Photosynthesis

Life depends on continuous transfers of energy. In plants energy from light is absorbed by chlorophyll, transferred to chemical energy allowing molecules form, which allow plant to produce ATP during respiration. Those organisms that are non-photosynthetic feeds on molecules produced by those that are, like plants, and use them to make their own ATP during respiration.

Site of photosynthesisLeaf is the main photosynthetic structure in eukaryotic plants. Chloroplast are cellular organelles where photosynthesis takes place.

Structure of the leaf:Leaves are adapted to get materials need for photosynthesis (water, CO2 and light) and remove its products (oxygen and glucose). Their adaptations include:

- Large surface to absorb as much light as possible- Leaves are arranged in a way to reduce overlapping and so increase

exposure to the sun- Thin, because light is absorbed in the first few micrometres, and to

create a short diffusion pathway for gases - A transparent cuticle and epidermis to give the photosynthetic

mesophyll cells access to light- Long, narrow upper mesophyll cells with lots of chloroplast – the

more organelles, the more light can be absorbed- Numerous stromata for gaseous exchange, to create a short diffusion

pathway from any mesophyll cell to stromata (outside environment)- Stomata open and close in response to changes in light intensity- Many air spaces in lower mesophyll layer to allow rapid diffusion in

the gas phase of carbon dioxide and oxygen- A network of xylem to bring water to leaf cells and phloem that

carries away sugars produced in photosynthesis

Photosynthesis is a complex metabolic pathway involving many intermediate reactions, so the equation above is high simplified. It is process of energy transferable where light energy is conserved in the form of chemical bonds. There are three main stages of photosynthesis:

- Capturing of light energy by chlorophyll (chloroplast pigment)- The light-dependent reaction – some of the light energy absorbed is conserved in chemical

bonds. Electron flow is created, causing water to split (photolysis) into protons, electrons and oxygen. Products are NADP, ATP and oxygen.

- Light-independent reaction – protons (hydrogen ions) are used to produce sugars and other organic molecules

Structure of chloroplast:They are typically disc-shaped, 2-10 micrometres long, 1 micrometre in diameterDouble membraneThere are two distinct regions inside the chloroplast:

- The grana – 100 disc-like structures, each disc is called a thylakoid – light-dependant reactions occur here. Thylakoids contain chlorophyll. Some thylakoids have tubular extensions – intergranal lamellae – to connect other grana

- The stoma – fluid-filled matrix – light-independent reaction occurs here. There are other structures present here, like starch grains.

Oxidation –gain oxygen, loss of electrons or loss of hydrogen Reduction – loss of oxygen, or gain of electrons or gain of hydrogenOxidation results in energy being give out; reducion results in it being taken in. They always take place together.

The light-dependant reaction involves the capture of light whose energy is used to:Make ATP by adding an inorganic phosphate molecule to ADP Spirt water into H+ ions (protons) and OH- ions – becaue they are sprit by light, this is known as photolysis

Process:

- Chlorophyll molecule absorbs light energy; the electrons get exicited enough to leave the atoms. The chlorophyll molecule become ionised – photoionisation and therefore became oxidised.

- An electron carrier takes up the lose electrons, becoming reduced. - There is a series of oxidation-reduction reactions as electrons are passed along a number of

electron carriers. The electron carriers form a transfer chain that is located in the membranes of the thylakoids. Each new carrier has a slightly lower energy level than the previous one, so electrons lose energy at each stage. Some of this energy is used to make ATP.

- The mechanism of making ATP can be explained by chemiosmotic theory. - In each thylakoid protons are pumped from the stroma using protein charriers in the

thylakoid membrane – proton pumps. - The energy to drive this process comes from electrons released when water molecules ae

split by light – photolusis of water. This also releases protons that further increases their concenrations inside the thylakoid, and so maintains the heigher concentration inside the thylakoid and low in the stoma (maintaining the concentration gradient).

- Protons can only cross the thylakoid membrane through the ATP synthase channel proteins; the rest of membrane is impermeable to proteins. The channels from small granules on the membrane surface, also called as stalked granules.

