Respiration & Photosynthesis

ATP is the immediate source of energy used by all cells to drive their metabolic reactions. 

ATP is a nucleotide. These are nitrogen containing organic substances. ATP occurs as a single molecule (mononucleotide). ATP is made from 3 types of molecules:

• Adenine - a nitrogen containing organic base (Adenine+Ribose=Make adenosine)
• Ribose - a 5-carbon sugar
• 3 phosphate groups

Breakdown of ATP. Hydrolysed=breakdown by the addition of water.

• Useful energy is mainly stored in the phosphate-phosphate bonds of the ATP molecule, between the 2nd and 3rd phosphate groups. 
• This is because the covalent bond linking these phosphate groups is unstable and easily broken by the enzyme ATPase in a HYDROLYSIS reaction.
• When this happens a phosphate group is removed, ENERGY IS RELEASED and ATP becomes ADP (Adenosine diphosphate) 

Synthesis of ATP. 

• ATP is synthesised by the addition of ADP to an inorganic phosphate, a reaction catalysed by the enzyme ATP synthase. 
• Addition of a phosphate molecule is known as PHOSPHORYLATION. This involves the removal of a molecule of water, so is a CONDENSATION reaction.
• ATP synthesis requires input of energy from a metabolic process. 

Photophosphorylation 

• Takes place in plant cells during the reactions of photosynthesis 
• Light dependent reaction
• ATP generated in chloroplast on thylakoid membranes

Oxidative phophorylation

• Occurs in the mitochondria of plant and animal cells during the process of electron transport
• Most ATP generated by this process
• Takes place at the end of respiration in cristae of mitochondria 

Substrate level phosphorylation 

• Occurs when phosphate groups are transferred from donor molecules to ADP to make ADP
• Glycosis and Krebs cycle

• ATP not a good long term energy store due to the INSTABILITY of its phosphate bonds.
• Cells can maintain only a few seconds supply.
• ATP is therefore the IMMEDIATE ENERGY SOURCE.
• This is not a problem as ATP is rapidly reformed from ADP and inorganic phosphate (Pi). The reactions are reversible.  

ATP CYCLE:

ATP is much more useful than glucose as an immediate source of energy because:

• Breakdown of ATP to ADP+Pi = SINGLE REACTION, making energy IMMEDIATELY available. Breakdown of glucose is complex involving several stages
• ATP can transfer its phosphate group to other molecules, PHOSPHORYLATING them and MAKING THEM MORE REACTIVE
• ATP is SOLUBLE and easily moved around inside cells, but cannot pass through cell membranes
• Breakdown of a molecule of ATP releases a SMALL AMOUNT OF ENERGY, ideal for fuelling the energy requiring reactions which occur in the cell. The breakdown of a molecule of glucose may produce more energy than is required at one time (inefficient - a lot of the energy would be wasted as heat)
• ATP can be reformed from ADP+Pi

ATP has a large number of roles in the metabolism of the cell.

ACTIVE TRANSPORT

• Energy is required to move substances AGAINST the concentration gradient using CARRIER proteins in plasma membranes.
• These protein pumps are also ATPase enzymes, since they catalyse the splitting of ATP to ADP+Pi, and use the energy released to change shape and pump the molecule.

EXOCYTOSIS 

• Energy is required to make vesicles, which are membrane-bound spheres synthesised by golgi appartus/body and used to package large molecules prior to SECRETION from cells.
• Energy is also required for the reverse process (ENDOCYTOSIS) used to bring large molecules INTO the cell.

SYNTHESIS OF SUBSTANCES (BIOSYNTHESIS)

• Energy is required to make large molecules (polymers) from smaller ones (monomers) E.g. Synthesis of proteins from condensation of amino acids

CELL DIVISION

• Energy required for synthesis of new DNA molecules (by DNA replication) prior to cell division.
• Mitosis and meiosis also require ATP (e.g. for spindle function).

MOVEMENT (MUSLCE CELLS ONLY)

• Energy required for muscle contraction - Require large amounts of energy

GLYCOLYSIS

• A phosphate molecule is transferred from ATP to glucose in the first stage of respiration.
• This makes it more reactive and provides the energy needed to begin the reactions of respiration.

