Microbial Metabolism: Structured Study Notes

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Microbial Metabolism

Overview of Metabolism

Metabolism refers to the collection of controlled biochemical reactions that occur within a microbe. The ultimate function of metabolism is to reproduce the organism. These reactions are guided by a series of elementary statements that describe how cells acquire nutrients, utilize energy, and grow.

Metabolism: All chemical reactions in a cell, including both catabolic and anabolic pathways.
Cells acquire nutrients and use energy from light or catabolism of nutrients.
Energy is stored in adenosine triphosphate (ATP).
Cells catabolize nutrients to form precursor metabolites, which are used in anabolic reactions to build macromolecules.
Growth and reproduction occur after cells assemble macromolecules and double in size.

Metabolism is composed of catabolic and anabolic reactions

Catabolism and Anabolism

Metabolic reactions are divided into two major classes: catabolic and anabolic pathways. These pathways are interconnected and essential for cellular function.

Catabolic pathways: Break larger molecules into smaller products; these reactions are exergonic (release energy).
Anabolic pathways: Synthesize large molecules from smaller products; these reactions are endergonic (require more energy than they release).
Energy released from catabolism is often used to drive anabolic reactions.

Oxidation and Reduction Reactions

Oxidation-reduction (redox) reactions are fundamental to metabolism, involving the transfer of electrons between molecules. These reactions always occur simultaneously, and cells use electron carriers to facilitate electron transfer.

Oxidation: Loss of electrons from a molecule.
Reduction: Gain of electrons by a molecule.
Important electron carriers: NAD+, NADP+, FAD.

Oxidation-Reduction, or Redox, Reactions

ATP Production and Energy Storage

Organisms release energy from nutrients and store it in high-energy phosphate bonds, primarily in ATP. ATP is produced by phosphorylation, which involves adding inorganic phosphate to ADP. There are three main mechanisms for ATP production:

Substrate-level phosphorylation: Direct transfer of phosphate between substrates.
Oxidative phosphorylation: Uses energy from redox reactions in the electron transport chain.
Photophosphorylation: Uses light energy to phosphorylate ADP.

The Roles of Enzymes in Metabolism

Enzymes are organic catalysts that increase the likelihood of chemical reactions. They lower the activation energy required for reactions, making metabolic processes more efficient.

Enzyme: Protein that speeds up chemical reactions without being consumed.
Enzymes bind substrates at their active sites, often inducing a fit for optimal catalysis.

The Effect of Enzymes on Chemical Reactions Enzymes Fitted to Substrates The Process of Enzymatic Activity

Factors Influencing Enzyme Activity

Several factors affect the rate of enzymatic reactions, including temperature, pH, enzyme and substrate concentrations, and the presence of inhibitors.

Optimal temperature and pH are required for maximal enzyme activity.
Enzyme denaturation occurs when conditions are too extreme, leading to loss of function.
Enzyme activity can be regulated by activators and inhibitors.

Representative Effects of Temperature, pH, and Substrate Concentration on Enzyme Activity Denaturation of Protein Enzymes

Enzyme Regulation: Activators and Inhibitors

Enzyme activity is controlled by activators and inhibitors. Activators bind to sites other than the active site (allosteric sites) to activate enzymes, while inhibitors block enzyme activity.

Allosteric activation: Cofactor binds to allosteric site, making the active site functional.
Competitive inhibitors: Bind to the active site, preventing substrate binding.
Noncompetitive inhibitors: Bind to allosteric sites, changing enzyme shape and reducing activity.
Feedback inhibition: End product of a pathway inhibits an earlier enzyme, regulating pathway activity.

Allosteric Activation Competitive Inhibition of Enzyme Activity Noncompetitive Inhibition at an Allosteric Site Feedback Inhibition

Carbohydrate Catabolism

Glucose Catabolism: Cellular Respiration and Fermentation

Many organisms use carbohydrates, especially glucose, as their primary energy source. Glucose is catabolized by cellular respiration or fermentation.

Cellular respiration: Complete oxidation of glucose to produce ATP via glycolysis, Krebs cycle, and electron transport chain.
Fermentation: Partial oxidation of glucose, providing cells with an alternative source of NAD+.

Summary of Glucose Catabolism

Glycolysis

Glycolysis occurs in the cytoplasm and involves splitting a six-carbon glucose into two three-carbon molecules. It consists of three stages and ten steps, resulting in a net gain of two ATP, two NADH, and pyruvic acid.

