3.5 Energy transfers in and between organisms

PAPER 2 3.5.1 Photosynthesis 3.5.2 Respiration 3.5.3 Energy and Ecosystems 3.5.4 Nutrient cycles

Coenzymes

molecules that aid the enzyme by transferring chemical group from one molecule to another

Types of coenzyme in respiration

NAD - transfer hydrogen between molecules
CoA - transfers acetate between molecules
FAD - transfer hydrogen between molecules

Processes of photosynthesis

light dependent reactions and light independent reactions

Background information about LDR

requires light energy
takes place in the thylakoid membrane
produces 3 things:
- ATP is produced from synthesis ADP and Pi with energy from proton gradient
- reduced NADP is produced from reduction of NADP by electron from PSI and a proton
- O2, electrons and protons are produced from photolysis of water by light energy

non-cyclic photophosphorylation process

1. Light is absorbed by PSII (680nm wavelength), light energy excites electrons, electrons reach higher energy level and are released from chlorophyll and move down electron transport chain
2. Light energy splits water into O2, electrons and H+ (protons)
3. Energy is released from electrons as they move down electron transport chain, energy is used to actively transport H+ from stroma to thylakoids
4. Proton gradient as high concentration of H+ in the thylakoid, H+ move down concentration gradient into stroma via ATP synthase (embedded in the thylakoid membrane) which synthesises ADP and Pi to make ATP.
5. PSI absorbs light energy which excites electrons to very high energy level, electron is released to reduce NADP along with a proton to make reduced NADP

Chemiosmosis

Process of electrons flowing down electron transport chain to create a proton gradient across the membrane to drive ATP synthesis

cyclic photophosphorylation

Only involves PSI, produces ATP
Electrons are not passed onto NADP, electron enters electron transport chain which releases energy to synthesise ATP
Electrons cycle back to PSI by electron carriers
Electrons are recycled, small amount of ATP is produced

background information about LIR

Light independent reaction is known as the Calvin cycle
Relies on products from LDR (ATP (energy) and reduced NADP (provides H+))
Takes place in the stroma
6 turns of the Calvin cycle produces 1 glucose molecule

Calvin cycle (LIR) process

1. CO2 enters the leaf through stomata which, diffuses into chloroplast, CO2 (1C) combines with RuBP (5C) to form initially an unstable 6C molecule which then splits into 2x GP (3C), this is catalysed by the enzyme rubisco

2. Hydrolysis of ATP and NADP from LDR provides energy and H+ to convert GP (3C) into TP (3C). Some TP is converted into useful organic materials such as glucose (carbohydrates, lipids, amino acids)

3. RuBP is regenerated, 5/6 molecules of TP are used to regenerate RuBP, rest of ATP is hydrolysed into ADP and Pi to generate energy for regeneration

Factors affecting photosynthesis

light intensity (affects LDR, high) , carbon dioxide concentration (affects LIR, 0.4%) and temperature (affects RoR, 25°C), water (mineral ion uptake, just enough but not waterlogged)

Agricultural practices to increase plant growth

Light intensity - growing plants under LED light, increases light intensity but maintains temperature
Burning fuels - increases CO2 concentration in the atmosphere as burning fuels releases CO2
Temperature - using a greenhouse, greenhouses trap heat energy from sunlight which warms the air, air circulation ensures temperature is even throughout the greenhouse

Compensation point

rate of respiration is equal to the rate of photosynthesis at the same time, no net movement of gases (0) which is caused by light being at a certain wavelength

Respiration types

aerobic and anaerobic

Aerobic respiration stages

glycolysis, link reaction, krebs cycle, oxidative phosphorylation

Anaerobic respiration stages

Glycolysis, oxidative phosphorylation

background information on glycolysis

takes place in the cytoplasm of the cell
first stage in both aerobic and anaerobic respiration
two stages: phosphorylation and oxidation

Glycolysis process

1. Glucose (6C) is phosphorylated using Pi from hydrolysis of ATP into glucose phosphate (6C) and ADP
2. Glucose phosphate is phosphorylated again into hexose biphosphate (6C) and ADP
3. Hexose biphosphate (6C) splits into two molecules of triose phosphate (3C)
4. Two molecules of triose phosphate (3C) oxidised to produce 2x pyruvate (3C), losing 2H+, 2H+ collected by NAD to form reduced NAD , 4x ADP and Pi synthesise to form 4 ATP
Glycolysis therefore produces net gain of 2 ATP (4-2\=+2 ATP)

background information on link reaction

link reaction takes place in the mitochondrial matrix, pyruvate is actively transported into the mitochondrial matrix from the cytoplasm
only involved in aerobic respiration
two link reactions occur per pyruvate molecule produced from link reaction