• Respiration occurs in all living cells. It's a series of ENZYME CONTROLLED REACTIONS, which release energy from organic molecules. 
• Energy released during respiration is transferred to ADENOSINE TRIPHOSPHATE (ATP). 
• ATP is the immediate short-tern source of energy in cells. During respiration energy in the form of heat is also released.

The reactions are REDOX reactions (OILRIG)

Reduction:

• Gain of electron
• Gain of hydrogen
• Loss of oxygen

Oxidation

• Loss of electron
• Loss of hydrogen
• Gain of oxygen

Glucose + Oxygen --> Carbon Dioxide + Water + ATP

Aerobic respiration occurs in 3 main stages: 

• Glycolysis
• The link reaction and Kreb's cycle
• Oxidative phosphorlyation 

Any factors that affect ENZYME ACTIVITY (e.g. temp & pH) will also affect the RATE of respiration

Molecules called COENZYMES (e.g. NAD & FAD) have an important role in the respiration reactions. 

Coenzymes are small organic molecules that can bind to enzymes and help them function. 

COENZYMES ARE NOT THEMSELVES ENZYMES.

NAD+FAD are dinucleotides (2 nucleotides joined together). Allow reactions to occur. Bind to H atoms so become reduced. NAD + FAD is a double nucleotide.

Takes place in CYTOPLASM of the cell, NOT mitochondria. Also does NOT require Oxygen & only needs a bit of ATP.

It's known as the COMMON PATHWAY as it takes place as part of aerobic AND anaerobic resp. 

Reactions of glycolysis can be summarised as:

• Glycolysis starts with the ACTIVATION OF GLUCOSE BY ATP. This makes the glucose more reactive. The glucose (6C molecule) is converted into a number of intermediates and finally into TWO molecules of PYRUVATE (each containing 3C atoms)
• These reactions are OXIDATION reactions as HYDROGEN IS REMOVED, i.e. oxidation by dehydrogentation
• The COENZYME NAD (nicotinamide adenine dinucleotide) is able to carry the pair of hydrogen atoms removed during glycolysis, thus becoming REDUCED in the process. This is shown by the equation: 

NAD   + 2H ----> NADH + H

GLYCOLYSIS RESULTS IN A NET GAIN OF ATP AND OF THE COENZYME REDUCED NAD.

This is substrate level phosphorylation

The pyruvate produced in glycolysis moved from the cytoplasm into the matrix of the mitochondria by active transport.

These reactions take place in the MATRIX OF THE MITOCHONDRIA. They will NOT occur in anaerobic conditions. 

The link reaction links glycolysis to the Krebs' cycle. (Carbon Dioxide is formed in this process)

• In the link reaction, pyruvate combines with COENZYME A to produce ACETYL-COENZYME A. This reaction involves the loss of 1 molecule of CO2 per pyruvate.
• Also an OXIDATION reaction & hydrogen that's lost is used to reduce NAD.
• Products: 2x reduced NAD & 2x CO2
• Acetyl has 2 Carbons
   

The acetyl coenzyme A enters the Kreb's cycle. Kreb's cycle:

• Acetyl coenzyme A is effectively a 2 carbon compound. It is fed into Kreb's cycle where it combines with a 4 carbon compound to produce a 6 carbon compound.
• The 6 carbon compound loses carbon dioxide. It also loses hydrogen in a series of oxidation reactions to produce the 4 carbon compound again.
• The hydrogen atoms given off are used to reduce coenzymes such as NAD
• A single molecule of ATP is produced by substrate level phosphorylation 
• The 4 carbon molecule can now combine with a new molecule of acetyl coenzyme A to begin the cycle again

The final stages of aerobic respiration occurs on the INNER MITOCHONDRIAL MEMBRANE which folds to form CRISTAE. It's here that the enzymes and electron transport proteins needed to synthesise most of the ATP are found. 

