Biochemistry and Microbial Metabolism

1. Living Cell and Biochemical Functions

The cell is the basic structural and functional unit of life. Microbial cells carry out numerous biochemical reactions that allow them to obtain nutrients, produce energy, synthesize cellular components, maintain internal organization and reproduce.

1.1 Origin and Importance of Biochemistry

Biochemistry is the branch of science that deals with the chemical substances and chemical reactions occurring in living organisms. It provides a molecular explanation of biological processes such as nutrition, respiration, growth, reproduction, heredity and metabolism.

1.2 Elements of Life

Living organisms contain several chemical elements. The major elements include carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur. Other elements such as calcium, potassium, sodium, magnesium, iron and chlorine are also essential for cellular functions.

1.3 Water: The Solvent of Life

Water is one of the most abundant components of living cells. Because of its polarity, it can dissolve many ionic and polar substances. It provides a medium for biochemical reactions, participates in some chemical reactions and contributes to transport and temperature regulation.

1.4 Biomembranes

Biological membranes are mainly composed of phospholipids and proteins. The plasma membrane separates the cell from its external environment and regulates the movement of substances across the membrane.

2. Macromolecules and Biomolecules

Biomolecules are chemical substances produced by living organisms. The major biological macromolecules are carbohydrates, proteins, lipids and nucleic acids.

2.1 Carbohydrates

Carbohydrates are organic compounds mainly composed of carbon, hydrogen and oxygen. They include monosaccharides, disaccharides and polysaccharides. Glucose is an important substrate for energy generation in many microorganisms.

2.2 Amino Acids

Amino acids are the basic units of proteins. Each amino acid has an amino group, carboxyl group, hydrogen atom and a variable side chain attached to a central carbon atom.

2.3 Proteins

Proteins are polymers of amino acids linked by peptide bonds. They perform catalytic, structural, transport, regulatory and protective functions.

2.4 Lipids

Lipids include fats, oils, phospholipids and other lipid molecules. They are important for energy storage and membrane structure.

2.5 Nucleic Acids

DNA and RNA are nucleic acids. DNA mainly stores hereditary information, whereas RNA participates in gene expression and protein synthesis.

3. Enzymes and Enzyme Kinetics

Enzymes are biological catalysts that increase the rate of biochemical reactions by lowering activation energy. Most enzymes are proteins, although some RNA molecules can also possess catalytic activity.

3.1 Characteristics of Enzymes

• They increase the rate of biochemical reactions.
• They generally show substrate specificity.
• They are not permanently consumed during the reaction.
• They function under suitable cellular conditions.
• Many require cofactors or coenzymes.

3.2 Classification of Enzymes

3.3 Cofactors and Coenzymes

Some enzymes require non-protein components for activity. These are called cofactors. Metal ions may act as inorganic cofactors, whereas organic cofactors are generally called coenzymes.

3.4 Isozymes

Isozymes are different molecular forms of an enzyme that catalyze the same reaction but may differ in their structure and properties.

3.5 Factors Affecting Enzyme Activity

• Temperature
• pH
• Substrate concentration
• Enzyme concentration
• Product concentration
• Inhibitors
• Activators

3.6 Enzyme Kinetics

Enzyme kinetics deals with the rate of enzyme-catalyzed reactions. As substrate concentration increases, reaction velocity increases until the enzyme approaches saturation.

Figure 1: Michaelis-Menten saturation curve showing the relationship between substrate concentration and reaction velocity.

4. Microbial Metabolism

Microbial metabolism is the sum of all biochemical reactions occurring within microbial cells. These reactions provide energy, reducing power and precursor molecules needed for growth, reproduction and maintenance.

Figure 2: General overview of cellular respiration and energy metabolism.

4.1 Catabolism

Catabolism involves the breakdown of complex molecules into simpler molecules. These reactions generally release energy, which can be conserved in ATP and reduced electron carriers.

4.2 Anabolism

Anabolism involves the synthesis of complex cellular molecules from simpler precursors. These reactions require energy and reducing power.

4.3 Exergonic and Endergonic Reactions

4.4 ATP: Energy Currency of the Cell

ATP or adenosine triphosphate is the major immediate energy carrier of the cell. Energy released during catabolic reactions may be conserved in ATP and subsequently used to perform cellular work.