- When protons pass through ATP synthase channels, they cause changes to the structure of the enzyme which then can cataluse ADP with Pi to form ATP.

Chlloroplast are structurally adapted to their function of capturing sunlight and carrying out the light-dependant reaction (which takes places in the thylakoids):

- The thylakoid membranes provide a large surface area for attachment of chlorophyll, electron carriers and enzymes

- A netweork of proteins in grana hold chlorophyll in a precise manner that allows maximum absorbtion of light

- The granal membranes have ATP suntahse channels within them, which cataluse the production of ATP. They also electrively permeable whih allows establishment of a proton gradient.

Chloroplast contain both DNA and ribosomes so they can quickly and easily manufacture some of the proteins invovled in the light-depndent reaction.

Photolysis of waterLight when striking a chlorophyll molecule photoionised i.e. loses electrons and for it to continue to absorb light energy, these electrons must be replaced. The replacement electrons are provided from water molecules which are split usin light energy, which also produces/yields protons.

These protons pass out of the of the thylakoid space through through ATP synthase channels and taken by an electron carried called NADP, which becomes reduced. The reduced NADP is the main product of the light-denepent stage and needed in light-independent reaction. It is another potention source of chemical energy to the plant. The oxygen by-product from photolysis of water is either used in respiration or diffuses out of the leaf as a waste product.

Light-independent reactionProducts of light-dependent reaction, ATP and NADPH, are used to reduce glycerate 3-phospate in the second stage of photosynthesis. It does not require light directly, but needs the products of light-dependent stage, so stops quickly when light is absent. It takes place in the stroma.

The Calvin cycleCarbon dioxide diffuses into the leaf through stomata and dissolves in water outside around mesophyll cells. It diffuses through the cell-surface membrane, cytoplasm and chloroplast membranes into the stroma. Carbon dioxide reacts with ribulose bisphosphate (RuBP) (pentose carbon), done by the enzyme rubisco or ribulose bisphosphate carboxylase. The reaction between carbon dioxide and RuBp produces glycerate 3-phosphate (GP).NADPH is used to reduce glycerate 3-phosphate to triose phosphate (TP) using energy supplied by ATP. The NADP is re-formed and goes back to the thylakoids. Some triose phosphate molecules are converted to organic substances that plants requires, such as starch, cellulose, lipids, glucose, amino acids, nucleotides.

Most triose phosphate molecules are used to regenerate ribulose bisphosphate using ATP from the light-dependent reaction.

Chloroplast is adapted to carrying out the light-independent reaction:- Fluids of stroma contains all enzymes needed to carry out the reaction- Self-surface membrane of chloroplast allows to maintain high concentration of enzymes and

substrates- Stroma surrounds the ground, so the product from grana can easily diffuse into stroma- Contains DNA and ribosomes, so it can manufacture proteins that are needed easily

Factors effecting photosynthesis

Limiting factor – a factor that limits the rate at which whole process can take place.

The law of limiting factors – At any given moment the rate of physiological process is limited by the factor that is at its least favourable value.

Respiration

There are two types of cellular respicration which is when ATP is produced from braking down of glucose:

- Aerobic respiration – requires oxygen, waste products are CO2, water and lots of ATP- Anaerobic respiration – no oxygen needs, waster products in animals is lactate or ethanol

and CO2 in plants and fungi, and little ATP in both cases

Aerobic respiration can be divide into four stages:- Glycolysis – the spilling of 6-carbon glucose molecule into two 3-carbon pyruvate molecule- Link reaction – the 3-carbon pyruvate molecules enter into a series of reactions which lead

to the fomration of acetylcoenzyme A, a 2-carbon moelcule- Krebs cycle – intro of acetylconezyme A into a cycle of oxidation-reduction reactions that

yield some ATP and a large quantity of reduced NAD and FAD- Oxidative phoshorylation – the use of electrons, associated with reduced NAD and FAD,

released from the Krebs cycle to synthesise ATP with water prodced as a by-product.