• Hydrogen is removed from the reduced NAD & FAD molecules produced during glycolysis, the link reaction & Kreb's cycle. The NAD & FAD are now oxidised (lose H atoms) and recycled in the process. 
• The hydrogens are split into electrons and hydrogen ions (protons):

2H atom ----> 2H+    + 2e-

• The electrons are transferred to the first molecule (protein) in the electron transport chain. They are then passed from one electron transport molecule to the next in a series of redox reactions: each carrier becomes reduced when it receives an electron, then reverts to its oxidised state when the electron is passed on. The electrons lose energy as they pass down the chain.
• This energy is used to actively pump the protons through the inner mitochondrial membrane.
• The protons accumulate in the space between the 2 mitochondrial membranes so that a steep conc. gradient builds up between here and the matrix of the mitochondria.

• The protons can only diffuse back into the matrix through special protein carriers known as stalked particles. These contain the enzyme ATP synthase.
• As the protons pass through the stalked particles, enough energy is released to allow the enzyme to attach inorganic phosphate groups to ADP molecules (Pi) to form ATP in a process described as OXIDATIVE PHOSPHORYLATION.
• During the electron transport chain, each reduced NAD molecule releases enough energy to produce 3 molecules of ATP. Each reduced FAD molecule releases enough energy to produce 2 molecules of ATP. 
• There's a difference in the number of ATPs produced because the reduced FAD enters later in the chain. Fewer H+ ions are transported, less ATP is produced. 
• The role of oxygen in this process is that it's the terminal electron acceptor at the end of the chain. (It combines with e- & H+ to make H2O)

1/2 O2 + 2H+  + 2e- ---> H2O

• In the absence of oxygen, the electrons & protons would 'back up' along the chain. The e- can't be passed through the chain if there's no oxygen to accept them. The reduced NAD & FAD would no longer be able to offload their Hydrogen & would not be recycled. This causes the Kreb's cycle to stop. Cells have a temp way out of this - anaerobic respiration.

• Reduced coenzyme releases its hydrogen, which becomes a proton and electron. Coenzyme returns to matrix to pick up more hydrogen
• The electron is passed along the electron transport chain in the inner mitochondrial membrane, releasing energy as it goes
• The energy is used to pump protons into intermembrane space
• Protons pass back into the matrix through ATP synthase enzyme
• Energy used to combine ADP and Pi to make ATP
• Oxygen acts as the terminal electron acceptor in the electron transport chain, combining with the electrong and proton to make water

Last electron acceptor/H+ ion acceptor is oxygen. Without oxygen everything backs up and respiration won't take place.

Oxygen combinesw with e- & H+ to form H2O.

NADH produces H+ . It splits to = H+ & e-         H --> H+ + e-

38 molecules of ATP are produced within a cell (net production) when one molecule of glucose is completely oxidised.

ATP Tally:

• 30 molecules of ATP produced following oxidation of 10 NADH molecules. 1 NAD=3 ATP
• 4 molecules of ATP produced following oxidation of 2 FADH molecules. 1 FAD=2 ATP
• 34 molecules produced by oxidative phosphorylation.
• 6 molecules of ATP produced by substrate level phosphorylation.
• 2 molecules of ATP used during glycolysis.
• 38 total net number of ATP molecules produced as a result of complete oxidation of one molecule of glucose.

• Inner mitochondrial membrane contains the electron transport chain. Cristae (folds) increase the surface area to make more ATP.
• Matrix contains the enzymes required for catalysis of the link reaction and Kreb's cycle.
• Outer member controls the movement of materials in and out of the mitochondrian.
• DNA (circular) and ribosomes (70S) allow mitochondrian to do protein synthesis.

Anaerobic respiration yields LESS ATP but glucose break down/turn over is FASTER

In the absence of oxygen neither Krebs cycle nor the electron transport chain can take place, leaving only glycolysis as a potential source of ATP.

For glycolysis to continue in the absence of oxygen:

• the pyruvate produced must be removed
• the reduced NAD produced must be oxidised and recycled so that it is available to accept further hydrogen

Reduced NAD --------------------> NAD

Animal cells do this by converting pyruvate to lactate. This reaction uses reduced NAD/NADH, oxidising it to NAD once more, so that it's available for use in glycolysis.

