5: Energy transfers in and between organisms

What are the stages to the nitrogen cycle?

• Nitrogen fixation

• Denitrification

• Nitrification

• Ammonification

What is the role of bacteria in nitrogen fixation?

Lightning can break the triple bond in nitrogen gas which is converted into ammonia which forms ammonium ions in soil by nitrogen-fixing bacteria 

What is the role of bacteria in denitrification?

Nitrates in soil converted into nitrogen gas by denitrifying bacterias in anaerobic conditions 

What is the role of bacteria in nitrification?

Ammonium ions in the soil is converted into nitrites than nitrates via a 2 step oxidation reaction for uptake by root hair cells by nitrifying bacteria in aerobic conditions

What is the role of bacteria in ammonification?

• Nitrogen containing compounds are broken down and converted into ammonia

• Ammonium ions in soil are formed by saprobionts which secrete enzymes for extracellular digestion

What is assimilation?

Plants will absorb ions in the soil and convert them to amino acids and nucleic acids

What is a sabprobiant?

Microorganisms that obtain nutrients by breaking down dead or waste organic matter (decomposers) and secrete ammonia

How are saprobionts used to recycle chemical elements?

• Decompose organic compounds in dead matter

• By secreting enzymes for extracellular digestion

• Absorb soluble needed nutrients

• Release minerals 

What is mycorrhizae?

Symbiotic relationships between fungi and the roots of plants

What is the role of mycorrhizae?

• Fungi act as an extension of plant roots to increase root surface area

• To increase rate of uptake of water and inorganic ions

• In return, fungi receive organic compounds

What is the process of the phosphorus cycle?

• Phosphate ions in rocks are released by erosion

• Phosphate ions are taken up by producers and are incorporated into their biomass

• The rate of absorption is increased by mycorrhizae 

• Phosphate ions are transferred through the food chain

• Some phosphate ions are lost from animals during excretion

• Saprobionts decompose organic compounds

What are the advantages/disadvantages of using natural fertilisers?

Advantages:

• Release nutrients slowly over time, so nutrients are less likely to be washed away into rivers and lakes after rain

• Contain organic matter, so can improve soil structure and water retention

Disadvantages:

• Less concentrated so large amounts needed

• Nutrient content is variable and harder to control

What are the advantages/disadvantages of using artificial fertilisers?

Advantages:

• Concentrated and easy to apply

• Precise nutrient content allows controlled dosing

Disadvantages:

• Highly soluble in water so can be leached out of soil into rivers and lakes when it rains

• Do not improve soil structure

What is leeching?

Soluble nutrients are washed out of the soil by rainwater and end up in rivers, lakes, or groundwater

What are the problems associated with leeching?

• Nitrate ions in drinking water can be harmful

• Loss of nutrients from soil reduces fertility so there is less productive crop growth

• Nitrates go into the water sources contributes to eutrophication

What is eutrophication?

Nutrient enrichment in bodies of water causes excessive plant and algal growth

What is the process of eutrophication?

• Mineral ions enter water bodies, causing rapid growth of algae at the surface

• Algae block sunlight, which prevents aquatic plants below the surface from photosynthesising

• These plants, and eventually the algae, begin to die

• Dead organic matter accumulates

• Bacteria decompose the dead matter, respiring aerobically and using up the oxygen dissolved in the water

• Oxygen levels fall and aquatic animals such as fish and insects can no longer survive

How can dry mass be measured?

Dry organisms in an oven at around 80°C until they reach a constant mass

How can chemical energy store in dry biomass be measured?

Calorimetry

What is Gross Primary Production (GPP)?

The total chemical energy store in plant biomass in a given area/volume in a given time

What is Net Primary Production (NPP)?

The chemical energy store in plant biomass after respiratory losses to the environment have been taken into account 

What is Net Primary Production used for?

• Growth

• Reproduction

• Consumers and decomposers

What is the formula for Net Primary Production (NPP)?

NPP = GPP- R(respiratory losses)

What is the formula for the net production of consumers?

I (chemical energy in ingested food)- (F(energy lost to faces and urine)+ R(respiratory lossess)

What is Primary Productivity and what is its unit?

The rate of primary production (kJ ha^–1 year^–1)

What is Secondary Productivity and what is its unit?

The rate of seccondary production (kJ ha^–1 year^–1)

Why is less energy available at each trophic level?

• Parts of the organism are not consumed

• Parts of the organism cannot be digested

• Energy is lost in secretions such as urine 

• Heat energy is transferred during respiration and is lost to the environment 

Why is such a small proportion (between 1-3%) of light energy captured by photosynthesising organisms?