Glycolsis is the initial stage of both aerobic and aberobic respiration. It occurs in cytoplasm of all living cells. Al encyme-controlled reactions can be divided into four stages:

- Phosphorylation of glucose to glucose phosphate – glucose is made more reactive by the addition of two phosphate molecules (phosphorylation). The phosphate molecules come from hydrolysis of two ATP molecules to ADP. This gives energy to activate glucose and lowers the anctivation enegry for upcoming enzyme-controlled reactions.

- Splitting of the phosphorylated glucose – glucose molecule is split into two 3-carbon molecules, triose phosphate

- Oxidation of triose phosphate – hydrogen is removed from the triose phosphate moelcuels and transferred to a hydrogen-carrier moelcule NAD to form reduced NAD (NADH)

- Production of ATP – the enzyme-controlled reactions convert each triose phosphate into another 3-carbon molecule pyruvate. Two molecules of ATP are produced during this process.

The pyruvate molecules possess potential energy that can be released in the Krebs cycle. To enter it, they must oxidised in the link reaction.

The overall yield of one glucose molecule undergoing glycolysis is:- 2 molecules of ATP (4 molecules are produced but 2 were used up in the initial

phosphorylation of glucose, so net profit is 2)- 2 molecules of NADH (these have potential to provide energy to produce more ATP)- 2 molecules of pyruvate

Glycolysis is a universal feature of every living organism and therefore provides indirect evidence for evolution. The enzyme for the glycolytic pathway are found in the cytoplasm of cells, so does not need any organelle. It does not require oxygen, taking place whether it is there or not. In absence of oxygen pyruvate produced can be converted into either lactate or ethanol during anaerobic respiration. This is necessary to re-oxidise NAD so glycolysis can continue. Anaerobic respiration gives/yields a small fraction of potential energy storied in pyruvate molecule. It release the energy, organisms use oxygen to break down pyruvate further.

The link reactionThe pyruvate molecules produced in the cytoplasm during glycolysis are actively transported into the matrix of mitochondria. They undergo a series of reactions during which:

- They are oxidised to acetate. They lose one carbon dioxide molecule and two hydrogen. The hydrogen are picked up by NAD to form reduced NAD/NADH, which is later used to produce ATP.

- 2-carbon acetate combines with coenzyme A (CoA) to produce a compound acetylcoenzyme A.

Pyruvate + NAD + CoA = acetyl CoA + NADH + CO2 (carbon dioxide)

Krebs cycleKrebs cycle involved a series of oxidation-reduction reactions that take place in the matrix of mitochondria. Process:

- 2-carbon acetyl CoA combine with 4-carbon molecule to produce a 6-carbon molecule- 6-carbon molecule loses Co2 and hydrogen to give a 4-carbon molecule and a single

molecule of ATP produced as a result of substrate-level phosphorylation. - 4-carbon molecule combine with new molecule of acetyl CoA to begin the cycle again.

For each molecule of pyruvate, the link reaction and Krebs cycle produce: - Reduced conenzymes, NADH and FADH2. They have the potential to provide energy to

produce ATP molecules by oxidative phosphorylation- one molecule of ATP- three molecules of C02

Two pyruvate molecules are produced from a single original glucose molecules, so the quantities described above should be doubled.

Coenzymes – molecules that some enzymes require in order to function. Coenzymes play a major role in photosynthesis and respiration where they carry hydrogen atoms from one molecule to another.

- NAD – respiration- FAD – Krebs cycle- NADP – photosynthesis

NAD is the most important carrier in respiration. It works with dehydrogenase enzymes that catalyse the removal of hydrogen atoms from substrates and transfer them to other molecules involved in oxidative phosphorylation.

Krebs cycle is significant because:- Breaks down macromolecules into smaller ones- Produced hydrogen atoms that are carried by NAD to electron transfer chain and provide

energy to oxidative phosphorylation, which leads to production of ATP- Regenerate the 4-carbon molecule that combines with acetyl CoA, which would otherwise

accumulate- Source of intermediate compounds used by cells to manufacture other importance

substances e.g. fatty acids, amino acids, chlorophyll.

