Chp 5 Microbial Metabolism: Foundations and Pathways

Microbial Metabolism

Overview of Metabolism

Metabolism is the sum of all controlled biochemical reactions that occur within a microbe. These reactions are essential for breaking down nutrients and building up the molecules required for cellular function and reproduction. The ultimate goal of metabolism is to enable the organism to reproduce.

• Catabolism: The breakdown of larger molecules into smaller products, releasing energy (exergonic).

• Anabolism: The synthesis of large molecules from smaller products, requiring energy input (endergonic).

• Energy from catabolism is stored in the form of ATP and used to drive anabolic reactions.

Eight Elementary Statements Guiding Metabolic Processes

• Every cell acquires nutrients.

• Metabolism requires energy from light or catabolism of nutrients.

• Energy is stored in ATP.

• Cells catabolize nutrients to form precursor metabolites.

• Precursor metabolites, ATP, and enzymes are used in anabolic reactions.

• Enzymes plus ATP form macromolecules.

• Cells grow by assembling macromolecules.

• Cells reproduce once they have doubled in size.

Catabolism and Anabolism

Catabolic and Anabolic Pathways

Catabolic pathways break down molecules and release energy, while anabolic pathways build complex molecules and consume energy. These processes are interconnected through the use of ATP and precursor metabolites.

• Catabolic reactions are exergonic (energy-releasing).

• Anabolic reactions are endergonic (energy-consuming).

Oxidation and Reduction Reactions

Redox Reactions in Metabolism

Oxidation-reduction (redox) reactions involve the transfer of electrons from an electron donor to an electron acceptor. These reactions are fundamental to energy production in cells and always occur simultaneously.

• Cells use electron carriers such as NAD+, NADP+, and FAD to shuttle electrons.

ATP: The Energy Currency

ATP Production and Energy Storage

Organisms release energy from nutrients and store it in the high-energy phosphate bonds of ATP. ATP is produced by phosphorylation, where inorganic phosphate is added to ADP. Anabolic pathways use the energy stored in ATP by breaking a phosphate bond.

• ATP is generated by substrate-level phosphorylation, oxidative phosphorylation, and photophosphorylation.

Enzymes in Metabolism

Role and Classification of Enzymes

Enzymes are organic catalysts that increase the likelihood of a reaction by lowering the activation energy required. They are essential for both catabolic and anabolic reactions.

• Enzymes are classified into six categories based on their mode of action:

  • Hydrolases: Catalyze hydrolysis reactions (catabolic).

  • Isomerases: Rearrange atoms within a molecule.

  • Ligases/Polymerases: Join molecules together (anabolic).

  • Lyases: Split molecules without water (catabolic).

  • Oxidoreductases: Transfer electrons or hydrogen atoms.

  • Transferases: Transfer functional groups between molecules.

Enzyme Structure and Function

Many enzymes are proteins that require nonprotein cofactors (inorganic ions or organic coenzymes) to be active. The combination of an apoenzyme and its cofactor forms a holoenzyme. Some enzymes are RNA molecules called ribozymes.

How Enzymes Work

Enzymes lower the activation energy of reactions, allowing them to proceed more rapidly. The substrate binds specifically to the enzyme's active site, forming an enzyme-substrate complex. The enzyme is unchanged after the reaction and can be reused.

Factors Affecting Enzyme Activity

Enzyme activity is influenced by several factors:

• Temperature

• pH

• Enzyme and substrate concentrations

• Presence of inhibitors

Enzyme Regulation

Enzyme activity can be regulated by activators and inhibitors:

• Allosteric activation: A cofactor binds to an allosteric site, making the active site functional.

• Competitive inhibition: An inhibitor competes with the substrate for the active site.

• Noncompetitive inhibition: An inhibitor binds to an allosteric site, changing the enzyme's shape and reducing activity.

• Feedback inhibition: The end product of a pathway inhibits an enzyme involved earlier in the pathway, preventing overproduction.

Carbohydrate Catabolism

Overview

Many organisms oxidize carbohydrates, primarily glucose, as their main energy source. Glucose catabolism occurs via two main processes: cellular respiration and fermentation.

Cellular Respiration

Cellular respiration is the complete oxidation of pyruvic acid (from glycolysis) to produce ATP through a series of redox reactions. It consists of three stages:

1. Glycolysis and synthesis of acetyl-CoA

2. Krebs cycle (Citric Acid Cycle)

3. Electron transport chain (ETC)

Glycolysis

• Occurs in the cytoplasm of most cells.

• Splits one six-carbon glucose into two three-carbon pyruvic acid molecules.

• Net gain: 2 ATP, 2 NADH, and 2 pyruvic acid.

Cellular Respiration Equation

The overall equation for aerobic respiration is:

$\mathrm{C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + ATP}$

Synthesis of Acetyl-CoA

• Pyruvic acid is converted to acetyl-CoA before entering the Krebs cycle.

• Products: 2 acetyl-CoA, 2 CO2, 2 NADH (per glucose molecule).

Krebs Cycle (Citric Acid Cycle)

• Occurs in the cytosol of prokaryotes and mitochondrial matrix of eukaryotes.

• Each acetyl-CoA enters the cycle, producing CO2, ATP, NADH, and FADH2.

• For each glucose: 4 CO2, 2 ATP, 6 NADH, 2 FADH2.

Electron Transport Chain (ETC) and Chemiosmosis

• Located in the inner mitochondrial membrane (eukaryotes) or cytoplasmic membrane (prokaryotes).

• Electrons from NADH and FADH2 are passed through a series of carriers to a final electron acceptor (O2 in aerobic respiration).

• Energy from electrons is used to pump protons, creating a proton gradient.

• Protons flow back through ATP synthase, generating ATP (oxidative phosphorylation).

• ~34 ATP produced per glucose in prokaryotes.

Summary Table: ATP Yield in Prokaryotic Aerobic Respiration

Pathway	ATP Produced
Glycolysis	4
Synthesis of acetyl-CoA and Krebs cycle	2
Electron transport chain	34
Total	40
Net Total	38

Additional info: In eukaryotes, the net total is 36 ATP due to differences in transport across mitochondrial membranes.

Fermentation

Fermentation is an alternative pathway for energy production when cells cannot completely oxidize glucose by cellular respiration. It regenerates NAD+ from NADH, allowing glycolysis to continue. Fermentation is less efficient than respiration and does not require oxygen.

Fermentation Products and Microbial Examples

Microbe	Fermentation Product	Commercial Use
Lactobacillus, Streptococcus	Lactic acid	Dairy products (yogurt, cheese)
Saccharomyces	Ethanol, CO2	Alcoholic beverages, bread
Propionibacterium	Propionic acid, CO2	Swiss cheese
Clostridium	Butyric acid, acetone, butanol	Industrial solvents

Comparison of Aerobic Respiration, Anaerobic Respiration, and Fermentation

Process	Oxygen Required	Final Electron Acceptor	ATP Yield (per glucose)
Aerobic Respiration	Yes	Oxygen	38 (prokaryotes), 36 (eukaryotes)
Anaerobic Respiration	No	NO3-, SO42-, CO32-	4–36
Fermentation	No	Cellular organic molecules	2

Clinical Relevance of Fermentation

Some pathogenic bacteria use fermentation pathways that can be harmful. For example, Clostridium perfringens produces fermentation products that destroy tissue, causing gangrene. Inhibiting certain fermentation pathways can reduce tissue damage during infection.