Microbial Metabolism: Structure, Function, and Regulation

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Microbial Metabolism

Overview of Metabolism

Metabolism encompasses all chemical reactions occurring within a living organism, balancing energy release and consumption. It is divided into two main classes: catabolism (energy-releasing, degradative reactions) and anabolism (energy-consuming, biosynthetic reactions).

Catabolism: Breaks down complex molecules into simpler ones, releasing energy.
Anabolism: Builds complex molecules from simpler ones, requiring energy input.

Catabolic pathways break down macromolecules into simple component parts, releasing energy in the process. Water is added in hydrolytic catabolic reactions. Anabolic pathways build up macromolecules by combining simpler molecules, using energy in the process.

Catabolic & Anabolic Pathways

Catabolic and anabolic pathways are interconnected, with catabolic reactions providing the energy needed for anabolic reactions. Energy is stored in ATP during catabolism and released for anabolism.

Catabolic and anabolic pathways are linked by energy. Catabolic reactions provide energy for anabolic reactions. Catabolism releases energy by oxidation of molecules; anabolism uses energy to synthesize macromolecules.

Enzymes: Chemical Reaction Helpers

Metabolic pathways are sequences of enzymatically catalyzed reactions. Enzymes, encoded by genes, determine the pathway and act as biological catalysts, speeding up reactions without being consumed.

Enzymes: Proteins that accelerate chemical reactions by lowering activation energy.
Catalysts: Substances that speed up reactions without permanent change.

Collision Theory & Activation Energy

The collision theory explains that reactions occur when molecules collide with sufficient energy. Enzymes increase reaction rates by lowering the activation energy required.

Effect of temperature on collision rate and reaction rate. Energy requirements of a chemical reaction: activation energy with and without enzyme.

Enzyme-Substrate Complex

Enzymes bind substrates at their active site, forming an enzyme-substrate complex. The substrate is transformed into products, and the enzyme remains unchanged.

Enzyme-substrate complex formation and product release. Lock and key model of enzyme specificity.

Enzyme Specificity and Efficiency

Enzymes are highly specific for their substrates and are extremely efficient, with turnover numbers ranging from 1 to 500,000 substrate molecules per second. Their activity is regulated by the cellular environment.

Enzyme Components

Most enzymes consist of a protein portion (apoenzyme) and a nonprotein component (cofactor). If the cofactor is organic, it is called a coenzyme. The active enzyme (holoenzyme) is formed when both components are present.

Apoenzyme: Protein portion, inactive alone.
Cofactor: Nonprotein activator (e.g., metal ions).
Coenzyme: Organic cofactor, often a vitamin.
Holoenzyme: Active enzyme (apoenzyme + cofactor).

Components of a holoenzyme: apoenzyme, cofactor, coenzyme, substrate. Edwin, the enzyme, was surprised how many substrates approached when he walked the cofactor.

Selected Vitamins and Their Coenzymatic Functions

Many coenzymes are derived from vitamins, which play essential roles in metabolism.

Vitamin	Function
Vitamin B1 (Thiamine)	Coenzyme in decarboxylase; metabolism of pyruvic acid
Vitamin B2 (Riboflavin)	Coenzyme in flavoproteins; electron transfers
Niacin (Nicotinic Acid)	Part of NAD molecule; electron transfers
Vitamin B6 (Pyridoxine)	Coenzyme in amino acid metabolism
Vitamin B12 (Cyanocobalamin)	Coenzyme in methyl group transfer; amino acid metabolism
Pantothenic Acid	Part of coenzyme A; metabolism of pyruvic acid and lipids
Biotin	Carbon dioxide fixation; fatty acid synthesis
Folic Acid	Synthesis of purines and pyrimidines
Vitamin E	Cellular and macromolecular syntheses
Vitamin K	Electron transport

Table of selected vitamins and their coenzymatic functions.

Factors Influencing Enzyme Activity

Enzyme activity is affected by temperature, pH, substrate concentration, and inhibitors. Extreme conditions can denature enzymes, rendering them inactive.

Active (functional) protein vs. denatured protein. Enzyme denaturation due to non-ideal pH levels. Graphs showing effects of temperature, pH, and substrate concentration on enzyme activity.

Enzyme Inhibitors

Enzyme inhibitors regulate metabolic pathways and can be used to control microbial growth. They are classified as competitive or noncompetitive.

Competitive inhibitors: Bind to the active site, blocking substrate access.
Noncompetitive inhibitors: Bind to an allosteric site, altering enzyme shape and function.