Oxidative Phosphorylation

Oxidative phosphorylation – mechanism by which some of the energy of electrons within the hydrogen atoms is conserved in the formation of ATP, electrons coming from coenzymes coming from hydrogen atoms carried by NAD and FAD. It involves transfer of electrons down a series of electron carrier molecules which together form the electron transfer chain (ETC).

Mitochondria are the site of oxidative phosphorylation. The enzymes and other proteins involved are found within cristae.

Process:- Hydrogen atoms produced during glycolysis and Krebs cycle combine with coenzymes NAD

and FAD, reducing them. - NADH and FADH2 donate electrons of hydrogen to first molecule in electron transport chain. - Electrons pass along chain of electron transfer carrier molecules in series of oxidation-

reduction reactions. Energy is released which is used for active transport of protons across the inner mitochondrial membrane and into inter-membranal space.

- Protons accumulate in inter-membranal space before they diffuse back into the mitochondrial matrix through ATP synthase channels embedded in the inner mitochondrial membrane.

- At the end of the chain electrons combine with protons and oxygen to form water. Oxygen is so the final acceptor of ETC.

The importance of oxygen in respiration is to act as the final acceptor of hydrogen atoms produced in glycolysis and Krebs cycle. Without the role in removing hydrogen atoms, electrons would ‘back up’ along the chain and process of aerobic respiration would end.

The greater the energy that is released in single step, the more of it is releases as heat and less used for useful purposes. When energy is released a little at a time, more of it can be harvested. This is why electrons are not transferred in one step but passed along a series of transfer carrier molecules, each which is at a slightly lower energy level. Electrons are transferred down an energy gradient, which allows energy to be gradually released.

Alternative respiratory substancesLipids and proteins can in certain circumstances be used as respiratory substances.

Respiration of lipids – lipids are first hydrolysed to glycerol and fatty acids. Glycerol is then phosphorylated, converted to triose phosphate that enters the Krebs cycle. Fatty acid component is broke down into 2-carbon fragments which are converted to acetyl coenzyme A, which also enters the Krebs cycle. Oxidation of lipids produces 2-carbon fragments of carbohydrate and hydrogen atoms. Hydrogen atoms are used in oxidative phosphorylation to produce ATP. For this reason lipids releases more than double energy of same mass of carbohydrate.

Energy and Ecosystems

All organisms found in an ecosystem rely on a source of energy to carry out all their activities. The ultimate source for almost all organisms is sunlight, which is conserved chemically by plants. Most plants used sunlight in making organic compounds from CO2 and water, which include sugars. They are used in respiration for the plant and by other organisms. These biological molecules form the biomass of plants.

Organisms can be divided into three groups according to how they obtain their energy and nutrients:- Producers – photosynthetic organisms that manufacture organic substances using light

energy, water, carbon dioxide and minerals. - Consumers – organisms that obtain energy by feeing on other organisms rather than using

sunlight energy directly. This can be further divided intoo Primary consumers – directly eat producers (green plants), called like this because they

are first in the chain of producers. o Secondary consumers – eat primary consumerso Tertiary consumers – those that eat secondary consumers. Secondary and tertiary are

usually predators but can be also scavengers or parasites. The line of consumers can go on quaternary consumers and so on.

- Saprobionts (decomposers) – group of organism that break down the complex materials in dead organisms into simple ones. This releases minerals and elements that can absorbed by plants (recycling). These are mostly fungi and bacteria.

Food chain – describes a feeding relationship, showing producers and their consumers. Each stage in the chain is referred to as a trophic level. The arrows on the food chain represent the direction of energy flow.

Food webs – many food chains linked together, as most organisms do not rely on a single food source in a habitat. The problem with them it is their complexity. In practise, most likely all organisms in an ecosystem will be linked to other food webs in other habitats.

