(a) Respiration and Combustion

The essential point: the equations are identical, but the path is what matters. The cell's strategy is to catabolise glucose so that not all the liberated energy goes out as heat, which requires oxidising it in small steps rather than one.

(b) Glycolysis and Krebs' cycle

(c) Aerobic respiration and Fermentation

Respiratory substrates are the organic compounds that are oxidised during respiration to release energy — that is, the molecules a cell feeds into the respiratory pathway as fuel.

The most common respiratory substrate is glucose. The chapter states that glucose is the favoured substrate for respiration, and that all carbohydrates are usually first converted into glucose before they are used for respiration.

Other respiratory substrates, and where each enters:

• Fats — first broken down into glycerol and fatty acids. Fatty acids are degraded to acetyl CoA and enter there; glycerol enters after being converted to PGAL.
• Proteins — degraded by proteases; the individual amino acids, after deamination, enter (depending on their structure) at some stage within Krebs' cycle, or even as pyruvate or acetyl CoA.

One caution to add: in living organisms, respiratory substrates are often more than one; pure proteins or fats are never used as respiratory substrates.

Points to write alongside the scheme:

• Site: cytoplasm; present in all living organisms; a chain of ten reactions under the control of different enzymes.
• ATP used at two steps: glucose → glucose-6-phosphate (by hexokinase) and fructose-6-phosphate → fructose-1,6-bisphosphate.
• NADH formed at one step: PGAL → BPGA, where two hydrogen atoms are transferred to NAD⁺.
• ATP formed at two steps: BPGA → PGA, and PEP → pyruvic acid — each twice per glucose.
• Net result per glucose: 2 pyruvic acid, 2 ATP net (4 gross − 2 used), 2 NADH + H⁺, and no CO₂.
• In plants the glucose comes from sucrose, split by invertase into glucose and fructose, or from storage carbohydrates.

Aerobic respiration is the process that leads to a complete oxidation of organic substances in the presence of oxygen, releasing CO₂, water and a large amount of the energy present in the substrate.

The two crucial events, as the chapter states them, are:

• the complete oxidation of pyruvate by the stepwise removal of all the hydrogen atoms, leaving three molecules of CO₂;
• the passing on of the electrons removed as part of the hydrogen atoms to molecular O₂, with simultaneous synthesis of ATP.

The main steps, in order, with their sites:

The overall location: aerobic respiration begins in the cytoplasm with glycolysis, but the aerobic steps proper take place within the mitochondria — the first process in the matrix and the second on the inner membrane. This is why the mitochondrion is called the powerhouse of the cell.

Points to write alongside the scheme:

• The cycle starts with the condensation of the acetyl group with oxaloacetic acid (OAA) and water to yield citric acid, catalysed by citrate synthase, with a molecule of CoA released.
• Citrate is isomerised to isocitrate, followed by two successive decarboxylations giving α-ketoglutaric acid and then succinyl-CoA.
• During the conversion of succinyl-CoA to succinic acid a molecule of GTP is synthesised — a substrate level phosphorylation; in a coupled reaction GTP → GDP with simultaneous synthesis of ATP from ADP.
• There are three points where NAD⁺ is reduced to NADH + H⁺ and one point where FAD⁺ is reduced to FADH₂.
• Continued operation requires continued replenishment of OAA and regeneration of NAD⁺ and FAD⁺.

Summary equation (which also covers the link reaction, so it starts from pyruvic acid):

Definition. The electron transport system (ETS) is the metabolic pathway through which the electron passes from one carrier to another, and it is present in the inner mitochondrial membrane.

Its purpose. The steps of the respiratory process that follow the Krebs' cycle serve to release and utilise the energy stored in NADH + H⁺ and FADH₂. This is accomplished when they are oxidised through the ETS and the electrons are passed on to O₂, resulting in the formation of H₂O.

