Microbial Metabolism

Introduction to Metabolism

Metabolism encompasses all controlled biochemical reactions within the cells of an organism. The ultimate function of metabolism is to enable the reproduction and survival of the organism. Metabolic processes are divided into two main categories: catabolism and anabolism.

• Catabolic pathways: Break down larger molecules into smaller products, releasing energy (exergonic reactions).

• Anabolic pathways: Synthesize large molecules from smaller products, requiring energy input (endergonic reactions).

Key Point: Energy released from catabolic reactions is often stored in the form of ATP and used to drive anabolic reactions.

Basic Chemical Reactions Underlying Metabolism

Oxidation and Reduction Reactions (Redox)

Redox reactions involve the transfer of electrons from one molecule (the donor) to another (the acceptor). These reactions always occur simultaneously and are essential for energy transfer in cells.

• Oxidation: Loss of electrons from a molecule.

• Reduction: Gain of electrons by a molecule.

• Cells use electron carrier molecules such as NAD+, NADP+, and FAD to shuttle electrons during metabolic reactions.

Example: In cellular respiration, glucose is oxidized and oxygen is reduced.

ATP Production and Energy Storage

Organisms release energy from nutrients and store it in the high-energy phosphate bonds of ATP. ATP is generated by phosphorylation of ADP in three main ways:

• Substrate-level phosphorylation

• Oxidative phosphorylation

• Photophosphorylation

Anabolic pathways use the energy stored in ATP by breaking a phosphate bond.

Enzyme Function in Metabolism

The Role of Enzymes

Enzymes are biological catalysts that speed up chemical reactions without being consumed. Many enzymes are proteins, but some RNA molecules (ribozymes) also have catalytic activity. Enzymes may require non-protein cofactors (ions or coenzymes) to be active.

• Apoenzyme: The protein portion of an enzyme, inactive without its cofactor.

• Cofactor: Non-protein component (inorganic ion or organic coenzyme).

• Holoenzyme: The complete, active enzyme with its cofactor.

Example: Many metabolic enzymes require NAD+ or FAD as coenzymes for redox reactions.

Factors Affecting Enzyme Activity

Enzyme activity is influenced by several factors:

• Temperature: Each enzyme has an optimal temperature for activity.

• pH: Enzymes function best within a specific pH range.

• Substrate concentration: Activity increases with substrate concentration up to a saturation point.

Protein conformation is crucial for enzyme function. Denaturation (loss of structure) leads to loss of activity.

Enzyme Inhibition and Regulation

Enzyme activity can be regulated by inhibitors:

• Competitive inhibitors: Bind to the active site, blocking substrate binding.

• Noncompetitive (allosteric) inhibitors: Bind to a different site, changing the enzyme's shape and reducing activity.

Feedback inhibition is a regulatory mechanism where the end product of a pathway inhibits an earlier step, preventing overproduction.

Carbohydrate Catabolism

Overview

Carbohydrate catabolism is the primary source of energy for many organisms. Glucose is the most common carbohydrate used and can be catabolized by cellular respiration or fermentation.

Glycolysis

Glycolysis is an ancient, nearly universal process that occurs in the cytoplasm. It splits one six-carbon glucose into two three-carbon pyruvic acid molecules, yielding a net gain of 2 ATP and 2 NADH.

• Energy-investment stage: ATP is used to phosphorylate glucose.

• Lysis stage: The six-carbon molecule is split into two three-carbon molecules.

• Energy-conserving stage: ATP and NADH are produced.

Substrate-level phosphorylation is a direct transfer of phosphate to ADP to form ATP during glycolysis.

Cellular Respiration

After glycolysis, pyruvic acid is completely oxidized to produce ATP, CO2, and H2O through three stages:

1. Synthesis of acetyl-CoA

2. Krebs cycle (Citric Acid Cycle)

3. Electron transport chain (ETC)

The Krebs cycle generates 2 ATP, 2 FADH2, 6 NADH, and 4 CO2 per glucose molecule.

Electron Transport Chain and Chemiosmosis

The ETC consists of a series of electron carriers that transfer electrons to a final electron acceptor, pumping protons across a membrane to create a proton motive force. Protons flow back through ATP synthase, driving oxidative phosphorylation and producing the majority of ATP.

Key Equation:

In aerobic respiration, oxygen is the final electron acceptor; in anaerobic respiration, other molecules (e.g., nitrate) serve this role.

Total ATP yield: Up to 38 ATP per glucose in prokaryotes.

Fermentation

Fermentation provides an alternative pathway for regenerating NAD+ when the ETC is not available. It results in the production of organic acids, alcohols, or gases, and yields only 2 ATP per glucose.

Comparison of Metabolic Pathways

Photosynthesis

Light-Dependent and Light-Independent Reactions

Photosynthesis consists of two stages:

• Light-dependent reactions: Convert light energy into ATP and NADPH using photosystems in the thylakoid membrane (or cytoplasmic membrane in prokaryotes).

• Calvin-Benson cycle (light-independent reactions): Uses ATP and NADPH to fix CO2 into organic molecules (G3P), which can be converted into glucose.

Key Point: For every 3 CO2 molecules entering the Calvin cycle, one G3P is produced; two G3P molecules can form one glucose.

Anabolic Pathways and Amphibolic Reactions

Overview of Anabolic Pathways

Anabolic reactions synthesize macromolecules and cellular structures from smaller precursors, using energy derived from ATP. Many anabolic pathways are the reverse of catabolic pathways and are termed amphibolic if they can proceed in both directions.

There are 12 basic precursor metabolites from which all macromolecules are synthesized, provided by glycolysis, the Krebs cycle, and the pentose phosphate pathway.

Integration and Regulation of Metabolic Function

Metabolic pathways are highly integrated and regulated to ensure efficient use of resources and energy. Feedback inhibition, allosteric regulation, and gene expression control are key mechanisms for metabolic regulation.