Energy and Respiration

• During cellular respiration, glucose is broken down through a series of chemical reactions in the mitochondria to produce ATP.
• Energy is needed for moving substances across membranes against their concentration gradients, movement inside a cell or of an organelle and for anabolic reactions such as DNA replication and protein synthesis
• ATP is a good universal energy currency because it can be made wherever it is needed, it is hydrolysed quickly, it produces a good amount of energy, and it is relatively stable in a normal cell pH.
• ATP is synthesised when ADP combines with a phosphate or in a substrate-linked reaction where the energy is provided directly from another chemical reaction.
• Chemiosmosis is when a phosphate is added to ADP using energy released by the movement of hydrogen down the concentration gradient across a membrane in a chloroplast or mitochondria
• The main organic molecule used in respiration is glucose. Lipids are used once all glucose has been used, and finally amino acids are a last resort.
• Carbohydrates make 15.8kJg-1, lipids make 39.4kJg-1 and protein makes 17.0kJg-1.
• RQ (standing for respritory quotient) is the ratio of carbon dioxide to oxygen. RQ = moles of Co2 given out in unit time / Moles of O2 taken in per unit time.
• The equation for aerobic respiration is:

  C6H12O6 + 6O2 -> 6CO2 + 6H20
• Glycolysis occurs in the cytoplasm of the cell, the link reaction takes place in the mitochondrial matrix, the Krebs cycle takes place in the mitochondrial matrix, and oxidative phosphorylation takes place in the inner membrane of the mitochondria.
• Glycolysis is a series of steps when glucose (6 Carbons) is split into two pyruvate molecules (3 carbons). The first step is phosphorylation where phosphate groups move from ATP to glucose raising it's energy level. Two ATP are required for each glucose molecule. The first phosphate makes glucose phosphate which is rearranged into fructose phosphate, the second phosphate makes fructose 1,6 biphosphate.
• In the second steps of glycolysis fructose 1,6 biphosphate (6 Carbons) is broken down into two triose phosphate molecules (3 carbons). Hydrogen is removed from the triose phosphates and transferred to NAD to make oxidised triose phosphate and reduced NAD. Two reduced NAD are produced per glucose molecule. Triose phosphate is then converted into 2 molecules of pyruvate (with a few intermediates in between) and 2ATP, 2H and 2ATP (after the intermediates) are made. There is a net gain of 2 ATP.
• When oxygen is available, pyruvate is moved by active transport through the envelope of the mitochondria into the matrix to partake in the link reaction,
• In the link reaction, pyruvate is immediately decarboxylated and dehydrogenated by the enzymes in the matrix. The remained of the molecule bonds with coenzyme A (CoA) to produce acetyl CoA.
• A coenzyme is a molecule that is needed for an enzyme to catalyse a reaction without taking part themselves.
• The link reaction as an equation:

  Pyruvate + CoA + NAD -> acetyl CoA + CO2 + reduced NAD
• The Krebs Cycle begins when Acetyl CoA (2 carbons) combines with oxaloacetate (4 Carbons) to form citrate (6 Carbons). The citrate is decarboxylated and dehydrogenated in a series of steps. NAD and FAD accept the hydrogens released and CO2 is released as a waste gas. Oxaloacetate is regenerated to repeat the cycle. For each repeat 2 CO2 molecules are produced and one FAD and three NAD are made. The ATP made is made by phosphate from one of the substrates to ADP.
• Reduced NAD and Reduced FAD move from the matrix to the inner membrane where their hydrogens are removed. Reduced NAD can be made in the cytoplasm but can be easily moved to the matrix for transportation.
• Hydrogen atoms are split into protons and electrons in oxidative phosphorylation. The electron is transferred to the first in series of electron carriers. Energetic electrons release energy as they move down the electron transport chain (some of which is used to move protons between the inner and outer membranes from the matrix to produce a concentration gradient). Protons return to the matrix by facilitated diffusion through ATP synthase which provides energy for ATP synthesis (this is chemiosmosis). Oxygen is the final electron acceptor in a chain.
• The equation for oxygen at the end of the electron transport chain:

  O2 + 4H+ + 4e- -> 2H2O
• Mitochondria are surrounded by an envelope of two phospholipid membranes, the outer of is very smooth and the inner one very folded. The membrane folds are cristae and provide the membrane with a large surface area. The outer membrane is more permeable to small molecules so things like oxygen, carbon dioxide, ATP, ADP and Pi can diffuse through. The inner membrane is less permeable and covered in ATP synthase. It is the site of the electron transport chain and the proteins needed for it.
• With no oxygen (anaerobic respiration) there is nothing to accept the electrons at the end of the electron transport chain meaning the Krebs Cycle, oxidative phosphorylation and the link reaction all stop. ATP is only made by glycolysis like this as long as NAD can be oxidised.
• Ethanol fermentation, mainly occurring in yeast, plant tissues and other microorganisms, is when the hydrogen from reduced NAD is passed to ethanal (made from pyruvate) to form ethanol (C2H5OH) when reduced by the enzyme alcohol dehydrogenase.
• Lactate fermentation occurs in mammalian muscles and other microorganisms and pyruvate acts as the hydrogen acceptor which uses lactate dehydrogenase to convert it to lactate. Lactate can be oxidised to become pyruvate again but required extra oxygen which is gained in EPOC (excess post-exercise oxygen consumption) or can be stored as glycogen.
• The energy yield for aerobic respiration is higher than anaerobic as aerobic respiration uses oxidative phosphorylation and the Krebs cycle along with glycolysis which have a high ATP yield. Anaerobic just uses glycolysis.
• Rice is adapted to grow in flooded plains as it grows higher as the water level increase to ensure that the leaves are above the water level so that photosynthesis can occur. Rice can with stand a much higher level of ethanol than a regular plant and contains more ethanol dehydrogenase so the plant can use the ethanol to grow when oxygen levels are low.
• Unlike rice, plants typically cannot survive in water as the oxygen levels are too low to respire aerobically and the high levels of ethanol kill them as it is toxic. They also do not grow tall enough so they cannot photosynthesise in the water. Plants would especially struggle in a rice paddie where other microorganisms would fight for oxygen.
• The dye DCPIP (Dichlorophenolindophenol) or methylene blue don't damage cells and when reduced become colourless. They act as redox indicators. Hydrogen removal is essential in respiration and NAD and FAD usually pick up hydrogen molecules, but with added dye the dye can pick up hydrogen too making it more colourless. The rate of change of colour is the rate of respiration. Effect of temperature can be tested using a controlled water bath and substrate amount can be tested by adding more substrate in the suspension liquid.