The carriers, in sequence:

• Complex I — NADH dehydrogenase. Electrons from NADH produced in the mitochondrial matrix during the citric acid cycle are oxidised here and transferred to ubiquinone, located within the inner membrane.
• Complex II. Ubiquinone also receives reducing equivalents via FADH₂, generated during the oxidation of succinate in the citric acid cycle.
• Complex III — cytochrome bc₁. The reduced ubiquinone (ubiquinol) is oxidised, with transfer of electrons to cytochrome c.
• Cytochrome c is a small protein attached to the outer surface of the inner membrane, acting as a mobile carrier between complexes III and IV.
• Complex IV — cytochrome c oxidase complex, containing cytochromes a and a₃ and two copper centres.
• Complex V — ATP synthase. As electrons pass from one carrier to another via complexes I to IV, they are coupled to ATP synthase for the production of ATP from ADP and inorganic phosphate.

The yield. The number of ATP molecules synthesised depends on the nature of the electron donor — oxidation of one NADH gives 3 ATP, while one FADH₂ gives 2 ATP (because FADH₂ joins at complex II and bypasses complex I).

The role of oxygen. Although aerobic respiration takes place only in the presence of oxygen, the role of oxygen is limited to the terminal stage. Yet its presence is vital, since it drives the whole process by removing hydrogen from the system. Oxygen acts as the final hydrogen acceptor and is reduced to water.

The ATP synthase. Complex V consists of F₁, a peripheral membrane protein complex containing the site for synthesis of ATP from ADP and inorganic phosphate, and F₀, an integral membrane protein complex forming the channel through which protons cross the inner membrane. For each ATP produced, 4H⁺ pass through F₀ from the intermembrane space to the matrix down the electrochemical proton gradient.

(a) Aerobic respiration and Anaerobic respiration

(b) Glycolysis and Fermentation

(c) Glycolysis and Citric acid cycle

Calculations of the net gain of ATP for every glucose molecule oxidised can be made only on four assumptions:

• There is a sequential, orderly pathway functioning, with one substrate forming the next, and with glycolysis, TCA cycle and ETS pathway following one after another.
• The NADH synthesised in glycolysis is transferred into the mitochondria and undergoes oxidative phosphorylation.
• None of the intermediates in the pathway are utilised to synthesise any other compound.
• Only glucose is being respired — no other alternative substrates are entering the pathway at any of the intermediary stages.

Why the question matters. These assumptions are not really valid in a living system: all pathways work simultaneously and do not take place one after another; substrates enter the pathways and are withdrawn from them as and when necessary; ATP is utilised as and when needed; and enzymatic rates are controlled by multiple means. The calculation therefore remains only a theoretical exercise — but a useful one, because it lets us appreciate the beauty and efficiency of the living system in extraction and storing of energy. On these assumptions, there can be a net gain of 38 ATP molecules during aerobic respiration of one molecule of glucose.

The traditional view. Since respiration involves breakdown of substrates, the respiratory process has traditionally been considered a catabolic process and the respiratory pathway a catabolic pathway. But is this understanding correct?

Where substrates enter, if they are to be respired.

• Fats are broken down into glycerol and fatty acids; fatty acids are degraded to acetyl CoA and enter there, while glycerol enters after conversion to PGAL.
• Proteins are degraded by proteases, and the amino acids, after deamination, enter at some stage within Krebs' cycle, or even as pyruvate or acetyl CoA, depending on their structure.

The key recognition. It is these very compounds that would be withdrawn from the respiratory pathway for the synthesis of the said substrates. So:

• Fatty acids are broken down to acetyl CoA before entering the respiratory pathway when acetyl CoA is used as a substrate;
• but when the organism needs to synthesise fatty acids, acetyl CoA is withdrawn from the respiratory pathway for it.

Hence the respiratory pathway comes into the picture both during breakdown and synthesis of fatty acids. Similarly, during breakdown and synthesis of protein too, respiratory intermediates form the link.

The conclusion. Breaking down processes within the living organism is catabolism, and synthesis is anabolism. Because the respiratory pathway is involved in both anabolism and catabolism, it is better to consider the respiratory pathway as an amphibolic pathway rather than as a catabolic one.

A way to picture it. The pathway is not a one-way demolition chute but a junction: molecules arrive from several directions to be dismantled, and molecules are also pulled off the line part-finished to be built into fats, amino acids and other compounds. Acetyl CoA is the clearest single example — the same molecule is the doorway for burning a fat and the starting block for making one.

