8.1 Energy, Matter, and Enzymes

Metabolism and Energy Acquisition

Metabolism is the sum of all chemical reactions happening inside a living organism. In microbes, these reactions serve three main purposes: generating ATP for energy, synthesizing essential biomolecules (proteins, nucleic acids, lipids, carbohydrates), and maintaining cellular homeostasis. Metabolism splits into two broad categories:

• Catabolism breaks down complex molecules and releases energy in the process. Glucose breakdown is a classic example.
• Anabolism uses energy to build complex molecules from simpler ones, like assembling amino acids into proteins.

These two processes are tightly linked. The energy released by catabolic reactions is what fuels anabolic ones.

Autotrophs vs. Heterotrophs

Microbes differ widely in how they get their carbon and energy. The two major categories:

Autotrophs produce their own organic compounds from inorganic sources. They're further divided by their energy source:

• Photoautotrophs use light energy to synthesize organic compounds. Examples include cyanobacteria and purple sulfur bacteria.
• Chemoautotrophs extract energy from inorganic chemical reactions. Sulfur-oxidizing bacteria and nitrifying bacteria fall into this group.

Heterotrophs depend on pre-made organic compounds for both energy and carbon:

• Chemoheterotrophs get energy by breaking down organic molecules through chemical reactions. Most bacteria and fungi are chemoheterotrophs.

Oxidation-Reduction in Microbial Metabolism

Redox reactions are electron transfers between molecules, and they're central to how microbes generate energy.

• Oxidation = loss of electrons (remember: OIL — Oxidation Is Loss)
• Reduction = gain of electrons (RIG — Reduction Is Gain)

These always happen in pairs. When one molecule is oxidized, another is reduced. In microbial metabolism, redox reactions drive the electron transport chain, power core metabolic pathways like glycolysis and the Krebs cycle, and help maintain the cell's overall redox balance.

Cellular Energy Processes and Enzymes

Energy Carriers in Cellular Processes

Cells use a handful of key molecules to capture, store, and shuttle energy. Each one has a distinct role:

ATP (adenosine triphosphate) is the universal energy currency of living cells. Energy is stored in the bonds between its phosphate groups and released when those bonds are broken. ATP powers biosynthesis, active transport, and motility.

NAD⁺ (nicotinamide adenine dinucleotide) is a coenzyme that picks up electrons during catabolic oxidation reactions, becoming reduced to NADH. NADH then donates those electrons to the electron transport chain, which uses them to generate more ATP.

FAD (flavin adenine dinucleotide) works similarly to NAD⁺. It accepts electrons during oxidation reactions to become FADH₂, then feeds those electrons into the electron transport chain. FADH₂ yields slightly less ATP than NADH because it enters the chain at a later point.

NADP⁺ (nicotinamide adenine dinucleotide phosphate) is structurally similar to NAD⁺ but plays a different role. When reduced to NADPH, it provides the reducing power needed for anabolic (biosynthetic) reactions rather than for ATP production.

Enzyme Structure in Microbes

Enzymes are proteins that catalyze (speed up) chemical reactions without being consumed in the process. Their function depends entirely on their three-dimensional shape, which is determined by their amino acid sequence.

Key structural components:

• Active site — the specific region where the substrate binds and the catalytic reaction occurs. Its shape is complementary to the substrate, often described by the "induced fit" model.
• Cofactors — non-protein molecules required for some enzymes to function. These can be metal ions (like zinc or iron) or vitamins.
• Coenzymes — organic cofactors that assist in catalysis. FAD, NAD⁺, and NADP⁺ all act as coenzymes.

Types of Enzyme Inhibitors

Enzyme inhibitors are molecules that reduce or eliminate enzyme activity. Understanding them matters for microbiology because many antimicrobial agents (antibiotics, antifungals) work by inhibiting microbial enzymes.

Competitive inhibitors are structurally similar to the substrate and bind directly to the active site, blocking the real substrate from entering. Key features:

• Inhibition is reversible — you can overcome it by increasing substrate concentration (outcompeting the inhibitor)
• Increases apparent $K_m$ (the enzyme appears to have lower affinity for its substrate)
• Does not affect $V_{max}$ (given enough substrate, the enzyme can still reach full speed)

Noncompetitive inhibitors bind to an allosteric site (somewhere other than the active site), causing a conformational change that reduces catalytic activity. Key features:

• Cannot be overcome by adding more substrate, since the inhibitor isn't competing for the active site
• Decreases $V_{max}$ (the enzyme simply can't work as fast)
• Does not affect $K_m$
• Can be reversible or irreversible depending on the inhibitor

Thermodynamics and Bioenergetics in Microbial Metabolism

Thermodynamic principles govern every energy transformation in microbial cells.

• Enthalpy is the total heat content of a system. Changes in enthalpy ($\Delta H$) tell you whether a reaction releases or absorbs heat.
• Entropy measures the degree of disorder in a system. Spontaneous processes tend to increase entropy.
• Free energy ($\Delta G$) combines both concepts. A negative $\Delta G$ means the reaction is spontaneous (exergonic); a positive $\Delta G$ means it requires energy input (endergonic).

Activation energy is the minimum energy needed to start a reaction. Even reactions with a negative $\Delta G$ won't proceed quickly without overcoming this energy barrier. Enzymes work by lowering the activation energy, allowing reactions to proceed much faster at normal cellular temperatures.

Enzyme kinetics studies the rates of enzyme-catalyzed reactions. The relationship between substrate concentration and reaction rate, described by the Michaelis-Menten model, is central to understanding how cells regulate their metabolic pathways.