Topic 5

What are the stages of photosynthesis?

Light dependent reaction :Thylakoid membrane of chloroplast

Light independent reaction :Stroma of chloroplast.

Describe photoionisation in the light dependent reaction (LDR)

Chlorophyll absorbs light energy which excites its electrons (higher energy level).

So electrons are released from chlorophyll (chlorophyll becomes positively charged)

Describe what happens after photoionisation in the LDR

Some energy from electrons released in photoionisation is conserved in the production of ATP / reduced NADP (NADPH) (chemiosmotic theory).

Electrons move along electron transfer chain (electron carriers), releasing energy.

This energy is used to actively pump protons from stroma into thylakoid.

Protons move by facilitated diffusion down electrochemical gradient into stroma via ATP synthase.

Energy used to join ADP and Pi to form ATP (photophosphorylation)

NADP accepts a proton and an electron to become reduced NADP (NADPH)

Describe photolysis of water in the LDR

Water splits to produce protons, electrons and oxygen (H₂O → ½ O₂ + 2e⁻ + 2H⁺).

Electrons replace those lost from chlorophyll

Describe the light independent reaction of photosynthesis (Calvin cycle)

CO₂ reacts with ribulose bisphosphate (RuBP).

Catalysed by the enzyme rubisco Forming 2 glycerate 3 phosphate (GP) molecules.

GP reduced to triose phosphate (TP)

Using products from light dependent reaction reduced NADP (NADPH) and energy from ATP.

Some TP converted to useful organic substances (eg. glucose).

Some TP used to regenerate RuBP in the Calvin cycle (using energy from ATP)

Describe how pigments from a leaf of a plant can be isolated with paper chromatography

Crush leaves with solvent to extract pigments.

Draw a pencil line on filter / chromatography paper, 1 cm above bottom

Add a drop of extract to line (point of origin)

Stand paper in boiling tube of (organic) solvent below point of origin

Add lid and leave to run (solvent moves up, carrying dissolved pigments)

Remove before solvent reaches top and mark solvent front with pencil

Explain why the origin should be drawn in pencil rather than ink.

Ink is soluble in solvent. So ink would mix with pigments / line would move

Explain why the point of origin should be above the level of the solvent.

Pigments are soluble in solvent ,so would run off paper / spots dissolve into solvent

Explain why a pigment may not move up the chromatography paper in one solvent.

May be soluble in one solvent but insoluble in another

Describe how pigments can be identified

Rf value = distance moved by spot / distance moved by solvent front

Compare Rf value to published value

Explain why the solvent front should be marked quickly once chromatography paper is removed.

Once solvent evaporates, solvent front not visible

Explain why the centre of each pigment spot should be measured.

Standardises readings as pigment is spread out. Which allows comparisons to be made

Explain why the obtained Rf values were similar, but not identical, to the published values.

Different solvent / paper / running conditions may affect Rf value

Explain why Rf values are used and not the distances moved by pigment spots.

Solvent / pigment moves different distances. Rf value is constant for same pigment / can be compared

Describe the role of the enzyme dehydrogenase in photosynthesis

Catalyses the reduction of NADP in the light-dependent reaction.

NADP accepts (gains) electrons from photoionisation of chlorophyll / photolysis of water

Describe how rate of dehydrogenase activity in extracts of chloroplasts can be measured

Extract chloroplasts from a leaf sample.

Set up test tubes as follows: Control 1 - set volume of DCPIP (redox indicator dye, electron acceptor), water and chloroplasts in isolation medium, covered in foil to block light

Control 2 - set volume of DCPIP, water and isolation medium without chloroplasts

Standard - set volume of water and chloroplasts in isolation medium, without DCPIP Experiment - set volume of DCPIP, water and chloroplasts in isolation medium

Shine light on test tubes and time how long to it takes for DCPIP to turn from blue (oxidised) to colourless (reduced) in tube D (tube A and B should show no change)

Compare to a colour standard (tube C) to identify end point.

Rate of dehydrogenase activity (s⁻¹) = 1 / time taken to investigate the effect of a named factor (eg. effect of wavelength of light), repeat and change that factor.

Give examples of variables that could be controlled.

Source of chloroplasts

Volume of chloroplast suspension

Volume / concentration of DCPIP

Explain the purpose of control 1 (tube A).

Shows light is required for DCPIP to decolourise.

Shows that chloroplasts alone do not cause DCPIP to decolourise

Explain why DCPIP in control 1 stays blue.

No light so no photoionisation of chlorophyll

So no electrons released to reduce DCPIP

Explain the purpose of control 2 (tube B).

Shows chloroplasts are required for DCPIP to decolourise

Shows that light alone does not cause DCPIP to decolourise

Explain why DCPIP changes from blue to colourless.