• Reflection by clouds

• Absorption by atmosphere

• Not all wavelengths of light can be absorbed

• Light may not fall on the chlorophyll molecule 

• Limiting factors (co2 concentration, temperature, light intensity, type/number of chlorophyll)

How can livestock farming practices increase the efficiency of energy transfer?

• Restricting movement, less muscle contraction so rate of respiration will be lowerso less energy can be used for biomass

• Regulating temperature to control the rate of respiration, homeostasis

• Treat livestock with antibiotics/vaccines- prevents loss of energy due to pathogens (leads to antibiotic resistance)

• Selective breeding to produce breeds with a higher growth rate

How can crop farming practices increase the efficiency of energy transfer?

• Simplifying food webs to reduce energy to non-human food chains

• Using herbicides to cell weeds so less competition

• Pesticides to reduce loss of biomass from crops

• Fungicides to reduce fungal infections

• Fertilisers to prevent stunted growth due to lack of nutrients

Why is respiration important?

• ATP is produced

• For processes that require energy (e.g, protein synthesis ext)

What are the stages in aerobic respiration and where do they take place?

• Glycolysis: cytoplasm

• Link reaction: matrix

• Krebs cycle: matrix

• Oxidative phosphorylation: inner mitochondrial membrane

What are the stages in anaerobic respiration?

• Glycolysis: cytoplasm

• NAD regeneration: cytoplasm

What is the process of glycolysis?

• Glucose is phosphorylated to glucose phosphate

• Using inorganic phosphates from 2 ATP molecules

• Hydrolysed to produce 2 triose phosphates

• Oxidised to produce 2 pyruvate, 2 reduced NAD and 4 ATP (net gain of 2)

What happens if glycolysis is anaerobic?

• Pyruvate produced in glycolysis is converted to lactate (animals) or ethanol (plants and yeast)

• Reduced NAD is oxidized to regenerate NAD

• Allows glycolysis to continue

Why does anaerobic respiration produce less ATP per molecule of glucose than aerobic respiration?

• Glycolysis is the only process involved in anaerobic respiration

• SO there is no oxidative phosphorylation which forms the majority of ATP

What is the process of the link reaction?

• Pyruvate is oxidized to acetate

• CO2 and reduced NAD is produced

• Acetate combines with coenzyme A, forming Acetyl Coenzyme A

• 2 of each product is produced per glucose molecule

What is the process of the Krebs Cycle?

• Acetyl coenzyme A (2C) reacts with an oxaloacetate (4C) molecule

• Coenzyme A and a 6C molecule is produced

• 6C molecule enters the krebs cycle

• A series of oxidation-reduction reactions, the 4C molecule is regenerated

• 2x CO2 lost

• Coenzymes NAD and FAD reduced

• Substrate level phosphorylation produces ATP

What is the importance of the Krebs Cycle?

• Oxaloacetate (4C) is regenerated allowing Krebs to continue

• Produces reduced NAD for oxidative phosphorylation

What is the process of oxidative phosphorylation?

• Reduced NAD and FAD are oxidised to release H+ ions and electrons

• Electrons are transferred down the electron transfer chain by a series of redox reactions

• Free energy released by electrons is used by carriers to actively pump protons from the matrix to intermembrane space

• Proton electrochemical gradient is established

• Oxygen is the final electron acceptor

• A conformational change in the ATP synthase provides the required energy to recombine

• So protons, electrons and oxygen combine to form water

What is chemiosmosis?

The movement of protons across a membrane via facilitated diffusion, providing a chemiosmotic potential gradient

How is a lipid used as a respiratory substrate?

• Lipids are hydrolysed into glycerol and fatty acids

• Glycerol is converted into triose phosphate which enters glycolysis

• Fatty acids are broken down into 2C compounds and convert into acetyl coenzyme A which enters the krebs cycle

How are proteins used as respiratory substrates?

• Proteins are hydrolysed into amino acids

• Amine group is removed from the amino acids 

• 3C compounds are converted into pyruvate (and enters links) 

• 4/5C compounds directly input themselves into different stages of the krebs cycle

What is the method for an investigation into a named variable into the rate of a named variable on respiration?

• Set up a water bath at 35°C

• Add 5cm3 of the yeast and glucose solution to three test tubes

• Place test tubes in the water bath and leave them, for the solution to equilibrate for 10 minutes

• Add 2cm3 of methylene blue to the test tubes and start the timer

• Shake for 10 seconds and place test tube back in water bath

• Record how long it takes for the methylene blue to turn colourless for each test tube

• Repeat the experiment using temperatures of 40°C, 50°C, 60°C and 70°C

• Find the mean of the results for each temperature and use to calculate the average rate of respiration.