Plant cells and yeast cells have different solution to the problem. They convert the pyruvate to ethanol and carbon dioxide. The result is similar, pyruvate is removed and NAD is regenerated.

• 38 molecules of ATP can be produced from a single molecule of glucose in aerobic respiration (net production)
• Anaerobic respiration produced 2 molecules of ATP as it relies on glycolysis to produce the ATP.
• Anaerobic respiration produces such a small amount of ATP that it can only fuel our cells for a very short period of time. The lactate/lactic acid produced is toxic, reducing pH of cells and therefore affecting enzyme activity. In muscle cells it can cause fatigue and cramp. However, the rate of turnover of glucose is high(so it's produced quickly)

Main point of anaerobic respiration:

To regenerate NAD so that glycolysis can continue. This will allow a small amount of ATP to be made in the absence of Oxygen.

• The energy we used has been captured by photosynthesis from sunlight. It also produces the oxygen we breathe by releasing it from water molecules. 
• Photosynthesis is a process in which light energy is used in the synthesis of organic molecules, such as glucose. 
• Photosynthesis is a series of enzyme catalysed reactions, and therefore any factor that affects enzyme activity will affect the rate of photosynthesis. 
• Photosynthesis takes place in the chloroplasts of cells in the leaves and other green parts of plants.
• The reactions involve the absorption of light by the pigment chlorophyll.
• Algae and cyanobacteria are also able to photosynthesise to make food. 
• The organisms then respire some of the food they make to provide them with energy for metabolic processes. 
• Excess food can be stored or used to make other substances such as cellulose, proteins, lipids etc, which are used for growth. 
• Photosynthesis: 6CO2 + 6H20 ------------------------> 6O2 + C6H12O6
• The reactions of photosynthesis occur in two distinct stages (both in chloroplasts): light dependent reactions (light) & light-independent reactions (dark-can occur in light)

The light dependent reactions involve the capture of light energy which is used for 3 purposes:

• To add inorganic phosphate molecule (Pi) to ADP, thereby making ATP. ADP+Pi -> ATP
• To split water into H+ ions (proton) and electrons. As the splitting is caused by light it is known as PHOTOLYSIS.
• To excite electrons in chlorophyll. 

The reactions occur on the thylakoid membranes of the chloroplasts, which contain tightly-packed chlorophyll molecules.

• When light falls on the chlorophyll molecules, a pair of electrons in the molecules gain energy, i.e. they become excited. The electrons become so energy that they leave the chlorophyll molecule and are taken up by a molecule called an electron carrier. 
• The electrons are now passed along a series of electron carriers in a series of REDOX reactions. The electron carriers form an electron transport chain located in the membranes of the thylakoids. 
• Each new carrier is at a slightly lower energy level than the previous one so that the electrons lose the energy they gained from light at each stage. 
• This energy is used to combine an inorganic phosphate molecule with ADP to make ATP, in a process called photophosphorylation. 
• At the same time a molecule of water is split into hydrogen ions (protons), electrons and oxygen in a process known as photolysis: 

H2O ------->2e- + 2H+   + 1/2 O2 

OXYGEN WASTE PRODUCT/USED IN RESPIRATION

• The electrons produced by photolysis are used to replace those lost from chlorophyll, allowing it to continually absorb light energy. 
• The protons produced by photolysis react with the oxidized coenzyme NADP, along with the electrons released at the end of the electron transfer chain to form reduced NADP.
• The oxygen produced by the photolysis of water is either used in respiration or diffuses out of the leaf as a waste product of photosynthesis. 

The ATP and reduced NADP formed by the light-dependent reactions provide the energy and the hydrogen necessary to form carbohydrate in the light-independent reactions.