Competitive inhibitor binding to enzyme active site. Sulfanilamide vs. PABA: competitive inhibition. Bactrim: Sulfamethoxazol + Trimethoprim, an example of competitive inhibition in antibiotics. Noncompetitive inhibitor binding to allosteric site. Feedback inhibition in metabolic pathways.

Energy Production and Redox Reactions

ATP: The Energy Currency

Cells capture energy released from catabolic reactions in the form of ATP, which contains high-energy bonds that are easily broken to release energy for cellular processes.

Oxidation-Reduction (Redox) Reactions

Redox reactions involve the transfer of electrons. Oxidation is the loss of electrons, while reduction is the gain of electrons. These reactions are always coupled, forming the basis of energy transfer in cells.

Oxidation: molecule loses electron; reduction: molecule gains electron. Coupled oxidation-reduction reactions. Dehydrogenation: removal of hydrogen atoms (electrons and protons). NAD+ and NADH: electron carriers in cellular metabolism.

ATP Generation

ATP is generated by phosphorylation, the addition of a phosphate group to ADP. There are three main mechanisms:

Substrate-level phosphorylation: Direct transfer of phosphate to ADP from a substrate.
Oxidative phosphorylation: Electrons transferred through the electron transport chain, generating ATP via chemiosmosis.
Photophosphorylation: (not covered here) Occurs in photosynthetic organisms.

ADP + Pi + energy forms ATP. Substrate-level phosphorylation: enzyme catalyzes transfer of phosphate to ADP.

Carbohydrate Catabolism

Aerobic Respiration

Aerobic respiration is the breakdown of carbohydrates to release energy, involving glycolysis, the transition step and Krebs cycle, and the electron transport chain.

Glycolysis: Oxidation of glucose to pyruvic acid, producing ATP and NADH.
Transition step & Krebs cycle: Further oxidation, producing NADH, FADH2, ATP, and CO2.
Electron transport chain: Electrons transferred through carrier molecules, generating ATP by chemiosmosis.

Carbohydrate catabolism pathways. Stages of aerobic respiration: glycolysis, Krebs cycle, ETC.

Glycolysis

Glycolysis occurs in the cytoplasm of all cells and does not require oxygen. It produces:

2 ATP
2 NADH
2 Pyruvate

Glycolysis: splitting of sugar. Energy end-products of glycolysis.

Transition Step & Krebs Cycle

The transition step converts pyruvate to acetyl-CoA, which enters the Krebs cycle. The cycle produces NADH, FADH2, ATP, and CO2.

Electron Transport Chain (ETC)

The ETC is located in the plasma membrane of prokaryotes and the inner mitochondrial membrane of eukaryotes. It consists of flavoproteins, cytochromes, and ubiquinones. Electrons are passed down the chain, and energy released is used to produce ATP by chemiosmosis.

Electron transport chain: carrier molecules and ATP production. Cytochrome C oxidase: last molecule to transfer electrons to O2. Location of ETC in prokaryotes and eukaryotes. ATP yield from NADH and FADH2 in ETC.

Total ATP Yield

Aerobic respiration in prokaryotes yields a total of 38 ATP per glucose molecule:

Stage	Net ATP Yield
Glycolysis	2 ATP
Transition step	0 ATP
Krebs cycle	2 ATP
ETC	34 ATP
Total	38 ATP

ATP yield table for aerobic respiration.

Anaerobic Respiration

Anaerobic respiration uses a final electron acceptor other than oxygen, resulting in less ATP production (5 to 37 ATP per glucose).

Aerobic vs. anaerobic respiration in prokaryotes.

Fermentation

Fermentation occurs when cells cannot carry out respiration due to lack of oxygen, electron transport system, or Krebs cycle enzymes. It releases energy from organic molecules, does not require oxygen, and produces small amounts of ATP.

Lactic acid fermentation: Produces lactic acid.
Alcohol fermentation: Produces ethanol and CO2.

Comparison of aerobic respiration, anaerobic respiration, and fermentation.

Catabolism of Macromolecules

Lipid Catabolism

Lipids are broken down by lipases into fatty acids and glycerol, which are then metabolized separately. The Krebs cycle oxidizes these components for energy production.

Protein Catabolism

Proteins are degraded by proteases and peptidases into amino acids, which are further processed (deaminated, decarboxylated, desulfurized) to enter the Krebs cycle.

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