• Rate of respiration = 1/mean time

What are the stages of photosynthesis and where do they take place?

• Light dependent reaction: thylakoid membrane

• Light independent reaction: stroma

What is the process of the light dependent reaction?

• Water splits to produce electrons, oxygen and protons (photolysis)

• Electrons replace those lost from chlorophyll

• Light strikes photosystem 2 and is absorbed

• Pigments in PS2 transfer the light energy until it reaches the primary pigment reaction centre 

• Electrons get excited by light energy, able to escape Mg

• The electrons replace the electrons that were excited when the light energy hit the chlorophyll 

• Electrons enter the electron transport chain, series of redox reactions cause free energy to be released 

• Hydrogen ions from the stroma enters into Thylakoid Space

• Light hits PS1, light energy is funneled into primary pigment reaction centre, electrons become excited

• Ferredoxin accepts electrons, takes them to the stroma 

• NADP and H+ ions combine to make reduced NADP

• Hydrogen ions move down proton gradient through ATP synthase 

• ATP produced as ATP synthase undergoes a conformational change 

What is the process of photolysis?

• Water splits to produce protons, electrons and oxygen

• Electrons replace those lost from chlorophyll

What is the process of photoionisation?

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

• 9So electrons are released from chlorophyll

• Chlorophyll becomes positively charged

What are the products of the light dependent reaction?

• 18 ATP

• 12 Reduced NAD

• 6 O₂

(per glucose molecule)

What is the process of the light independent reaction?

• Carbon dioxide combines with RuBP

• Produces two GP catalysed by enzyme RuBisCo

• GP reduced to triose phosphate

• Using reduced NADP and energy from ATP

• Some triose phosphate converted to RuBP

• Some TP converted into glucose

How does temperature affect the rate of photosynthesis?

• As temperature increases, rate increases

• Enzymes (RuBisCo) gain kinetic energy

• So more enzyme-substrate complexes form

• Above an optimum temperature, rate decreases

• Enzymes denature as Hydrogen bonds in tertiary structure break

• So fewer enzyme-substrate complexes form

How does light intensity affect the rate of photosynthesis?

• As light intensity increases, rate increases

• Light-dependent reaction increases (more photoionisation of chlorophyll)

• More ATP and reduced NADP produced

• So light-independent reaction increases as more GP reduced to TP and more TP regenerates RuBP

• Above a certain light intensity, rate stops increasing as another factor is limiting

How does CO₂ concentration affect the rate of photosynthesis?

• As CO2 concentration increases, rate increases

• Light-independent reaction increases

• As more CO2 combines with RuBP to form GP

• So more GP reduced to TP

• So more TP converted to organic substances and more RuBP regenerated

• Above a certain CO2 concentration, rate stops increasing as another factor is limiting
  

What is the method of chromatography to investigate the pigments isolated in the leaves of different plants from shade-tolerant and shade-intolerant plants or leaves of different colours?

• Draw a straight line in pencil approximately 1 cm above the bottom of the filter paper being used

• Make sure not to use a pen as the ink will blur the line and obscure the results

• Cut a section of leaf and place it in a mortar

• Add 20 drops of acetone and use the pestle to grind up the leaf sample and release the pigments

• Use a capillary tube to extract some of the pigment and blot it onto the centre of the pencil line you have drawn

• Suspend the paper in the solvent so that the level of the liquid does not lie above the pencil line and leave the paper until the solvent has run up the paper to near the top.

• Remove the paper from the solvent and draw a pencil line marking where the solvent moved up to

• Calculate the Rf value for each spot (distance travelled by solute/distance travelled by solvent)

What is the method for an Investigation into the effect of a named factor onto the rate of dehydrogenase activity in extracts of chloroplasts?

• Remove stalks from leaf samples. Grind sample using a pestle and mortar and place into a chilled isolation solution. 

• Use a muslin cloth and funnel to filter the sample into a beaker. Suspend the beaker in an ice water bath to keep the sample chilled

• Transfer to centrifuge tubes and centrifuge at high speed for 10 minutes. This will separate chloroplasts into the pellet.

• Remove supernatant and add pellet to the fresh isolation medium. Store isolation solution on ice. 

• Set the colorimeter to the red filter. Zero using a cuvette containing chloroplast extract and distilled water. 

• Place the test tube in the rack 30cm from the light source and add DCPIP. Immediately take a sample and add to the cuvette. Measure the absorbance of the sample using the colorimeter. 

• Take a sample and measure its absorbance every 2 minutes for 10 minutes. 

• Repeat for different distances from the lamp up to 100 cm. This will vary the light intensity.