Energy-investment stage: ATP is used to phosphorylate glucose.
Lysis stage: Glucose is split into two three-carbon molecules.
Energy-conserving stage: ATP and NADH are produced.

Glycolysis by the EMP Pathway

Cellular Respiration

Cellular respiration consists of three stages: synthesis of acetyl-CoA, Krebs cycle, and electron transport chain. Pyruvic acid is completely oxidized to produce ATP.

Synthesis of acetyl-CoA: Pyruvic acid is converted to acetyl-CoA, producing NADH and CO2.
Krebs cycle: Acetyl-CoA is oxidized, transferring energy to NAD+ and FAD.
Electron transport chain (ETC): Electrons are passed through carrier molecules, generating a proton gradient used for ATP synthesis.

The Pyruvate Dehydrogenase Complex The Citric Acid Cycle One Possible Arrangement of Electron Transport Chain Molecules

Chemiosmosis and ATP Yield

Chemiosmosis is the use of electrochemical gradients to generate ATP. Protons flow through ATP synthase, phosphorylating ADP to ATP. This process is called oxidative phosphorylation.

Total ATP yield from one molecule of glucose in prokaryotic aerobic respiration is approximately 34 ATP.

Fermentation

Fermentation provides cells with an alternative source of NAD+ when cellular respiration cannot occur. It involves partial oxidation of sugar, using an organic molecule as the final electron acceptor.

Fermentation products include lactic acid, ethanol, and other organic acids.
Different organisms produce different fermentation products.

Examples of Fermentation Representative Fermentation Products and the Organisms That Produce Them

Photosynthesis

Photosynthetic Structures and Pigments

Photosynthesis is the process by which organisms synthesize organic molecules from inorganic carbon dioxide using light energy. Chlorophylls are key pigments that capture light energy.

Chlorophylls: Pigments with a hydrocarbon tail and light-absorbing active site centered on magnesium ion.
Photosystems: Arrangements of chlorophyll and other pigments in thylakoid membranes.
In prokaryotes, thylakoids are infoldings of the cytoplasmic membrane; in eukaryotes, they are part of chloroplasts.

Photosynthetic Structures in a Prokaryote

Light-Dependent and Light-Independent Reactions

Photosynthesis consists of light-dependent and light-independent reactions. Light-dependent reactions use light energy to generate ATP and NADPH, while light-independent reactions synthesize glucose from CO2 and water.

Light-dependent reactions: Photophosphorylation can be cyclic or noncyclic.
Light-independent reactions: Carbon fixation via the Calvin-Benson cycle.

Reaction Center of a Photosystem The Light-Dependent Reactions of Photosynthesis: Cyclic and Noncyclic Photophosphorylation

Calvin-Benson Cycle

The Calvin-Benson cycle is the key light-independent reaction in photosynthesis. It consists of three steps: fixation of CO2, reduction, and regeneration of RuBP.

ATP and NADPH generated by light-dependent reactions are used in the Calvin-Benson cycle.

Simplified Diagram of the Calvin-Benson Cycle

Summary Table: Comparison of Metabolic Pathways

Below is a summary table comparing aerobic respiration, anaerobic respiration, and fermentation (Additional info: Table inferred from context).

Pathway	Final Electron Acceptor	ATP Yield	End Products
Aerobic Respiration	O2	~34 ATP	CO2, H2O
Anaerobic Respiration	Other inorganic molecules (e.g., NO3-, SO42-)	Variable, less than aerobic	CO2, reduced inorganic compounds
Fermentation	Organic molecules	2 ATP	Organic acids, alcohols, gases

Key Terms and Concepts

Metabolism: All chemical reactions in a cell.
Catabolism: Breakdown of molecules, releasing energy.
Anabolism: Synthesis of molecules, requiring energy.
ATP: Main energy currency of the cell.
Enzyme: Protein catalyst for biochemical reactions.
Glycolysis: First step in glucose catabolism.
Krebs cycle: Central metabolic pathway in cellular respiration.
Electron transport chain: Series of carriers for electron transfer and ATP synthesis.
Fermentation: Alternative pathway for energy production.
Photosynthesis: Light-driven synthesis of organic molecules.

Important Equations

ATP formation:
Glucose catabolism (aerobic):
Photosynthesis:

Additional info: Table and equations were inferred for completeness and academic context.