DCPIP is a redox indicator / DCPIP gets reduced by electrons

From photoionisation of chlorophyll

Suggest a limitation with the method and how the experiment could be modified to overcome this.

End point (colour change) is subjective

Use a colorimeter

Measure light absorbance of sample at set time intervals

Zero colorimeter using the colour standard

Why is respiration important?

Respiration produces ATP (to release energy)

For active transport, protein synthesis etc.

Summarise the stages of aerobic & anaerobic respiration

Aerobic respiration

1. Glycolysis - cytoplasm (anaerobic)

2. Link reaction - mitochondrial matrix

3. Krebs cycle - mitochondrial matrix

4. Oxidative phosphorylation - inner mitochondrial membrane Anaerobic respiration

1. Glycolysis - cytoplasm

2. NAD regeneration - cytoplasm

Describe the process of glycolysis

1. Glucose phosphorylated to glucose phosphate. Using inorganic phosphates from 2 ATP

2. Hydrolysed to 2 x triose phosphate

3. Oxidised to 2 pyruvate 2 NAD reduced 4 ATP regenerated (net gain of 2)

Explain what happens after glycolysis if respiration is anaerobic

1. Pyruvate converted to lactate (animals & some bacteria) or ethanol (plants & yeast)

2. Oxidising reduced NAD → NAD regenerated

3. So glycolysis can continue (which needs NAD) allowing continued production of ATP

Suggest why anaerobic respiration produces less ATP per molecule of glucose than aerobic respiration

Only glycolysis involved which produces little ATP (2 molecules).

No oxidative phosphorylation which forms majority of ATP (around 34 molecules)

What happens after glycolysis if respiration is aerobic?

Pyruvate is actively transported into the mitochondrial matrix.

Describe the link reaction

1. Pyruvate oxidised (and decarboxylated) to acetate. CO2 produced Reduced NAD produced (picks up H)

2. Acetate combines with coenzyme A, forming Acetyl Coenzyme A .

Products per glucose molecule: 2 x Acetyl Coenzyme A, 2 X CO2 and 2 X reduced NAD

Describe the Krebs cycle

1. Acetyl coenzyme A (2C) reacts with a 4C molecule.

Releasing coenzyme A Producing a 6C molecule that enters the Krebs cycle 2. In a series of oxidation-reduction reactions, the 4C molecule is regenerated and: 2 x CO2 lost Coenzymes NAD & FAD reduced Substrate level phosphorylation (direct transfer of Pi from intermediate compound to ADP) → ATP produced Products per glucose molecule: 6 x reduced NAD, 2 x reduced FAD, 2 x ATP and 4 x CO2

Describe the process of oxidative phosphorylation

1. Reduced NAD/FAD oxidised to release H atoms → split into protons (H⁺) and electrons (e⁻) 2. Electrons transferred down electron transfer chain (chain of carriers at decreasing energy levels) By redox reactions 3. Energy released by electrons used in the production of ATP from ADP + Pi (chemiosmotic theory): Energy used by electron carriers to actively pump protons from matrix → intermembrane space Protons diffuse into matrix down an electrochemical gradient, via ATP synthase (embedded) Releasing energy to synthesise ATP from ADP + Pi 4. In matrix at end of ETC, oxygen is final electron acceptor (electrons can’t pass along otherwise) So protons, electrons and oxygen combine to form water

Give examples of other respiratory substrates

Breakdown products of lipids and amino acids, which enter the Krebs cycle. For example: Fatty acids from hydrolysis of lipids → converted to Acetyl Coenzyme A Amino acids from hydrolysis of proteins → converted to intermediates in Krebs cycle

Describe how a respirometer can be used to measure the rate of aerobic respiration

Measures O2 uptake: 1. Add a set mass of single-celled organism eg. yeast to a set volume / concentration of substrate eg. glucose 2. Add a buffer to keep pH constant 3. Add a chemical that absorbs CO2 eg. sodium hydroxide 4. Place in water bath at a set temperature and allow to equilibrate 5. Measure distance moved by coloured liquid in a set time

Explain why the liquid moves.

Organisms aerobically respire → take in O2 CO2 given out but absorbed by sodium hydroxide solution So volume of gas and pressure in container decrease So fluid in capillary tube moves down a pressure gradient towards organism

Explain why the respirometer apparatus is left open for 10 minutes.

Allow apparatus to equilibrate Allow for overall pressure expansion/change throughout Allow respiration rate of organisms to stabilise

Explain why the apparatus must be airtight.

Prevent air entering or leaving Would change volume and pressure, affecting movement of liquid

Describe a more accurate way to measure volume of gas.

