Metabolism, Enzymes, and Cellular Respiration

Structure and Function

An enzyme's ability to function is highly specific, determined by its active site, a unique pocket where the reaction occurs. When a specific molecule, known as a substrate, binds to the active site, they form an enzyme-substrate complex.

Not all enzymes are functional on their own. Some consist of:

• Apoenzyme: The protein portion of the enzyme that is inactive without a helper.
• Cofactor/Coenzyme: Non-protein helpers (such as metal ions or organic molecules) that assist in catalysis.
• Holoenzyme: The complete, active form of the enzyme, consisting of the apoenzyme plus its required cofactor or coenzyme.

Regulation and Inhibition

Enzyme activity is sensitive to environmental factors like temperature and pH; each enzyme has an optimal range where it functions most efficiently. Furthermore, cells regulate metabolic pathways through inhibition:

• Competitive Inhibitors: These molecules compete with the substrate for access to the active site.
• Noncompetitive Inhibitors: These bind to a different part of the enzyme (an allosteric site), changing the enzyme's shape so the substrate can no longer bind effectively.
• Feedback Inhibition: A regulatory mechanism where the end product of a metabolic pathway acts as a noncompetitive inhibitor on an enzyme earlier in the pathway, preventing the overproduction of that product.

Energy Capture: Phosphorylation Pathways

Cells capture energy primarily by adding a phosphate group to ADP to create ATP. This process is called phosphorylation, and there are three main types:

1. Substrate-level phosphorylation: The direct transfer of a phosphate group from a substrate molecule to ADP.
2. Oxidative phosphorylation: The production of ATP using an electron transport chain (ETC) and the energy released from redox reactions.
3. Photophosphorylation: The production of ATP using light energy, typically seen in photosynthetic organisms.

Cellular Respiration and Fermentation

Organisms have evolved different strategies to extract energy from nutrients, depending on the availability of oxygen and the types of electron acceptors available.

Aerobic vs. Anaerobic Respiration

• Aerobic Respiration: This process uses oxygen as the final electron acceptor. It involves the complete oxidation of glucose and produces the maximum amount of ATP through a combination of substrate-level and oxidative phosphorylation.
• Anaerobic Respiration: This process also uses an electron transport chain but utilizes inorganic molecules other than oxygen (such as nitrate, sulfate, or carbonate) as the final electron acceptor.

Fermentation

When oxygen is absent and an electron transport chain cannot be used, some organisms rely on fermentation. Fermentation is an anaerobic process that uses an organic molecule (such as pyruvate) as the final electron acceptor. Because it relies solely on substrate-level phosphorylation, it produces significantly less ATP per glucose molecule than respiration.

Photosynthesis and Nutritional Classifications

While respiration breaks down molecules, photosynthesis allows certain organisms to build them using light.

Photosynthesis Types

• Oxygenic Photosynthesis: Produces oxygen as a byproduct (e.g., plants and cyanobacteria).
• Anoxygenic Photosynthesis: Does not produce oxygen (e.g., certain green sulfur bacteria).

How Organisms are Classified

We can categorize organisms based on how they obtain their energy and carbon:

Note: An organism can be a combination of these, such as a photoautotroph (uses light and $CO_2$) or a chemoorganoheterotroph (uses organic compounds for both).

Exam Summary Table: Respiration Comparison

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