organisms need nitrogen?

what form do plants take up nitrogen in?

how is this absorbed?

Answer 36

proteins, nucleic acid, etc

NO3- ions

active transport from the soil to the roots

Question 37

Importance and stages of nitrogen cycle

Answer 37

Importance:
-shows how nitrogen is recycled in ecosystems
-nitrogen needed for proteins and DNA/RNA
-78% of the atmosphere is nitrogen gas
-plants and animals cannot access gaseous nitrogen
-because they can’t break triple bond between nitrogen atoms
-hence rely on certain bacteria to convert N2 (g) into nitrates, which can be taken up by plants
-also shows how nitrogen in the nitrogen-containing compounds is then passed between trophic levels or between living organisms and the non-living environment

The role of bacteria in the nitrogen cycle
Nitrogen fixation:
-carried out by nitrogen-fixing bacteria such as Rhizobium
-bacteria convert nitrogen gas from atmosphere into ammonia, which forms ammonium ions (in solution) that can then be used by plants
-nitrogen-fixing bacteria are found inside root nodules of leguminous plants (e.g. peas, beans and clover)
-bacteria have a symbiotic (mutually beneficial) relationship with these plants
-bacteria provide plants with nitrogen-containing compounds
-plants provide the bacteria with organic compounds e.g. carbohydrates

Ammonification:
-nitrogen compounds in waste products (e.g. urine/faeces) and dead organisms are converted into ammonia
-by saprobionts (type of decomposer including some fungi and bacteria)
-ammonia forms ammonium ions in soil

Nitrification:
-ammonium ions in soil are converted by nitrifying bacteria (e.g. Nitrosomonas) into nitrites
-different nitrifying bacteria (e.g. Nitrobacter) then convert these nitrites into nitrates
-can be used by plants

Denitrification:
-produces nitrogen gas, which returns to the atmosphere
-denitrifying bacteria use nitrates in the soil during respiration
-occurs in anaerobic conditions (little/no oxygen available, e.g. in waterlogged soil)

Question 38

Importance and stages of phosphorus cycle

Answer 38

-shows how phosphorus is recycled in ecosystems
-phosphorus needed for:
-phospholipids (cell membranes)
-nucleic acids (DNA and RNA)
-ATP

Process:
-phosphorus in rocks is slowly released into soil and water sources in the form of phosphate ions (PO₄³⁻)
-done by the process of weathering (slow erosion of rocks over time)
-PO₄³⁻ ions are taken up from soil by plants through their roots or absorbed from water by algae
-PO₄³⁻ ions are transferred to consumers during feeding
-saprobionts release PO₄³⁻ ions in waste products and dead organisms into soil/water during decomposition
-can now be taken up and used once again by producers
-may be trapped in sediments that, over very long geological time periods may turn into phosphorus-containing rock once again

Question 39

Role of mycorrhiza

Answer 39

-fungal associations between plants roots and beneficial fungi

-increases SA for water and mineral absorption
-acts as a sponge, holding water and minerals around the roots
-makes plant more resistant to drought
-also increases uptake of inorganic ions
-mutualistic relationship with plants

Question 40

use of natural and artificial fertilisers to replace the nitrates and phosphates lost by harvesting plants and removing livestock.

Answer 40

Artificial fertilisers (e.g. ammonium nitrate) are inorganic.
Artificial fertilisers are produced specifically for replacing nutrients.

Natural fertilisers (e.g. composted food waste, manure) are organic.
Natural fertilisers are taken from organic matter and used to replace nutrients.

Eutrophication:
-can happen when too much fertiliser is used
-excess soluble nitrates and phosphates leach into water sources like ponds from the soil.
-leads to the rapid growth of algae at the surface of the water source, sometimes called an ‘algal bloom’.
-algae then block light to plants and algae at lower depths.
-these plants and algae die due to insufficient light for photosynthesis.
-levels of aerobic saprobiontic bacteria increase as they decompose the dead plant material.
-depletes oxygen levels in the water, results in the death of fish and other aquatic life, disrupting food webs.
-anaerobic organisms increase in number, further decomposing dead material and releasing more nitrates and toxic wastes.

Artificial fertilisers are particularly prone to leaching because their mineral nutrients dissolve easily in water, and are the main cause of eutrophication. The risk of eutrophication may also be increased with increased use of organic manures or animal slurry, human sewage, ploughing old grassland, or natural leaching.

Fertilisers that are sprayed onto fields can leach through the soil or flow into ponds, rivers and lakes.
Leaching is when water-soluble plant nutrients are lost from the soil.
This causes a build up of nutrients in the water.

algal overgrowth:

plant death:

Bacteria decompose the dead plants.
As numbers of bacteria increase, the oxygen concentration in the water decreases.
Fish and other organisms will now die because there is not enough oxygen.

Question 41

environmental issues arising from the use of fertilisers including leaching and eutrophication.