Use a gas syringe

Describe how the rate of respiration can be calculated

1. Calculate volume of O2 / CO2 consumed / released (calculate area of a cylinder) Calculate cross-sectional area of capillary tube using π r² Multiply by distance liquid has moved 2. Divide by mass of organism and time taken 3. Units - unit for volume per unit time per unit mass eg. cm³min⁻¹g⁻¹

Describe how a respirometer can be used to measure the rate of anaerobic respiration

Measures CO2 release: Repeat experiment as above but remove chemical that absorbs CO2 Make conditions anaerobic, for example: Layer of oil / liquid paraffin above yeast → stop O2 diffusing in Add a chemical that absorbs O2 Leave for an hour to allow O2 to be respired and used up

Explain why the liquid moves.

Yeast anaerobically respire → release CO2 So volume of gas and pressure in container increase So fluid in capillary tube moves down a pressure gradient away from organism

Explain why the apparatus is left for an hour after the culture has reached a constant temperature.

Allow time for oxygen to be used / respired

Describe how redox indicator dyes such as Methylene blue can be used to measure rate of respiration

Redox indicators (eg. methylene blue) change colour when they accept electrons becoming reduced Redox indicators take up hydrogens and get reduced instead of NAD / FAD → modelling their reactions 1. Add a set volume of organism eg. yeast and a set volume of respiratory substrate eg. glucose to tubes 2. Add a buffer to keep pH constant 3. Place in water bath at a set temperature and allow to equilibrate for 5 mins 4. Add a set volume of methylene blue, shake for a set time (do not shake again) 5. Record time taken for colour to disappear in tube Rate of respiration (s⁻¹) = 1 / time (sec)

Give examples of variables that could be controlled.

Volume of single-celled organism Volume / conc. / type of respiratory substrate Temperature (with a water bath) pH (with a buffer) Volume of redox indicator (only control)

Why leave tubes in the water bath for 5 minutes?

Allow for solutions to equilibrate and reach the same temperature as the water bath

Describe a control experiment and why it would be done.

Add methylene blue to boiled / inactive / dead yeast (boiling denatures enzymes) All other conditions the same To show change is due to respiration in organisms

Suggest and explain why you must not shake tubes containing methylene blue.

Shaking would mix solution with oxygen Which would oxidise methylene blue / cause it to lose its electrons So methylene blue would turn back to its original blue colour

Suggest one source of error in using methylene blue. Explain how this can be reduced.

Subjective as to determination of colour change / end point Compare results to a colour standard (one that has already chan

Describe how biomass is formed in plants

During photosynthesis, plants make organic (carbon) compounds from atmospheric or aquatic CO2 Most sugars synthesised are used by the plant as respiratory substrates Rest used to make other groups of biological molecules (eg. carbs, lipids & proteins) → form biomass

How can biomass be measured?

Mass of carbon or dry mass of tissue per given area

Describe how dry mass of tissue can be measured

1. Sample dried in an oven eg. at 100°C (avoid combustion) 2. Sample weighed and reheated at regular intervals until mass remains constant (all water evaporated)

Explain why dry mass is more representative than fresh (wet) mass

Water volume in wet samples will vary but will not affect dry mass.

Describe how the chemical energy stored in dry biomass can be estimated

Using calorimetry: 1. Known mass of dry biomass is fully combusted (burnt) 2. Heat energy released heats a known volume of water 3. Increase in temperature of water is used to calculate chemical energy of biomass

Explain how features of a calorimeter enable valid measurement of heat energy released

Stirrer → evenly distributes heat energy (in water) Air / insulation → reduces heat loss & gain to & from surroundings Water → has a high specific heat capacity

What is gross primary production (GPP)?

Chemical energy store in plant biomass, in a given area or volume, in a given time Total energy transferred into chemical energy from light energy during photosynthesis

What is net primary production (NPP)?

Chemical energy store in plant biomass after respiratory losses to environment taken into account

State the formula for NPP

NPP = GPP – R R = respiratory losses to the environment

Explain the importance of NPP in ecosystems

NPP is available for plant growth and reproduction NPP is also available to other trophic levels in the ecosystem, such as herbivores and decomposers

What is primary or secondary productivity?

The rate of primary or secondary production, respectively.