Link reaction process

1. Pyruvate (3C) is actively transported into the matrix, pyruvate (3C) is decarboxylated to produce CO2
2. Pyruvate is oxidised to form Acetate (2C) and NAD is then reduced by the H+ released to produce reduced NAD
3. Acetate (2C) combines with co-enzyme A to form Acetyl CoA (2C)
No ATP is produced from this reaction

Glycolysis products

2 pyruvate, 2 ATP, 2 NADH

Link Reaction Products

2 acetyl CoA (Krebs cycle) , 2 CO2 (waste product), 2 NADH (oxidative phosphorylation)

background information on Krebs cycle

occurs in the mitochondrial matrix
reduced coenzymes and ATP are produced
series of reduction and oxidation reactions
cycles twice for each glucose molecule (produce two molecules of acetyl CoA from link reaction)

Krebs cycle process

1. Acetyl CoA (2C) from link reaction combines with 4C molecule to form 6C molecule, CoA is released and goes back to link reaction to reused
2. 6C molecule is decarboxylated and dehydrogenated to make 5C molecule releasing CO2 and a H+ which reduces NAD into reduced NAD
3. 5C molecule regenerates 4C molecule by decarboxylation and dehydrogenation, H+ released reduces FAD into reduced FAD and two molecules of NAD reduced into 2x reduced NAD
ATP is produced by substrate-level phosphorylation.

Krebs cycle products and destinations

2x CoA - link reaction
2x 4C molecule - regenerated next Krebs cycle
4x CO2 - waste product
2x ATP - used for energy
6x reduced NADP - oxidative phosphorylation
2x reduced FAD - oxidative phosphorylation

substrate-level phosphorylation

Direct transfer of phosphate from respiratory intermediate to ADP to produce ATP. Occurs in glycolysis and Krebs cycle.

oxidative phosphorylation

The indirect linking of Pi to ADP to produce ATP involving energy and hydrogen atoms that are carried on NAD/FAD

background information on oxidative phosphorylation

involves electron transport chain, involves oxidation and phosphorylation , uses reduced coenzymes from Krebs cycle which split into protons and electrons

Oxidative phosphorylation process

1. Reduced coenzymes (FAD/NAD) are oxidised and release hydrogen. Hydrogen splits into protons and electrons
2. Electrons move down electron transport chain, reducing when entering an electron carrier and then oxidising it when electron leaves. Energy from electrons moving is used to pump protons into the intermembrane space. This creates a electrochemical gradient (difference in concentration of ions across membrane)
3. H+ transported in facilitated diffusion via ATP synthase into matrix. Causes drive in synthesis (phosphorylation) of 2x ADP + Pi -\> 2x ATP
4. Finally, Oxygen is final electron acceptor and accepts a H+ ion to produce water

Why is oxygen important in oxidative phosphorylation?

Final electron acceptor if this didn't happen, electron transport chain would not be maintained, proton would not be transported. Therefore, electrochemical gradient would not happen, no chemiosmosis, no ATP production

Background info on anaerobic respiration

no oxygen
occurs in the cytoplasm only
oxidises NAD in order to be used in glycolysis to produce small amounts of ATP
only two ATP produced during anaerobic respiration

alcoholic fermentation process

occurs in plants and yeast
1. Pyruvate is decarboxylated to form ethanal
2. Ethanal is reduced by reduced NAD to produce ethanol, reduced NAD is oxidised and produces NAD
3. NAD is reused in glycolysis to produce small amount of ATP

lactate production process

occurs in animals
1. Pyruvate is reduced by reduced NAD to produce lactic acid, reduced NAD is oxidised and produces NAD
2. NAD is reused in glycolysis to produce small amount of ATP

Ecosystem

form of biological community containing all living and non-living factors

Producers

photosynthetic organisms, energy provided from the sun

Consumers

obtain energy and nutrients by eating other organisms

Why is energy important in organisms?

Synthesises organic compounds using energy as well as CO2 in plants

How does a plant produce its biomass?

Sugars are synthesised in plants using energy which produce respiratory substances
Rest of energy synthesises other biological molecules, this makes up the plants biomass

Biomass

the total mass of living materials in a specific area at a given time

How can biomass be measured?

Two ways:
- Dry mass - mass of carbon/dry mass of tissue per given area
- Chemical energy store in dry biomass obtained using calorimeter

Dry biomass method

Heat sample at 100°C so water evaporates
Weigh and reheat until no further change in mass is recorded
(Dry biomass on land is in g/m2, Dry biomass at sea/pond is g/m3)

Calorimetry method

1. Dry material is weighed
2. Burned in pure oxygen within sealed chamber
3. Surrounded by water bath - heat of combustion causes change in temperature
4. Use specific heat capacity of water to calculate energy released from mass of burned biomass

Food chain

A series of steps in which organisms transfer energy by eating and being eaten. Energy is lost when going to a higher trophic level.

basic food chain

primary producer, primary consumer, secondary consumer, tertiary consumer

energy efficiency formula

energy available after transfer / energy available before transfer x 100

Why do we lose energy between trophic levels?