• Unlike the first stage of photosynthesis, this stage does not require light directly. 
• In practice however, it soon stops in the absence of light as it requires the products of the light dependent reactions, ATP and reduced NADP.
• The ATP and reduced NADP are now used to reduce carbon dioxide from the atmosphere, building it into carbohydrates. 
• The light independent reactions occur in the STROMA of the chloroplast, and are catalysed by enzymes. 
• They are often referred to as the Calvin cycle: 

• In these reactions CO2 combines with a 5 carbon molecule called ribulose biphosphate (RuBP) to form 2 molecules of the 3 carbon compounds, glycerate-3-phosphate (GP).
•  In the next stage the ATP and the reduced NADP produced in the LDR's is used to reduce the glycerate-3-phosphate (GP) to triose phosphate (TP).
• The ATP provides the necessary energy for this reaction (i.e. it activates GP) and the reduced NADP provides the hydrogen for the reduction reaction.
• The NADP is reformed and goes back to the LDP's to be reduced again by accepting more hydrogen. 
• Some (about one-sixth) of the triose phosphate is converted into carbohydrates such as glucose, sucrose, starch or cellulose. 
• The rest of the triose phosphate (about five-sixths) is used to regenerate RUBP, using ATP from the LDR. ATP is required as it supplies the phosphate ncessary to convert ribulose phosphate into rublose biphosphate. 

CALVIN CYCLE = part of photosynthesis

KREBS CYCLE = part of respiration

LDR:

• Occur in thylakoids 
• Chlorophyll in the thylakoids absorb light energy
• Grana increase efficiency of LDR by capurting as much light as possible

LIR:

• Stroma contains most enzymes for LIR
• Outer membrane control movement in and out of chloroplast

Environmental factors that affect rate of PS:

• light intensity
• temp
• CO2 conc. 

If one of these factors falls below a certain level, it will start to limit the rate of photosynthesis. Although temp, co2 and light may all affect rates of photosynthesis, only the one that is in shortest supply will limit the rate at any particular point in time. This factor is called the limiting factor. The rate of photosynthesis can be increased by increasing that factor. 

Light intensity

• As light increases, rate of photosynthesis also increases. 

Temperature 

• When light intensity is high, increasing temperature will have a significant effect on the rate of photosynthesis. 
• Between 10 - 35 degrees, a 10 degree rise in temp will double the rate of photosynthesis. 
• Increasing temp increases the rate of photosynthesis as enzymes work faster - more kinetic energy, more collisoons and so more enezyme substrate complexes form. 
• If photosynthesis starts to decline it would be due to the temp going above the optimum temp of the enzymes. Enzymes denature, hydrogen bonds break and this changes the tertiary structure.

CO2 usually makes up only 0.04% of the volume of the air. This is lower than the optimum value (0.1%) for photosynthesis. This means that co2 conc. will often be the limiting factor, particularly in tropical areas where temp and light intensity are high. 

co2 is needed for photosynthesis.

Knowledge of limiting factors can enable growers to increase the yield of crops grown in glasshouses. The costs of maintaining optimum temp, light intensity and CO2 conc. need to be outweighed by the greater income from the crop. 

Benefits of producing crops in glasshouses in UK:

• Can control temp/light intensity/co2 conc.
• Soil replaced with mineral solution - removing soil means no risk of soil organisms causing disease.

Growers need to control possible limiting factors inside commercial glasshouses. The faster the rates of photosynthesis, the more carbohydrates the plants can make. The more carbohydrates made. the more energy and materials are available for growth and fruit formation.

How each factor could be controlled:

1) Light intensity 

• Artificial lighting
• Specific wavelengths used

2) Carbon dioxide conc.

• Pump CO2 into glasshouse
• Use paraffin heaters
• Ventilation

3) Temperature

• Glass - stops heat escaping
• Optimal temp achieved - heating/cooling mechanisms

At ideal temps for photosynthesis, water loss by transpiration is likely to be high. Excessive water loss can lead to plants closing their stomata to limit this loss. This means that carbon dioxide would not be able to enter the leaves and rates of photosynthesis would be dramatically reduced. Growers need to ensure plants have plenty of water and many glasshouses have automatic watering systems with sprinklers and humidifiers. 

How will a humidifer ensure plants have plenty of water?

• Increase amount of water vapour in air (in glasshouse)
• Increases water potential gradient (between leaves and air)

All of the above factors can be controlled by computers. Sensors are used to monitor the level of each factor.

There are costs involved in controlling the environment and these are only worthwhile if the increased yield produced enough profit to exceed these costs. A grower will try to achieve an optimum tield to balance out these factors.