State the units used for primary or secondary productivity

kJ ha⁻¹ year⁻¹ (unit for energy, per unit area, per year)

Explain why these units for primary or secondary productivity are used

Per unit area → takes into account that different environments vary in size Standardising results to enable comparison between environments Per year → takes into account effect of seasonal variation (temperature etc.) on biomass More representative and enables comparison between environments

Explain why most light falling on producers is not used in photosynthesis

Light is reflected or wrong wavelength Light misses chlorophyll / chloroplasts / photosynthetic tissue CO2 concentration or temperature is a limiting factor

State the formula for net production of consumers (N)

N = I – (F + R) I = the chemical energy store in ingested food F = the chemical energy lost to the environment in faeces and urine

State the formula for efficiency of energy transfer

Energy or biomass available after transfer / energy or biomass available before transfer x 100 if a %

Explain why energy transfer between trophic levels is inefficient

Heat energy is lost via respiration Energy lost via parts of organism that aren’t eaten (eg. bones) Energy lost via food not digested → lost as faeces Energy lost via excretion eg. urea in urine

Explain how crop farming practices increase efficiency of energy transfer

Simplifying food webs to reduce energy / biomass losses to non-human food chains eg. Herbicides kill weeds → less competition (eg. for light) so more energy to create biomass Pesticides kill insects (pests) → reduce loss of biomass from crops Fungicides reduce fungal infections → more energy to create biomass Fertilisers e.g. nitrates to prevent poor growth due to lack of nutrients

Explain how livestock farming practices increase efficiency of energy transfer

Reducing respiratory losses within a human food chain (so more energy to create biomass): Restrict movement and keep warm → less energy lost as heat from respiration Slaughter animal while still growing / young, when most of their energy is used for growth Treated with antibiotics → prevent loss of energy due to pathogens Selective breeding to produce breeds with higher growth rates

Explain the role of saprobionts in recycling chemical elements

Decompose (break down) organic compounds eg. proteins / urea / DNA in dead matter / organic waste By secreting enzymes for extracellular digestion (saprobiotic nutrition) Absorb soluble needed nutrients and release minerals ions eg. phosphate ions

Explain the role of mycorrhizae

Mycorrhizae = symbiotic association between fungi and plant roots Fungi (hyphae) act as an extension of plant roots to increase surface area of root system To increase rate of uptake / absorption of water and inorganic ions In return, fungi receive organic compounds eg. carbohydrates

Give examples of biological molecules that contain nitrogen

Amino acids / proteins or enzymes / urea / DNA or RNA / chlorophyll / ATP or ADP / NAD or NADP

Describe the role of bacteria in nitrogen fixation

Nitrogen gas (N2) converted into ammonia (NH3), which forms ammonium ions (NH4⁺) in soil By nitrogen-fixing bacteria (may be found in root nodules)

Describe the role of bacteria in ammonification

Nitrogen-containing compounds eg. proteins / urea from dead organisms / waste are broken down / decomposed Converted to ammonia, which forms ammonium ions in soil By saprobionts - secrete enzymes for extracellular digestion

Describe the role of bacteria in nitrification

Ammonium ions in soil converted into nitrites then nitrates, via a two-step oxidation reaction For uptake by plant root hair cells by active transport By nitrifying bacteria in aerobic conditions (oxygen)

Describe the role of bacteria in denitrification

Nitrates in soil converted into nitrogen gas (reduction) By denitrifying bacteria in anaerobic conditions (no oxygen, eg. waterlogged soil)

Suggest why ploughing (aerating) soil increases its fertility

More ammonium converted into nitrite and nitrate / more nitrification / more (active) nitrifying bacteria Less nitrate converted to nitrogen gas / less denitrification / fewer (active) nitrifying bacteria

Give examples of biological molecules that contain phosphorus

Phospholipids / DNA or RNA / ATP or ADP / NADP / TP or GP / RuBP

Describe the phosphorus cycle

1. Phosphate ions in rocks released (into soils / oceans) by erosion / weathering 2. Phosphate ions taken up by producers / plants / algae and incorporated into their biomass Rate of absorption increased by mycorrhizae 3. Phosphate ions transferred through food chain eg. as herbivores eat producers 4. Some phosphate ions lost from animals in waste products (excretion) 5. Saprobionts decompose organic compounds eg. DNA in dead matter / organic waste, releasing phosphate ions

Explain why fertilisers are used

To replace nitrates / phosphates lost when plants are harvested and livestock are removed Those removed from soil and incorporated into biomass can’t be released back into the soil through decomposition by saprobionts So improve efficiency of energy transfer → increase productivity / yield

Describe the difference between artificial and natural fertilisers

Natural Contain inorganic compounds of nitrogen, phosphorus and potassium Artificial Organic, eg. manure, compost, sewage → ions released during decomposition by saprobionts

Explain the key environmental issue arising from use of fertilisers

Phosphates / nitrates dissolve in water, leading to leaching of nutrients into lakes / rivers / oceans This leads to eutrophication 1. Rapid growth of algae in pond / river (algal bloom) so light blocked 2. So submerged plants die as they cannot photosynthesise 3. So saprobionts decompose dead plant matter, using oxygen in aerobic respiration 4. So less oxygen for fish to aerobically respire, leading to their death

Explain the key advantage of using natural fertiliser over artificial fertiliser

Less water soluble so less leaching → eutrophication less likely Organic molecules require breaking down by saprobionts → slow release of nitrate / phosphate etc.