Biomass – total mass of living material in a specific area at a given time. It is measured using dry mass per given area, in a given time, grams per square metre where an area is being sampled. Where a volume is being sampled, it is measured in grams per cubic metre. Usually mass of carbon or dry mass is measure, as fresh mass due to water is unreliable, but only a small sample can be made as organisms must be killed to do that.

The chemical energy stored in dry mass can be estimated using calorimetry. In bomb calorimetry, a sample of dry material is weighed, burnt in pure oxygen in a sealed container, placed in a water bath and the bomb’s heat raises water temperature.As we know the specific heat capacity of water (4.184 J), the volume of water and temperature rise, we can calculate the energy released from biomass in jJkg-1.

Nutrient cycles

The flow of energy through an ecosystem is in one direction i.e. it is linear. While with the light energy it is not a problem, with nutrients it is as they do not have an extra-terrestrial source and so there is limited availability of nutrient ions in usable form. Therefore it is important for elements like carbon, nitrogen and phosphorus to be recycle. So their flow is mostly cyclic rather than linear.

All nutrients cycles follow this basic sequence:1) Nutrient is taken up by producers as inorganic ions 2) The producers incorporate the nutrient into complex organic molecules3) The consumer ingest the nutrient by eating the producer4) The nutrient passes along the food chain when the consumer is eaten by the next consumer

in the food chain5) When producers and consumers die, their complex molecules are broken down by

saprobiontic microorganisms who release nutrients in its original simple form. The saprobionts actions are vital for the cycle as they allow the nutrients to be released and therefore reused.

Nitrogen cycle Living organisms require nitrogen to manufacture proteins, nucleic acids and other nitrogen-containing compounds. Only few organisms can use nitrogen gas directly from the atmosphere (which consists of 78% of nitrogen). Plants take up nitrogen in a form of nitrate ions (NO3

-) by active transport from the soil. Consumers obtain nitrogen-containing components by eating and digesting plants. Nitrate concentration is restored largely by recycling of nitrogen-containing compounds.

Four steps of nitrogen cycle:1) Ammonification – production of ammonia from organic nitrogen-containing compounds.

There include urea, proteins, nucleic acids and vitamins (found in faeces and dead organisms). Saprobiontic organisms, mainly fungi and bacteria, feed on faeces and dead

organisms and release ammonia. It is then forms ammonium ions in the soil. Nitrogen returns as a non-living component.

2) Nitrification – bacteria using light energy converts ammonium ions to nitrate ions. This is an oxidation reaction and so releases energy. First ammonium ions are oxides to form nitrite ions (NO2

-); then nitrite ions are oxidised to form nitrate ions (NO3

-). 3) Nitrogen fixation – process in which nitrogen gas is converted into nitrogen containing

compounds. Free-living nitrogen-fixing bacteria reduce gaseous nitrogen to ammonia, use it to manufacture amino acids, and then release it when they die and decay. Mutualistic nitrogen-fixing bacteria live in nodules on the roots of plants, like peas and beans, obtaining carbohydrates from the plant while the plants gains amino acids from bacteria.

4) Denitrification – anaerobic denitrifying bacteria converts soil nitrates into gaseous nitrogen. This reduces the availability of nitrogen-containing compounds for plants. This occurs when soil is waterlogged (not enough air spaces/aerated or bad drainage of water) which reduces the amount of aerobic nitrifying and nitrogen-fixing bacteria and increases the amount of anaerobic denitrifying bacteria.

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Phosphorus cycle

Phosphorus is a component of ATP, phospholipids and nucleic acids. - The main reservoir of phosphorus is in mineral form. It is found mainly in a form of

phosphate ions (PO43-) in sedimentary rock deposits. They have origin in the sea and are brought to the surface by geological uplifting of rocks. Weathering and erosion dissolves phosphate ions and allows them to be absorbed by plants.

- The ions are passed to consumers who ingest these plants. Excess phosphate ions are excreted and may accumulate in waste materials.

- When plants and animals die, they are decomposed by certain bacteria and fungi and released into water or soil. Some phosphate ions remain in parts of animals, like bones or shells, and are very slow to breakdown.