Energy loss due to respiration, excretion (urine/faeces), death, some parts not eaten/indigestible

Conserving energy (factory farming)

restricting movement of livestock, less energy for muscle contraction
warmer environment to reduce heat loss in respiration
controlled feeding - optimum amount of food no excess
exclusion of predators

Conserving energy (crop farmers)

Eliminating organisms that are part of food web which compete with plant
(weeds - compete for water and minerals
insects/pests - cause damage, spread disease, eat crops
monoculture - same plant in one area, spreads disease)

gross primary productivity (GPP)

The chemical energy store in a plant biomass in a given area or volume. (disregarding respiratory losses)

GPP differs in certain areas due to

light intensity
higher temperature
higher water availability
higher plant density

net primary productivity (NPP)

The chemical energy store in plant biomass after respiratory losses to the environment have been taken into account (mainly for plants, herbivores and microorganisms)

net primary productivity equation

NPP \= GPP - R

net production equation

N \= I - (F + R)

How do nutrients cycle?

Nutrients are recycled within natural ecosystem, microorganisms pay vital role in recycling chemical elements such as nitrogen and phosphorus

Saprobionts

organisms that digest their food externally and then absorb the products (e.g. bacteria, fungi)

Mycorrhizae

fungal associations between plant roots and bacterial fungi
Forms mutualistic relationship with plant (plant gains water and inorganic ions from fungi, fungi gains carbohydrates and photosynthesis products from plant)

Mycorrhizae advantages

1. Increases the SA between plant roots and bacterial fungi
2. Acts like a sponge and holds water and mineral ions close to the roots
so makes plants more drought resistant, higher intake of inorganic ions

Why is nitrogen important?

Nitrogen needed to make DNA, RNA, amino acids, ATP etc.

nitrogen cycle steps

nitrogen fixation
ammonification
nitrification
denitrification

nitrogen fixation

Nitrogen fixing bacteria convert atmospheric nitrogen into ammonium ions (N2 -\> NH4+)

Where are nitrogen fixing bacteria found?

- Free living in the soil
- Root nodules of leguminous plants

Ammonification

Nitrogen compounds (proteins, ATP, DNA, urea) from decomposition of dead organisms and waste material are converted into ammonium ions which are released in the soil by saprobionts

Nitrification

Ammonium in the soil is oxidised to nitrites and then oxidised again to form nitrates by nitrifying bacteria (NH4+ -\> NO2\- -\> NO3-)

How can farmers maximise nitrification?

ploughing to keep the soil aerated
good drainage to prevent waterlogging

Denifitrication

Anaerobic nitrifying bacteria convert nitrogen back into atmospheric nitrogen, this is a disadvantage to plants and is caused by waterlogging
(NH4+ -\> N2)

Why is phosphorus important?

Phosphorus is essential to life because it is part of molecules such as DNA and RNA and phospholipid bilayers.

phosphorus cycle steps

1. Environmental conditions cause erosion/weathering of rocks which release phosphate ions
2. Phosphate ions end up in bodies of water and into soil, plants assimilate ions
3. Animals consume plants and use ions to synthesise organic compounds
4. Animals die and phosphorus ions are released back into soil
5. Decomposing bacteria convert phosphate ions into inorganic phosphate that end up in waterways and are assimilated by plants again

Why do we use fertilisers?

Fertilisers replace nitrates and phosphates lost from harvesting crops and removing livestock, allowing plants to grow bigger and taller

Types of fertilizers

Natural and Artificial

natural fertilizer

manure, seaweed, peat, sludge, guano

evaluation of natural fertilizer

cheap, may be free due to livestock
not very concentrated, cannot control exact mineral proportion, released over long time period, need a lot of it

Artificial fertilisers

inorganic compounds, pure chemical as powders/pellets

evaluation of artificial fertilizer

expensive, highly-water soluble so can leach
contain exact amount of chemicals, easy to apply, contains at least 3 chemical compounds

Leaching

process that nutrients (water-soluble) are washed away into bodies of water (e.g. rivers and ponds)
if nitrogen fertilisers leach, eutrophication occurs

What type of fertiliser leaches easily?

Artificial fertilisers more likely to be leached as they are readily soluble and highly concentrated compared to natural fertilisers which still contains organic compounds

Leaching is more likely in nitrogen or phosphate?

leaching of phosphate is less, leaching of nitrates is more as nitrates are more readily soluble than phosphates

Eutrophication

1. Nitrogen ions leached from fertiliser, stimulate rapid growth of algae in a body of water
2. Algal bloom blocks light from reaching plants at the bottom of the water
3. Plants die as they cannot photosynthesise
4. Decomposing bacteria feed on dead matter, increasing number of bacteria reducing oxygen concentration
5. Fish/aquatic organisms die due to very low oxygen concentration