Definition. The respiratory quotient (RQ), also called the respiratory ratio, is the ratio of the volume of CO₂ evolved to the volume of O₂ consumed in respiration.

The RQ depends upon the type of respiratory substrate used during respiration.

Value for fats: less than 1 — and specifically 0.7 for the fatty acid tripalmitin, as calculated in the chapter:

For comparison: carbohydrates completely oxidised give RQ = 1 (6CO₂ / 6O₂), because equal amounts of CO₂ and O₂ are evolved and consumed; proteins give about 0.9.

Why fat gives a value below 1. A fat molecule is very rich in hydrogen and poor in oxygen, so a large volume of atmospheric O₂ must be consumed simply to convert all that hydrogen into water, while relatively less CO₂ is released. A small numerator over a large denominator gives a ratio well below one.

Caution to add. In living organisms respiratory substrates are often more than one; pure proteins or fats are never used as respiratory substrates, so any measured RQ is a mixture value.

Oxidative phosphorylation is the synthesis of ATP from ADP and inorganic phosphate at the inner mitochondrial membrane, using the energy released as electrons pass down the electron transport system to oxygen.

Why it carries that name. The chapter draws the contrast explicitly: unlike photophosphorylation, where it is the light energy that is utilised for the production of the proton gradient required for phosphorylation, in respiration it is the energy of oxidation-reduction utilised for the same process. It is for this reason that the process is called oxidative phosphorylation.

How it works, step by step.

• NADH + H⁺ and FADH₂ from glycolysis, the link reaction and the Krebs' cycle are oxidised through the ETS, and the electrons are passed on to O₂, resulting in the formation of H₂O.
• As electrons pass from one carrier to another via complexes I to IV, the energy released builds a proton gradient, protons accumulating in the intermembrane space.
• The electrons' passage is coupled to ATP synthase (complex V) for the production of ATP from ADP and inorganic phosphate, the mechanism being the chemiosmotic hypothesis studied in the earlier chapter.
• ATP synthase has F₁, a peripheral complex carrying the catalytic site for ATP synthesis, and F₀, an integral complex forming the proton channel. For each ATP produced, 4H⁺ pass through F₀ from the intermembrane space to the matrix down the electrochemical proton gradient.
• The yield depends on the donor: one NADH gives 3 ATP, one FADH₂ gives 2 ATP.

Distinguish it from substrate level phosphorylation, the other kind of ATP synthesis in respiration — for instance the GTP formed during the conversion of succinyl-CoA to succinic acid, which needs no membrane, no gradient and no electron transport.

The chapter's own statement of the principle is the core of the answer: the complete combustion of glucose yields energy most of which is given out as heat. If this energy is to be useful to the cell, it should be able to utilise it to synthesise other molecules that the cell requires. The strategy the cell uses is to catabolise the glucose molecule in such a way that not all the liberated energy goes out as heat. The key is to oxidise glucose not in one step but in several small steps, enabling some steps to be just large enough that the energy released can be coupled to ATP synthesis.

The specific advantages:

• Energy is captured in a usable chemical form. Small packets of energy can be coupled to the synthesis of ATP; one enormous release could not, and would simply be lost as heat.
• The cell is not damaged. A single-step oxidation would raise the temperature sharply and destroy enzymes, membranes and the cell itself. Respiration proceeds at ordinary cell temperature.
• The process can be regulated. With many steps, each under a different enzyme, enzymatic rates are controlled by multiple means, so the cell can speed up or slow down respiration to match demand — and ATP is utilised as and when needed.
• Useful intermediates become available. Because the breakdown passes through many compounds, those compounds can be withdrawn from the respiratory pathway for the synthesis of fats, amino acids and other molecules — which is exactly why the pathway is amphibolic. A single-step combustion would yield no intermediates at all.
• Energy is released as and when required, rather than all at once, so the cell is neither starved nor overwhelmed.
• Efficiency. The stepwise route allows a theoretical 38 ATP per glucose against the 2 ATP of the shortest anaerobic route.