- Phosphate ions in excreta (waste matter e.g. faeces and urine), decomposed and dissolved out of rocks, are transported by streams and rivers into lakes and oceans where they form sedimentary rocks.

Mycorrhizae – associations between certain types of fungi and roots of most plants. The fungi acts like the extensions of roots, increasing the total surface area of absorption of minerals and water. It also acts like a sponge, containing water and in minerals useful for times when there is lack of it, e.g. in drought. In return, it gains sugars and amino acids from the plants.

Fertilisers

Agricultural ecosustems increase the efficiency of energy transfer along human food chains. In doing so they improve productive, which includes the use of fertilisers. Fertilisers contain mineral ions essential for the plant. In natural ecosystems, the minerals that are removed from the soil are returned when the plant dies and is decomposed by microogranisms. In agricultural ecosystem this does not happen, as the plants are harvested and transported. So the concentration of mineral ions will fall and will become the limiting factor of plant gownth and therefore productivity. Fertilisers provide these mineral ions.

There are two types:- Natural (organic) fertilisers – consist of dead and decaying remains of plants and animals as

well as animal wastes, like manure, slirry and bone meal. - Artificial (inorganic) fertilers - mined from rocks an reposits and the converted into

different forms, blended to gether to give appropriate balance of minerals for a particular crip. Compounds of nitrogen, phosphorys and potassium are always presend.

Researchers suggests that a combination of natural and artificial fertilisers gives the greatest long-term increase in productivity. An approprate amount of minerals must be given, as there is a point when an increase of quantity of fertiliser no longer results in increased productivity.

Nitrogen is essential compoent of amino acids, ATP and nucleotides in DNA. All of these are needed for plant growth, making them more likely to develop earlier, grow taller and have a greater leaf area. So increases the rate of photosynthesis and improves crop productivity. Nitrogen-containing fetriliers have helped to provide cheaper food, mostly due to larger amount of nitrogen. However, nitrogen-containing fertilisers have detrimental effects:

- Reduces species diversty, as nitrogen rich soils favours growth of grasses, nettles and other rapidly growing species.

- Leaching, which may lead to pollution of watercourses- Eutrophication, caused by leaching of fertilers into waercourses.

Leaching – process by which nutrients are removed from the soil. Rainwater will dissolve soluble nutrients, like phosphate and nitrate ions (though as phosphate ions are less soluble they are less likely to be leached than nitrate ions), and carry them deep into the soil, eventually beyond the reach of the plant. The leached ions will be carried into freshwater lakes. Effects:

- Harmful for consumption of water, as high nitrate concenrtation can prevent efficient oxygen tranport in babies and there a link to stomach cancer.

- Can cause eutrophication.

Eutrophication – process by which nurtients concentrations increase in bodies of water. It occurs mostly in freshwater lakes and lower reaches of rivers. It can be caused by other things like manures, slurry, human sewage, ploughing olf grassland and natural leaching, but leaching of artificial fertilisers is the main cause. Sequence of events:

1) Most lakes and rivers have naturally very low concntration of nitrate, which becomes the limiting factor for plant and algal growth.

2) If nitrate concentration increases due to leaching, there is an increase in plants and algal growth as this limiting factor is removied.

3) Algal bloom occurs, when upper layers of water become desnely populated with algae (as most algae grow at the surface).

4) Algae layer absrobs light and prevents in from penetrating lower depths. 5) The light becomes the limiting factor for plants growth and algae that live at lower depth,

and eventually die. 6) This provides food for saprobiontic bacteria, and as this is no longer their limiting factor,

their populations gorw. 7) This bacteria require oxygen for respiration, creating an increased demand for oxygen. Its

concentration is reduced. 8) Oxygen becomes the limiting factor of aerobic orgaisms, like fish. These organisms

ultimateley die. 9) The dead organisms, like plants and fish are broken down by saprobiontic bacteria,

releasting nitrates. As also anaerbobic organisms grow, due to lack of oxygen, they also release toxic waste like hydrogen sulphid, which make the water putrid/rotten/moldy.