Figure 3: Simplified representation of ATP.

4.5 Heterotrophic and Autotrophic Metabolism

Heterotrophic microorganisms obtain organic compounds from the environment as sources of carbon and energy. Autotrophic microorganisms obtain their cellular carbon mainly from carbon dioxide and obtain energy either from light or from oxidation of inorganic substances.

5. Glycolysis

Glycolysis is a major pathway of glucose degradation. It occurs in the cytoplasm and converts one molecule of glucose into two molecules of pyruvate.

Figure 4: Glycolytic pathway showing conversion of glucose to pyruvate.

5.1 Major Phases

1. Energy investment phase: ATP is consumed.
2. Cleavage phase: The six-carbon intermediate is divided into two three-carbon molecules.
3. Energy generation phase: ATP and NADH are produced.

6. Pyruvate Oxidation and TCA / Krebs Cycle

6.1 Pyruvate Oxidation

Under suitable respiratory conditions, pyruvate is converted into acetyl-CoA. This reaction connects glycolysis with the TCA cycle.

6.2 TCA / Krebs Cycle

The tricarboxylic acid cycle is a central metabolic pathway in which acetyl-CoA is oxidized through a series of reactions. It produces reduced electron carriers and carbon dioxide and provides intermediates for biosynthetic pathways.

Figure 5: Tricarboxylic acid cycle showing the major intermediates.

6.3 Importance of TCA Cycle

• Oxidation of acetyl-CoA.
• Production of NADH and FADH₂.
• Generation of ATP or GTP at one step.
• Production of carbon dioxide.
• Provision of biosynthetic intermediates.

7. Electron Transport Chain and Oxidative Phosphorylation

The electron transport chain consists of a series of electron carriers through which electrons are transferred. The energy released during electron transfer is used to establish a proton motive force that can drive ATP synthesis.

Figure 6: General representation of electron transport and oxidative phosphorylation.

7.1 Oxidative Phosphorylation

Oxidative phosphorylation is the process of ATP synthesis driven by the energy associated with electron transport and the proton motive force. In aerobic respiration, oxygen commonly acts as the terminal electron acceptor.

8. Fermentation

Fermentation is a metabolic process in which an organic molecule acts as the terminal electron acceptor. It allows microorganisms to regenerate NAD⁺ and continue substrate-level phosphorylation.

Figure 7: Simplified representation of fermentation pathways.

9. Pentose Phosphate Pathway

The pentose phosphate pathway is an alternative pathway of glucose metabolism. Its major functions are the production of NADPH and pentose phosphates.

Importance

• Produces NADPH.
• Provides pentose sugars for nucleotide synthesis.
• Provides intermediates for other metabolic pathways.

10. Entner-Doudoroff Pathway

The Entner-Doudoroff pathway is an alternative route for glucose degradation found in several bacteria. It produces pyruvate, glyceraldehyde-3-phosphate, ATP and reduced electron carriers.

11. Lipid Metabolism

Lipids are important structural molecules and energy reserves. Fatty acids can be degraded through beta-oxidation to produce acetyl-CoA and reduced electron carriers.

11.1 Beta-Oxidation

Beta-oxidation is a cyclic process in which fatty acids are progressively shortened by two carbon atoms. Acetyl-CoA produced during this process can enter the TCA cycle.

12. Protein and Amino Acid Metabolism

Proteins can be hydrolyzed into amino acids. Amino acids are mainly used for protein synthesis, but they can also be degraded when required. Their carbon skeletons can enter different points of central metabolic pathways.

12.1 Major Processes

• Proteolysis: Breakdown of proteins into peptides and amino acids.
• Transamination: Transfer of an amino group between an amino acid and a keto acid.
• Deamination: Removal of an amino group from an amino acid.
• Decarboxylation: Removal of the carboxyl group from an amino acid.

13. Intermediary Metabolism

Intermediary metabolism refers to the interconnected network of metabolic reactions involving carbohydrates, lipids and proteins. Metabolic pathways share intermediates and therefore function as an integrated network rather than as isolated processes.

Figure 8: General overview of interconnected metabolic pathways.

🔬 Overall Flow of Microbial Energy Metabolism

Figure 9: Overall relationship among glycolysis, pyruvate oxidation, TCA cycle and respiratory energy generation.