The relative energy values of carbohydrates, lipids, and proteins as respiratory substrates differ significantly due to the nature of the chemical bonds storing energy within their structures. Carbohydrates are primarily composed of glucose, a simple sugar. Glucose contains numerous C-H and C-C bonds, and the glycosidic bonds that link glucose molecules together. These bonds store potential energy. During respiration, these bonds are broken, releasing energy. The high number of these bonds in glucose means a large amount of energy can be released through their breakdown.

Lipids, such as fats and oils, are primarily composed of glycerol and fatty acids. Fatty acids contain many C-H and C-C bonds, and triglycerides contain ester bonds. Ester bonds are stronger than glycosidic bonds in carbohydrates, and the number of C-H bonds in fatty acids is substantial. This results in lipids storing a considerable amount of potential energy. However, the strength of the ester bonds means that less energy is released per gram of lipid compared to carbohydrates. The energy yield is also affected by the degree of saturation of the fatty acids; saturated fats yield more energy than unsaturated fats due to fewer double bonds.

Proteins are composed of amino acids linked by peptide bonds. Peptide bonds are very strong covalent bonds. The energy stored in peptide bonds is less than that stored in glycosidic or ester bonds. Furthermore, proteins often contain significant amounts of hydrogen bonds, which require energy to break. Therefore, proteins yield the least amount of energy per gram when respired. The complex structure of proteins also means that the breakdown process is more energetically demanding.

In summary, the energy yield is related to the number and strength of the bonds that are broken during respiration. Carbohydrates have a high number of relatively weaker bonds, lipids have a large number of stronger bonds, and proteins have a smaller number of very strong bonds. This explains the order of energy yield: carbohydrates > lipids > proteins.

The respiratory quotient (RQ) is significant because it provides information about the type of fuel being used for respiration and, consequently, the amount of energy being released. The RQ is the ratio of CO₂ produced to O₂ consumed.

A RQ of 1 indicates that glucose is being fully oxidized (aerobic respiration), producing CO₂ and water. A RQ of 0.7 indicates that fat is being respired (aerobic respiration), which is less fully oxidized than glucose and produces less CO₂. A RQ of 0.8 indicates that protein is being respired (aerobic respiration), which is the least fully oxidized and produces the least CO₂.

The RQ relates to the level of oxidation of the fuel. Higher RQ values (closer to 1) indicate a more fully oxidized fuel source (like glucose), while lower RQ values (closer to 0) indicate a less fully oxidized fuel source (like protein). This difference in oxidation state directly affects the amount of CO₂ produced.

ATP synthesis occurs through two primary mechanisms: substrate-linked reactions and chemiosmosis.

Substrate-linked reactions (or photophosphorylation in chloroplasts): This process involves the direct transfer of a phosphate group from a high-energy substrate to ADP, forming ATP. This occurs in the cytoplasm of prokaryotes and in the stroma of chloroplasts. The energy released from the phosphorylation reaction is used to drive other cellular processes. The key principle is the direct chemical bond formation between ADP and phosphate, requiring an enzyme to catalyze the reaction.

Chemiosmosis (in mitochondria and chloroplasts): This mechanism involves the movement of protons (H+) across a membrane, creating an electrochemical gradient. This gradient stores potential energy, which is then used by ATP synthase to phosphorylate ADP. In mitochondria, the proton gradient is established by the electron transport chain during aerobic respiration. In chloroplasts, the proton gradient is established during the light-dependent reactions of photosynthesis. The key principle is the use of a proton motive force to drive ATP synthesis.