Microbial Metabolism: Chapter Five

Microbial Metabolism

Overview of Metabolism

Microbial metabolism encompasses all the controlled biochemical reactions that occur within a microbe. These reactions are essential for breaking down nutrients and synthesizing the molecules required for cellular function and reproduction. Metabolism is divided into two major classes: catabolism (energy-releasing breakdown of molecules) and anabolism (energy-consuming synthesis of macromolecules).

• Catabolic pathways: Break larger molecules into smaller products; exergonic (release energy).

• Anabolic pathways: Synthesize large molecules from smaller products; endergonic (require energy input).

• The ultimate function of metabolism is to reproduce the organism.

Basic Chemical Reactions Underlying Metabolism

• All cells acquire nutrients and require energy from light or catabolism of nutrients.

• Energy is stored in adenosine triphosphate (ATP).

• Cells catabolize nutrients to form precursor metabolites, which, along with ATP and enzymes, are used in anabolic reactions to build macromolecules.

• Cells grow by assembling macromolecules and reproduce once they have doubled in size.

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 always occur simultaneously and are essential for energy transfer in cells. Cells use electron carriers such as NAD+, NADP+, and FAD to shuttle electrons during metabolic processes.

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

ATP as Energy

ATP Production and Energy Storage

Organisms release energy from nutrients, which is stored in the high-energy phosphate bonds of ATP. Phosphorylation is the process of adding inorganic phosphate to ADP to form ATP. Anabolic pathways use the energy of ATP by breaking a phosphate bond.

The Roles of Enzymes in Metabolism

Enzyme Function and Classification

Enzymes are organic catalysts that increase the likelihood of a reaction by lowering the activation energy required. They are highly specific for their substrates and can be reused multiple times.

• Six categories of enzymes based on their mode of action:

Class	Type of Reaction Catalyzed	Example
Hydrolase	Hydrolysis (catabolic)	Lipase—breaks down lipid molecules
Isomerase	Rearrangement of atoms within a molecule	Phosphoglucoisomerase—converts glucose 6-phosphate into fructose 6-phosphate during glycolysis
Ligase or Polymerase	Joining two or more chemicals together (anabolic)	Acetyl-CoA synthetase—combines acetate and coenzyme A to form acetyl-CoA for the citric acid cycle
Lyase	Splitting a chemical into smaller parts without using water (catabolic)	Fructose-1,6-bisphosphate aldolase—splits fructose 1,6-bisphosphate into G3P and DHAP
Oxidoreductase	Transfer of electrons or hydrogen atoms from one molecule to another	Lactic acid dehydrogenase—oxidizes lactic acid to form pyruvic acid during fermentation
Transferase	Moving a functional group from one molecule to another (may be anabolic)	Hexokinase—transfers phosphate from ATP to glucose in the first step of glycolysis

Enzyme Structure and Cofactors

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

Cofactors	Examples of Use in Enzymatic Activity	Substance Transferred in Enzymatic Activity	Vitamin Source (of Coenzyme)
Magnesium (Mg2+)	Forms bond with ADP during phosphorylation	Phosphate	None
NAD+	Carrier of reducing power	Two electrons and a hydrogen ion	Niacin (B3)
NADP+	Carrier of reducing power	Two electrons and a hydrogen ion	Niacin (B3)
FAD	Carrier of reducing power	Two hydrogen atoms	Riboflavin (B2)
Tetrahydrofolate	Used in synthesis of nucleotides and some amino acids	One-carbon molecule	Folic acid (B9)
Coenzyme A	Formation of acetyl-CoA in citric acid cycle and beta-oxidation	Two-carbon molecule	Pantothenic acid (B5)
Pyridoxal phosphate	Used in synthesis of amino acids	Amine group	Pyridoxine (B6)
Thiamine pyrophosphate	Decarboxylation of pyruvic acid	Aldehyde group	Thiamine (B1)

Enzyme Activity and Regulation

Enzymes lower the activation energy required for reactions, increasing the rate of metabolic processes. Their activity is influenced by temperature, pH, and substrate concentration. Enzymes can be regulated by activators, inhibitors, and feedback mechanisms.

• Enzymes are unchanged by the reaction and can be reused.

• Substrates fit specifically into the enzyme's active site (lock and key model).

Factors Affecting Enzyme Activity

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

• pH: Enzyme activity is highest at an optimal pH; extreme pH can denature enzymes.

• Substrate concentration: Activity increases with substrate concentration until a saturation point is reached.

Enzyme Regulation: Inhibitors and Activators

• Allosteric activation: Some enzymes are activated when a cofactor binds to a site other than the active site, changing the enzyme's shape to allow substrate binding.

• Competitive inhibition: Inhibitors compete with the substrate for the active site.

• Noncompetitive inhibition: Inhibitors bind to an allosteric site, changing the enzyme's shape and reducing activity.

• Feedback inhibition: The end product of a metabolic pathway inhibits an enzyme involved earlier in the pathway, regulating the pathway's activity.

Carbohydrate Catabolism

Overview

Carbohydrates, especially glucose, are the primary energy source for most organisms. Glucose catabolism occurs via two main processes: cellular respiration and fermentation.

• Cellular respiration: Complete oxidation of glucose to produce ATP through glycolysis, the Krebs cycle, and the electron transport chain.

• Fermentation: Partial oxidation of glucose when oxygen is not available, regenerating NAD+ for glycolysis.

Glycolysis

Glycolysis occurs in the cytoplasm and involves splitting a six-carbon glucose into two three-carbon pyruvic acid molecules. It yields a net gain of 2 ATP, 2 NADH, and 2 pyruvic acid molecules.

Cellular Respiration

Cellular respiration consists of three stages:

1. Glycolysis and synthesis of acetyl-CoA

2. Krebs cycle (Citric Acid Cycle)

3. Electron transport chain (ETC)

Synthesis of Acetyl-CoA

Pyruvic acid from glycolysis is converted to acetyl-CoA, producing NADH and CO2 in the process.

Krebs Cycle (Citric Acid Cycle)

Acetyl-CoA enters the Krebs cycle, where it is oxidized, transferring energy to NAD+ and FAD. The cycle produces CO2, ATP, NADH, and FADH2. In prokaryotes, this occurs in the cytosol; in eukaryotes, in the mitochondrial matrix.

Electron Transport Chain (ETC) and Chemiosmosis

The ETC is a series of carrier molecules that transfer electrons to a final electron acceptor, generating a proton gradient across the membrane. The energy from this gradient is used by ATP synthase to produce ATP in a process called chemiosmosis. In aerobic respiration, oxygen is the final electron acceptor; in anaerobic respiration, other molecules serve this role.

ATP Yield from Aerobic Respiration

Pathway	ATP Produced	ATP Used	NADH Produced	FADH2 Produced
Glycolysis	4	2	2	0
Synthesis of acetyl-CoA and citric acid cycle	2	0	8	2
Electron transport chain	34	0	0	0
Total	40	2	10	2
Net Total	38

Fermentation

Fermentation allows cells to regenerate NAD+ from NADH, enabling glycolysis to continue in the absence of oxygen. It produces less ATP than respiration and results in various end products, such as lactic acid, ethanol, and other organic acids, depending on the organism.

Comparison of Aerobic Respiration, Anaerobic Respiration, and Fermentation

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

Clinical Relevance: Fermentation and Disease

Some pathogenic bacteria, such as Clostridium perfringens, use fermentation pathways that produce toxins and destroy tissue, leading to diseases like gangrene.

Applications of Fermentation

Fermentation is used industrially to produce a variety of products, including dairy products, alcoholic beverages, and solvents.